1
|
King MR, Ruff KM, Pappu RV. Emergent microenvironments of nucleoli. Nucleus 2024; 15:2319957. [PMID: 38443761 PMCID: PMC10936679 DOI: 10.1080/19491034.2024.2319957] [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: 09/04/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.
Collapse
Affiliation(s)
- Matthew R. King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| |
Collapse
|
2
|
Wan L, Zhu Y, Zhang W, Mu W. Recent advances in design and application of synthetic membraneless organelles. Biotechnol Adv 2024; 73:108355. [PMID: 38588907 DOI: 10.1016/j.biotechadv.2024.108355] [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: 08/12/2023] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) have been extensively studied due to their spatiotemporal control of biochemical and cellular processes in living cells. These findings have provided valuable insights into the physicochemical principles underlying the formation and functionalization of biomolecular condensates, which paves the way for the development of versatile phase-separating systems capable of addressing a variety of application scenarios. Here, we highlight the potential of constructing synthetic MLOs with programmable and functional properties. Notably, we organize how these synthetic membraneless compartments have been capitalized to manipulate enzymatic activities and metabolic reactions. The aim of this review is to inspire readerships to deeply comprehend the widespread roles of synthetic MLOs in the regulation enzymatic reactions and control of metabolic processes, and to encourage the rational design of controllable and functional membraneless compartments for a broad range of bioengineering applications.
Collapse
Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
3
|
Wu L, Zhu K, Xue S, Wu B, Xiao Z, Feng Z, Yin Y, Li J, Yu D, Cao Z. Dual-Mode Arginine Assay Based on the Conformation Switch of a Ferrocene-Grafted Polypeptide. Anal Chem 2024. [PMID: 38918973 DOI: 10.1021/acs.analchem.4c01050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Both controllable regulation of the conformational structure of a polypeptide and specific recognition of an amino acid are still arduous challenges. Here, a novel dual-mode (electrochemical and colorimetric) biosensor was built for arginine (Arg) recognition based on a conformation switch, utilizing controllable and synergistic self-assembly of a ferrocene-grafted hexadecapeptide (P16Fc) with gold nanoparticles (AuNPs). Benefiting from the flexibility and unique topological structure of P16Fc formed nanospheres, the assembly and disassembly can undergo a conformation transition induced by Arg through controlling the distance and number of Fc detached from the gold surface, producing on-off electrical signals. Also, they can induce aggregation and dispersion of AuNPs in solution, causing a color change. The mechanism of Arg recognition with polypeptide conformation regulation was well explored by combining microstructure characterizations with molecular mechanics calculations. The electrochemical and colorimetric assays for Arg were successfully established in sensitive and selective manner, not only obtaining a very low detection limit, but also effectively eliminating the interference from other amino acids and overcoming the limitation of AuNP aggregation. Notably, the conformational change-based assay with the peptide regulated by the target will make a powerful tool for the amino acid biosensing and health diagnosis.
Collapse
Affiliation(s)
- Ling Wu
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Kaijie Zhu
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Shulei Xue
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Bowen Wu
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Zhongliang Xiao
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Zemeng Feng
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Yulong Yin
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Jishan Li
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Donghong Yu
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, East, Denmark
| | - Zhong Cao
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
| |
Collapse
|
4
|
Waterbury AL, Kwok HS, Lee C, Narducci DN, Freedy AM, Su C, Raval S, Reiter AH, Hawkins W, Lee K, Li J, Hoenig SM, Vinyard ME, Cole PA, Hansen AS, Carr SA, Papanastasiou M, Liau BB. An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. Mol Cell 2024; 84:2238-2254.e11. [PMID: 38870936 PMCID: PMC11193646 DOI: 10.1016/j.molcel.2024.05.017] [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: 09/12/2023] [Revised: 03/21/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
Transcriptional coregulators and transcription factors (TFs) contain intrinsically disordered regions (IDRs) that are critical for their association and function in gene regulation. More recently, IDRs have been shown to promote multivalent protein-protein interactions between coregulators and TFs to drive their association into condensates. By contrast, here we demonstrate how the IDR of the corepressor LSD1 excludes TF association, acting as a dynamic conformational switch that tunes repression of active cis-regulatory elements. Hydrogen-deuterium exchange shows that the LSD1 IDR interconverts between transient open and closed conformational states, the latter of which inhibits partitioning of the protein's structured domains with TF condensates. This autoinhibitory switch controls leukemic differentiation by modulating repression of active cis-regulatory elements bound by LSD1 and master hematopoietic TFs. Together, these studies unveil alternative mechanisms by which disordered regions and their dynamic crosstalk with structured regions can shape coregulator-TF interactions to control cis-regulatory landscapes and cell fate.
Collapse
Affiliation(s)
- Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hui Si Kwok
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ceejay Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Domenic N Narducci
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Allyson M Freedy
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Cindy Su
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shaunak Raval
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew H Reiter
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - William Hawkins
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jiaming Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Samuel M Hoenig
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anders S Hansen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| |
Collapse
|
5
|
Latham AP, Zhu L, Sharon DA, Ye S, Willard AP, Zhang X, Zhang B. Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.30.534967. [PMID: 37034777 PMCID: PMC10081284 DOI: 10.1101/2023.03.30.534967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences to the physical properties of condensates, i.e., the molecular grammar, are hampered by a lack of effective approaches for probing high-resolution structural details. Using a combination of multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored a series of systems consisting of diblock elastin-like polypeptides (ELP). The simulations succeeded in reproducing the variation of condensate stability upon amino acid substitution and revealed different microenvironments within a single condensate, which we verified with environmentally sensitive fluorophores. The interspersion of hydrophilic and hydrophobic residues and a lack of secondary structure formation result in an interfacial environment, which explains both the strong correlation between ELP condensate stability and interfacial hydrophobicity scales, as well as the prevalence of protein-water hydrogen bonds. Our study uncovers new mechanisms for condensate stability and organization that may be broadly applicable.
Collapse
|
6
|
Liu J, Jiang Y, Liu R, Jin J, Wei S, Ji W, He X, Wu F, Yu P, Mao L. Vitamin C Drives Reentrant Actin Phase Transition: Biphasic Exocytosis Regulation Revealed by Single-Vesicle Electrochemistry. J Am Chem Soc 2024. [PMID: 38889317 DOI: 10.1021/jacs.4c02710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Unveiling molecular mechanisms that dominate protein phase dynamics has been a pressing need for deciphering the intricate intracellular modulation machinery. While ions and biomacromolecules have been widely recognized for modulating protein phase separations, effects of small molecules that essentially constitute the cytosolic chemical atmosphere on the protein phase behaviors are rarely understood. Herein, we report that vitamin C (VC), a key small molecule for maintaining a reductive intracellular atmosphere, drives reentrant phase transitions of myosin II/F-actin (actomyosin) cytoskeletons. The actomyosin bundle condensates dissemble in the low-VC regime and assemble in the high-VC regime in vitro or inside neuronal cells, through a concurrent myosin II protein aggregation-dissociation process with monotonic VC concentration increase. Based on this finding, we employ in situ single-cell and single-vesicle electrochemistry to demonstrate the quantitative modulation of catecholamine transmitter vesicle exocytosis by intracellular VC atmosphere, i.e., exocytotic release amount increases in the low-VC regime and decreases in the high-VC regime. Furthermore, we show how VC regulates cytomembrane-vesicle fusion pore dynamics through counteractive or synergistic effects of actomyosin phase transitions and the intracellular free calcium level on membrane tensions. Our work uncovers the small molecule-based reversive protein phase regulatory mechanism, paving a new way to chemical neuromodulation and therapeutic repertoire expansion.
Collapse
Affiliation(s)
- Jing Liu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Ying Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ran Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jing Jin
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Shiyi Wei
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Wenliang Ji
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiulan He
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Fei Wu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
7
|
Zhou HX, Kota D, Qin S, Prasad R. Fundamental Aspects of Phase-Separated Biomolecular Condensates. Chem Rev 2024. [PMID: 38885177 DOI: 10.1021/acs.chemrev.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.
