1
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Boyd-Shiwarski CR, Shiwarski DJ, Subramanya AR. A New Phase for WNK Kinase Signaling Complexes as Biomolecular Condensates. Physiology (Bethesda) 2024; 39:0. [PMID: 38624245 DOI: 10.1152/physiol.00013.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
The purpose of this review is to highlight transformative advances that have been made in the field of biomolecular condensates, with special emphasis on condensate material properties, physiology, and kinases, using the With-No-Lysine (WNK) kinases as a prototypical example. To convey how WNK kinases illustrate important concepts for biomolecular condensates, we start with a brief history, focus on defining features of biomolecular condensates, and delve into some examples of how condensates are implicated in cellular physiology (and pathophysiology). We then highlight how WNK kinases, through the action of "WNK droplets" that ubiquitously regulate intracellular volume and kidney-specific "WNK bodies" that are implicated in distal tubule salt reabsorption and potassium homeostasis, exemplify many of the defining features of condensates. Finally, this review addresses the controversies within this emerging field and questions to address.
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Affiliation(s)
- Cary R Boyd-Shiwarski
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Pittsburgh Heart, Lung, Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Daniel J Shiwarski
- Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Arohan R Subramanya
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Pittsburgh Heart, Lung, Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, United States
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2
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Maraldo A, Rnjak-Kovacina J, Marquis C. Tyrosine - a structural glue for hierarchical protein assembly. Trends Biochem Sci 2024; 49:633-648. [PMID: 38653686 DOI: 10.1016/j.tibs.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Protein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their natural counterparts, emerges as a promising strategy for creating adaptive, self-assembling systems with diverse applications. This review explores the central role of tyrosine in orchestrating protein self-assembly, delving into key interactions and examining its potential in innovative applications, including responsive biomaterials and bioengineering.
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Affiliation(s)
- Anton Maraldo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Jelena Rnjak-Kovacina
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, Australia.
| | - Christopher Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
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3
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Rekhi S, Garcia CG, Barai M, Rizuan A, Schuster BS, Kiick KL, Mittal J. Expanding the molecular language of protein liquid-liquid phase separation. Nat Chem 2024; 16:1113-1124. [PMID: 38553587 PMCID: PMC11230844 DOI: 10.1038/s41557-024-01489-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/27/2024] [Indexed: 04/07/2024]
Abstract
Understanding the relationship between a polypeptide sequence and its phase separation has important implications for analysing cellular function, treating disease and designing novel biomaterials. Several sequence features have been identified as drivers for protein liquid-liquid phase separation (LLPS), schematized as a 'molecular grammar' for LLPS. Here we further probe how sequence modulates phase separation and the material properties of the resulting condensates, targeting sequence features previously overlooked in the literature. We generate sequence variants of a repeat polypeptide with either no charged residues, high net charge, no glycine residues or devoid of aromatic or arginine residues. All but one of 12 variants exhibited LLPS, albeit to different extents, despite substantial differences in composition. Furthermore, we find that all the condensates formed behaved like viscous fluids, despite large differences in their viscosities. Our results support the model of multiple interactions between diverse residue pairs-not just a handful of residues-working in tandem to drive the phase separation and dynamics of condensates.
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Affiliation(s)
- Shiv Rekhi
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Mayur Barai
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA.
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA.
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA.
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4
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Dao TP, Rajendran A, Galagedera SKK, Haws W, Castañeda CA. Short disordered termini and proline-rich domain are major regulators of UBQLN1/2/4 phase separation. Biophys J 2024; 123:1449-1457. [PMID: 38041404 PMCID: PMC11163289 DOI: 10.1016/j.bpj.2023.11.3401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/03/2023] Open
Abstract
Highly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2, and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates, and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2, and UBQLN4 exhibit distinct phase behaviors in vitro. Strikingly, UBQLN4 phase separates at a much lower saturation concentration than UBQLN1. However, neither UBQLN1 nor UBQLN4 phase separates with a strong temperature dependence, unlike UBQLN2. We determined that the temperature-dependent phase behavior of UBQLN2 stems from its unique proline-rich region, which is absent in the other UBQLNs. We found that the short N-terminal disordered regions of UBQLN1, UBQLN2, and UBQLN4 inhibit UBQLN phase separation via electrostatics interactions. Charge variants of the N-terminal regions exhibit altered phase behaviors. Consistent with the sensitivity of UBQLN phase separation to the composition of the N-terminal regions, epitope tags placed on the N-termini of the UBQLNs tune phase separation. Overall, our in vitro results have important implications for studies of UBQLNs in cells, including the identification of phase separation as a potential mechanism to distinguish the cellular roles of UBQLNs and the need to apply caution when using epitope tags to prevent experimental artifacts.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | - Anitha Rajendran
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | | | - William Haws
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York; Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, New York; BioInspired Institute, Syracuse University, Syracuse, New York.
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5
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Kar M, Vogel LT, Chauhan G, Felekyan S, Ausserwöger H, Welsh TJ, Dar F, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Solutes unmask differences in clustering versus phase separation of FET proteins. Nat Commun 2024; 15:4408. [PMID: 38782886 PMCID: PMC11116469 DOI: 10.1038/s41467-024-48775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Phase separation and percolation contribute to phase transitions of multivalent macromolecules. Contributions of percolation are evident through the viscoelasticity of condensates and through the formation of heterogeneous distributions of nano- and mesoscale pre-percolation clusters in sub-saturated solutions. Here, we show that clusters formed in sub-saturated solutions of FET (FUS-EWSR1-TAF15) proteins are affected differently by glutamate versus chloride. These differences on the nanoscale, gleaned using a suite of methods deployed across a wide range of protein concentrations, are prevalent and can be unmasked even though the driving forces for phase separation remain unchanged in glutamate versus chloride. Strikingly, differences in anion-mediated interactions that drive clustering saturate on the micron-scale. Beyond this length scale the system separates into coexisting phases. Overall, we find that sequence-encoded interactions, mediated by solution components, make synergistic and distinct contributions to the formation of pre-percolation clusters in sub-saturated solutions, and to the driving forces for phase separation.
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Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anjana R Kamath
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Anthony A Hyman
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany.
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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6
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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7
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Wake N, Weng SL, Zheng T, Wang SH, Kirilenko V, Mittal J, Fawzi NL. Expanding the molecular grammar of polar residues and arginine in FUS prion-like domain phase separation and aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580391. [PMID: 38405719 PMCID: PMC10888811 DOI: 10.1101/2024.02.15.580391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A molecular grammar governing low-complexity prion-like domains phase separation (PS) has been proposed based on mutagenesis experiments that identified tyrosine and arginine as primary drivers of phase separation via aromatic-aromatic and aromatic-arginine interactions. Here we show that additional residues make direct favorable contacts that contribute to phase separation, highlighting the need to account for these contributions in PS theories and models. We find that tyrosine and arginine make important contacts beyond only tyrosine-tyrosine and tyrosine-arginine, including arginine-arginine contacts. Among polar residues, glutamine in particular contributes to phase separation with sequence/position-specificity, making contacts with both tyrosine and arginine as well as other residues, both before phase separation and in condensed phases. For glycine, its flexibility, not its small solvation volume, favors phase separation by allowing favorable contacts between other residues and inhibits the liquid-to-solid (LST) transition. Polar residue types also make sequence-specific contributions to aggregation that go beyond simple rules, which for serine positions is linked to formation of an amyloid-core structure by the FUS low-complexity domain. Hence, here we propose a revised molecular grammar expanding the role of arginine and polar residues in prion-like domain protein phase separation and aggregation.
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Affiliation(s)
- Noah Wake
- Therapeutic Sciences Graduate Program, Brown University, Providence, RI 02912
| | - Shuo-Lin Weng
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Tongyin Zheng
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Valentin Kirilenko
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Jeetain Mittal
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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8
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Galagedera SKK, Dao TP, Enos SE, Chaudhuri A, Schmit JD, Castañeda CA. Polyubiquitin ligand-induced phase transitions are optimized by spacing between ubiquitin units. Proc Natl Acad Sci U S A 2023; 120:e2306638120. [PMID: 37824531 PMCID: PMC10589717 DOI: 10.1073/pnas.2306638120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023] Open
Abstract
Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or posttranslational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to either the UBQLN2-binding surface of Ub or the spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model based on polyphasic linkage principles that accurately described the effects of different hubs on UBQLN2 phase separation, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. The extent to which polyubiquitin hubs promote UBQLN2 phase separation is encoded in the spacings between Ub units. This spacing is modulated by chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. The spacing in naturally occurring linear polyubiquitin chains is already optimized to promote phase separation with UBQLN2. We expect our findings to extend to other condensates, emphasizing the importance of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.
