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Zhao P, Gao Y, Zhou Y, Huang M, Fan S, Bi H. Exogenous Pregnane X Receptor Does Not Undergo Liquid-Liquid Phase Separation in Nucleus under Cell-Based In Vitro Conditions. Drug Metab Dispos 2024; 52:1161-1169. [PMID: 38296653 DOI: 10.1124/dmd.123.001570] [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: 10/19/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 02/02/2024] Open
Abstract
Pregnane X receptor (PXR) belongs to the nuclear receptor superfamily that plays a crucial role in hepatic physiologic and pathologic conditions. Phase separation is a process in which biomacromolecules aggregate and condense into a dense phase as liquid condensates and coexist with a dilute phase, contributing to various cellular and biologic functions. Until now, whether PXR could undergo phase separation remains unclear. This study aimed to investigate whether PXR undergoes phase separation. Analysis of the intrinsically disordered regions (IDRs) using algorithm tools indicated a low propensity of PXR to undergo phase separation. Experimental assays such as hyperosmotic stress, agonist treatment, and optoDroplets assay demonstrated the absence of phase separation for PXR. OptoDroplets assay revealed the inability of the fusion protein of Cry2 with PXR to form condensates upon blue light stimulation. Moreover, phase separation of PXR did not occur even though the mRNA and protein expression levels of PXR target, cytochrome P450 3A4, changed after sorbitol treatment. In conclusion, for the first time, these findings suggested that exogenous PXR does not undergo phase separation following activation or under hyperosmotic stress in nucleus of cells. SIGNIFICANCE STATEMENT: PXR plays a critical role in hepatic physiological and pathological processes. The present study clearly demonstrated that exogenous PXR does not undergo phase separation after activation by agonist or under hyperosmotic stress in nucleus. These findings may help understand PXR biology.
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Affiliation(s)
- Pengfei Zhao
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., Y.G., Y.Z., M.H., S.F., H.B.); and NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (S.F., H.B.)
| | - Yue Gao
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., Y.G., Y.Z., M.H., S.F., H.B.); and NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (S.F., H.B.)
| | - Yanying Zhou
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., Y.G., Y.Z., M.H., S.F., H.B.); and NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (S.F., H.B.)
| | - Min Huang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., Y.G., Y.Z., M.H., S.F., H.B.); and NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (S.F., H.B.)
| | - Shicheng Fan
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., Y.G., Y.Z., M.H., S.F., H.B.); and NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (S.F., H.B.)
| | - Huichang Bi
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., Y.G., Y.Z., M.H., S.F., H.B.); and NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (S.F., H.B.)
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2
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Allegri G, Huskens J, Martinho RP, Lindhoud S. Distribution of polyelectrolytes and counterions upon polyelectrolyte complexation. J Colloid Interface Sci 2024; 672:654-663. [PMID: 38865879 DOI: 10.1016/j.jcis.2024.06.062] [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: 05/06/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
HYPOTHESIS Understanding polyelectrolyte complexation remains limited due to the absence of a systematic methodology for analyzing the distribution of components between the polyelectrolyte complex (PEC) and the dilute phases. EXPERIMENTS We developed a methodology based on NMR to quantify all components of solid-like PECs and their supernatant phases formed by mixing different ratios of poly(allylamine hydrochloride) (PAH) and poly(acrylic acid)-sodium salt (PAA). This approach allowed for determining relative and absolute concentrations of polyelectrolytes in both phases by 1H NMR studies. Using 23Na and 35Cl NMR spectroscopy we measured the concentration of counterions in both phases. FINDINGS Regardless of the mixing ratio of the polyelectrolytes the PEC is charge-stoichiometric, and any excess polyelectrolytes to achieve charge stoichiometry remains in the supernatant phase. The majority of counterions were found in the supernatant phase, confirming counterion release being a major thermodynamic driving force for PEC formation. The counterion concentrations in the PEC phase were approximately twice as high as in the supernatant phase. The complete mass balance of PEC formation could be determined and translated into a molecular picture. It appears that PAH is fully charged, while PAA is more protonated, so less charged, and some 10% extrinsic PAH-Cl- pairs are present in the complex.
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Affiliation(s)
- Giulia Allegri
- Molecular Nanofabrication Group, Department for Molecules & Materials, MESA+ Institute & Faculty of Science Technology, University of Twente, 7500 AE Enschede, the Netherlands.
| | - Jurriaan Huskens
- Molecular Nanofabrication Group, Department for Molecules & Materials, MESA+ Institute & Faculty of Science Technology, University of Twente, 7500 AE Enschede, the Netherlands.
| | - Ricardo P Martinho
- Biomolecular Nanotechnology Group, Department for Molecules & Materials, MESA+ Institute & Faculty of Science Technology, University of Twente, 7500 AE Enschede, the Netherlands.
| | - Saskia Lindhoud
- Molecular Nanofabrication Group, Department for Molecules & Materials, MESA+ Institute & Faculty of Science Technology, University of Twente, 7500 AE Enschede, the Netherlands.
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3
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Nishio T, Schiessel H. Coalescence of liquid or gel-like DNA-encapsulating microdroplets. J Chem Phys 2024; 161:134904. [PMID: 39356067 DOI: 10.1063/5.0223951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 09/19/2024] [Indexed: 10/03/2024] Open
Abstract
Liquid-liquid phase separation plays a prominent role in the physics of life, providing the cells with various membrane-less compartments. These structures exhibit a range of material properties that, in many cases, change over time. Inspired by this, we investigate here an aqueous two-phase system formed by mixing polyethylene glycol with dextran. We modulate the material properties of the resulting dextran droplets by adding DNA that readily enters the droplets. We find a non-monotonic dependence of the physical properties of the droplets under the imposed ionic conditions.
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Affiliation(s)
- Takashi Nishio
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, 01307 Dresden, Germany
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, 01307 Dresden, Germany
- Institut für Theoretische Physik, TUD Dresden University of Technology, 01062 Dresden, Germany
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4
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Sanchez-Fernandez A, Insua I, Montenegro J. Supramolecular fibrillation in coacervates and other confined systems towards biomimetic function. Commun Chem 2024; 7:223. [PMID: 39349583 PMCID: PMC11442845 DOI: 10.1038/s42004-024-01308-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 09/13/2024] [Indexed: 10/04/2024] Open
Abstract
As in natural cytoskeletons, the cooperative assembly of fibrillar networks can be hosted inside compartments to engineer biomimetic functions, such as mechanical actuation, transport, and reaction templating. Coacervates impose an optimal liquid-liquid phase separation within the aqueous continuum, functioning as membrane-less compartments that can organise such self-assembling processes as well as the exchange of information with their environment. Furthermore, biological fibrillation can often be controlled or assisted by intracellular compartments. Thus, the reconstitution of analogues of natural filaments in simplified artificial compartments, such as coacervates, offer a suitable model to unravel, mimic, and potentially exploit cellular functions. This perspective summarises the latest developments towards assembling fibrillar networks under confinement inside coacervates and related compartments, including a selection of examples ranging from biological to fully synthetic monomers. Comparative analysis between coacervates, lipid vesicles, and droplet emulsions showcases the interplay between supramolecular fibres and the boundaries of the corresponding compartment. Combining inspiration from natural systems and the custom properties of tailored synthetic fibrillators, rational monomer and compartment design will contribute towards engineering increasingly complex and more realistic artificial protocells.
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Affiliation(s)
- Adrian Sanchez-Fernandez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Departamento de Enxeñaría Química, Universidade de Santaigo de Compostela, Santiago de Compostela, Spain
| | - Ignacio Insua
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
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5
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Yuzu K, Lin CY, Yi PW, Huang CH, Masuhara H, Chatani E. Spatiotemporal formation of a single liquid-like condensate and amyloid fibrils of α-synuclein by optical trapping at solution surface. Proc Natl Acad Sci U S A 2024; 121:e2402162121. [PMID: 39292741 PMCID: PMC11441557 DOI: 10.1073/pnas.2402162121] [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: 02/01/2024] [Accepted: 08/14/2024] [Indexed: 09/20/2024] Open
Abstract
Liquid-like protein condensates have recently attracted much attention due to their critical roles in biological phenomena. They typically show high fluidity and reversibility for exhibiting biological functions, while occasionally serving as sites for the formation of amyloid fibrils. To comprehend the properties of protein condensates that underlie biological function and pathogenesis, it is crucial to study them at the single-condensate level; however, this is currently challenging due to a lack of applicable methods. Here, we demonstrate that optical trapping is capable of inducing the formation of a single liquid-like condensate of α-synuclein in a spatiotemporally controlled manner. The irradiation of tightly focused near-infrared laser at an air/solution interface formed a condensate under conditions coexisting with polyethylene glycol. The fluorescent dye-labeled imaging showed that the optically induced condensate has a gradient of protein concentration from the center to the edge, suggesting that it is fabricated through optical pumping-up of the α-synuclein clusters and the expansion along the interface. Furthermore, Raman spectroscopy and thioflavin T fluorescence analysis revealed that continuous laser irradiation induces structural transition of protein molecules inside the condensate to β-sheet rich structure, ultimately leading to the condensate deformation and furthermore, the formation of amyloid fibrils. These observations indicate that optical trapping is a powerful technique for examining the microscopic mechanisms of condensate appearance and growth, and furthermore, subsequent aging leading to amyloid fibril formation.