Collapse
|
8
|
Dhamankar S, Webb MA. Asymmetry in Polymer-Solvent Interactions Yields Complex Thermoresponsive Behavior. ACS Macro Lett 2024:818-825. [PMID: 38874369 DOI: 10.1021/acsmacrolett.4c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
We introduce a lattice framework that incorporates elements of Flory-Huggins solution theory and the q-state Potts model to study the phase behavior of polymer solutions and single-chain conformational characteristics. Without empirically introducing temperature-dependent interaction parameters, standard Flory-Huggins theory describes systems that are either homogeneous across temperatures or exhibit upper critical solution temperatures. The proposed Flory-Huggins-Potts framework extends these capabilities by predicting lower critical solution temperatures, miscibility loops, and hourglass-shaped spinodal curves. We particularly show that including orientation-dependent interactions, specifically between monomer segments and solvent particles, is alone sufficient to observe such phase behavior. Signatures of emergent phase behavior are found in single-chain Monte Carlo simulations, which display heating- and cooling-induced coil-globule transitions linked to energy fluctuations. The framework also capably describes a range of experimental systems. Importantly, and by contrast to many prior theoretical approaches, the framework does not employ any temperature- or composition-dependent parameters. This work provides new insights regarding the microscopic physics that underpin complex thermoresponsive behavior in polymers.
Collapse
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Michael A Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
9
|
Cohen SR, Banerjee PR, Pappu RV. Direct computations of viscoelastic moduli of biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598543. [PMID: 38915484 PMCID: PMC11195242 DOI: 10.1101/2024.06.11.598543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
In vitro facsimiles of biomolecular condensates are formed by different types of intrinsically disordered proteins including prion-like low complexity domains (PLCDs). PLCD condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model and information regarding intra- and inter-chain contacts that is extracted from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations. The key ingredient of the generalized Rouse model is the Zimm matrix that we compute from equilibrium MMC simulations. We compute two flavors of Zimm matrices, one referred to as the single-chain model that accounts only for intra-chain contacts, and the other referred to as a collective model, that accounts for inter-chain interactions. The single-chain model systematically overestimates the storage and loss moduli, whereas the collective model reproduces the measured moduli with greater fidelity. However, in the long time, low-frequency domain, a mixture of the two models proves to be most accurate. In line with the theory of Rouse, we find that a continuous distribution of relaxation times exists in condensates. The single crossover frequency between dominantly elastic versus dominantly viscous behaviors is influenced by the totality of the relaxation modes. Hence, our analysis suggests that viscoelastic fluid-like condensates are best described as generalized Maxwell fluids. Finally, we show that the complex shear moduli can be used to solve an inverse problem to obtain distributions of relaxation times that underlie the dynamics within condensates.
Collapse
|
10
|
Mitra R, Usher ET, Dedeoğlu S, Crotteau MJ, Fraser OA, Yennawar NH, Gadkari VV, Ruotolo BT, Holehouse AS, Salmon L, Showalter SA, Bardwell JCA. Molecular insights into the interaction between a disordered protein and a folded RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598678. [PMID: 38915483 PMCID: PMC11195163 DOI: 10.1101/2024.06.12.598678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Intrinsically disordered protein regions (IDRs) are well-established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition to folded RNA-binding domains that contribute to RBP function. To understand the dynamic interactions of an IDR-RNA complex, we characterized the RNA-binding features of a small (68 residues), positively charged IDR-containing protein, SERF. At high concentrations, SERF and RNA undergo charge-driven associative phase separation to form a protein- and RNA-rich dense phase. A key advantage of this model system is that this threshold for demixing is sufficiently high that we could use solution-state biophysical methods to interrogate the stoichiometric complexes of SERF with RNA in the one-phase regime. Herein, we describe our comprehensive characterization of SERF alone and in complex with a small fragment of the HIV-1 TAR RNA (TAR) with complementary biophysical methods and molecular simulations. We find that this binding event is not accompanied by the acquisition of structure by either molecule; however, we see evidence for a modest global compaction of the SERF ensemble when bound to RNA. This behavior likely reflects attenuated charge repulsion within SERF via binding to the polyanionic RNA and provides a rationale for the higher-order assembly of SERF in the context of RNA. We envision that the SERF-RNA system will lower the barrier to accessing the details that support IDR-RNA interactions and likewise deepen our understanding of the role of IDR-RNA contacts in complex formation and liquid-liquid phase separation. SIGNIFICANCE Subcellular organization through the formation of biomolecular condensates has emerged as an important contributor to myriad cellular functions, with implications in homeostasis, stress response, and disease. To understand the general and specific principles that support condensate formation, we must interrogate the interactions and assembly of their constituent biomolecules. To this end, this study introduces a simple model system comprised of a small, disordered protein and small RNA that undergo charge-driven, associative phase separation. In addition to extensive biophysical characterization of these molecules and their complex, we also generate new insights into mode of interaction and assembly between an unstructured protein and a structured RNA.
Collapse
|
11
|
Chen F, Li X, Guo W, Wang Y, Guo M, Shum HC. Size Scaling of Condensates in Multicomponent Phase Separation. J Am Chem Soc 2024; 146:16000-16009. [PMID: 38809420 DOI: 10.1021/jacs.4c02906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Constant proportionalities between cells and their intracellular organelles have been widely observed in various types of cells, known as intracellular size scaling. However, the mechanism underlying the size scaling and its modulation by environmental factors in multicomponent systems remain poorly understood. Here, we study the size scaling of membrane-less condensates using microdroplet-encapsulated minimalistic condensates formed by droplet microfluidics and mean-field theory. We demonstrate that the size scaling of condensates is an inherent characteristic of liquid-liquid phase separation. This concept is supported by experiments showing the occurrence of size scaling phenomena in various condensate systems and a generic lever rule acquired from mean-field theory. Moreover, it is found that the condensate-to-microdroplet scaling ratio can be affected by the solute and salt concentrations, with good agreement between experiments and predictions by theory. Notably, we identify a noise buffering mechanism whereby condensates composed of large macromolecules effectively maintain constant volumes and counteract concentration fluctuations of small molecules. This mechanism is achieved through the dynamic rearrangement of small molecules in and out of membrane-free interfaces. Our work provides crucial insights into understanding mechanistic principles that govern the size of cells and intracellular organelles as well as associated biological functions.
Collapse
Affiliation(s)
- Feipeng Chen
- Department of Mechanical Engineering, the University of Hong Kong, Pokfulam Road, Hong Kong (SAR) 999077, China
| | - Xiufeng Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR) 999077, China
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Wei Guo
- Department of Mechanical Engineering, the University of Hong Kong, Pokfulam Road, Hong Kong (SAR) 999077, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR) 999077, China
| | - Yuchao Wang
- Department of Mechanical Engineering, the University of Hong Kong, Pokfulam Road, Hong Kong (SAR) 999077, China
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ho Cheung Shum
- Department of Mechanical Engineering, the University of Hong Kong, Pokfulam Road, Hong Kong (SAR) 999077, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR) 999077, China
| |
Collapse
|
12
|
Davis MC, André AAM, Kjaergaard M. Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates. J Mol Biol 2024:168645. [PMID: 38848869 DOI: 10.1016/j.jmb.2024.168645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Biomolecular condensates are increasingly recognized as important drivers of cellular function; their dysregulation leads to pathology and disease. We discuss three questions in terms of the impending utility of data-driven techniques to predict condensate-driven biological outcomes, i.e., the impact of cellular state changes on condensates, the effect of condensates on biochemical processes within, and condensate properties that result in cellular dysregulation and disease.