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Affiliation(s)
- Sarasi K. K. Galagedera
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
| | - Thuy P. Dao
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
| | - Suzanne E. Enos
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
| | - Antara Chaudhuri
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
| | - Jeremy D. Schmit
- Department of Physics, Kansas State University, Manhattan, KS66506
| | - Carlos A. Castañeda
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY13244
- BioInspired Institute, Syracuse University, Syracuse, NY13244
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9
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Dao TP, Rajendran A, Galagedera SKK, Haws W, Castañeda CA. Short N-terminal disordered regions and the proline-rich domain are major regulators of phase transitions for full-length UBQLN1, UBQLN2 and UBQLN4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559790. [PMID: 37808720 PMCID: PMC10557701 DOI: 10.1101/2023.09.27.559790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Highly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2 and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2 and UBQLN4 exhibit distinct phase behaviors in vitro. Strikingly, UBQLN4 phase separates at a much lower saturation concentration than UBQLN1. However, neither UBQLN1 nor UBQLN4 phase separates with a strong temperature dependence, unlike UBQLN2. We determined that the temperature-dependent phase behavior of UBQLN2 stems from its unique proline-rich (Pxx) region, which is absent in the other UBQLNs. We found that the short N-terminal disordered regions of UBQLN1, UBQLN2 and UBQLN4 inhibit UBQLN phase separation via electrostatics interactions. Charge variants of the N-terminal regions exhibit altered phase behaviors. Consistent with the sensitivity of UBQLN phase separation to the composition of the N-terminal regions, epitope tags placed on the N-termini of the UBQLNs tune phase separation. Overall, our in vitro results have important implications for studies of UBQLNs in cells, including the identification of phase separation as a potential mechanism to distinguish the cellular roles of UBQLNs, and the need to apply caution when using epitope tags to prevent experimental artifacts.
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Affiliation(s)
- Thuy P. Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Anitha Rajendran
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | | | - William Haws
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Carlos A. Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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10
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Nicy, Collepardo-Guevara R, Joseph JA, Wales DJ. Energy landscapes and heat capacity signatures for peptides correlate with phase separation propensity. QRB DISCOVERY 2023; 4:e7. [PMID: 37771761 PMCID: PMC10523320 DOI: 10.1017/qrd.2023.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/09/2023] [Accepted: 07/17/2023] [Indexed: 09/30/2023] Open
Abstract
Phase separation plays an important role in the formation of membraneless compartments within the cell and intrinsically disordered proteins with low-complexity sequences can drive this compartmentalisation. Various intermolecular forces, such as aromatic-aromatic and cation-aromatic interactions, promote phase separation. However, little is known about how the ability of proteins to phase separate under physiological conditions is encoded in their energy landscapes and this is the focus of the present investigation. Our results provide a first glimpse into how the energy landscapes of minimal peptides that contain - and cation- interactions differ from the peptides that lack amino acids with such interactions. The peaks in the heat capacity () as a function of temperature report on alternative low-lying conformations that differ significantly in terms of their enthalpic and entropic contributions. The analysis and subsequent quantification of frustration of the energy landscape suggest that the interactions that promote phase separation lead to features (peaks or inflection points) at low temperatures in . More features may occur for peptides containing residues with better phase separation propensity and the energy landscape is more frustrated for such peptides. Overall, this work links the features in the underlying single-molecule potential energy landscapes to their collective phase separation behaviour and identifies quantities ( and frustration metric) that can be utilised in soft material design.
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Affiliation(s)
- Nicy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Physics, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Jerelle A. Joseph
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - David J. Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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11
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Abstract
Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.
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Affiliation(s)
- Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Samuel R Cohen
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Furqan Dar
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307 Dresden, Germany
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12
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Zhang Z, Huang G, Song Z, Gatch AJ, Ding F. Amyloid Aggregation and Liquid-Liquid Phase Separation from the Perspective of Phase Transitions. J Phys Chem B 2023; 127:6241-6250. [PMID: 37414583 PMCID: PMC10404378 DOI: 10.1021/acs.jpcb.3c01426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Amyloid aggregation describes the aberrant self-assembly of peptides into ordered fibrils characterized by cross-β spine cores and is associated with many neurodegenerative diseases and Type 2 diabetes. Oligomers, populated during the early stage of aggregation, are found to be more cytotoxic than mature fibrils. Recently, many amyloidogenic peptides have been reported to undergo liquid-liquid phase separation (LLPS)─a biological process important for the compartmentalization of biomolecules in living cells─prior to fibril formation. Understanding the relationship between LLPS and amyloid aggregation, especially the formation of oligomers, is essential for uncovering disease mechanisms and mitigating amyloid toxicity. In this Perspective, available theories and models of amyloid aggregation and LLPS are first briefly reviewed. By drawing analogies to gas, liquid, and solid phases in thermodynamics, a phase diagram of protein monomer, droplet, and fibril states separated by coexistence lines can be inferred. Due to the high free energy barrier of fibrillization kinetically delaying the formation of fibril seeds out of the droplets, a "hidden" monomer-droplet coexistence line extends into the fibril phase. Amyloid aggregation can then be described as the equilibration process from the initial "out-of-equilibrium" state of a homogeneous solution of monomers to the final equilibrium state of stable amyloid fibrils coexisting with monomers and/or droplets via the formation of metastable or stable droplets as the intermediates. The relationship between droplets and oligomers is also discussed. We suggest that the droplet formation of LLPS should be considered in future studies of amyloid aggregation, which may help to better understand the aggregation process and develop therapeutic strategies to mitigate amyloid toxicity.
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Affiliation(s)
- Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Gangtong Huang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Zhiyuan Song
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Adam J. Gatch
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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13
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Malhotra I, Potoyan DA. Re-entrant transitions of locally stiff RNA chains in the presence of polycations leads to gelated architectures. SOFT MATTER 2023. [PMID: 37449795 PMCID: PMC10369498 DOI: 10.1039/d3sm00320e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
The liquid-liquid phase separation of protein and nucleic acid mixtures drives the formation of numerous membraneless compartments in cells. Temperature variation is commonly used for mapping condensate phase diagrams, which often display unique upper critical temperatures. Recent report on peptide-RNA mixtures has shown the existence of lower and upper critical solution temperatures, highlighting the importance of temperature-dependent solvent and ion-mediated forces. In the present work, we employ residue-level coarse-grained models of RNA and polycation peptide chains for simulating temperature-induced re-entrant transitions and shedding light on the role played by mobile ions, temperature-dependent dielectric permittivity, and local chain stiffness. We show that differences in bending rigidity can significantly modulate condensate topology leading to the formation of gelated or fibril like architectures. The study also finds that temperature dependence of water permittivity is generally sufficient for recapitulating experimentally observed closed loop and LCST phase diagrams of highly charged protein-RNA mixtures. However, we find that similar-looking closed-loop phase diagrams can correspond to vastly different condensate topologies.
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Affiliation(s)
- Isha Malhotra
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, USA.
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, USA.
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14
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Swasthi HM, Basalla JL, Dudley CE, Vecchiarelli AG, Chapman MR. Cell surface-localized CsgF condensate is a gatekeeper in bacterial curli subunit secretion. Nat Commun 2023; 14:2392. [PMID: 37100792 PMCID: PMC10133297 DOI: 10.1038/s41467-023-38089-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/14/2023] [Indexed: 04/28/2023] Open
Abstract
Curli are functional amyloids present on the outer membrane of E. coli. CsgF is required for the proper assembly of curli. Here, we found that the CsgF phase separates in vitro and that the ability of CsgF variants to phase-separate is tightly correlated with CsgF function during curli biogenesis. Substitution of phenylalanine residues in the CsgF N-terminus both reduced the propensity of CsgF to phase-separate and impaired curli assembly. Exogenous addition of purified CsgF complemented csgF - cells. This exogenous addition assay was used to assess the ability of CsgF variants to complement csgF ‒ cells. CsgF on the cell surface modulated the secretion of CsgA, the curli major subunit, to the cell surface. We also found that the CsgB nucleator protein can form SDS-insoluble aggregates within the dynamic CsgF condensate. We propose that these multicomponent CsgF-B condensates form a nucleation-competent complex that templates CsgA amyloid formation on the cell surface.