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Affiliation(s)
- Keisuke Yuzu
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Ching-Yang Lin
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Po-Wei Yi
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Chih-Hao Huang
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Hiroshi Masuhara
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
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6
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Liang T, Dong Y, Cheng I, Wen P, Li F, Liu F, Wu Q, Ren E, Liu P, Li H, Gu Z. In situ formation of biomolecular condensates as intracellular drug reservoirs for augmenting chemotherapy. Nat Biomed Eng 2024:10.1038/s41551-024-01254-y. [PMID: 39271933 DOI: 10.1038/s41551-024-01254-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/10/2024] [Indexed: 09/15/2024]
Abstract
Biomolecular condensates, which arise from liquid-liquid phase separation within cells, may provide a means of enriching and prolonging the retention of small-molecule drugs within cells. Here we report a method for the controlled in situ formation of biomolecular condensates as reservoirs for the enrichment and retention of chemotherapeutics in cancer cells, and show that the approach can be leveraged to enhance antitumour efficacies in mice with drug-resistant tumours. The method involves histones as positively charged proteins and doxorubicin-intercalated DNA strands bioorthogonally linked via a click-to-release reaction between trans-cyclooctene and tetrazine groups. The reaction temporarily impaired the phase separation of histones in vitro, favoured the initiation of liquid-liquid phase separation within cells and led to the formation of biomolecular condensates that were sufficiently large to be retained within tumour cells. The controlled formation of biomolecular condensates as drug reservoirs within cells may offer new options for boosting the efficacies of cancer therapies.
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Affiliation(s)
- Tingxizi Liang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yuxiang Dong
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Irina Cheng
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ping Wen
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Fengqin Li
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Liu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qing Wu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - En Ren
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Peifeng Liu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Hongjun Li
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Zhen Gu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Jinhua Institute of Zhejiang University, Jinhua, China.
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.
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7
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Mouland AJ, Chau BA, Uversky VN. Methodological approaches to studying phase separation and HIV-1 replication: Current and future perspectives. Methods 2024; 229:147-155. [PMID: 39002735 DOI: 10.1016/j.ymeth.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 06/26/2024] [Accepted: 07/11/2024] [Indexed: 07/15/2024] Open
Abstract
This article reviews tried-and-tested methodologies that have been employed in the first studies on phase separating properties of structural, RNA-binding and catalytic proteins of HIV-1. These are described here to stimulate interest for any who may want to initiate similar studies on virus-mediated liquid-liquid phase separation. Such studies serve to better understand the life cycle and pathogenesis of viruses and open the door to new therapeutics.
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Affiliation(s)
- Andrew J Mouland
- Department of Medicine, McGill University, Montreal, Quebec, Canada.
| | - Bao-An Chau
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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8
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Cao Y, Chao Y, Shum HC. Affinity-Controlled Partitioning of Biomolecules at Aqueous Interfaces and Their Bioanalytic Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2409362. [PMID: 39171488 DOI: 10.1002/adma.202409362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Indexed: 08/23/2024]
Abstract
All-aqueous phase separation systems play essential roles in bioanalytical and biochemical applications. Compared to conventional oil and organic solvent-based systems, these systems are characterized by their rich bulk and interfacial properties, offering superior biocompatibility. In particular, phase separation in all-aqueous systems facilitates the creation of compartments with specific physicochemical properties, and therefore largely enhances the accessibility of the systems. In addition, the all-aqueous compartments have diverse affinities, with an important property known as partitioning, which can concentrate (bio)molecules toward distinct immiscible phases. This partitioning affinity imparts all-aqueous interfaces with selective permeability, enabling the controlled enrichment of target (bio)molecules. This review introduces the basic principles and applications of partitioning-induced interfacial phenomena in a typical all-aqueous system, namely aqueous two-phase systems (ATPSs); these applications include interfacial chemical reactions, bioprinting, and assembly, as well as bio-sensing and detection. The primary challenges associated with designing all-aqueous phase separation systems and several future directions are also discussed, such as the stabilization of aqueous interfaces, the handling of low-volume samples, and exploration of suitable ATPSs compositions with the efficient protocol.
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Affiliation(s)
- Yang Cao
- 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
| | - Youchuang Chao
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - 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
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9
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Stormo BM, McLaughlin GA, Jalihal AP, Frederick LK, Cole SJ, Seim I, Dietrich FS, Chilkoti A, Gladfelter AS. Intrinsically disordered sequences can tune fungal growth and the cell cycle for specific temperatures. Curr Biol 2024; 34:3722-3734.e7. [PMID: 39089255 PMCID: PMC11372857 DOI: 10.1016/j.cub.2024.07.015] [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: 11/21/2023] [Revised: 05/16/2024] [Accepted: 07/02/2024] [Indexed: 08/03/2024]
Abstract
Temperature can impact every reaction essential to a cell. For organisms that cannot regulate their own temperature, adapting to temperatures that fluctuate unpredictably and on variable timescales is a major challenge. Extremes in the magnitude and frequency of temperature changes are increasing across the planet, raising questions as to how the biosphere will respond. To examine mechanisms of adaptation to temperature, we collected wild isolates from different climates of the fungus Ashbya gossypii, which has a compact genome of only ∼4,600 genes. We found control of the nuclear division cycle and polarized morphogenesis, both critical processes for fungal growth, were temperature sensitive and varied among the isolates. The phenotypes were associated with naturally varying sequences within the glutamine-rich region (QRR) IDR of an RNA-binding protein called Whi3. This protein regulates both nuclear division and polarized growth via its ability to form biomolecular condensates. In cells and in cell-free reconstitution assays, we found that temperature tunes the properties of Whi3-based condensates. Exchanging Whi3 sequences between isolates was sufficient to rescue temperature-sensitive phenotypes, and specifically, a heptad repeat sequence within the QRR confers temperature-sensitive behavior. Together, these data demonstrate that sequence variation in the size and composition of an IDR can promote cell adaptation to growth at specific temperature ranges. These data demonstrate the power of IDRs as tuning knobs for rapid adaptation to environmental fluctuations.
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Affiliation(s)
- Benjamin M Stormo
- Duke University, Department of Cell Biology, 308 Research Drive, Durham, NC 27705, USA
| | - Grace A McLaughlin
- Duke University, Department of Cell Biology, 308 Research Drive, Durham, NC 27705, USA; University of North Carolina-Chapel Hill, Department of Biology, 120 South Road, Chapel Hill, NC 27599, USA
| | - Ameya P Jalihal
- Duke University, Department of Cell Biology, 308 Research Drive, Durham, NC 27705, USA
| | - Logan K Frederick
- University of North Carolina-Chapel Hill, Department of Biology, 120 South Road, Chapel Hill, NC 27599, USA
| | - Sierra J Cole
- Duke University, Department of Cell Biology, 308 Research Drive, Durham, NC 27705, USA; University of North Carolina-Chapel Hill, Department of Biochemistry and Biophysics, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Ian Seim
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Fred S Dietrich
- Duke University, Department of Molecular Genetics and Microbiology, 213 Research Drive, Durham, NC 27710, USA
| | - Ashutosh Chilkoti
- Duke University, Department of Biomedical Engineering, 101 Science Drive, Durham, NC 27705, USA
| | - Amy S Gladfelter
- Duke University, Department of Cell Biology, 308 Research Drive, Durham, NC 27705, USA.
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10
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Castelletto V, Seitsonen J, Pollitt A, Hamley IW. Minimal Peptide Sequences That Undergo Liquid-Liquid Phase Separation via Self-Coacervation or Complex Coacervation with ATP. Biomacromolecules 2024; 25:5321-5331. [PMID: 39066731 PMCID: PMC11323023 DOI: 10.1021/acs.biomac.4c00738] [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: 05/31/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
The simple (self-)coacervation of the minimal tryptophan/arginine peptide sequences W2R2 and W3R3 was observed in salt-free aqueous solution. The phase diagrams were mapped using turbidimetry and optical microscopy, and the coacervate droplets were imaged using confocal microscopy complemented by cryo-TEM to image smaller droplets. The droplet size distribution and stability were probed using dynamic light scattering, and the droplet surface potential was obtained from zeta potential measurements. SAXS was used to elucidate the structure within the coacervate droplets, and circular dichroism spectroscopy was used to probe the conformation of the peptides, a characteristic signature for cation-π interactions being present under conditions of coacervation. These observations were rationalized using a simple model for the Rayleigh stability of charged coacervate droplets, along with atomistic molecular dynamics simulations which provide insight into stabilizing π-π stacking interactions of tryptophan as well as arginine-tryptophan cation-π interactions (which modulate the charge of the tryptophan π-electron system). Remarkably, the dipeptide WR did not show simple coacervation under the conditions examined, but complex coacervation was observed in mixtures with ATP (adenosine triphosphate). The electrostatically stabilized coacervation in this case provides a minimal model for peptide/nucleotide membraneless organelle formation. These are among the simplest model peptide systems observed to date able to undergo either simple or complex coacervation and are of future interest as protocell systems.