Collapse
Affiliation(s)
- Maria C Davis
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alain A M André
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; The Danish Research Institute for Translational Neuroscience (DANDRITE), Denmark.
| |
Collapse
|
13
|
Chauhan G, Bremer A, Dar F, Mittag T, Pappu RV. Crowder titrations enable the quantification of driving forces for macromolecular phase separation. Biophys J 2024; 123:1376-1392. [PMID: 37717144 PMCID: PMC11163301 DOI: 10.1016/j.bpj.2023.09.006] [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: 07/03/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023] Open
Abstract
Macromolecular solubility is an important contributor to the driving forces for phase separation. Formally, the driving forces in a binary mixture comprising a macromolecule dissolved in a solvent can be quantified in terms of the saturation concentration, which is the threshold macromolecular concentration above which the mixture separates into coexisting dense and dilute phases. In addition, the second virial coefficient, which measures the effective strength of solvent-mediated intermolecular interactions provides direct assessments of solvent quality. The sign and magnitude of second virial coefficients will be governed by a combination of solution conditions and the nature of the macromolecule of interest. Here, we show, using a combination of theory, simulation, and in vitro experiments, that titrations of crowders, providing they are true depletants, can be used to extract the intrinsic driving forces for macromolecular phase separation. This refers to saturation concentrations in the absence of crowders and the second virial coefficients that quantify the magnitude of the incompatibility between macromolecules and the solvent. Our results show how the depletion-mediated attractions afforded by crowders can be leveraged to obtain comparative assessments of macromolecule-specific, intrinsic driving forces for phase separation.
Collapse
Affiliation(s)
- Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri.
| |
Collapse
|
14
|
Chew PY, Joseph JA, Collepardo-Guevara R, Reinhardt A. Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures. Biophys J 2024; 123:1342-1355. [PMID: 37408305 PMCID: PMC11163273 DOI: 10.1016/j.bpj.2023.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023] Open
Abstract
Multiphasic architectures are found ubiquitously in biomolecular condensates and are thought to have important implications for the organization of multiple chemical reactions within the same compartment. Many of these multiphasic condensates contain RNA in addition to proteins. Here, we investigate the importance of different interactions in multiphasic condensates comprising two different proteins and RNA using computer simulations with a residue-resolution coarse-grained model of proteins and RNA. We find that in multilayered condensates containing RNA in both phases, protein-RNA interactions dominate, with aromatic residues and arginine forming the key stabilizing interactions. The total aromatic and arginine content of the two proteins must be appreciably different for distinct phases to form, and we show that this difference increases as the system is driven toward greater multiphasicity. Using the trends observed in the different interaction energies of this system, we demonstrate that we can also construct multilayered condensates with RNA preferentially concentrated in one phase. The "rules" identified can thus enable the design of synthetic multiphasic condensates to facilitate further study of their organization and function.
Collapse
Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jerelle A Joseph
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Physics, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
15
|
Ginell GM, Emenecker RJ, Lotthammer JM, Usher ET, Holehouse AS. Direct prediction of intermolecular interactions driven by disordered regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597104. [PMID: 38895487 PMCID: PMC11185574 DOI: 10.1101/2024.06.03.597104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for a wide variety of cellular functions, many of which involve interactions with partner proteins. Molecular recognition is typically considered through the lens of sequence-specific binding events. However, a growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of the amino acid order, instead driven by complementary chemical interactions leading to disordered bound-state complexes. Despite this emerging paradigm, we lack tools to describe, quantify, predict, and interpret these types of structurally heterogeneous interactions from the underlying amino acid sequences. Here, we repurpose the chemical physics developed originally for molecular simulations to develop an approach for predicting intermolecular interactions between IDRs and partner proteins. Our approach enables the direct prediction of phase diagrams, the identification of chemically-specific interaction hotspots on IDRs, and a route to develop and test mechanistic hypotheses regarding IDR function in the context of molecular recognition. We use our approach to examine a range of systems and questions to highlight its versatility and applicability.
Collapse
Affiliation(s)
- Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Ryan. J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Jeffrey M. Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| |
Collapse
|
16
|
Alston JJ, Soranno A, Holehouse AS. Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. RESEARCH SQUARE 2024:rs.3.rs-4477977. [PMID: 38883712 PMCID: PMC11177979 DOI: 10.21203/rs.3.rs-4477977/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for cellular function yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. Here, we focus on the first two domains of coronavirus nucleocapsid proteins: the disordered N-terminal domain (NTD) and the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system for exploring the interplay between an IDR adjacent to a folded domain and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved dynamic and disordered RNA:protein complex is found across nucleocapsid protein orthologs despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
Collapse
Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
- Present Address, Program In Cellular and Molecular Medicine (PCMM), Boston Children’s Hospital, Boston, MA, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, 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 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| |
Collapse
|
17
|
Mathias KM, Liu Y, Wan L. Dysregulation of transcriptional condensates in human disease: mechanisms, biological functions, and open questions. Curr Opin Genet Dev 2024; 86:102203. [PMID: 38788489 PMCID: PMC11162900 DOI: 10.1016/j.gde.2024.102203] [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: 10/30/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
Precise gene expression, crucial for normal development and health, depends on the co-ordinated assembly and function of various factors within the crowded nucleus. Recent evidence suggests that this process is in part regulated by mesoscale compartmentalization and concentration of transcriptional components within condensates, offering a new perspective on gene regulation. Dysregulation of transcriptional condensates is increasingly associated with diseases, indicating a potential role in pathogenesis. In this mini-review, we provide a concise overview of the current understanding of the formation and function of transcriptional condensates, with a specific focus on recent advances in their dysregulation and implications in diseases, notably cancer. We also address limitations in the field and highlight open questions for future research.
Collapse
Affiliation(s)
- Kaeli M Mathias
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiman Liu
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Liling Wan
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
18
|
Sood A, Zhang B. Preserving condensate structure and composition by lowering sequence complexity. Biophys J 2024:S0006-3495(24)00373-4. [PMID: 38824391 DOI: 10.1016/j.bpj.2024.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/25/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024] Open
Abstract
Biomolecular condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent interactions, leading to spontaneous aggregation. Theoretical advancements are critical at connecting IDP sequences with condensate emergent properties to establish the so-called molecular grammar. We proposed an extension to the stickers and spacers model, incorporating heterogeneous, nonspecific pairwise interactions between spacers alongside specific interactions among stickers. Our investigation revealed that although spacer interactions contribute to phase separation and co-condensation, their nonspecific nature leads to disorganized condensates. Specific sticker-sticker interactions drive the formation of condensates with well-defined networked structures and molecular composition. We discussed how evolutionary pressures might emerge to affect these interactions, leading to the prevalence of low-complexity domains in IDP sequences. These domains suppress spurious interactions and facilitate the formation of biologically meaningful condensates.
Collapse
Affiliation(s)
- Amogh Sood
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| |
Collapse
|
19
|
Kuzin S, Stolba D, Wu X, Syryamina VN, Boulos S, Jeschke G, Nyström L, Yulikov M. Quantification of Distributions of Local Proton Concentrations in Heterogeneous Soft Matter and Non-Anfinsen Biomacromolecules. J Phys Chem Lett 2024; 15:5625-5632. [PMID: 38758534 PMCID: PMC11145652 DOI: 10.1021/acs.jpclett.4c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/18/2024]
Abstract
A new method to quantitatively analyze heterogeneous distributions of local proton densities around paramagnetic centers in unstructured and weakly structured biomacromolecules and soft matter is introduced, and its feasibility is demonstrated on aqueous solutions of stochastically spin-labeled polysaccharides. This method is based on the pulse EPR experiment ih-RIDME (intermolecular hyperfine relaxation-induced dipolar modulation enhancement). Global analysis of a series of RIDME traces allows for a mathematically stable transformation of the time-domain data to the distribution of local proton concentrations. Two pulse sequences are proposed and tested, which combine the ih-RIDME block and the double-electron-electron resonance (DEER) experiment. Such experiments can be potentially used to correlate the local proton concentration with the macromolecular chain conformation. We anticipate an application of this approach in studies of intrinsically disordered proteins, biomolecular aggregates, and biomolecular condensates.