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Affiliation(s)
- Hema M Swasthi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Joseph L Basalla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Claire E Dudley
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Matthew R Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA.
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15
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Galagedera SKK, Dao TP, Enos SE, Chaudhuri A, Schmit JD, Castañeda CA. Decoding optimal ligand design for multicomponent condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532222. [PMID: 36993708 PMCID: PMC10054939 DOI: 10.1101/2023.03.13.532222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or post-translational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules for various cellular processes. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to the UBQLN2-binding surface of Ub or deviations from the optimal spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model that accurately described the effects of different hubs on UBQLN2 phase diagrams, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. Importantly, the extent to which polyubiquitin hubs can promote UBQLN2 phase separation are encoded in the spacings between Ub units as found for naturally-occurring chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. We expect our findings to extend to other condensates necessitating the consideration of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.
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Affiliation(s)
| | - Thuy P. Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Suzanne E. Enos
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Antara Chaudhuri
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Jeremy D. Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Carlos A. Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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16
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Dao TP, Castañeda CA. We con-dense if we want to; We can't leave AZUL outside. Structure 2023; 31:369-371. [PMID: 37028393 DOI: 10.1016/j.str.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 04/09/2023]
Abstract
In this issue of Structure, Buel et al. (2023) combined NMR data with AlphaFold2 to map out the interaction between the AZUL domain of ubiquitin ligase E6AP and UBQLN1/2 UBA. The authors demonstrated that this interaction enhances the self-association of the helix neighboring UBA and enables E6AP to localize to UBQLN2 droplets.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA; Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA; Program in Neuroscience, Syracuse University, Syracuse, NY 13244, USA.
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17
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Ginell GM, Holehouse AS. An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates. Methods Mol Biol 2023; 2563:95-116. [PMID: 36227469 DOI: 10.1007/978-1-0716-2663-4_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cellular organization is determined by a combination of membrane-bound and membrane-less biomolecular assemblies that range from clusters of tens of molecules to micrometer-sized cellular bodies. Over the last decade, membrane-less assemblies have come to be referred to as biomolecular condensates, reflecting their ability to condense specific molecules with respect to the remainder of the cell. In many cases, the physics of phase transitions provides a conceptual framework and a mathematical toolkit to describe the assembly, maintenance, and dissolution of biomolecular condensates. Among the various quantitative and qualitative models applied to understand intracellular phase transitions, the stickers-and-spacers framework offers an intuitive yet rigorous means to map biomolecular sequences and structure to the driving forces needed for higher-order assembly. This chapter introduces the fundamental concepts behind the stickers-and-spacers model, considers its application to different biological systems, and discusses limitations and misconceptions around the model.
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Affiliation(s)
- Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
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18
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Raymond-Smiedy P, Bucknor B, Yang Y, Zheng T, Castañeda CA. A Spectrophotometric Turbidity Assay to Study Liquid-Liquid Phase Separation of UBQLN2 In Vitro. Methods Mol Biol 2023; 2551:515-541. [PMID: 36310223 DOI: 10.1007/978-1-0716-2597-2_32] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Liquid-liquid phase separation (LLPS) is hypothesized to be the underlying mechanism for how membraneless organelles or biomolecular condensates form inside both prokaryotic and eukaryotic cells. Protein LLPS is a biophysical process during which proteins demix from homogeneous solution to form protein-dense droplets with liquid-like properties. Disruptions to LLPS, such as changes to material properties of condensates or physicochemical parameters for LLPS onset, are implicated in neurodegenerative diseases and cancer. Therefore, it is essential to determine the physicochemical parameters that promote protein LLPS. Here, we present our UV-Vis spectrophotometric turbidity assay to characterize the temperature and concentration dependence of LLPS for UBQLN2, a protein that undergoes LLPS via homotypic interactions in vitro and forms stress-induced condensates in cells. Mutations in UBQLN2 cause amyotrophic lateral sclerosis (ALS) and disrupt UBQLN2 LLPS. We present a detailed expression and purification protocol for a C-terminal construct of UBQLN2 and how we use microscopy to image UBQLN2 LLPS. We use our UV-Vis assay to construct temperature-concentration phase diagrams for wild-type and mutant UBQLN2 constructs to determine the effects of domain deletions and/or mutations on UBQLN2 phase separation.
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Affiliation(s)
| | - Barrington Bucknor
- Department of Biology, Syracuse University, Syracuse, NY, USA
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
- Program in Neuroscience, Syracuse University, Syracuse, NY, USA
| | - Yiran Yang
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Tongyin Zheng
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Carlos A Castañeda
- Department of Biology, Syracuse University, Syracuse, NY, USA.
- Department of Chemistry, Syracuse University, Syracuse, NY, USA.
- Program in Neuroscience, Syracuse University, Syracuse, NY, USA.
- BioInspired Institute, Syracuse University, Syracuse, NY, USA.
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19
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Safren N, Sharkey LM, Barmada SJ. Neuronal Puncta/Aggregate Formation by WT and Mutant UBQLN2. Methods Mol Biol 2023; 2551:561-573. [PMID: 36310225 PMCID: PMC10519613 DOI: 10.1007/978-1-0716-2597-2_34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein aggregates are a common feature of nearly all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS). Here we describe a method to quickly and accurately measure protein aggregation in cells expressing a fluorescently tagged aggregation-prone protein. This unbiased method obviates the need for manual scoring and facilitates the identification of factors governing protein self-assembly and its downstream consequences for cell heath.
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Affiliation(s)
- Nathaniel Safren
- Department of Neurology, University of Michigan Health System, Ann Arbor, MI, USA
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan Health System, Ann Arbor, MI, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan Health System, Ann Arbor, MI, USA.
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20
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Ibrahim AY, Khaodeuanepheng NP, Amarasekara DL, Correia JJ, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. Intrinsically disordered regions that drive phase separation form a robustly distinct protein class. J Biol Chem 2022; 299:102801. [PMID: 36528065 PMCID: PMC9860499 DOI: 10.1016/j.jbc.2022.102801] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Protein phase separation is thought to be a primary driving force for the formation of membrane-less organelles, which control a wide range of biological functions from stress response to ribosome biogenesis. Among phase-separating (PS) proteins, many have intrinsically disordered regions (IDRs) that are needed for phase separation to occur. Accurate identification of IDRs that drive phase separation is important for testing the underlying mechanisms of phase separation, identifying biological processes that rely on phase separation, and designing sequences that modulate phase separation. To identify IDRs that drive phase separation, we first curated datasets of folded, ID, and PS ID sequences. We then used these sequence sets to examine how broadly existing amino acid property scales can be used to distinguish between the three classes of protein regions. We found that there are robust property differences between the classes and, consequently, that numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. This result indicates that multiple, redundant mechanisms contribute to the formation of phase-separated droplets from IDRs. The top-performing scales were used to further optimize our previously developed predictor of PS IDRs, ParSe. We then modified ParSe to account for interactions between amino acids and obtained reasonable predictive power for mutations that have been designed to test the role of amino acid interactions in driving protein phase separation. Collectively, our findings provide further insight into the classification of IDRs and the elements involved in protein phase separation.