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Affiliation(s)
- Valeria Castelletto
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Jani Seitsonen
- Nanomicroscopy
Center, Aalto University, Puumiehenkuja 2, Espoo 02150, Finland
| | - Alice Pollitt
- Institute
for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading, Reading RG6 6AS, U.K.
| | - Ian W. Hamley
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
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11
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Chang CC, Coyle SM. Regulatable assembly of synthetic microtubule architectures using engineered microtubule-associated protein-IDR condensates. J Biol Chem 2024; 300:107544. [PMID: 38992434 PMCID: PMC11342785 DOI: 10.1016/j.jbc.2024.107544] [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: 05/23/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
Microtubule filaments are assembled into higher-order structures using microtubule-associated proteins. However, synthetic MAPs that direct the formation of new structures are challenging to design, as nanoscale biochemical activities must be organized across micron length-scales. Here, we develop modular MAP-IDR condensates (synMAPs) that enable inducible assembly of higher-order microtubule structures for synthetic exploration in vitro and in mammalian cells. synMAPs harness a small microtubule-binding domain from oligodendrocytes (TPPP) whose activity we show can be rewired by interaction with unrelated condensate-forming IDR sequences. This combination is sufficient to allow synMAPs to self-organize multivalent structures that bind and bridge microtubules into higher-order architectures. By regulating the connection between the microtubule-binding domain and condensate-forming components of a synMAP, the formation of these structures can be triggered by small molecules or cell-signaling inputs. We systematically test a panel of synMAP circuit designs to define how the assembly of these synthetic microtubule structures can be controlled at the nanoscale (via microtubule-binding affinity) and microscale (via condensate formation). synMAPs thus provide a modular starting point for the design of higher-order microtubule systems and an experimental testbed for exploring condensate-directed mechanisms of higher-order microtubule assembly from the bottom-up.
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Affiliation(s)
- Chih-Chia Chang
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Scott M Coyle
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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12
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Kobayashi R, Nabika H. Liquid-liquid phase separation induced by crowding condition affects amyloid-β aggregation mechanism. SOFT MATTER 2024; 20:5331-5342. [PMID: 38847095 DOI: 10.1039/d4sm00470a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is common in the aggregation of proteins associated with neurodegenerative diseases. Many efforts have been made to reproduce crowded conditions with artificial polymeric materials to understand the effect of LLPS in physiological conditions with significantly highly concentrated proteins, such as intrinsically disordered proteins. Although the possibility that LLPS is involved in intracellular amyloid-β (Aβ) aggregation, a protein related to the pathogenesis of Alzheimer's disease, has been investigated, the relationship between LLPS and the aggregation of Aβ is poorly characterized. Thus, in this study, we mimicked the intracellular crowding environment using polyethylene glycol and dextran, used commonly as model polymers, to examine the relationship of Aβ with LLPS and aggregation dynamics in vitro. We confirmed that Aβ undergoes LLPS under specific polymer coexistence conditions. Moreover, the addition of different electrolytes modulated LLPS and fibril formation. These results suggest that hydrophobic and electrostatic interactions are the driving forces for the LLPS of Aβ. Similar to the role of the liposome interface, the interface of droplets induced by LLPS functioned as the site for heterogeneous nucleation. These findings offer valuable insights into the complex mechanisms of Aβ aggregation in vivo and may be useful in establishing therapeutic methods for Alzheimer's disease.
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Affiliation(s)
- Ryuki Kobayashi
- Department of Science, Graduate School of Science and Engineering, Yamagata University, 1-4-12, Kojirakawa, Yamagata 990-8560, Japan
| | - Hideki Nabika
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa, Yamagata 990-8560, Japan.
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13
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Zhao P, Fan S, Zhou Y, Huang M, Gao Y, Bi H. Constitutive Androstane Receptor and Peroxisome Proliferator-Activated Receptor α Do Not Perform Liquid-Liquid Phase Separation in Cells. J Pharmacol Exp Ther 2024; 390:88-98. [PMID: 38719477 DOI: 10.1124/jpet.124.002174] [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: 02/08/2024] [Accepted: 04/23/2024] [Indexed: 06/23/2024] Open
Abstract
Constitutive androstane receptor (CAR) and peroxisome proliferator-activated receptor α (PPARα) are members of the nuclear receptor superfamily, which regulates various physiologic and pathologic processes. Phase separation is a dynamic biophysical process in which biomacromolecules form liquid-like condensates, which have been identified as contributors to many cellular functions, such as signal transduction and transcription regulation. However, the possibility of phase separation for CAR and PPARα remains unknown. This study explored the potential phase separation of CAR and PPARα The computational analysis utilizing algorithm tools examining the intrinsically disordered regions of CAR and PPARα suggested a limited likelihood of undergoing phase separation. Experimental assays under varying conditions of hyperosmotic stress and agonist treatments confirmed the absence of phase separation for these receptors. Additionally, the optoDroplets assay, which utilizes blue light stimulation to induce condensate formation, showed that there was no condensate formation of the fusion protein of Cry2 with CAR or PPARα Furthermore, phase separation of CAR or PPARα did not occur despite reduced target expression under hyperosmotic stress. In conclusion, these findings revealed that neither the activation of CAR and PPARα nor hyperosmotic stress induces phase separation of CAR and PPARα in cells. SIGNIFICANCE STATEMENT: Constitutive androstane receptor (CAR) and peroxisome proliferator-activated receptor α (PPARα) are key regulators of various functions in the body. This study showed that CAR and PPARα do not exhibit phase separation under hyperosmotic stress or after agonist-induced activation. These findings provide new insights into the CAR and PPARα biology and physiology.
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Affiliation(s)
- Pengfei Zhao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening and Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (P.Z., S.F., H.B.); Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., S.F., Y.Z., M.H., Y.G., H.B.); and The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China (H.B.)
| | - Shicheng Fan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening and Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (P.Z., S.F., H.B.); Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., S.F., Y.Z., M.H., Y.G., H.B.); and The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China (H.B.)
| | - Yanying Zhou
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening and Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (P.Z., S.F., H.B.); Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., S.F., Y.Z., M.H., Y.G., H.B.); and The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China (H.B.)
| | - Min Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening and Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (P.Z., S.F., H.B.); Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., S.F., Y.Z., M.H., Y.G., H.B.); and The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China (H.B.)
| | - Yue Gao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening and Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (P.Z., S.F., H.B.); Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., S.F., Y.Z., M.H., Y.G., H.B.); and The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China (H.B.)
| | - Huichang Bi
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong Provincial Key Laboratory of New Drug Screening and Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China (P.Z., S.F., H.B.); Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China (P.Z., S.F., Y.Z., M.H., Y.G., H.B.); and The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China (H.B.)
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14
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Wyle Y, Lu N, Hepfer J, Sayal R, Martinez T, Wang A. The Role of Biophysical Factors in Organ Development: Insights from Current Organoid Models. Bioengineering (Basel) 2024; 11:619. [PMID: 38927855 PMCID: PMC11200479 DOI: 10.3390/bioengineering11060619] [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: 04/17/2024] [Revised: 05/26/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Biophysical factors play a fundamental role in human embryonic development. Traditional in vitro models of organogenesis focused on the biochemical environment and did not consider the effects of mechanical forces on developing tissue. While most human tissue has a Young's modulus in the low kilopascal range, the standard cell culture substrate, plasma-treated polystyrene, has a Young's modulus of 3 gigapascals, making it 10,000-100,000 times stiffer than native tissues. Modern in vitro approaches attempt to recapitulate the biophysical niche of native organs and have yielded more clinically relevant models of human tissues. Since Clevers' conception of intestinal organoids in 2009, the field has expanded rapidly, generating stem-cell derived structures, which are transcriptionally similar to fetal tissues, for nearly every organ system in the human body. For this reason, we conjecture that organoids will make their first clinical impact in fetal regenerative medicine as the structures generated ex vivo will better match native fetal tissues. Moreover, autologously sourced transplanted tissues would be able to grow with the developing embryo in a dynamic, fetal environment. As organoid technologies evolve, the resultant tissues will approach the structure and function of adult human organs and may help bridge the gap between preclinical drug candidates and clinically approved therapeutics. In this review, we discuss roles of tissue stiffness, viscoelasticity, and shear forces in organ formation and disease development, suggesting that these physical parameters should be further integrated into organoid models to improve their physiological relevance and therapeutic applicability. It also points to the mechanotransductive Hippo-YAP/TAZ signaling pathway as a key player in the interplay between extracellular matrix stiffness, cellular mechanics, and biochemical pathways. We conclude by highlighting how frontiers in physics can be applied to biology, for example, how quantum entanglement may be applied to better predict spontaneous DNA mutations. In the future, contemporary physical theories may be leveraged to better understand seemingly stochastic events during organogenesis.
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Affiliation(s)
- Yofiel Wyle
- Department of Surgery, School of Medicine, University of California-Davis, Sacramento, CA 95817, USA; (Y.W.); (N.L.); (J.H.); (R.S.); (T.M.)