Collapse
Affiliation(s)
- Sergei Kuzin
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Dario Stolba
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Xiaowen Wu
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
- Max
Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Victoria N. Syryamina
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
- Voevodsky
Institute of Chemical Kinetics and Combustion, Novosibirsk 630090, Russia
| | - Samy Boulos
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Gunnar Jeschke
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Laura Nyström
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Maxim Yulikov
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| |
Collapse
|
20
|
Netzer A, Baruch Leshem A, Veretnik S, Edelstein I, Lampel A. Regulation of Peptide Liquid-Liquid Phase Separation by Aromatic Amino Acid Composition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401665. [PMID: 38804888 DOI: 10.1002/smll.202401665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/25/2024] [Indexed: 05/29/2024]
Abstract
Membraneless organelles are cellular biomolecular condensates that are formed by liquid-liquid phase separation (LLPS) of proteins and nucleic acids. LLPS is driven by multiple weak attractive forces, including intermolecular interactions mediated by aromatic amino acids. Considering the contribution of π-electron bearing side chains to protein-RNA LLPS, systematically study sought to how the composition of aromatic amino acids affects the formation of heterotypic condensates and their physical properties. For this, a library of minimalistic peptide building blocks is designed containing varying number and compositions of aromatic amino acids. It is shown that the number of aromatics in the peptide sequence affect LLPS propensity, material properties and (bio)chemical stability of peptide/RNA heterotypic condensates. The findings shed light on the contribution of aromatics' composition to the formation of heterotypic condensates. These insights can be applied for regulation of condensate material properties and improvement of their (bio)chemical stability, for various biomedical and biotechnological applications.
Collapse
Affiliation(s)
- Amit Netzer
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Avigail Baruch Leshem
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shirel Veretnik
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ilan Edelstein
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ayala Lampel
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
- Sagol Center for Regenerative Biotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
- Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, 69978, Israel
| |
Collapse
|
21
|
Kacirani A, Uralcan B, Domingues TS, Haji-Akbari A. Effect of Pressure on the Conformational Landscape of Human γD-Crystallin from Replica Exchange Molecular Dynamics Simulations. J Phys Chem B 2024; 128:4931-4942. [PMID: 38685567 DOI: 10.1021/acs.jpcb.4c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Human γD-crystallin belongs to a crucial family of proteins known as crystallins located in the fiber cells of the human lens. Since crystallins do not undergo any turnover after birth, they need to possess remarkable thermodynamic stability. However, their sporadic misfolding and aggregation, triggered by environmental perturbations or genetic mutations, constitute the molecular basis of cataracts, which is the primary cause of blindness in the globe according to the World Health Organization. Here, we investigate the impact of high pressure on the conformational landscape of wild-type HγD-crystallin using replica exchange molecular dynamics simulations augmented with principal component analysis. We find pressure to have a modest impact on global measures of protein stability, such as root-mean-square displacement and radius of gyration. Upon projecting our trajectories along the first two principal components from principal component analysis, however, we observe the emergence of distinct free energy basins at high pressures. By screening local order parameters previously shown or hypothesized as markers of HγD-crystallin stability, we establish correlations between a tyrosine-tyrosine aromatic contact within the N-terminal domain and the protein's end-to-end distance with projections along the first and second principal components, respectively. Furthermore, we observe the simultaneous contraction of the hydrophobic core and its intrusion by water molecules. This exploration sheds light on the intricate responses of HγD-crystallin to elevated pressures, offering insights into potential mechanisms underlying its stability and susceptibility to environmental perturbations, crucial for understanding cataract formation.
Collapse
Affiliation(s)
- Arlind Kacirani
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Betül Uralcan
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemical Engineering, Boğaziçi University, Istanbul 34342, Turkey
| | - Tiago S Domingues
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Graduate Program in Applied Mathematics, Yale University, New Haven, Connecticut 06520, United States
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
Collapse
Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
24
|
Zhang Y, Prasad R, Su S, Lee D, Zhou HX. Amino Acid-Dependent Material Properties of Tetrapeptide Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594233. [PMID: 38798623 PMCID: PMC11118382 DOI: 10.1101/2024.05.14.594233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Condensates formed by intrinsically disordered proteins mediate a myriad of cellular processes and are linked to pathological conditions including neurodegeneration. Rules of how different types of amino acids (e.g., π-π pairs) dictate the physical properties of biomolecular condensates are emerging, but our understanding of the roles of different amino acids is far from complete. Here we studied condensates formed by tetrapeptides of the form XXssXX, where X is an amino acid and ss represents a disulfide bond along the backbone. Eight peptides form four types of condensates at different concentrations and pH values: droplets (X = F, L, M, P, V, A); amorphous dense liquids (X = L, M, P, V, A); amorphous aggregates (X = W), and gels (X = I, V, A). The peptides exhibit enormous differences in phase equilibrium and material properties, including a 368-fold range in the threshold concentration for phase separation and a 3856-fold range in viscosity. All-atom molecular dynamics simulations provide physical explanations of these results. The present work also reveals widespread critical behaviors, including critical slowing down manifested by the formation of amorphous dense liquids and critical scaling obeyed by fusion speed, with broad implications for condensate function.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Siyuan Su
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Daesung Lee
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago IL 60607, USA
| |
Collapse
|
25
|
Jambon-Puillet E, Testa A, Lorenz C, Style RW, Rebane AA, Dufresne ER. Phase-separated droplets swim to their dissolution. Nat Commun 2024; 15:3919. [PMID: 38724503 PMCID: PMC11082165 DOI: 10.1038/s41467-024-47889-y] [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: 10/30/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Biological macromolecules can condense into liquid domains. In cells, these condensates form membraneless organelles that can organize chemical reactions. However, little is known about the physical consequences of chemical activity in and around condensates. Working with model bovine serum albumin (BSA) condensates, we show that droplets swim along chemical gradients. Active BSA droplets loaded with urease swim toward each other. Passive BSA droplets show diverse responses to externally applied gradients of the enzyme's substrate and products. In all these cases, droplets swim toward solvent conditions that favor their dissolution. We call this behavior "dialytaxis", and expect it to be generic, as conditions which favor dissolution typically reduce interfacial tension, whose gradients are well-known to drive droplet motion through the Marangoni effect. These results could potentially suggest alternative physical mechanisms for active transport in living cells, and may enable the design of fluid micro-robots.
Collapse
Affiliation(s)
- Etienne Jambon-Puillet
- Department of Materials, ETH Zürich, Zürich, Switzerland
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Andrea Testa
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Charlotta Lorenz
- Department of Materials, ETH Zürich, Zürich, Switzerland
- Department of Materials Science and Engineering, Department of Physics, Cornell University, Ithaca, NY, USA
| | - Robert W Style
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Aleksander A Rebane
- Department of Materials, ETH Zürich, Zürich, Switzerland
- Life Molecules and Materials Lab, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Eric R Dufresne
- Department of Materials, ETH Zürich, Zürich, Switzerland.
- Department of Materials Science and Engineering, Department of Physics, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
26
|
Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
Collapse
Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
| |
Collapse
|
27
|
Liang Q, Peng N, Xie Y, Kumar N, Gao W, Miao Y. MolPhase, an advanced prediction algorithm for protein phase separation. EMBO J 2024; 43:1898-1918. [PMID: 38565952 PMCID: PMC11065880 DOI: 10.1038/s44318-024-00090-9] [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: 09/20/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
We introduce MolPhase, an advanced algorithm for predicting protein phase separation (PS) behavior that improves accuracy and reliability by utilizing diverse physicochemical features and extensive experimental datasets. MolPhase applies a user-friendly interface to compare distinct biophysical features side-by-side along protein sequences. By additional comparison with structural predictions, MolPhase enables efficient predictions of new phase-separating proteins and guides hypothesis generation and experimental design. Key contributing factors underlying MolPhase include electrostatic pi-interactions, disorder, and prion-like domains. As an example, MolPhase finds that phytobacterial type III effectors (T3Es) are highly prone to homotypic PS, which was experimentally validated in vitro biochemically and in vivo in plants, mimicking their injection and accumulation in the host during microbial infection. The physicochemical characteristics of T3Es dictate their patterns of association for multivalent interactions, influencing the material properties of phase-separating droplets based on the surrounding microenvironment in vivo or in vitro. Robust integration of MolPhase's effective prediction and experimental validation exhibit the potential to evaluate and explore how biomolecule PS functions in biological systems.