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Affiliation(s)
- Ayyam Y. Ibrahim
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | | | - John J. Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Karen A. Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | - Loren E. Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA,For correspondence: Steven T. Whitten; Loren E. Hough
| | - Steven T. Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA,For correspondence: Steven T. Whitten; Loren E. Hough
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21
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Molecular and environmental determinants of biomolecular condensate formation. Nat Chem Biol 2022; 18:1319-1329. [DOI: 10.1038/s41589-022-01175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/15/2022] [Indexed: 11/21/2022]
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22
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Palumbo RJ, McKean N, Leatherman E, Namitz KEW, Connell L, Wolfe A, Moody K, Gostinčar C, Gunde-Cimerman N, Bah A, Hanes SD. Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance. SCIENCE ADVANCES 2022; 8:eabq3235. [PMID: 36070379 PMCID: PMC9451162 DOI: 10.1126/sciadv.abq3235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/21/2022] [Indexed: 06/14/2023]
Abstract
Most of the world's biodiversity lives in cold (-2° to 4°C) and hypersaline environments. To understand how cells adapt to such conditions, we isolated two key components of the transcription machinery from fungal species that live in extreme polar environments: the Ess1 prolyl isomerase and its target, the carboxy-terminal domain (CTD) of RNA polymerase II. Polar Ess1 enzymes are conserved and functional in the model yeast, Saccharomyces cerevisiae. By contrast, polar CTDs diverge from the consensus (YSPTSPS)26 and are not fully functional in S. cerevisiae. These CTDs retain the critical Ess1 Ser-Pro target motifs, but substitutions at Y1, T4, and S7 profoundly affected their ability to undergo phase separation in vitro and localize in vivo. We propose that environmentally tuned phase separation by the CTD and other intrinsically disordered regions plays an adaptive role in cold tolerance by concentrating enzymes and substrates to overcome energetic barriers to metabolic activity.
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Affiliation(s)
- Ryan J. Palumbo
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Nathan McKean
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Erinn Leatherman
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Kevin E. W. Namitz
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Laurie Connell
- School of Marine Sciences and Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - Aaron Wolfe
- Ichor Life Sciences Inc., 2651 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Kelsey Moody
- Ichor Life Sciences Inc., 2651 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Alaji Bah
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Steven D. Hanes
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
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23
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Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA. Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep 2022; 23:e55056. [PMID: 35762418 PMCID: PMC9346500 DOI: 10.15252/embr.202255056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ubiquitin‐binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48‐ and K63‐linked polyubiquitin chains, respectively. UBQLN2 comprises self‐associating regions that drive its homotypic liquid–liquid phase separation (LLPS). Specific interactions between one of these regions and ubiquitin inhibit UBQLN2 LLPS. Here, we show that, unlike ubiquitin, the effects of multivalent polyubiquitin chains on UBQLN2 LLPS are highly dependent on chain types. Specifically, K11‐Ub4 and K48‐Ub4 chains generally inhibit UBQLN2 LLPS, whereas K63‐Ub4, M1‐Ub4 chains, and a designed tetrameric ubiquitin construct significantly enhance LLPS. We demonstrate that these opposing effects stem from differences in chain conformations but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin‐binding surface promote UBQLN2 LLPS by enabling a switch between homotypic to partially heterotypic LLPS that is driven by both UBQLN2 self‐interactions and interactions between multiple UBQLN2 units with each polyubiquitin chain. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic LLPS with ubiquitin‐binding shuttles and adaptors.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
| | - Yiran Yang
- Department of Chemistry Syracuse University Syracuse NY USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Weikang Ma
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
- Interdisciplinary Neuroscience Program Syracuse University Syracuse NY USA
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24
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Liu J, Zhorabek F, Dai X, Huang J, Chau Y. Minimalist Design of an Intrinsically Disordered Protein-Mimicking Scaffold for an Artificial Membraneless Organelle. ACS CENTRAL SCIENCE 2022; 8:493-500. [PMID: 35505868 PMCID: PMC9052801 DOI: 10.1021/acscentsci.1c01021] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 05/05/2023]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging and universal mechanism for intracellular organization, particularly, by forming membraneless organelles (MLOs) hosting intrinsically disordered proteins (IDPs) as scaffolds. Genetic engineering is generally applied to reconstruct IDPs harboring over 100 amino acid residues. Here, we report the first design of synthetic hybrids consisting of short oligopeptides of fewer than 10 residues as "stickers" and dextran as a "spacer" to recapitulate the characteristics of IDPs, as exemplified by the multivalent FUS protein. Hybrids undergo LLPS into micron-sized liquid droplets resembling LLPS in vitro and in living cells. Moreover, the droplets formed are capable of recruiting proteins and RNAs and providing a favorable environment for a biochemical reaction with highly enriched components, thereby mimicking the function of natural MLOs. This simple yet versatile model system can help elucidate the molecular interactions implicated in MLOs and pave ways to a new type of biomimetic materials.
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Affiliation(s)
- Jianhui Liu
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Fariza Zhorabek
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Xin Dai
- Department
of Chemistry, The Hong Kong University of
Science and Technology, Clear Water
Bay, Kowloon, Hong Kong SAR, China
| | - Jinqing Huang
- Department
of Chemistry, The Hong Kong University of
Science and Technology, Clear Water
Bay, Kowloon, Hong Kong SAR, China
| | - Ying Chau
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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25
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Kuechler ER, Jacobson M, Mayor T, Gsponer J. GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents. Nucleic Acids Res 2022; 50:W384-W391. [PMID: 35474477 PMCID: PMC9252806 DOI: 10.1093/nar/gkac279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/27/2022] [Accepted: 04/09/2022] [Indexed: 01/30/2023] Open
Abstract
Phase separation-based condensate formation is a novel working paradigm in biology, helping to rationalize many important cellular phenomena including the assembly of membraneless organelles. Uncovering the functional impact of cellular condensates requires a better knowledge of these condensates’ constituents. Herein, we introduce the webserver GraPES (Granule Protein Enrichment Server), a user-friendly online interface containing the MaGS and MaGSeq predictors, which provide propensity scores for proteins’ localization into cellular condensates. Our webpage contains models trained on human (Homo sapiens) and yeast (Saccharomyces cerevisiae) stress granule proteins. MaGS utilizes experimentally-based protein features for prediction, whereas MaGSeq is an entirely protein sequence-based implementation. GraPES is implemented in HTML/CSS and Javascript and is freely available for public use at https://grapes.msl.ubc.ca/. Documentation for using the provided webtools, descriptions of their methodology, and implementation notes can be found on the webpage.
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Affiliation(s)
- Erich R Kuechler
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Jacobson
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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26
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RNA chain length and stoichiometry govern surface tension and stability of protein-RNA condensates. iScience 2022; 25:104105. [PMID: 35378855 PMCID: PMC8976129 DOI: 10.1016/j.isci.2022.104105] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/23/2022] [Accepted: 03/15/2022] [Indexed: 12/28/2022] Open
Abstract
Proteomic studies have shown that cellular condensates are frequently enriched in diverse RNA molecules, which is suggestive of mechanistic links between phase separation and transcriptional activities. Here, we report a systematic experimental and computational study of thermodynamic landscapes and interfacial properties of protein-RNA condensates. We have studied the affinity of protein-RNA condensation as a function of variable RNA sequence length and RNA-protein stoichiometry under different ionic environments and external crowding. We have chosen the PolyU sequences for RNA and arginine/glycine-rich intrinsically disordered peptide (RGG) for proteins as a model system of RNA-protein condensates, which we then investigate through in vitro microscopy measurements and coarse-grained molecular dynamics simulations. We find that crowding and RNA chain length can have a major stabilizing effect on the condensation. We also find that the RNA-protein charge ratio is a crucial variable controlling stability, interfacial properties, and the reentrant phase behavior of RGG-RNA mixtures. LLPS with long RNAs is favored because of the lower entropic penalty of dissociation RNA chain length modulates interfacial and material properties of condensates Crowding can stabilize condensates with shorter RNAs Salt reduces the reentrant LLPS window but does not change the optimal stoichiometry
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27
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Role of the Ubiquitin System in Stress Granule Metabolism. Int J Mol Sci 2022; 23:ijms23073624. [PMID: 35408984 PMCID: PMC8999021 DOI: 10.3390/ijms23073624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/01/2023] Open
Abstract
Eukaryotic cells react to various stress conditions with the rapid formation of membrane-less organelles called stress granules (SGs). SGs form by multivalent interactions between RNAs and RNA-binding proteins and are believed to protect stalled translation initiation complexes from stress-induced degradation. SGs contain hundreds of different mRNAs and proteins, and their assembly and disassembly are tightly controlled by post-translational modifications. The ubiquitin system, which mediates the covalent modification of target proteins with the small protein ubiquitin (‘ubiquitylation’), has been implicated in different aspects of SG metabolism, but specific functions in SG turnover have only recently emerged. Here, we summarize the evidence for the presence of ubiquitylated proteins at SGs, review the functions of different components of the ubiquitin system in SG formation and clearance, and discuss the link between perturbed SG clearance and the pathogenesis of neurodegenerative disorders. We conclude that the ubiquitin system plays an important, medically relevant role in SG biology.