- Institute for Pediatric Regenerative Medicine, Shriners Children’s, Sacramento, CA 95817, USA
| | - Nathan Lu
- Department of Surgery, School of Medicine, University of California-Davis, Sacramento, CA 95817, USA; (Y.W.); (N.L.); (J.H.); (R.S.); (T.M.)
| | - Jason Hepfer
- Department of Surgery, School of Medicine, University of California-Davis, Sacramento, CA 95817, USA; (Y.W.); (N.L.); (J.H.); (R.S.); (T.M.)
| | - Rahul Sayal
- Department of Surgery, School of Medicine, University of California-Davis, Sacramento, CA 95817, USA; (Y.W.); (N.L.); (J.H.); (R.S.); (T.M.)
| | - Taylor Martinez
- Department of Surgery, School of Medicine, University of California-Davis, Sacramento, CA 95817, USA; (Y.W.); (N.L.); (J.H.); (R.S.); (T.M.)
| | - Aijun Wang
- Department of Surgery, School of Medicine, University of California-Davis, Sacramento, CA 95817, USA; (Y.W.); (N.L.); (J.H.); (R.S.); (T.M.)
- Institute for Pediatric Regenerative Medicine, Shriners Children’s, Sacramento, CA 95817, USA
- Department of Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA
- Center for Surgical Bioengineering, Department of Surgery, School of Medicine, University of California, Davis, 4625 2nd Ave., Research II, Suite 3005, Sacramento, CA 95817, USA
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15
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Litschel T, Kelley CF, Cheng X, Babl L, Mizuno N, Case LB, Schwille P. Membrane-induced 2D phase separation of the focal adhesion protein talin. Nat Commun 2024; 15:4986. [PMID: 38862544 PMCID: PMC11166923 DOI: 10.1038/s41467-024-49222-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: 05/16/2023] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
Focal adhesions form liquid-like assemblies around activated integrin receptors at the plasma membrane. How they achieve their flexible properties is not well understood. Here, we use recombinant focal adhesion proteins to reconstitute the core structural machinery in vitro. We observe liquid-liquid phase separation of the core focal adhesion proteins talin and vinculin for a spectrum of conditions and interaction partners. Intriguingly, we show that binding to PI(4,5)P2-containing membranes triggers phase separation of these proteins on the membrane surface, which in turn induces the enrichment of integrin in the clusters. We suggest a mechanism by which 2-dimensional biomolecular condensates assemble on membranes from soluble proteins in the cytoplasm: lipid-binding triggers protein activation and thus, liquid-liquid phase separation of these membrane-bound proteins. This could explain how early focal adhesions maintain a structured and force-resistant organization into the cytoplasm, while still being highly dynamic and able to quickly assemble and disassemble.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| | - Charlotte F Kelley
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Xiaohang Cheng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leon Babl
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Naoko Mizuno
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Laboratory of Structural Cell Biology, National Institutes of Health, Bethesda, MD, USA
| | - Lindsay B Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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16
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Ou X, Tang Z, Ye Y, Chen X, Huang Y. Macromolecular Crowding Effect on Chitosan-Hyaluronic Acid Complexation and the Activity of Encapsulated Catalase. Biomacromolecules 2024; 25:3840-3849. [PMID: 38801711 DOI: 10.1021/acs.biomac.4c00445] [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: 05/29/2024]
Abstract
The associative phase separation of charged biomacromolecules plays a key role in many biophysical events that take place in crowded intracellular environments. Such natural polyelectrolyte complexation and phase separation often occur at nonstoichiometric charge ratios with the incorporation of bioactive proteins, which is not studied as extensively as those complexations at stoichiometric ratios. In this work, we investigated how the addition of a crowding agent (polyethylene glycol, PEG) affected the complexation between chitosan (CS) and hyaluronic acid (HA), especially at nonstoichiometric ratios, and the encapsulation of enzyme (catalase, CAT) by the colloidal complexes. The crowded environment promoted colloidal phase separation at low charge ratios, forming complexes with increased colloidal and dissolution stability, which resulted in a smaller size and polydispersity (PDI). The binding isotherms revealed that the addition of PEG greatly enhanced the ion-pairing strength (with increased ion-pairing equilibrium constant Ka from 4.92 × 104 without PEG to 1.08 × 106 with 200 g/L PEG) and switched the coacervation from endothermic to exothermic, which explained the promoted complexation and phase separation. At the stoichiometric charge ratio, the enhanced CS-HA interaction in crowded media generated a more solid-like coacervate phase with a denser network, slower chain relaxation, and higher modulus. Moreover, both crowding and complex encapsulation enhanced the activity and catalytic efficiency of CAT, represented by a 2-fold increase in catalytic efficiency (Kcat/Km) under 100 g/L PEG crowding and CS-HA complex encapsulation. This is likely due to the lower polarity in the microenvironment surrounding the enzyme molecules. By a systematic investigation of both nonstoichiometric and stoichiometric charge ratios under macromolecular crowding, this work provided new insights into the complexation between natural polyelectrolytes in a scenario closer to an intracellular environment.
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Affiliation(s)
- Xiatong Ou
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Ziyao Tang
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Yanqi Ye
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
| | - Xiaochao Chen
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
- Chuanhua Kechuang Building, Ningwei Street, Xiaoshan District, Zhejiang Novofacies Biotech Co., Ltd., Hangzhou 311215, Zhejiang, China
| | - Yan Huang
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Minhou County, Fuzhou 350108, Fujian, China
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17
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Singh A, Gupta M, Rastogi H, Khare K, Chowdhury PK. Deeper Insights into Mixed Crowding through Enzyme Activity, Dynamics, and Crowder Diffusion. J Phys Chem B 2024; 128:5293-5309. [PMID: 38808573 DOI: 10.1021/acs.jpcb.4c00337] [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: 05/30/2024]
Abstract
Given the fact that the cellular interior is crowded by many different kinds of macromolecules, it is important that in vitro studies be carried out in the presence of mixed crowder systems. In this regard, we have used binary crowders formed by the combination of some of the commonly used crowding agents, namely, Ficoll 70, Dextran 70, Dextran 40, and PEG 8000 (PEG 8), to study how these affect enzyme activity, dynamics, and crowder diffusion. The enzyme chosen is AK3L1, an isoform of adenylate kinase. To investigate its dynamics, we have carried out three single point mutations (A74C, A132C, and A209C) with the cysteine residues being labeled with a coumarin-based solvatochromic probe [CPM: (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin)]. Both enzyme activity and dynamics decreased in the binary mixtures as compared with the sum of the individual crowders, suggesting a reduction in excluded volume (in the mixture). To gain deeper insights into the binary mixtures, fluorescence correlation spectroscopy studies were carried out using fluorescein isothiocyanate-labeled Dextran 70 and tetramethylrhodamine-labeled AK3L1 as the diffusion probes. Diffusion in binary mixtures was observed to be much more constrained (relative to the sum of the individual crowders) for the labeled enzyme as compared to the labeled crowder showing different environments being faced by the two species. This was further confirmed during imaging of the phase-separated droplets formed in the binary mixtures having PEG as one of the crowding agents. The interior of these droplets was found to be rich in crowders and densely packed, as shown by confocal and digital holographic microscopy images, with the enzymes predominantly residing outside these droplets, that is, in the relatively less crowded regions. Taken together, our data provide important insights into various aspects of the simplest form of mixed crowding, that is, composed of just two components, and also hint at the enhanced complexity that the cellular interior presents toward having a detailed and comprehensive understanding of the same.
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Affiliation(s)
- Arvind Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Kedar Khare
- Optics and Photonics Centre, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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18
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Islam M, Shen F, Regmi D, Petersen K, Karim MRU, Du D. Tau liquid-liquid phase separation: At the crossroads of tau physiology and tauopathy. J Cell Physiol 2024; 239:e30853. [PMID: 35980344 PMCID: PMC9938090 DOI: 10.1002/jcp.30853] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 12/14/2022]
Abstract
Abnormal deposition of tau in neurons is a hallmark of Alzheimer's disease and several other neurodegenerative disorders. In the past decades, extensive efforts have been made to explore the mechanistic pathways underlying the development of tauopathies. Recently, the discovery of tau droplet formation by liquid-liquid phase separation (LLPS) has received a great deal of attention. It has been reported that tau condensates have a biological role in promoting and stabilizing microtubule (MT) assembly. Furthermore, it has been hypothesized that the transition of phase-separated tau droplets to a gel-like state and then to fibrils is associated with the pathology of neurodegenerative diseases. In this review, we outline LLPS, the structural disorder that facilitates tau droplet formation, the effects of posttranslational modification of tau on condensate formation, the physiological function of tau droplets, the pathways from droplet to toxic fibrils, and the therapeutic strategies for tauopathies that might evolve from toxic droplets. We expect a deeper understanding of tau LLPS will provide additional insights into tau physiology and tauopathies.