Collapse
Affiliation(s)
- Qiyu Liang
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Nana Peng
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Yi Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Nivedita Kumar
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Weibo Gao
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore, Singapore.
| |
Collapse
|
28
|
Firouzbakht A, Haider A, Gaalswyk K, Alaeen S, Ghosh K, Gruebele M. HYPK: A marginally disordered protein sensitive to charge decoration. Proc Natl Acad Sci U S A 2024; 121:e2316408121. [PMID: 38657047 PMCID: PMC11067017 DOI: 10.1073/pnas.2316408121] [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: 09/20/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) that lie close to the empirical boundary separating IDPs and folded proteins in Uversky's charge-hydropathy plot may behave as "marginal IDPs" and sensitively switch conformation upon changes in environment (temperature, crowding, and charge screening), sequence, or both. In our search for such a marginal IDP, we selected Huntingtin-interacting protein K (HYPK) near that boundary as a candidate; PKIα, also near that boundary, has lower secondary structure propensity; and Crk1, just across the boundary on the folded side, has higher secondary structure propensity. We used a qualitative Förster resonance energy transfer-based assay together with circular dichroism to simultaneously probe global and local conformation. HYPK shows several unique features indicating marginality: a cooperative transition in end-to-end distance with temperature, like Crk1 and folded proteins, but unlike PKIα; enhanced secondary structure upon crowding, in contrast to Crk1 and PKIα; and a cross-over from salt-induced expansion to compaction at high temperature, likely due to a structure-to-disorder transition not seen in Crk1 and PKIα. We then tested HYPK's sensitivity to charge patterning by designing charge-flipped variants including two specific sequences with identical amino acid composition that markedly differ in their predicted size and response to salt. The experimentally observed trends, also including mutants of PKIα, verify the predictions from sequence charge decoration metrics. Marginal proteins like HYPK show features of both folded and disordered proteins that make them sensitive to physicochemical perturbations and structural control by charge patterning.
Collapse
Affiliation(s)
- Arash Firouzbakht
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
| | - Austin Haider
- Department of Molecular and Cellular Biophysics, University of Denver, Denver, CO80210
| | - Kari Gaalswyk
- Department of Physics and Astronomy, University of Denver, Denver, CO80210
| | - Sepehr Alaeen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO80210
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Department of Physics, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Carle-Illinois College of Medicine, University of Illinois Urbana Champaign, Urbana Champaign, IL61801
- Center for Advanced Study, University of Illinois Urbana Champaign, Urbana Champaign, IL61801
| |
Collapse
|
29
|
Jankowski MS, Griffith D, Shastry DG, Pelham JF, Ginell GM, Thomas J, Karande P, Holehouse AS, Hurley JM. Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator. Nat Commun 2024; 15:3523. [PMID: 38664421 PMCID: PMC11045787 DOI: 10.1038/s41467-024-47761-z] [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: 09/07/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but the contribution of these disordered regions to clock protein interactions had not been elucidated. To determine the functionality of these disordered regions, we applied a synthetic peptide microarray approach to the disordered clock protein FRQ in Neurospora crassa. We identified residues required for FRQ's interaction with its partner protein FRH, the mutation of which demonstrated FRH is necessary for persistent clock oscillations but not repression of transcriptional activity. Additionally, the microarray demonstrated an enrichment of FRH binding to FRQ peptides with a net positive charge. We found that positively charged residues occurred in significant "blocks" within the amino acid sequence of FRQ and that ablation of one of these blocks affected both core clock timing and physiological clock output. Finally, we found positive charge clusters were a commonly shared molecular feature in repressive circadian clock proteins. Overall, our study suggests a mechanistic purpose for positive charge blocks and yielded insights into repressive arm protein roles in clock function.
Collapse
Affiliation(s)
- Meaghan S Jankowski
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Divya G Shastry
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jacqueline F Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joshua Thomas
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Pankaj Karande
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| |
Collapse
|
30
|
Maraldo A, Rnjak-Kovacina J, Marquis C. Tyrosine - a structural glue for hierarchical protein assembly. Trends Biochem Sci 2024:S0968-0004(24)00080-X. [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] [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.
Collapse
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.
| |
Collapse
|
31
|
Dar F, Cohen SR, Mitrea DM, Phillips AH, Nagy G, Leite WC, Stanley CB, Choi JM, Kriwacki RW, Pappu RV. Biomolecular condensates form spatially inhomogeneous network fluids. Nat Commun 2024; 15:3413. [PMID: 38649740 PMCID: PMC11035652 DOI: 10.1038/s41467-024-47602-z] [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: 10/07/2023] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.
Collapse
Affiliation(s)
- Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Samuel R Cohen
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Diana M Mitrea
- Dewpoint Therapeutics Inc., 451 D Street, Boston, MA, 02210, USA
| | - Aaron H Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Gergely Nagy
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington C Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| |
Collapse
|
32
|
Jung J, Tan C, Sugita Y. GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nat Commun 2024; 15:3370. [PMID: 38643169 PMCID: PMC11032353 DOI: 10.1038/s41467-024-47654-1] [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: 09/07/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models.
Collapse
Affiliation(s)
- Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan.
| |
Collapse
|
33
|
Hardy JC, Pool EH, Bruystens JGH, Zhou X, Li Q, Zhou DR, Palay M, Tan G, Chen L, Choi JLC, Lee HN, Strack S, Wang D, Taylor SS, Mehta S, Zhang J. Molecular determinants and signaling effects of PKA RIα phase separation. Mol Cell 2024; 84:1570-1584.e7. [PMID: 38537638 PMCID: PMC11031308 DOI: 10.1016/j.molcel.2024.03.002] [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: 02/21/2023] [Revised: 12/07/2023] [Accepted: 03/01/2024] [Indexed: 04/09/2024]
Abstract
Spatiotemporal regulation of intracellular signaling molecules, such as the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA), ensures proper cellular function. Liquid-liquid phase separation (LLPS) of the ubiquitous PKA regulatory subunit RIα promotes cAMP compartmentation and signaling specificity. However, the molecular determinants of RIα LLPS remain unclear. Here, we reveal that two separate dimerization interfaces, combined with the cAMP-induced unleashing of the PKA catalytic subunit (PKA-C) from the pseudosubstrate inhibitory sequence, drive RIα condensate formation in the cytosol of mammalian cells, which is antagonized by docking to A-kinase anchoring proteins. Strikingly, we find that the RIα pseudosubstrate region is critically involved in forming a non-canonical R:C complex, which recruits active PKA-C to RIα condensates to maintain low basal PKA activity in the cytosol. Our results suggest that RIα LLPS not only facilitates cAMP compartmentation but also spatially restrains active PKA-C, thus highlighting the functional versatility of biomolecular condensates in driving signaling specificity.