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Li L, Casalini T, Arosio P, Salvalaglio M. Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations. J Chem Theory Comput 2022; 18:1915-1928. [PMID: 35174713 PMCID: PMC9097291 DOI: 10.1021/acs.jctc.1c00889] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 01/08/2023]
Abstract
Intrinsically disordered proteins play a key role in many biological processes, including the formation of biomolecular condensates within cells. A detailed characterization of their configurational ensemble and structure-function paradigm is crucial for understanding their biological activity and for exploiting them as building blocks in material sciences. In this work, we incorporate bias-exchange metadynamics and parallel-tempering well-tempered metadynamics with CHARMM36m and CHARMM22* to explore the structural and thermodynamic characteristics of a short archetypal disordered sequence derived from a DEAD-box protein. The conformational landscapes emerging from our simulations are largely congruent across methods and force fields. Nevertheless, differences in fine details emerge from varying combinations of force-fields and sampling methods. For this protein, our analysis identifies features that help to explain the low propensity of this sequence to undergo self-association in vitro, which are common to all force-field/sampling method combinations. Overall, our work demonstrates the importance of using multiple force-field and sampling method combinations for accurate structural and thermodynamic information in the study of disordered proteins.
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Affiliation(s)
- Lunna Li
- Thomas
Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, U.K.
| | - Tommaso Casalini
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Matteo Salvalaglio
- Thomas
Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, U.K.
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29
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Bremer A, Farag M, Borcherds WM, Peran I, Martin EW, Pappu RV, Mittag T. Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains. Nat Chem 2022; 14:196-207. [PMID: 34931046 PMCID: PMC8818026 DOI: 10.1038/s41557-021-00840-w] [Citation(s) in RCA: 174] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 10/19/2021] [Indexed: 12/20/2022]
Abstract
Prion-like low-complexity domains (PLCDs) have distinctive sequence grammars that determine their driving forces for phase separation. Here we uncover the physicochemical underpinnings of how evolutionarily conserved compositional biases influence the phase behaviour of PLCDs. We interpret our results in the context of the stickers-and-spacers model for the phase separation of associative polymers. We find that tyrosine is a stronger sticker than phenylalanine, whereas arginine is a context-dependent auxiliary sticker. In contrast, lysine weakens sticker-sticker interactions. Increasing the net charge per residue destabilizes phase separation while also weakening the strong coupling between single-chain contraction in dilute phases and multichain interactions that give rise to phase separation. Finally, glycine and serine residues act as non-equivalent spacers, and thus make the glycine versus serine contents an important determinant of the driving forces for phase separation. The totality of our results leads to a set of rules that enable comparative estimates of composition-specific driving forces for PLCD phase separation.
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Affiliation(s)
- Anne Bremer
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mina Farag
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St Louis, St Louis, MO, USA
| | - Wade M Borcherds
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ivan Peran
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Erik W Martin
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St Louis, St Louis, MO, USA.
| | - Tanja Mittag
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
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30
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Michels JJ, Brzezinski M, Scheidt T, Lemke EA, Parekh SH. Role of Solvent Compatibility in the Phase Behavior of Binary Solutions of Weakly Associating Multivalent Polymers. Biomacromolecules 2022; 23:349-364. [PMID: 34866377 PMCID: PMC8753604 DOI: 10.1021/acs.biomac.1c01301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/23/2021] [Indexed: 11/29/2022]
Abstract
Condensate formation of biopolymer solutions, prominently those of various intrinsically disordered proteins (IDPs), is often driven by "sticky" interactions between associating residues, multivalently present along the polymer backbone. Using a ternary mean-field "stickers-and-spacers" model, we demonstrate that if sticker association is of the order of a few times the thermal energy, a delicate balance between specific binding and nonspecific polymer-solvent interactions gives rise to a particularly rich ternary phase behavior under physiological circumstances. For a generic system represented by a solution comprising multiassociative scaffold and client polymers, the difference in solvent compatibility between the polymers modulates the nature of isothermal liquid-liquid phase separation (LLPS) between associative and segregative. The calculations reveal regimes of dualistic phase behavior, where both types of LLPS occur within the same phase diagram, either associated with the presence of multiple miscibility gaps or a flip in the slope of the tie-lines belonging to a single coexistence region.
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Affiliation(s)
- Jasper J. Michels
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mateusz Brzezinski
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tom Scheidt
- Institute
for Molecular Biology, Johannes Gutenberg
University, Ackermannweg
4, 55128 Mainz, Germany
| | - Edward A. Lemke
- Institute
for Molecular Biology, Johannes Gutenberg
University, Ackermannweg
4, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street Stop C0800, Austin, Texas 78712, United States
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31
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Kanekura K, Hayamizu Y, Kuroda M. Order controls disordered droplets: structure-function relationships in C9orf72-derived poly(PR). Am J Physiol Cell Physiol 2021; 322:C197-C204. [PMID: 34910602 DOI: 10.1152/ajpcell.00372.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) have been thought as two distinct neurodegenerative diseases. However, recent genetic screening and careful investigations found the genetic and pathological overlap among these disorders. Hexanucleotide expansions in intron 1 of C9orf72 are a leading cause of familial ALS and familial FTD. These expansions facilitate the repeat-associated non-ATG initiated translation (RAN translation), producing five dipeptide repeat proteins (DRPs), including Arg-rich poly(PR: Pro-Arg) and poly-(GR: Gly-Arg) peptides. Arg is a positively charged, highly polar amino acid that facilitates interactions with anionic molecules such as nucleic acids and acidic amino acids via electrostatic forces and aromatic amino acids via cation-pi interaction, suggesting that Arg-rich DRPs underlie the pathophysiology of ALS via Arg-mediated molecular interactions. Arg-rich DRPs have also been reported to induce neurodegeneration in cellular and animal models via multiple mechanisms; however, it remains unclear why the Arg-rich DRPs exhibit such diverse toxic properties, because not all Arg-rich peptides are toxic. In this mini-review, we discuss the current understanding of the pathophysiology of Arg-rich C9orf72 DRPs and introduce recent findings on the role of Arg distribution as a determinant of the toxicity and its contribution to the pathogenesis of ALS.
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Affiliation(s)
- Kohsuke Kanekura
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Tokyo, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Tokyo, Japan
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32
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Holehouse AS, Ginell GM, Griffith D, Böke E. Clustering of Aromatic Residues in Prion-like Domains Can Tune the Formation, State, and Organization of Biomolecular Condensates. Biochemistry 2021; 60:3566-3581. [PMID: 34784177 PMCID: PMC8638251 DOI: 10.1021/acs.biochem.1c00465] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/29/2021] [Indexed: 12/12/2022]
Abstract
In immature oocytes, Balbiani bodies are conserved membraneless condensates implicated in oocyte polarization, the organization of mitochondria, and long-term organelle and RNA storage. In Xenopus laevis, Balbiani body assembly is mediated by the protein Velo1. Velo1 contains an N-terminal prion-like domain (PLD) that is essential for Balbiani body formation. PLDs have emerged as a class of intrinsically disordered regions that can undergo various different types of intracellular phase transitions and are often associated with dynamic, liquid-like condensates. Intriguingly, the Velo1 PLD forms solid-like assemblies. Here we sought to understand why Velo1 phase behavior appears to be biophysically distinct from that of other PLD-containing proteins. Through bioinformatic analysis and coarse-grained simulations, we predict that the clustering of aromatic residues and the amino acid composition of residues between aromatics can influence condensate material properties, organization, and the driving forces for assembly. To test our predictions, we redesigned the Velo1 PLD to test the impact of targeted sequence changes in vivo. We found that the Velo1 design with evenly spaced aromatic residues shows rapid internal dynamics, as probed by fluorescent recovery after photobleaching, even when recruited into Balbiani bodies. Our results suggest that Velo1 might have been selected in evolution for distinctly clustered aromatic residues to maintain the structure of Balbiani bodies in long-lived oocytes. In general, our work identifies several tunable parameters that can be used to augment the condensate material state, offering a road map for the design of synthetic condensates.