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Affiliation(s)
- Majedul Islam
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Fengyun Shen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Deepika Regmi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Katherine Petersen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Md Raza Ul Karim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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19
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Batisse C, Lapaillerie D, Humbert N, Real E, Zhu R, Mély Y, Parissi V, Ruff M, Batisse J. Integrase-LEDGF/p75 complex triggers the formation of biomolecular condensates that modulate HIV-1 integration efficiency in vitro. J Biol Chem 2024; 300:107374. [PMID: 38762180 PMCID: PMC11208922 DOI: 10.1016/j.jbc.2024.107374] [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: 05/20/2023] [Revised: 04/27/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024] Open
Abstract
The pre-integration steps of the HIV-1 viral cycle are some of the most valuable targets of recent therapeutic innovations. HIV-1 integrase (IN) displays multiple functions, thanks to its considerable conformational flexibility. Recently, such flexible proteins have been characterized by their ability to form biomolecular condensates as a result of Liquid-Liquid-Phase-Separation (LLPS), allowing them to evolve in a restricted microenvironment within cells called membrane-less organelles (MLO). The LLPS context constitutes a more physiological approach to study the integration of molecular mechanisms performed by intasomes (complexes containing viral DNA, IN, and its cellular cofactor LEDGF/p75). We investigated here if such complexes can form LLPS in vitro and if IN enzymatic activities were affected by this LLPS environment. We observed that the LLPS formed by IN-LEDGF/p75 functional complexes modulate the in vitro IN activities. While the 3'-processing of viral DNA ends was drastically reduced inside LLPS, viral DNA strand transfer was strongly enhanced. These two catalytic IN activities appear thus tightly regulated by the environment encountered by intasomes.
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Affiliation(s)
- Claire Batisse
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory (MFP), UMR-5234 CNRS-University of Bordeaux, Bordeaux, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Nicolas Humbert
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Eleonore Real
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Rui Zhu
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Yves Mély
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory (MFP), UMR-5234 CNRS-University of Bordeaux, Bordeaux, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
| | - Marc Ruff
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
| | - Julien Batisse
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
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20
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Lu X, Lu J, Li S, Feng S, Wang Y, Cui L. The Role of Liquid-Liquid Phase Separation in the Accumulation of Pathological Proteins: New Perspectives on the Mechanism of Neurodegenerative Diseases. Aging Dis 2024:AD.2024.0209. [PMID: 38739933 DOI: 10.14336/ad.2024.0209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/20/2024] [Indexed: 05/16/2024] Open
Abstract
It is widely accepted that living organisms form highly dynamic membrane-less organelles (MLOS) with various functions through phase separation, and the indispensable role that phase separation plays in the mechanisms of normal physiological functions and pathogenesis is gradually becoming clearer. Pathological aggregates, regarded as hallmarks of neurodegenerative diseases, have been revealed to be closely related to aberrant phase separation. Specific proteins are assembled into condensates and transform into insoluble inclusions through aberrant phase separation, contributing to the development of diseases. In this review, we present an overview of the progress of phase separation research, involving its biological mechanisms and the status of research in neurodegenerative diseases, focusing on five main disease-specific proteins, tau, TDP-43, FUS, α-Syn and HTT, and how exactly these proteins reside within dynamic liquid-like compartments and thus turn into solid deposits. Further studies will yield new perspectives for understanding the aggregation mechanisms and potential therapeutic strategies, and future research directions are anticipated.
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Affiliation(s)
- Xingyu Lu
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jiongtong Lu
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Shengnan Li
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Sifan Feng
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yan Wang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Lili Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- The Marine Biomedical Research Institute of Guangdong, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, Guangdong, China
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21
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Hedtfeld M, Dammers A, Koerner C, Musacchio A. A validation strategy to assess the role of phase separation as a determinant of macromolecular localization. Mol Cell 2024; 84:1783-1801.e7. [PMID: 38614097 DOI: 10.1016/j.molcel.2024.03.022] [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: 06/04/2023] [Revised: 12/11/2023] [Accepted: 03/22/2024] [Indexed: 04/15/2024]
Abstract
Liquid-liquid phase separation (LLPS) of putative assembly scaffolds has been proposed to drive the biogenesis of membraneless compartments. LLPS scaffolds are usually identified through in vitro LLPS assays with single macromolecules (homotypic), but the predictive value of these assays remains poorly characterized. Here, we apply a strategy to evaluate the robustness of homotypic LLPS assays. When applied to the chromosomal passenger complex (CPC), which undergoes LLPS in vitro and localizes to centromeres to promote chromosome biorientation, LLPS propensity in vitro emerged as an unreliable predictor of subcellular localization. In vitro CPC LLPS in aqueous buffers was enhanced by commonly used crowding agents. Conversely, diluted cytomimetic media dissolved condensates of the CPC and of several other proteins. We also show that centromeres do not seem to nucleate LLPS, nor do they promote local, spatially restrained LLPS of the CPC. Our strategy can be adapted to purported LLPS scaffolds of other membraneless compartments.
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Affiliation(s)
- Marius Hedtfeld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Alicia Dammers
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Carolin Koerner
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.
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22
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Zhang M, Zhang Z, Niu X, Ti H, Zhou Y, Gao B, Li Y, Liu J, Chen X, Li H. Interplay Between Intracellular Transport Dynamics and Liquid‒Liquid Phase Separation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308338. [PMID: 38447188 PMCID: PMC11109639 DOI: 10.1002/advs.202308338] [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: 11/02/2023] [Revised: 01/22/2024] [Indexed: 03/08/2024]
Abstract
Liquid‒liquid phase separation (LLPS) is a ubiquitous process in which proteins, RNA, and biomolecules assemble into membrane-less compartments, playing important roles in many biological functions and diseases. The current knowledge on the biophysical and biochemical principles of LLPS is largely from in vitro studies; however, the physiological environment in living cells is complex and not at equilibrium. The characteristics of intracellular dynamics and their roles in physiological LLPS remain to be resolved. Here, by using single-particle tracking of quantum dots and dynamic monitoring of the formation of stress granules (SGs) in single cells, the spatiotemporal dynamics of intracellular transport in cells undergoing LLPS are quantified. It is shown that intracellular diffusion and active transport are both reduced. Furthermore, the formation of SG droplets contributes to increased spatial heterogeneity within the cell. More importantly, the study demonstrated that the LLPS of SGs can be regulated by intracellular dynamics in two stages: the reduced intracellular diffusion promotes SG assembly and the microtubule-associated transport facilitates SG coalescences. The work on intracellular dynamics not only improves the understanding of the mechanism of physiology phase separations occurring in nonequilibrium environments but also reveals an interplay between intracellular dynamics and LLPS.
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Affiliation(s)
- Ming‐Li Zhang
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Ziheng Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xue‐Zhi Niu
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Hui‐Ying Ti
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Yu‐Xuan Zhou
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Bo Gao
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics and Molecular Imaging Key LaboratoryDepartment of Biomedical EngineeringCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
| | - Ji‐Long Liu
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xiaosong Chen
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
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23
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Nesterov SV, Ilyinsky NS, Plokhikh KS, Manuylov VD, Chesnokov YM, Vasilov RG, Kuznetsova IM, Turoverov KK, Gordeliy VI, Fonin AV, Uversky VN. Order wrapped in chaos: On the roles of intrinsically disordered proteins and RNAs in the arrangement of the mitochondrial enzymatic machines. Int J Biol Macromol 2024; 267:131455. [PMID: 38588835 DOI: 10.1016/j.ijbiomac.2024.131455] [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: 11/11/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
The analysis of cryo-electron tomography images of human and rat mitochondria revealed that the mitochondrial matrix is at least as crowded as the cytosol. To mitigate the crowding effects, metabolite transport in the mitochondria primarily occurs through the intermembrane space, which is significantly less crowded. The scientific literature largely ignores how enzyme systems and metabolite transport are organized in the crowded environment of the mitochondrial matrix. Under crowded conditions, multivalent interactions carried out by disordered protein regions (IDRs), may become extremely important. We analyzed the human mitochondrial proteome to determine the presence and physiological significance of IDRs. Despite mitochondrial proteins being generally more ordered than cytosolic or overall proteome proteins, disordered regions plays a significant role in certain mitochondrial compartments and processes. Even in highly ordered enzyme systems, there are proteins with long IDRs. Some IDRs act as binding elements between highly ordered subunits, while the roles of others are not yet established. Mitochondrial systems, like their bacterial ancestors, rely less on IDRs and more on RNA for LLPS compartmentalization. More evolutionarily advanced subsystems that enable mitochondria-cell interactions contain more IDRs. The study highlights the crucial and often overlooked role played by IDRs and non-coding RNAs in mitochondrial organization.