Collapse
Affiliation(s)
- Julia C Hardy
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily H Pool
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica G H Bruystens
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingrong Li
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daojia R Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Max Palay
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gerald Tan
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lisa Chen
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jaclyn L C Choi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ha Neul Lee
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stefan Strack
- Department of Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Dong Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
34
|
Kang CY, Chang Y, Zieske K. Lipid Membrane Topographies Are Regulators for the Spatial Distribution of Liquid Protein Condensates. NANO LETTERS 2024; 24:4330-4335. [PMID: 38579181 PMCID: PMC11036382 DOI: 10.1021/acs.nanolett.3c04169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/07/2024]
Abstract
Liquid protein condensates play important roles in orchestrating subcellular organization and as biochemical reaction hubs. Recent studies have linked lipid membranes to proteins capable of forming liquid condensates, and shown that biophysical parameters, like protein enrichment and restricted diffusion at membranes, regulate condensate formation and size. However, the impact of membrane topography on liquid condensates remains poorly understood. Here, we devised a cell-free system to reconstitute liquid condensates on lipid membranes with microstructured topographies and demonstrated that lipid membrane topography is a significant biophysical regulator. Using membrane surfaces designed with microwells, we observed ordered condensate patterns. Furthermore, we demonstrate that membrane topographies influence the shape of liquid condensates. Finally, we show that capillary forces, mediated by membrane topographies, lead to the directed fusion of liquid condensates. Our results demonstrate that membrane topography is a potent biophysical regulator for the localization and shape of mesoscale liquid protein condensates.
Collapse
Affiliation(s)
- Chae Yeon Kang
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
| | - Yoohyun Chang
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
| | - Katja Zieske
- Biophysics, Max
Planck Institute for the Science of Light, 91058 Erlangen, Germany
| |
Collapse
|
35
|
Murai T. Transmembrane signaling through single-spanning receptors modulated by phase separation at the cell surface. Eur J Cell Biol 2024; 103:151413. [PMID: 38631097 DOI: 10.1016/j.ejcb.2024.151413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
A wide variety of transmembrane signals are transduced by cell-surface receptors that activate intracellular signaling molecules. In particular, receptor clustering in the plasma membrane plays a critical role in these processes. Single-spanning or single-pass transmembrane proteins are among the most significant types of membrane receptors, which include adhesion receptors, such as integrins, CD44, cadherins, and receptor tyrosine kinases. Elucidating the molecular mechanisms underlying the regulation of the activity of these receptors is of great significance. Liquid-liquid phase separation (LLPS) is a recently emerging paradigm in cellular physiology for the ubiquitous regulation of the spatiotemporal dynamics of various signaling pathways. This study describes the emerging features of transmembrane signaling through single-spanning receptors from the perspective of phase separation. Possible physicochemical modulations of LLPS-based transmembrane signaling are also discussed.
Collapse
Affiliation(s)
- Toshiyuki Murai
- Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
36
|
King MR, Ruff KM, Lin AZ, Pant A, Farag M, Lalmansingh JM, Wu T, Fossat MJ, Ouyang W, Lew MD, Lundberg E, Vahey MD, Pappu RV. Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient. Cell 2024; 187:1889-1906.e24. [PMID: 38503281 DOI: 10.1016/j.cell.2024.02.029] [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: 07/18/2023] [Revised: 01/02/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
Collapse
Affiliation(s)
- Matthew R King
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrew Z Lin
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Avnika Pant
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Mina Farag
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jared M Lalmansingh
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tingting Wu
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Martin J Fossat
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Wei Ouyang
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Matthew D Lew
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Emma Lundberg
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael D Vahey
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
37
|
Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haesaerts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3105. [PMID: 38600130 PMCID: PMC11006873 DOI: 10.1038/s41467-024-47296-3] [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: 05/21/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.
Collapse
Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
| |
Collapse
|
38
|
Sanchez‐Martinez S, Nguyen K, Biswas S, Nicholson V, Romanyuk AV, Ramirez J, Kc S, Akter A, Childs C, Meese EK, Usher ET, Ginell GM, Yu F, Gollub E, Malferrari M, Francia F, Venturoli G, Martin EW, Caporaletti F, Giubertoni G, Woutersen S, Sukenik S, Woolfson DN, Holehouse AS, Boothby TC. Labile assembly of a tardigrade protein induces biostasis. Protein Sci 2024; 33:e4941. [PMID: 38501490 PMCID: PMC10949331 DOI: 10.1002/pro.4941] [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: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.
Collapse
Affiliation(s)
| | - K. Nguyen
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Biswas
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - V. Nicholson
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. V. Romanyuk
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
| | - J. Ramirez
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Kc
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. Akter
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - C. Childs
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. K. Meese
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. T. Usher
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - G. M. Ginell
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - F. Yu
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - E. Gollub
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - M. Malferrari
- Dipartimento di Chimica “Giacomo Ciamician”Università di BolognaBolognaItaly
| | - F. Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
| | - G. Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o Dipartimento di Fisica e Astronomia (DIFA)Università di BolognaBolognaItaly
| | - E. W. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - F. Caporaletti
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - G. Giubertoni
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Woutersen
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Sukenik
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - D. N. Woolfson
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
- School of BiochemistryUniversity of Bristol, Biomedical Sciences BuildingBristolUK
| | - A. S. Holehouse
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - T. C. Boothby
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| |
Collapse
|
39
|
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 2024:10.1038/s41557-024-01489-x. [PMID: 38553587 DOI: 10.1038/s41557-024-01489-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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.
Collapse
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.
| |
Collapse
|
40
|
Wegeng WR, Bogus SM, Ruiz M, Chavez SR, Noori KSM, Niesman IR, Ernst AM. A Hollow TFG Condensate Spatially Compartmentalizes the Early Secretory Pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586876. [PMID: 38585729 PMCID: PMC10996658 DOI: 10.1101/2024.03.26.586876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
In the early secretory pathway, endoplasmic reticulum (ER) and Golgi membranes form a nearly spherical interface. In this ribosome-excluding zone, bidirectional transport of cargo coincides with a spatial segregation of anterograde and retrograde carriers by an unknown mechanism. We show that at physiological conditions, Trk-fused gene (TFG) self-organizes to form a hollow, anisotropic condensate that matches the dimensions of the ER-Golgi interface. Regularly spaced hydrophobic residues in TFG control the condensation mechanism and result in a porous condensate surface. We find that TFG condensates act as a molecular sieve, enabling molecules corresponding to the size of anterograde coats (COPII) to access the condensate interior while restricting retrograde coats (COPI). We propose that a hollow TFG condensate structures the ER-Golgi interface to create a diffusion-limited space for bidirectional transport. We further propose that TFG condensates optimize membrane flux by insulating secretory carriers in their lumen from retrograde carriers outside TFG cages.
Collapse
Affiliation(s)
- William R. Wegeng
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Savannah M. Bogus
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Miguel Ruiz
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Sindy R. Chavez
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Khalid S. M. Noori
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Ingrid R. Niesman
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Andreas M. Ernst
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093 USA
| |
Collapse
|
41
|
Shepherdson JL, Granas DM, Li J, Shariff Z, Plassmeyer SP, Holehouse AS, White MA, Cohen BA. Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585809. [PMID: 38585983 PMCID: PMC10996540 DOI: 10.1101/2024.03.21.585809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.
Collapse
Affiliation(s)
- James L. Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - David M. Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Jie Li
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Zara Shariff
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Stephen P. Plassmeyer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Michael A. White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| |
Collapse
|
42
|
Johnson CN, Sojitra KA, Sohn EJ, Moreno-Romero AK, Baudin A, Xu X, Mittal J, Libich DS. Insights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS. J Am Chem Soc 2024; 146:8071-8085. [PMID: 38492239 DOI: 10.1021/jacs.3c12034] [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] [Indexed: 03/18/2024]
Abstract
The FET protein family, comprising FUS, EWS, and TAF15, plays crucial roles in mRNA maturation, transcriptional regulation, and DNA damage response. Clinically, they are linked to Ewing family tumors and neurodegenerative diseases such as amyotrophic lateral sclerosis. The fusion protein EWS::FLI1, the causative mutation of Ewing sarcoma, arises from a genomic translocation that fuses a portion of the low-complexity domain (LCD) of EWS (EWSLCD) with the DNA binding domain of the ETS transcription factor FLI1. This fusion protein modifies transcriptional programs and disrupts native EWS functions, such as splicing. The exact role of the intrinsically disordered EWSLCD remains a topic of active investigation, but its ability to phase separate and form biomolecular condensates is believed to be central to EWS::FLI1's oncogenic properties. Here, we used paramagnetic relaxation enhancement NMR, microscopy, and all-atom molecular dynamics (MD) simulations to better understand the self-association and phase separation tendencies of the EWSLCD. Our NMR data and mutational analysis suggest that a higher density and proximity of tyrosine residues amplify the likelihood of condensate formation. MD simulations revealed that the tyrosine-rich termini exhibit compact conformations with unique contact networks and provided critical input on the relationship between contacts formed within a single molecule (intramolecular) and inside the condensed phase (intermolecular). These findings enhance our understanding of FET proteins' condensate-forming capabilities and underline differences between EWS, FUS, and TAF15.