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Affiliation(s)
- Alex S. Holehouse
- Department
of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center
for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, Missouri 63130, United States
| | - Garrett M. Ginell
- Department
of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center
for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, Missouri 63130, United States
| | - Daniel Griffith
- Department
of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center
for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, Missouri 63130, United States
| | - Elvan Böke
- Centre
for Genomic Regulation (CRG), The Barcelona
Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat
Pompeu Fabra (UPF), Barcelona 08002, Spain
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33
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Paiz EA, Allen JH, Correia JJ, Fitzkee NC, Hough LE, Whitten ST. Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins. J Biol Chem 2021; 297:101343. [PMID: 34710373 PMCID: PMC8592878 DOI: 10.1016/j.jbc.2021.101343] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
The complex cellular milieu can spontaneously demix, or phase separate, in a process controlled in part by intrinsically disordered (ID) proteins. A protein's propensity to phase separate is thought to be driven by a preference for protein-protein over protein-solvent interactions. The hydrodynamic size of monomeric proteins, as quantified by the polymer scaling exponent (v), is driven by a similar balance. We hypothesized that mean v, as predicted by protein sequence, would be smaller for proteins with a strong propensity to phase separate. To test this hypothesis, we analyzed protein databases containing subsets of proteins that are folded, disordered, or disordered and known to spontaneously phase separate. We find that the phase-separating disordered proteins, on average, had lower calculated values of v compared with their non-phase-separating counterparts. Moreover, these proteins had a higher sequence-predicted propensity for β-turns. Using a simple, surface area-based model, we propose a physical mechanism for this difference: transient β-turn structures reduce the desolvation penalty of forming a protein-rich phase and increase exposure of atoms involved in π/sp2 valence electron interactions. By this mechanism, β-turns could act as energetically favored nucleation points, which may explain the increased propensity for turns in ID regions (IDRs) utilized biologically for phase separation. Phase-separating IDRs, non-phase-separating IDRs, and folded regions could be distinguished by combining v and β-turn propensity. Finally, we propose a new algorithm, ParSe (partition sequence), for predicting phase-separating protein regions, and which is able to accurately identify folded, disordered, and phase-separating protein regions based on the primary sequence.
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Affiliation(s)
- Elisia A Paiz
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Jeffre H Allen
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - John J Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Loren E Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA.
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA.
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34
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Ryu JK, Hwang DE, Choi JM. Current Understanding of Molecular Phase Separation in Chromosomes. Int J Mol Sci 2021; 22:10736. [PMID: 34639077 PMCID: PMC8509192 DOI: 10.3390/ijms221910736] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation. Recent studies have found that biomolecular phase separation is involved in a wide range of cellular processes. In particular, phase separation is involved in the formation and regulation of chromosome structures at various levels. Here, we review the current understanding of biomolecular phase separation related to chromosomes. First, we discuss the fundamental principles of phase separation and introduce several examples of nuclear/chromosomal biomolecular assemblies formed by phase separation. We also briefly explain the experimental and computational methods used to study phase separation in chromosomes. Finally, we discuss a recent phase separation model, termed bridging-induced phase separation (BIPS), which can explain the formation of local chromosome structures.
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Affiliation(s)
- Je-Kyung Ryu
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea;
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea;
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35
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Therapeutics-how to treat phase separation-associated diseases. Emerg Top Life Sci 2021; 4:307-318. [PMID: 32364240 PMCID: PMC7733670 DOI: 10.1042/etls20190176] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022]
Abstract
Liquid-liquid phase separation has drawn attention as many neurodegeneration or cancer-associated proteins are able to form liquid membraneless compartments (condensates) by liquid-liquid phase separation. Furthermore, there is rapidly growing evidence that disease-associated mutation or post-translational modification of these proteins causes aberrant location, composition or physical properties of the condensates. It is ambiguous whether aberrant condensates are always causative in disease mechanisms, however they are likely promising potential targets for therapeutics. The conceptual framework of liquid-liquid phase separation provides opportunities for novel therapeutic approaches. This review summarises how the extensive recent advances in understanding control of nucleation, growth and composition of condensates by protein post-translational modification has revealed many possibilities for intervention by conventional small molecule enzyme inhibitors. This includes the first proof-of-concept examples. However, understanding membraneless organelle formation as a physical chemistry process also highlights possible physicochemical mechanisms of intervention. There is huge demand for innovation in drug development, especially for challenging diseases of old age including neurodegeneration and cancer. The conceptual framework of liquid-liquid phase separation provides a new paradigm for thinking about modulating protein function and is very different from enzyme lock-and-key or structured binding site concepts and presents new opportunities for innovation.
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36
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Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof. Emerg Top Life Sci 2021; 4:307-329. [PMID: 33078839 DOI: 10.1042/etls20190164] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered protein regions (IDRs) - regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations - have recently entered mainstream cell biology in the context of liquid-liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than 'disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.
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37
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Wohl S, Jakubowski M, Zheng W. Salt-Dependent Conformational Changes of Intrinsically Disordered Proteins. J Phys Chem Lett 2021; 12:6684-6691. [PMID: 34259536 DOI: 10.1021/acs.jpclett.1c01607] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The flexible structure of an intrinsically disordered protein (IDP) is known to be perturbed by salt concentrations, which can be understood by electrostatic screening on charged amino acids. However, an IDP usually contains more uncharged residues that are influenced by the salting-out effect. Here we have parametrized the salting-out effect into a coarse-grained model using a set of Förster resonance energy transfer data and verified with experimental salt-dependent liquid-liquid phase separation (LLPS) of 17 proteins. The new model can correctly capture the behavior of 6 more sequences, resulting in a total of 13 when varying salt concentrations. Together with a survey of more than 500 IDP sequences, we conclude that the salting-out effect, which was considered to be secondary to electrostatic screening, is important for IDP sequences with moderately charged residues at physiological salt concentrations. The presented scheme is generally applicable to other computational models for capturing salt-dependent IDP conformations.
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Affiliation(s)
- Samuel Wohl
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthew Jakubowski
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
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38
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Zheng T, Galagedera SKK, Castañeda CA. Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation. Protein Sci 2021; 30:1467-1481. [PMID: 34029402 DOI: 10.1002/pro.4128] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023]
Abstract
Shuttle protein UBQLN2 functions in protein quality control (PQC) by binding to proteasomal receptors and ubiquitinated substrates via its N-terminal ubiquitin-like (UBL) and C-terminal ubiquitin-associated (UBA) domains, respectively. Between these two folded domains are low-complexity STI1-I and STI1-II regions, connected by disordered linkers. The STI1 regions bind other components, such as HSP70, that are important to the PQC functions of UBQLN2. We recently determined that the STI1-II region enables UBQLN2 to undergo liquid-liquid phase separation (LLPS) to form liquid droplets in vitro and biomolecular condensates in cells. However, how the interplay between the folded (UBL/UBA) domains and the intrinsically disordered regions mediates phase separation is largely unknown. Using engineered domain deletion constructs, we found that removing the UBA domain inhibits UBQLN2 LLPS while removing the UBL domain enhances LLPS, suggesting that UBA and UBL domains contribute asymmetrically in modulating UBQLN2 LLPS. To explain these differential effects, we interrogated the interactions that involve the UBA and UBL domains across the entire UBQLN2 molecule using nuclear magnetic resonance spectroscopy. To our surprise, aside from well-studied canonical UBL:UBA interactions, there also exist moderate interactions between the UBL and several disordered regions, including STI1-I and residues 555-570, the latter of which is a known contributor to UBQLN2 LLPS. Our findings are essential for the understanding of both the molecular driving forces of UBQLN2 LLPS and the effects of ligand binding to UBL, UBA, or disordered regions on the phase behavior and physiological functions of UBQLN2.
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Affiliation(s)
- Tongyin Zheng
- Department of Chemistry, Syracuse University, Syracuse, New York, USA
| | | | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, New York, USA.,BioInspired Institute, Syracuse University, Syracuse, New York, USA
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39
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Ruff KM, Dar F, Pappu RV. Polyphasic linkage and the impact of ligand binding on the regulation of biomolecular condensates. BIOPHYSICS REVIEWS 2021; 2:021302. [PMID: 34179888 PMCID: PMC8211317 DOI: 10.1063/5.0050059] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/30/2022]
Abstract
Cellular matter can be spatially and temporally organized into membraneless biomolecular condensates. The current thinking is that these condensates form and dissolve via phase transitions driven by one or more condensate-specific multivalent macromolecules known as scaffolds. Cells likely regulate condensate formation and dissolution by exerting control over the concentrations of regulatory molecules, which we refer to as ligands. Wyman and Gill introduced the framework of polyphasic linkage to explain how ligands can exert thermodynamic control over phase transitions. This review focuses on describing the concepts of polyphasic linkage and the relevance of such a mechanism for controlling condensate formation and dissolution. We describe how ligand-mediated control over scaffold phase behavior can be quantified experimentally. Further, we build on recent studies to highlight features of ligands that make them suppressors vs drivers of phase separation. Finally, we highlight areas where advances are needed to further understand ligand-mediated control of condensates in complex cellular environments. These advances include understanding the effects of networks of ligands on condensate behavior and how ligands modulate phase transitions controlled by different combinations of homotypic and heterotypic interactions among scaffold macromolecules. Insights gained from the application of polyphasic linkage concepts should be useful for designing novel pharmaceutical ligands to regulate condensates.