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Affiliation(s)
- Semen V Nesterov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia; Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia; Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia.
| | - Nikolay S Ilyinsky
- Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia.
| | | | - Vladimir D Manuylov
- Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia
| | - Yuriy M Chesnokov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Raif G Vasilov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Irina M Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | | | - Valentin I Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027 Grenoble, France
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
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24
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Wilcox K, Yamagami KR, Roopnarine BK, Linscott A, Morozova S. Effect of Polymer Gel Elasticity on Complex Coacervate Phase Behavior. ACS POLYMERS AU 2024; 4:109-119. [PMID: 38618006 PMCID: PMC11010254 DOI: 10.1021/acspolymersau.3c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 04/16/2024]
Abstract
Gels are key materials in biological systems such as tissues and may control biocondensate formation and structure. To further understand the effects of elastic environments on biomacromolecular assembly, we have investigated the phase behavior and radii of complex coacervate droplets in polyacrylamide (PAM) networks as a function of gel modulus. Poly-l-lysine (PLL) and sodium hyaluronate (HA) complex coacervate phases were prepared in PAM gels with moduli varying from 0.035 to 15.0 kPa. The size of the complex coacervate droplets is reported from bright-field microscopy and confocal fluorescence microscopy. Overall, the complex coacervate droplet volume decreases inversely with the modulus. Fluorescence microscopy is also used to determine the phase behavior and concentration of fluorescently tagged HA in the complex coacervate phases as a function of ionic strength (100-270 mM). We find that the critical ionic strength and complex coacervate stability are nonmonotonic as a function of the network modulus and that the local gel concentration can be used to control phase behavior and complex coacervate droplet size scale. By understanding how elastic environments influence simple electrostatic assembly, we can further understand how biomacromolecules exist in complex, crowded, and elastic cellular environments.
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Affiliation(s)
- Kathryn
G. Wilcox
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
| | - Kai R. Yamagami
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
| | - Brittany K. Roopnarine
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
| | - Adam Linscott
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
| | - Svetlana Morozova
- Department of Macromolecular
Science and Engineering, Case Western Reserve
University, Cleveland, Ohio 44106, United States
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25
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Pedrozo-Romero JJ, Pérez-Ángel G. Depletion forces in dense mixtures of spheres and rods. J Chem Phys 2024; 160:134502. [PMID: 38557848 DOI: 10.1063/5.0189387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
We evaluate depletion forces in molecular dynamics simulation of a binary mixture of spheres (depleted particles) and rods (depletant particles) for a wide range of densities for both species. This evaluation was carried out using a recently proposed least squares fitting algorithm. We found that the restriction of the rods' rotational degrees of freedom, when the distance between two spheres is less than the rods length, creates a shallow, and apparently linear, attractive force ramp. For intersphere distances smaller than the rods' diameter, a much stronger attractive force is found, and a large repulsive barrier appears between these aforementioned regimes, roughly at the distance of the rods' thickness. The evaluated forces are validated via a comparison of the pairwise correlation functions obtained from molecular dynamics simulation of a mono-disperse sphere fluid, using the evaluated effective forces, against the original (full system) pairwise correlation functions. Agreement is excellent. We also record the angular pairwise correlation function, using the P2(x) Legendre polynomial, and find that for high densities of both species, a local nematic ordering starts to appear. This nematic order may be a factor in the small differences found between original and effective pairwise correlation functions at high densities of rods.
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Affiliation(s)
- Jorge J Pedrozo-Romero
- CINVESTAV Unidad Mérida, Departamento de Física Aplicada, A.P. 73 "Cordemex," 97310 Mérida, Yucatán, Mexico
| | - Gabriel Pérez-Ángel
- CINVESTAV Unidad Mérida, Departamento de Física Aplicada, A.P. 73 "Cordemex," 97310 Mérida, Yucatán, Mexico
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26
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Kovács ZJ, Harami GM, Pálinkás J, Kuljanishvili N, Hegedüs J, Harami‐Papp H, Mahmudova L, Khamisi L, Szakács G, Kovács M. DNA-dependent phase separation by human SSB2 (NABP1/OBFC2A) protein points to adaptations to eukaryotic genome repair processes. Protein Sci 2024; 33:e4959. [PMID: 38511671 PMCID: PMC10955726 DOI: 10.1002/pro.4959] [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: 10/19/2023] [Revised: 02/04/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Single-stranded DNA binding proteins (SSBs) are ubiquitous across all domains of life and play essential roles via stabilizing and protecting single-stranded (ss) DNA as well as organizing multiprotein complexes during DNA replication, recombination, and repair. Two mammalian SSB paralogs (hSSB1 and hSSB2 in humans) were recently identified and shown to be involved in various genome maintenance processes. Following our recent discovery of the liquid-liquid phase separation (LLPS) propensity of Escherichia coli (Ec) SSB, here we show that hSSB2 also forms LLPS condensates under physiologically relevant ionic conditions. Similar to that seen for EcSSB, we demonstrate the essential contribution of hSSB2's C-terminal intrinsically disordered region (IDR) to condensate formation, and the selective enrichment of various genome metabolic proteins in hSSB2 condensates. However, in contrast to EcSSB-driven LLPS that is inhibited by ssDNA binding, hSSB2 phase separation requires single-stranded nucleic acid binding, and is especially facilitated by ssDNA. Our results reveal an evolutionarily conserved role for SSB-mediated LLPS in the spatiotemporal organization of genome maintenance complexes. At the same time, differential LLPS features of EcSSB and hSSB2 point to functional adaptations to prokaryotic versus eukaryotic genome metabolic contexts.
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Affiliation(s)
- Zoltán J. Kovács
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
- HUN‐REN–ELTE Motor Pharmacology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Gábor M. Harami
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - János Pálinkás
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Natalie Kuljanishvili
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - József Hegedüs
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Hajnalka Harami‐Papp
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Lamiya Mahmudova
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Lana Khamisi
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Gergely Szakács
- HUN‐REN Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapestHungary
- Center for Cancer ResearchMedical University of ViennaWienAustria
| | - Mihály Kovács
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
- HUN‐REN–ELTE Motor Pharmacology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
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27
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Xu G, Cheng K, Liu M, Li C. Studying protein stability in crowded environments by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2024; 140-141:42-48. [PMID: 38705635 DOI: 10.1016/j.pnmrs.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/07/2024]
Abstract
Most proteins perform their functions in crowded and complex cellular environments where weak interactions are ubiquitous between biomolecules. These complex environments can modulate the protein folding energy landscape and hence affect protein stability. NMR is a nondestructive and effective method to quantify the kinetics and equilibrium thermodynamic stability of proteins at an atomic level within crowded environments and living cells. Here, we review NMR methods that can be used to measure protein stability, as well as findings of studies on protein stability in crowded environments mimicked by polymer and protein crowders and in living cells. The important effects of chemical interactions on protein stability are highlighted and compared to spatial excluded volume effects.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China.
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28
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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29
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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.
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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
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30
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Rai S, Pramanik S, Mukherjee S. Deciphering the liquid-liquid phase separation induced modulation in the structure, dynamics, and enzymatic activity of an ordered protein β-lactoglobulin. Chem Sci 2024; 15:3936-3948. [PMID: 38487243 PMCID: PMC10935713 DOI: 10.1039/d3sc06802a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 03/17/2024] Open
Abstract
Owing to the significant role in the subcellular organization of biomolecules, physiology, and the realm of biomimetic materials, studies related to biomolecular condensates formed through liquid-liquid phase separation (LLPS) have emerged as a growing area of research. Despite valuable contributions of prior research, there is untapped potential in exploring the influence of phase separation on the conformational dynamics and enzymatic activities of native proteins. Herein, we investigate the LLPS of β-lactoglobulin (β-LG), a non-intrinsically disordered protein, under crowded conditions. In-depth characterization through spectroscopic and microscopic techniques revealed the formation of dynamic liquid-like droplets, distinct from protein aggregates, driven by hydrophobic interactions. Our analyses revealed that phase separation can alter structural flexibility and photophysical properties. Importantly, the phase-separated β-LG exhibited efficient enzymatic activity as an esterase; a characteristic seemingly exclusive to β-LG droplets. The droplets acted as robust catalytic crucibles, providing an ideal environment for efficient ester hydrolysis. Further investigation into the catalytic mechanism suggested the involvement of specific amino acid residues, rather than general acid or base catalysis. Also, the alteration in conformational distribution caused by phase separation unveils the latent functionality. Our study delineates the understanding of protein phase separation and insights into the diverse catalytic strategies employed by proteins. It opens exciting possibilities for designing functional artificial compartments based on phase-separated biomolecules.
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Affiliation(s)
- Saurabh Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
| | - Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road Bhopal 462066 Madhya Pradesh India
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31
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Mondal S, Cui Q. Sequence Sensitivity in Membrane Remodeling by Polyampholyte Condensates. J Phys Chem B 2024; 128:2087-2099. [PMID: 38407041 DOI: 10.1021/acs.jpcb.3c08149] [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: 02/27/2024]
Abstract
Intrinsically disordered peptides (IDPs) have been found to undergo liquid-liquid phase separation (LLPS) and produce complex coacervates that play numerous regulatory roles in the cell. Recent experimental studies have discovered that LLPS at or near the membrane surface helps in the biomolecular organization during signaling events and can significantly alter the membrane morphology. However, the molecular mechanism and microscopic details of such processes still remain unclear. Here we study the effect of polyampholyte and polyelectrolyte condensation on two different anionic membranes, as they represent a majority of naturally occurring IDPs. The polyampholytes are fifty-residue polymers, made of glutamate(E) and lysine(K) with different charge patterns. The polyelectrolytes are separate chains of E25 and K25. We first calibrate the MARTINI v3.0 force field and then perform long-time-scale coarse-grained molecular dynamics simulations. We find that condensates formed by all the polyampholytes get adsorbed on the membrane. However, the strong polyampholytes (i.e., blocky sequences) can remodel the membranes more prominently than the weaker ones (i.e., scrambled sequences). Condensates formed by the blocky sequences induce a significant negative curvature (∼0.1 nm-1) and local demixing of lipids, whereas those by the scrambled sequences tend to wet the membrane to a greater extent without generating significant curvature or demixing. We perform several microscopic analyses to characterize the nature of the interaction between membranes and these condensates. Our analyses of interaction energetics reveal that membrane remodeling and/or wetting are favored by enhanced interactions between polyampholytes with lipids and the counterions.