Collapse
Affiliation(s)
- Courtney N Johnson
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Kandarp A Sojitra
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Erich J Sohn
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Alma K Moreno-Romero
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Antoine Baudin
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Xiaoping Xu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| | - David S Libich
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| |
Collapse
|
43
|
Sun J, Qu J, Zhao C, Zhang X, Liu X, Wang J, Wei C, Liu X, Wang M, Zeng P, Tang X, Ling X, Qing L, Jiang S, Chen J, Chen TSR, Kuang Y, Gao J, Zeng X, Huang D, Yuan Y, Fan L, Yu H, Ding J. Precise prediction of phase-separation key residues by machine learning. Nat Commun 2024; 15:2662. [PMID: 38531854 DOI: 10.1038/s41467-024-46901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Understanding intracellular phase separation is crucial for deciphering transcriptional control, cell fate transitions, and disease mechanisms. However, the key residues, which impact phase separation the most for protein phase separation function have remained elusive. We develop PSPHunter, which can precisely predict these key residues based on machine learning scheme. In vivo and in vitro validations demonstrate that truncating just 6 key residues in GATA3 disrupts phase separation, enhancing tumor cell migration and inhibiting growth. Glycine and its motifs are enriched in spacer and key residues, as revealed by our comprehensive analysis. PSPHunter identifies nearly 80% of disease-associated phase-separating proteins, with frequent mutated pathological residues like glycine and proline often residing in these key residues. PSPHunter thus emerges as a crucial tool to uncover key residues, facilitating insights into phase separation mechanisms governing transcriptional control, cell fate transitions, and disease development.
Collapse
Affiliation(s)
- Jun Sun
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiale Qu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cai Zhao
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyao Zhang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyu Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mulan Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoru Ling
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiahao Chen
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tara S R Chen
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yalan Kuang
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Jinhang Gao
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Xiaoxi Zeng
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Dongfeng Huang
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yong Yuan
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Haopeng Yu
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Junjun Ding
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
| |
Collapse
|
44
|
Tariq D, Maurici N, Bartholomai BM, Chandrasekaran S, Dunlap JC, Bah A, Crane BR. Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock. eLife 2024; 12:RP90259. [PMID: 38526948 PMCID: PMC10963029 DOI: 10.7554/elife.90259] [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: 03/27/2024] Open
Abstract
Circadian clocks are composed of transcription-translation negative feedback loops that pace rhythms of gene expression to the diurnal cycle. In the filamentous fungus Neurospora crassa, the proteins Frequency (FRQ), the FRQ-interacting RNA helicase (FRH), and Casein-Kinase I (CK1) form the FFC complex that represses expression of genes activated by the white-collar complex (WCC). FRQ orchestrates key molecular interactions of the clock despite containing little predicted tertiary structure. Spin labeling and pulse-dipolar electron spin resonance spectroscopy provide domain-specific structural insights into the 989-residue intrinsically disordered FRQ and the FFC. FRQ contains a compact core that associates and organizes FRH and CK1 to coordinate their roles in WCC repression. FRQ phosphorylation increases conformational flexibility and alters oligomeric state, but the changes in structure and dynamics are non-uniform. Full-length FRQ undergoes liquid-liquid phase separation (LLPS) to sequester FRH and CK1 and influence CK1 enzymatic activity. Although FRQ phosphorylation favors LLPS, LLPS feeds back to reduce FRQ phosphorylation by CK1 at higher temperatures. Live imaging of Neurospora hyphae reveals FRQ foci characteristic of condensates near the nuclear periphery. Analogous clock repressor proteins in higher organisms share little position-specific sequence identity with FRQ; yet, they contain amino acid compositions that promote LLPS. Hence, condensate formation may be a conserved feature of eukaryotic clocks.
Collapse
Affiliation(s)
- Daniyal Tariq
- Department of Chemistry & Chemical Biology, Cornell UniversityIthacaUnited States
| | - Nicole Maurici
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical UniversitySyracuseUnited States
| | - Bradley M Bartholomai
- Department of Molecular and Systems Biology, Geisel School of Medicine at DartmouthHanoverUnited States
| | | | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Alaji Bah
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical UniversitySyracuseUnited States
| | - Brian R Crane
- Department of Chemistry & Chemical Biology, Cornell UniversityIthacaUnited States
| |
Collapse
|
45
|
Ramirez DA, Hough LE, Shirts MR. Coiled-coil domains are sufficient to drive liquid-liquid phase separation in protein models. Biophys J 2024; 123:703-717. [PMID: 38356260 PMCID: PMC10995412 DOI: 10.1016/j.bpj.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/09/2023] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) is thought to be a main driving force in the formation of membraneless organelles. Examples of such organelles include the centrosome, central spindle, and stress granules. Recently, it has been shown that coiled-coil (CC) proteins, such as the centrosomal proteins pericentrin, spd-5, and centrosomin, might be capable of LLPS. CC domains have physical features that could make them the drivers of LLPS, but it is unknown if they play a direct role in the process. We developed a coarse-grained simulation framework for investigating the LLPS propensity of CC proteins, in which interactions that support LLPS arise solely from CC domains. We show, using this framework, that the physical features of CC domains are sufficient to drive LLPS of proteins. The framework is specifically designed to investigate how the number of CC domains, as well as the multimerization state of CC domains, can affect LLPS. We show that small model proteins with as few as two CC domains can phase separate. Increasing the number of CC domains up to four per protein can somewhat increase LLPS propensity. We demonstrate that trimer-forming and tetramer-forming CC domains have a dramatically higher LLPS propensity than dimer-forming coils, which shows that multimerization state has a greater effect on LLPS than the number of CC domains per protein. These data support the hypothesis of CC domains as drivers of protein LLPS, and have implications in future studies to identify the LLPS-driving regions of centrosomal and central spindle proteins.
Collapse
Affiliation(s)
- Dominique A Ramirez
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado.
| |
Collapse
|
46
|
Peltan EL, Riley NM, Flynn RA, Roberts DS, Bertozzi CR. Galectin-3 does not interact with RNA directly. Glycobiology 2024; 34:cwad076. [PMID: 37815932 DOI: 10.1093/glycob/cwad076] [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: 04/28/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023] Open
Abstract
Galectin-3, well characterized as a glycan binding protein, has been identified as a putative RNA binding protein, possibly through participation in pre-mRNA maturation through interactions with splicosomes. Given recent developments with cell surface RNA biology, the putative dual-function nature of galectin-3 evokes a possible non-classical connection between glycobiology and RNA biology. However, with limited functional evidence of a direct RNA interaction, many molecular-level observations rely on affinity reagents and lack appropriate genetic controls. Thus, evidence of a direct interaction remains elusive. We demonstrate that antibodies raised to endogenous human galectin-3 can isolate RNA-protein crosslinks, but this activity remains insensitive to LGALS3 knock-out. Proteomic characterization of anti-galectin-3 IPs revealed enrichment of galectin-3, but high abundance of hnRNPA2B1, an abundant, well-characterized RNA-binding protein with weak homology to the N-terminal domain of galectin-3, in the isolate. Genetic ablation of HNRNPA2B1, but not LGALS3, eliminates the ability of the anti-galectin-3 antibodies to isolate RNA-protein crosslinks, implying either an indirect interaction or cross-reactivity. To address this, we introduced an epitope tag to the endogenous C-terminal locus of LGALS3. Isolation of the tagged galectin-3 failed to reveal any RNA-protein crosslinks. This result suggests that the galectin-3 does not directly interact with RNA and may be misidentified as an RNA-binding protein, at least in HeLa where the putative RNA associations were first identified. We encourage further investigation of this phenomenon employ gene deletions and, when possible, endogenous epitope tags to achieve the specificity required to evaluate potential interactions.