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Affiliation(s)
- Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Furqan Dar
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, USA
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40
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Lei L, Wu Z, Winklhofer KF. Protein quality control by the proteasome and autophagy: A regulatory role of ubiquitin and liquid-liquid phase separation. Matrix Biol 2021; 100-101:9-22. [DOI: 10.1016/j.matbio.2020.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
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41
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Regy RM, Thompson J, Kim YC, Mittal J. Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins. Protein Sci 2021; 30:1371-1379. [PMID: 33934416 DOI: 10.1002/pro.4094] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 12/28/2022]
Abstract
We present improvements to the hydropathy scale (HPS) coarse-grained (CG) model for simulating sequence-specific behavior of intrinsically disordered proteins (IDPs), including their liquid-liquid phase separation (LLPS). The previous model based on an atomistic hydropathy scale by Kapcha and Rossky (KR scale) is not able to capture some well-known LLPS trends such as reduced phase separation propensity upon mutations (R-to-K and Y-to-F). Here, we propose to use the Urry hydropathy scale instead, which was derived from the inverse temperature transitions in a model polypeptide with guest residues X. We introduce two free parameters to shift (Δ) and scale (µ) the overall interaction strengths for the new model (HPS-Urry) and use the experimental radius of gyration for a diverse group of IDPs to find their optimal values. Interestingly, many possible (Δ, µ) combinations can be used for typical IDPs, but the phase behavior of a low-complexity (LC) sequence FUS is only well described by one of these models, which highlights the need for a careful validation strategy based on multiple proteins. The CG HPS-Urry model should enable accurate simulations of protein LLPS and provide a microscopically detailed view of molecular interactions.
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Affiliation(s)
- Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Jacob Thompson
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
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42
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Dong X, Bera S, Qiao Q, Tang Y, Lao Z, Luo Y, Gazit E, Wei G. Liquid-Liquid Phase Separation of Tau Protein Is Encoded at the Monomeric Level. J Phys Chem Lett 2021; 12:2576-2586. [PMID: 33686854 DOI: 10.1021/acs.jpclett.1c00208] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Liquid-liquid phase separation (LLPS) is involved in both physiological and pathological processes. The intrinsically disordered protein Tau and its K18 construct can undergo LLPS in a distinct temperature-dependent manner, and the LLPS of Tau protein can initiate Tau aggregation. However, the underlying mechanism driving Tau LLPS remains largely elusive. To understand the temperature-dependent LLPS behavior of Tau at the monomeric level, we explored the conformational ensemble of Tau at different temperatures by performing all-atom replica-exchange molecular dynamic simulation on K18 monomer with an accumulated simulation time of 26.4 μs. Our simulation demonstrates that the compactness, β-structure propensity, and intramolecular interaction of K18 monomer exhibit nonlinear temperature-dependent behavior. 295DNIKHV300/326GNIHHK331/337VEVKSE342 make significant contributions to the temperature dependence of the β propensity of K18 monomer, while the two fibril-nucleating cores display relatively high β propensity at all temperatures. At a specific temperature, K18 monomer adopts the most collapsed state with exposed sites for both persistent and transient interactions. Given that more collapsed polypeptide chains were reported to be more prone to phase separate, our results suggest that K18 monomer inherently possesses conformational characteristics favoring LLPS. Our simulation predicts the importance of 295DNIKHV300/326GNIHHK331/337VEVKSE342 to the temperature-dependent conformational properties of K18, which is corroborated by CD spectra, turbidity assays, and DIC microscopy. Taken together, we offer a computational and experimental approach to comprehend the structural basis for LLPS by amyloidal building blocks.
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Affiliation(s)
- Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Santu Bera
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Qin Qiao
- Digital Medical Research Center, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai 200032, People's Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Yin Luo
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
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43
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Schuster BS, Regy RM, Dolan EM, Kanchi Ranganath A, Jovic N, Khare SD, Shi Z, Mittal J. Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties. J Phys Chem B 2021; 125:3441-3451. [PMID: 33661634 DOI: 10.1021/acs.jpcb.0c11606] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This perspective article highlights recent progress and emerging challenges in understanding the formation and function of membraneless organelles (MLOs). A long-term goal in the MLO field is to identify the sequence-encoded rules that dictate the formation of compositionally controlled biomolecular condensates, which cells utilize to perform a wide variety of functions. The molecular organization of the different components within a condensate can vary significantly, ranging from a homogeneous mixture to core-shell droplet structures. We provide many examples to highlight the richness of the observed behavior and potential research directions for improving our mechanistic understanding. The tunable environment within condensates can, in principle, alter enzymatic activity significantly. We examine recent examples where this was demonstrated, including applications in synthetic biology. An important question about MLOs is the role of liquid-like material properties in biological function. We discuss the need for improved quantitative characterization tools and the development of sequence-structure-dynamics relationships.
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Affiliation(s)
- Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Elliott M Dolan
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Aishwarya Kanchi Ranganath
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Zheng Shi
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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44
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Dao TP, Castañeda CA. Ubiquitin-Modulated Phase Separation of Shuttle Proteins: Does Condensate Formation Promote Protein Degradation? Bioessays 2020; 42:e2000036. [PMID: 32881044 PMCID: PMC7737676 DOI: 10.1002/bies.202000036] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/29/2020] [Indexed: 12/14/2022]
Abstract
Liquid-liquid phase separation (LLPS) has recently emerged as a possible mechanism that enables ubiquitin-binding shuttle proteins to facilitate the degradation of ubiquitinated substrates via distinct protein quality control (PQC) pathways. Shuttle protein LLPS is modulated by multivalent interactions among their various domains as well as heterotypic interactions with polyubiquitin chains. Here, the properties of three different shuttle proteins (hHR23B, p62, and UBQLN2) are closely examined, unifying principles for the molecular determinants of their LLPS are identified, and how LLPS is connected to their functions is discussed. Evidence supporting LLPS of other shuttle proteins is also found. In this review, it is proposed that shuttle protein LLPS leads to spatiotemporal regulation of PQC activities by mediating the recruitment of PQC machinery (including proteasomes or autophagic components) to biomolecular condensates, assembly/disassembly of condensates, selective enrichment of client proteins, and extraction of ubiquitinated proteins from condensates in cells.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY, 13244, USA
- Bioinspired Institute, Syracuse University, Syracuse, NY, 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY, 13244, USA
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45
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Zheng T, Yang Y, Castañeda CA. Structure, dynamics and functions of UBQLNs: at the crossroads of protein quality control machinery. Biochem J 2020; 477:3471-3497. [PMID: 32965492 PMCID: PMC7737201 DOI: 10.1042/bcj20190497] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Cells rely on protein homeostasis to maintain proper biological functions. Dysregulation of protein homeostasis contributes to the pathogenesis of many neurodegenerative diseases and cancers. Ubiquilins (UBQLNs) are versatile proteins that engage with many components of protein quality control (PQC) machinery in cells. Disease-linked mutations of UBQLNs are most commonly associated with amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and other neurodegenerative disorders. UBQLNs play well-established roles in PQC processes, including facilitating degradation of substrates through the ubiquitin-proteasome system (UPS), autophagy, and endoplasmic-reticulum-associated protein degradation (ERAD) pathways. In addition, UBQLNs engage with chaperones to sequester, degrade, or assist repair of misfolded client proteins. Furthermore, UBQLNs regulate DNA damage repair mechanisms, interact with RNA-binding proteins (RBPs), and engage with cytoskeletal elements to regulate cell differentiation and development. Important to the myriad functions of UBQLNs are its multidomain architecture and ability to self-associate. UBQLNs are linked to numerous types of cellular puncta, including stress-induced biomolecular condensates, autophagosomes, aggresomes, and aggregates. In this review, we focus on deciphering how UBQLNs function on a molecular level. We examine the properties of oligomerization-driven interactions among the structured and intrinsically disordered segments of UBQLNs. These interactions, together with the knowledge from studies of disease-linked mutations, provide significant insights to UBQLN structure, dynamics and function.