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Affiliation(s)
- Sayantan Mondal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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32
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McCarthy E, Manna RK, Damavandi O, Manning ML. Demixing in Binary Mixtures with Differential Diffusivity at High Density. PHYSICAL REVIEW LETTERS 2024; 132:098301. [PMID: 38489657 DOI: 10.1103/physrevlett.132.098301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 03/17/2024]
Abstract
Spontaneous phase separation, or demixing, is important in biological phenomena such as cell sorting. In particle-based models, an open question is whether differences in diffusivity can drive such demixing. While differential-diffusivity-induced phase separation occurs in mixtures with a packing fraction up to 0.7 [S. N. Weber et al. Binary mixtures of particles with different diffusivities demix, Phys. Rev. Lett. 116, 058301 (2016)PRLTAO0031-900710.1103/PhysRevLett.116.058301], here we investigate whether demixing persists at even higher densities relevant for cells. For particle packing fractions between 0.7 and 1.0 the system demixes, but at packing fractions above unity the system remains mixed, exposing re-entrant behavior in the phase diagram that occurs when phase separation can no longer drive a change in entropy production at high densities. We also find that a confluent Voronoi model for tissues does not phase separate, consistent with particle-based simulations.
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Affiliation(s)
- Erin McCarthy
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
| | - Raj Kumar Manna
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
| | - Ojan Damavandi
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
| | - M Lisa Manning
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
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33
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [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: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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34
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Rozhkov S, Goryunov A, Rozhkova N. Molecular Serum Albumin Unmask Nanobio Properties of Molecular Graphenes in Shungite Carbon Nanoparticles. Int J Mol Sci 2024; 25:2465. [PMID: 38473711 DOI: 10.3390/ijms25052465] [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: 01/13/2024] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Serum albumin is a popular macromolecule for studying the effect of proteins on the colloidal stability of nanoparticle (NP) dispersions, as well as the protein-nanoparticle interaction and protein corona formation. In this work, we analyze the specific conformation-dependent phase, redox, and fatty acid delivery properties of bovine albumin in the presence of shungite carbon (ShC) molecular graphenes stabilized in aqueous dispersions in the form of NPs in order to reveal the features of NP bioactivity. The formation of NP complexes with proteins (protein corona around NP) affects the transport properties of albumin for the delivery of fatty acids. Being acceptors of electrons and ligands, ShC NPs are capable of exhibiting both their own biological activity and significantly affecting conformational and phase transformations in protein systems.
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Affiliation(s)
- Sergey Rozhkov
- Institute of Biology, Karelian Research Centre RAS, 185910 Petrozavodsk, Russia
| | - Andrey Goryunov
- Institute of Biology, Karelian Research Centre RAS, 185910 Petrozavodsk, Russia
| | - Natalia Rozhkova
- Institute of Geology, Karelian Research Centre RAS, 185910 Petrozavodsk, Russia
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35
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Ong Q, Xufeng X, Stellacci F. Versatile Capillary Cells for Handling Concentrated Samples in Analytical Ultracentrifugation. Anal Chem 2024; 96:2567-2573. [PMID: 38301115 PMCID: PMC10867799 DOI: 10.1021/acs.analchem.3c05006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
In concentrated macromolecular dispersions, far-from-ideal intermolecular interactions determine the dispersion behaviors including phase transition, crystallization, and liquid-liquid phase separation. Here, we present a novel versatile capillary-cell design for analytical ultracentrifugation-sedimentation equilibrium (AUC-SE), ideal for studying samples at high concentrations. Current setups for such studies are difficult and unreliable to handle, leading to a low experimental success rate. The design presented here is easy to use, robust, and reusable for samples in both aqueous and organic solvents while requiring no special tools or chemical modification of AUC cells. The key and unique feature is the fabrication of liquid reservoirs directly on the bottom window of AUC cells, which can be easily realized by laser ablation or mechanical drilling. The channel length and optical path length are therefore tunable. The success rate for assembling this new cell is close to 100%. We demonstrate the practicality of this cell by studying: (1) the equation of state and second virial coefficients of concentrated gold nanoparticle dispersions in water and bovine serum albumin (BSA) as well as lysozyme solution in aqueous buffers, (2) the gelation phase transition of DNA and BSA solutions, and (3) liquid-liquid phase separation of concentrated BSA/polyethylene glycol (PEG) droplets.
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Affiliation(s)
- Quy Ong
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
| | - Xu Xufeng
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
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36
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Subramanya AR, Boyd-Shiwarski CR. Molecular Crowding: Physiologic Sensing and Control. Annu Rev Physiol 2024; 86:429-452. [PMID: 37931170 PMCID: PMC11472293 DOI: 10.1146/annurev-physiol-042222-025920] [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: 11/08/2023]
Abstract
The cytoplasm is densely packed with molecules that contribute to its nonideal behavior. Cytosolic crowding influences chemical reaction rates, intracellular water mobility, and macromolecular complex formation. Overcrowding is potentially catastrophic; to counteract this problem, cells have evolved acute and chronic homeostatic mechanisms that optimize cellular crowdedness. Here, we provide a physiology-focused overview of molecular crowding, highlighting contemporary advances in our understanding of its sensing and control. Long hypothesized as a form of crowding-induced microcompartmentation, phase separation allows cells to detect and respond to intracellular crowding through the action of biomolecular condensates, as indicated by recent studies. Growing evidence indicates that crowding is closely tied to cell size and fluid volume, homeostatic responses to physical compression and desiccation, tissue architecture, circadian rhythm, aging, transepithelial transport, and total body electrolyte and water balance. Thus, molecular crowding is a fundamental physiologic parameter that impacts diverse functions extending from molecule to organism.
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Affiliation(s)
- Arohan R Subramanya
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; ,
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Pittsburgh Center for Kidney Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Cary R Boyd-Shiwarski
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; ,
- Pittsburgh Center for Kidney Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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37
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Fu H, Huang J, van der Tol JJB, Su L, Wang Y, Dey S, Zijlstra P, Fytas G, Vantomme G, Dankers PYW, Meijer EW. Supramolecular polymers form tactoids through liquid-liquid phase separation. Nature 2024; 626:1011-1018. [PMID: 38418913 PMCID: PMC10901743 DOI: 10.1038/s41586-024-07034-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 01/05/2024] [Indexed: 03/02/2024]
Abstract
Liquid-liquid phase separation (LLPS) of biopolymers has recently been shown to play a central role in the formation of membraneless organelles with a multitude of biological functions1-3. The interplay between LLPS and macromolecular condensation is part of continuing studies4,5. Synthetic supramolecular polymers are the non-covalent equivalent of macromolecules but they are not reported to undergo LLPS yet. Here we show that continuously growing fibrils, obtained from supramolecular polymerizations of synthetic components, are responsible for phase separation into highly anisotropic aqueous liquid droplets (tactoids) by means of an entropy-driven pathway. The crowding environment, regulated by dextran concentration, affects not only the kinetics of supramolecular polymerizations but also the properties of LLPS, including phase-separation kinetics, morphology, internal order, fluidity and mechanical properties of the final tactoids. In addition, substrate-liquid and liquid-liquid interfaces proved capable of accelerating LLPS of supramolecular polymers, allowing the generation of a myriad of three-dimensional-ordered structures, including highly ordered arrays of micrometre-long tactoids at surfaces. The generality and many possibilities of supramolecular polymerizations to control emerging morphologies are demonstrated with several supramolecular polymers, opening up a new field of matter ranging from highly structured aqueous solutions by means of stabilized LLPS to nanoscopic soft matter.
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Affiliation(s)
- Hailin Fu
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Jingyi Huang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Biomedical Engineering and Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Joost J B van der Tol
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Lu Su
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Swayandipta Dey
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Peter Zijlstra
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - George Fytas
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Max Planck Institute for Polymer Research, Mainz, Germany
- Institute of Electronic Structure and Laser, FO.R.T.H, Heraklion, Greece
| | - Ghislaine Vantomme
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Patricia Y W Dankers
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Biomedical Engineering and Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
- School of Chemistry and RNA Institute, University of New South Wales, Sydney, New South Wales, Australia.