Collapse
Affiliation(s)
- Egan L Peltan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 269 Campus Drive CCSR 4145 Stanford, CA 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
| | - Nicholas M Riley
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, 1 Blackfan Circle, Boston, MA 02445, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138, United States
| | - David S Roberts
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
| | - Carolyn R Bertozzi
- Sarafan ChEM-H, Stanford University, Stanford ChEM-H Building 290 Jane Stanford Way Stanford, CA 94305, United States
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, CA 94305, United States
- Howard Hughes Medical Institute, Stanford University, 279 Campus Drive Room B202 Stanford, CA 94305-5323, United States
| |
Collapse
|
47
|
Lee G, Kim S, Hwang DE, Eom YG, Jang G, Park HY, Choi JM, Ko J, Shin Y. Thermodynamic modulation of gephyrin condensation by inhibitory synapse components. Proc Natl Acad Sci U S A 2024; 121:e2313236121. [PMID: 38466837 PMCID: PMC10963017 DOI: 10.1073/pnas.2313236121] [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: 08/08/2023] [Accepted: 02/05/2024] [Indexed: 03/13/2024] Open
Abstract
Phase separation drives compartmentalization of intracellular contents into various biomolecular condensates. Individual condensate components are thought to differentially contribute to the organization and function of condensates. However, how intermolecular interactions among constituent biomolecules modulate the phase behaviors of multicomponent condensates remains unclear. Here, we used core components of the inhibitory postsynaptic density (iPSD) as a model system to quantitatively probe how the network of intra- and intermolecular interactions defines the composition and cellular distribution of biomolecular condensates. We found that oligomerization-driven phase separation of gephyrin, an iPSD-specific scaffold, is critically modulated by an intrinsically disordered linker region exhibiting minimal homotypic attractions. Other iPSD components, such as neurotransmitter receptors, differentially promote gephyrin condensation through distinct binding modes and affinities. We further demonstrated that the local accumulation of scaffold-binding proteins at the cell membrane promotes the nucleation of gephyrin condensates in neurons. These results suggest that in multicomponent systems, the extent of scaffold condensation can be fine-tuned by scaffold-binding factors, a potential regulatory mechanism for self-organized compartmentalization in cells.
Collapse
Affiliation(s)
- Gyehyun Lee
- Department of Mechanical Engineering, Seoul National University, Seoul08826, Republic of Korea
| | - Seungjoon Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu42988, Republic of Korea
- Center for Synapse Diversity and Specificity, Daegu Gyeongbuk Institute of Science and Technology, Daegu42988, Republic of Korea
| | - Da-Eun Hwang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan46241, Republic of Korea
| | - Yu-Gon Eom
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan46241, Republic of Korea
| | - Gyubin Jang
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu42988, Republic of Korea
- Center for Synapse Diversity and Specificity, Daegu Gyeongbuk Institute of Science and Technology, Daegu42988, Republic of Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul08826, Republic of Korea
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN55455
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan46241, Republic of Korea
| | - Jaewon Ko
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu42988, Republic of Korea
- Center for Synapse Diversity and Specificity, Daegu Gyeongbuk Institute of Science and Technology, Daegu42988, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul08826, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Republic of Korea
| |
Collapse
|
48
|
Uozumi R, Mori K, Gotoh S, Miyamoto T, Kondo S, Yamashita T, Kawabe Y, Tagami S, Akamine S, Ikeda M. PABPC1 mediates degradation of C9orf72-FTLD/ALS GGGGCC repeat RNA. iScience 2024; 27:109303. [PMID: 38444607 PMCID: PMC10914486 DOI: 10.1016/j.isci.2024.109303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
GGGGCC hexanucleotide repeat expansion in C9orf72 causes frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Expanded GGGGCC repeat RNA accumulates within RNA foci and is translated into toxic dipeptide repeat proteins; thus, efficient repeat RNA degradation may alleviate diseases. hnRNPA3, one of the repeat RNA-binding proteins, has been implicated in the destabilization of repeat RNA. Using APEX2-mediated proximity biotinylation, here, we demonstrate PABPC1, a cytoplasmic poly (A)-binding protein, interacts with hnRNPA3. Knockdown of PABPC1 increased the accumulation of repeat RNA and RNA foci to the same extent as the knockdown of hnRNPA3. Proximity ligation assays indicated PABPC1-hnRNPA3 and PABPC1-RNA exosomes, a complex that degrades repeat RNA, preferentially co-localized when repeat RNA was present. Our results suggest that PABPC1 functions as a mediator of polyadenylated GGGGCC repeat RNA degradation through interactions with hnRNPA3 and RNA exosome complex.
Collapse
Affiliation(s)
- Ryota Uozumi
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kohji Mori
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shiho Gotoh
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tesshin Miyamoto
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shizuko Kondo
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoko Yamashita
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuya Kawabe
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Psychiatry, Minoh Neuropsychiatric Hospital, Minoh, Osaka 562-0004, Japan
| | - Shinji Tagami
- Psychiatry, Minoh Neuropsychiatric Hospital, Minoh, Osaka 562-0004, Japan
- Health and Counseling Center, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shoshin Akamine
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Manabu Ikeda
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
49
|
Gan P, Eppert M, De La Cruz N, Lyons H, Shah AM, Veettil RT, Chen K, Pradhan P, Bezprozvannaya S, Xu L, Liu N, Olson EN, Sabari BR. Coactivator condensation drives cardiovascular cell lineage specification. SCIENCE ADVANCES 2024; 10:eadk7160. [PMID: 38489358 PMCID: PMC10942106 DOI: 10.1126/sciadv.adk7160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
During development, cells make switch-like decisions to activate new gene programs specifying cell lineage. The mechanisms underlying these decisive choices remain unclear. Here, we show that the cardiovascular transcriptional coactivator myocardin (MYOCD) activates cell identity genes by concentration-dependent and switch-like formation of transcriptional condensates. MYOCD forms such condensates and activates cell identity genes at critical concentration thresholds achieved during smooth muscle cell and cardiomyocyte differentiation. The carboxyl-terminal disordered region of MYOCD is necessary and sufficient for condensate formation. Disrupting this region's ability to form condensates disrupts gene activation and smooth muscle cell reprogramming. Rescuing condensate formation by replacing this region with disordered regions from functionally unrelated proteins rescues gene activation and smooth muscle cell reprogramming. Our findings demonstrate that MYOCD condensate formation is required for gene activation during cardiovascular differentiation. We propose that the formation of transcriptional condensates at critical concentrations of cell type-specific regulators provides a molecular switch underlying the activation of key cell identity genes during development.
Collapse
Affiliation(s)
- Peiheng Gan
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mikayla Eppert
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nancy De La Cruz
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Heankel Lyons
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Akansha M. Shah
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reshma T. Veettil
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Pradhan
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin R. Sabari
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
50
|
de Vries T, Novakovic M, Ni Y, Smok I, Inghelram C, Bikaki M, Sarnowski CP, Han Y, Emmanouilidis L, Padroni G, Leitner A, Allain FHT. Specific protein-RNA interactions are mostly preserved in biomolecular condensates. SCIENCE ADVANCES 2024; 10:eadm7435. [PMID: 38446881 PMCID: PMC10917357 DOI: 10.1126/sciadv.adm7435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.
Collapse
Affiliation(s)
- Tebbe de Vries
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mihajlo Novakovic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Yinan Ni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Izabela Smok
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Clara Inghelram
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Maria Bikaki
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Chris P. Sarnowski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Yaning Han
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - Giacomo Padroni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | |
Collapse
|