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Affiliation(s)
- Tongyin Zheng
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, U.S.A
| | - Yiran Yang
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, U.S.A
| | - Carlos A. Castañeda
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, U.S.A
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, U.S.A
- Bioinspired Institute, and the Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, U.S.A
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46
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Schuster BS, Dignon GL, Tang WS, Kelley FM, Ranganath AK, Jahnke CN, Simpkins AG, Regy RM, Hammer DA, Good MC, Mittal J. Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior. Proc Natl Acad Sci U S A 2020; 117:11421-11431. [PMID: 32393642 PMCID: PMC7261017 DOI: 10.1073/pnas.2000223117] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phase separation of intrinsically disordered proteins (IDPs) commonly underlies the formation of membraneless organelles, which compartmentalize molecules intracellularly in the absence of a lipid membrane. Identifying the protein sequence features responsible for IDP phase separation is critical for understanding physiological roles and pathological consequences of biomolecular condensation, as well as for harnessing phase separation for applications in bioinspired materials design. To expand our knowledge of sequence determinants of IDP phase separation, we characterized variants of the intrinsically disordered RGG domain from LAF-1, a model protein involved in phase separation and a key component of P granules. Based on a predictive coarse-grained IDP model, we identified a region of the RGG domain that has high contact probability and is highly conserved between species; deletion of this region significantly disrupts phase separation in vitro and in vivo. We determined the effects of charge patterning on phase behavior through sequence shuffling. We designed sequences with significantly increased phase separation propensity by shuffling the wild-type sequence, which contains well-mixed charged residues, to increase charge segregation. This result indicates the natural sequence is under negative selection to moderate this mode of interaction. We measured the contributions of tyrosine and arginine residues to phase separation experimentally through mutagenesis studies and computationally through direct interrogation of different modes of interaction using all-atom simulations. Finally, we show that despite these sequence perturbations, the RGG-derived condensates remain liquid-like. Together, these studies advance our fundamental understanding of key biophysical principles and sequence features important to phase separation.
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Affiliation(s)
- Benjamin S Schuster
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ 08854
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Wai Shing Tang
- Department of Physics, Brown University, Providence, RI 02912
| | - Fleurie M Kelley
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ 08854
| | | | - Craig N Jahnke
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Alison G Simpkins
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015
| | - Daniel A Hammer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Matthew C Good
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015;
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47
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Abstract
Many biomolecular condensates appear to form via spontaneous or driven processes that have the hallmarks of intracellular phase transitions. This suggests that a common underlying physical framework might govern the formation of functionally and compositionally unrelated biomolecular condensates. In this review, we summarize recent work that leverages a stickers-and-spacers framework adapted from the field of associative polymers for understanding how multivalent protein and RNA molecules drive phase transitions that give rise to biomolecular condensates. We discuss how the valence of stickers impacts the driving forces for condensate formation and elaborate on how stickers can be distinguished from spacers in different contexts. We touch on the impact of sticker- and spacer-mediated interactions on the rheological properties of condensates and show how the model can be mapped to known drivers of different types of biomolecular condensates.
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Affiliation(s)
- Jeong-Mo Choi
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
- Natural Science Research Institute, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Alex S Holehouse
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
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48
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Kuechler ER, Budzyńska PM, Bernardini JP, Gsponer J, Mayor T. Distinct Features of Stress Granule Proteins Predict Localization in Membraneless Organelles. J Mol Biol 2020; 432:2349-2368. [PMID: 32105731 DOI: 10.1016/j.jmb.2020.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/31/2022]
Abstract
Recently generated proteomic data provides unprecedented insight into stress granule composition and stands as fruitful ground for further analysis. Stress granules are stress-induced biological assemblies that are of keen interest due to being linked to both long-term cell viability and a variety of protein aggregation-based diseases. Herein, we compile recently published stress granule composition data, formed specifically through heat and oxidative stress, for both mammalian (Homo sapiens) and yeast (Saccharomyces cerevisiae) cells. Interrogation of the data reveals that stress granule proteins are enriched in features that favor protein liquid-liquid phase separation, being highly disordered, soluble, and abundant while maintaining a high level of protein-protein interactions under basal conditions. Furthermore, these "stress granuleomes" are shown to be enriched for multidomained, RNA-binding proteins with increased potential for post-translational modifications. Findings are consistent with the notion that stress granule formation is driven by protein liquid-liquid phase separation. Furthermore, stress granule proteins appear poised near solubility limits while possessing the ability to dynamically alter their phase behavior in response to external threat. Interestingly, several features, such as protein disorder, are more prominent among stress granule proteins that share homologs between yeast and mammalian systems also found within stress-induced foci. We culminate results from our stress granule analysis into novel predictors for granule incorporation and validate the mammalian predictor's performance against multiple types of membraneless condensates and by colocalization microscopy.
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Affiliation(s)
- Erich R Kuechler
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Paulina M Budzyńska
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Jonathan P Bernardini
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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49
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Renaud L, Picher-Martel V, Codron P, Julien JP. Key role of UBQLN2 in pathogenesis of amyotrophic lateral sclerosis and frontotemporal dementia. Acta Neuropathol Commun 2019; 7:103. [PMID: 31319884 PMCID: PMC6889556 DOI: 10.1186/s40478-019-0758-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 06/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ubiquilin-2 (UBQLN2) is a member of the ubiquilin family, actively implicated in the degradation of misfolded and redundant proteins through the ubiquitin-proteasome system and macroautophagy. UBQLN2 received much attention after the discovery of gene mutations in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). The abnormal presence of positive UBQLN2 inclusion in the cytosol of degenerating motor neurons of familial and sporadic forms of ALS patients has been newly related to neurodegeneration. Only recently, data have emerged on its role in liquid-liquid phase separation, in stress granule development and in the formation of secondary amyloid structures. Furthermore, several animal models are available to investigate its involvement in TDP-43 pathology and neuroinflammation in ALS. This review addresses the molecular pathogenetic pathways involving UBQLN2 abnormalities which are converging toward defects in clearance mechanisms. UBQLN2.
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50
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Cable J, Brangwynne C, Seydoux G, Cowburn D, Pappu RV, Castañeda CA, Berchowitz LE, Chen Z, Jonikas M, Dernburg A, Mittag T, Fawzi NL. Phase separation in biology and disease-a symposium report. Ann N Y Acad Sci 2019; 1452:3-11. [PMID: 31199001 DOI: 10.1111/nyas.14126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 01/28/2023]
Abstract
Phase separation of multivalent protein and RNA molecules enables cells the formation of reversible nonstoichiometric, membraneless assemblies. These assemblies, referred to as biomolecular condensates, help with the spatial organization and compartmentalization of cellular matter. Each biomolecular condensate is defined by a distinct macromolecular composition. Distinct condensates have distinct preferential locations within cells, and they are associated with distinct biological functions, including DNA replication, RNA metabolism, signal transduction, synaptic transmission, and stress response. Several proteins found in biomolecular condensates have also been implicated in disease, including Huntington's disease, amyotrophic lateral sclerosis, and several types of cancer. Disease-associated mutations in these proteins have been found to affect the material properties of condensates as well as the driving forces for phase separation. Understanding the intrinsic and extrinsic forces driving the formation and dissolution of biomolecular condensates via spontaneous and driven phase separation is an important step in understanding the processes associated with biological regulation in health and disease.
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Affiliation(s)
| | - Clifford Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David Cowburn
- Departments of Biochemistry and Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Science and Engineering of Living Systems, McKelvey School of Engineering, St. Louis, Missouri
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Program in Neuroscience, Syracuse University, Syracuse, New York
| | - Luke E Berchowitz
- Departments of Genetics and Development, Columbia University, New York, New York
| | - Zhijuan Chen
- University of Texas Southwestern Medical Center, Dallas, Texas
| | - Martin Jonikas
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Abby Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island
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