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38
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Wang F, Zhang Y. Physiology and pharmacological targeting of phase separation. J Biomed Sci 2024; 31:11. [PMID: 38245749 PMCID: PMC10800077 DOI: 10.1186/s12929-024-00993-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: 08/30/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) in biology describes a process by which proteins form membraneless condensates within a cellular compartment when conditions are met, including the concentration and posttranslational modifications of the protein components, the condition of the aqueous solution (pH, ionic strength, pressure, and temperature), and the existence of assisting factors (such as RNAs or other proteins). In these supramolecular liquid droplet-like inclusion bodies, molecules are held together through weak intermolecular and/or intramolecular interactions. With the aid of LLPS, cells can assemble functional sub-units within a given cellular compartment by enriching or excluding specific factors, modulating cellular function, and rapidly responding to environmental or physiological cues. Hence, LLPS is emerging as an important means to regulate biology and physiology. Yet, excessive inclusion body formation by, for instance, higher-than-normal concentrations or mutant forms of the protein components could result in the conversion from dynamic liquid condensates into more rigid gel- or solid-like aggregates, leading to the disruption of the organelle's function followed by the development of human disorders like neurodegenerative diseases. In summary, well-controlled formation and de-formation of LLPS is critical for normal biology and physiology from single cells to individual organisms, whereas abnormal LLPS is involved in the pathophysiology of human diseases. In turn, targeting these aggregates or their formation represents a promising approach in treating diseases driven by abnormal LLPS including those neurodegenerative diseases that lack effective therapies.
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Affiliation(s)
- Fangfang Wang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA.
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39
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Hilditch AT, Romanyuk A, Cross SJ, Obexer R, McManus JJ, Woolfson DN. Assembling membraneless organelles from de novo designed proteins. Nat Chem 2024; 16:89-97. [PMID: 37710047 PMCID: PMC10774119 DOI: 10.1038/s41557-023-01321-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Recent advances in de novo protein design have delivered a diversity of discrete de novo protein structures and complexes. A new challenge for the field is to use these designs directly in cells to intervene in biological processes and augment natural systems. The bottom-up design of self-assembled objects such as microcompartments and membraneless organelles is one such challenge. Here we describe the design of genetically encoded polypeptides that form membraneless organelles in Escherichia coli. To do this, we combine de novo α-helical sequences, intrinsically disordered linkers and client proteins in single-polypeptide constructs. We tailor the properties of the helical regions to shift protein assembly from arrested assemblies to dynamic condensates. The designs are characterized in cells and in vitro using biophysical methods and soft-matter physics. Finally, we use the designed polypeptide to co-compartmentalize a functional enzyme pair in E. coli, improving product formation close to the theoretical limit.
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Affiliation(s)
- Alexander T Hilditch
- School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Andrey Romanyuk
- School of Chemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Stephen J Cross
- Wolfson Bioimaging Facility, University of Bristol, Bristol, UK
| | - Richard Obexer
- School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Jennifer J McManus
- HH Wills Physics Laboratory, School of Physics, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Bristol, UK.
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.
- School of Biochemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Bristol, UK.
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40
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Su WC, Ho JCS, Gettel DL, Rowland AT, Keating CD, Parikh AN. Kinetic control of shape deformations and membrane phase separation inside giant vesicles. Nat Chem 2024; 16:54-62. [PMID: 37414881 DOI: 10.1038/s41557-023-01267-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
A variety of cellular processes use liquid-liquid phase separation (LLPS) to create functional levels of organization, but the kinetic pathways by which it proceeds remain incompletely understood. Here in real time, we monitor the dynamics of LLPS of mixtures of segregatively phase-separating polymers inside all-synthetic, giant unilamellar vesicles. After dynamically triggering phase separation, we find that the ensuing relaxation-en route to the new equilibrium-is non-trivially modulated by a dynamic interplay between the coarsening of the evolving droplet phase and the interactive membrane boundary. The membrane boundary is preferentially wetted by one of the incipient phases, dynamically arresting the progression of coarsening and deforming the membrane. When the vesicles are composed of phase-separating mixtures of common lipids, LLPS within the vesicular interior becomes coupled to the membrane's compositional degrees of freedom, producing microphase-separated membrane textures. This coupling of bulk and surface phase-separation processes suggests a physical principle by which LLPS inside living cells might be dynamically regulated and communicated to the cellular boundaries.
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Affiliation(s)
- Wan-Chih Su
- Chemistry Graduate Program, University of California, Davis, CA, USA
| | - James C S Ho
- Singapore Centre for Environmental Life Sciences Engineering and Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Nanyang Technological University, Singapore, Singapore
| | - Douglas L Gettel
- Chemical Engineering Graduate Program, University of California, Davis, CA, USA
| | - Andrew T Rowland
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
| | - Atul N Parikh
- Chemistry Graduate Program, University of California, Davis, CA, USA.
- Singapore Centre for Environmental Life Sciences Engineering and Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Nanyang Technological University, Singapore, Singapore.
- Chemical Engineering Graduate Program, University of California, Davis, CA, USA.
- Biomedical Engineering Graduate Programs, University of California, Davis, CA, USA.
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41
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Hong L, Wang Z, Zhang Z, Luo S, Zhou T, Zhang J. Phase separation reduces cell-to-cell variability of transcriptional bursting. Math Biosci 2024; 367:109127. [PMID: 38070763 DOI: 10.1016/j.mbs.2023.109127] [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: 09/11/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
Gene expression is a stochastic and noisy process often occurring in "bursts". Experiments have shown that the compartmentalization of proteins by liquid-liquid phase separation is conducive to reducing the noise of gene expression. Therefore, an important goal is to explore the role of bursts in phase separation noise reduction processes. We propose a coupled model that includes phase separation and a two-state gene expression process. Using the timescale separation method, we obtain approximate solutions for the expectation, variance, and noise strength of the dilute phase. We find that a higher burst frequency weakens the ability of noise reduction by phase separation, but as the burst size increases, this ability first increases and then decreases. This study provides a deeper understanding of phase separation to reduce noise in the stochastic gene expression with burst kinetics.
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Affiliation(s)
- Lijun Hong
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, PR China; School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong Province, 510275, PR China
| | - Zihao Wang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, PR China; School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong Province, 510275, PR China
| | - Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, PR China; School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong Province, 510275, PR China
| | - Songhao Luo
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, PR China; School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong Province, 510275, PR China; Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, PR China; School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong Province, 510275, PR China
| | - Jiajun Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, PR China; School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong Province, 510275, PR China.
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42
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Krevert C, Chavez D, Chatterjee S, Stelzl LS, Pütz S, Roeters SJ, Rudzinski JF, Fawzi NL, Girard M, Parekh SH, Hunger J. Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics. J Phys Chem Lett 2023; 14:11224-11234. [PMID: 38056002 PMCID: PMC10726384 DOI: 10.1021/acs.jpclett.3c02790] [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: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale. Interestingly, these dynamics are markedly slower for proteins in the condensate than in a homogeneous protein solution, indicative of different hydration dynamics. All-atom molecular dynamics simulations confirm that lifetimes of hydrogen-bonds between water and the protein are longer in the condensates than in the protein in solution. Altered hydrogen-bonding dynamics may contribute to unique solvation and reaction dynamics in such condensates.
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Affiliation(s)
- Carola
S. Krevert
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Chavez
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sayantan Chatterjee
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Lukas S. Stelzl
- KOMET 1,
Institute of Physics, Johannes Gutenberg
University, Staudingerweg 7, 55099 Mainz, Germany
- Faculty of
Biology, Johannes Gutenberg University Mainz, Gresemundweg 2, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), Ackermannweg 2, 55128 Mainz, Germany
| | - Sabine Pütz
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Steven J. Roeters
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department
of Anatomy and Neurosciences, Amsterdam
UMC, Vrije Universiteit, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Joseph F. Rudzinski
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- IRIS
Adlershof, Humboldt-Universität zu
Berlin, Zum Großen
Windkanal 2, 12489 Berlin, Germany
| | - Nicolas L. Fawzi
- Department
of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Providence, Rhode Island 02912, United States
| | - Martin Girard
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Johannes Hunger
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Perego E, Zappone S, Castagnetti F, Mariani D, Vitiello E, Rupert J, Zacco E, Tartaglia GG, Bozzoni I, Slenders E, Vicidomini G. Single-photon microscopy to study biomolecular condensates. Nat Commun 2023; 14:8224. [PMID: 38086853 PMCID: PMC10716487 DOI: 10.1038/s41467-023-43969-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Biomolecular condensates serve as membrane-less compartments within cells, concentrating proteins and nucleic acids to facilitate precise spatial and temporal orchestration of various biological processes. The diversity of these processes and the substantial variability in condensate characteristics present a formidable challenge for quantifying their molecular dynamics, surpassing the capabilities of conventional microscopy. Here, we show that our single-photon microscope provides a comprehensive live-cell spectroscopy and imaging framework for investigating biomolecular condensation. Leveraging a single-photon detector array, single-photon microscopy enhances the potential of quantitative confocal microscopy by providing access to fluorescence signals at the single-photon level. Our platform incorporates photon spatiotemporal tagging, which allowed us to perform time-lapse super-resolved imaging for molecular sub-diffraction environment organization with simultaneous monitoring of molecular mobility, interactions, and nano-environment properties through fluorescence lifetime fluctuation spectroscopy. This integrated correlative study reveals the dynamics and interactions of RNA-binding proteins involved in forming stress granules, a specific type of biomolecular condensates, across a wide range of spatial and temporal scales. Our versatile framework opens up avenues for exploring a broad spectrum of biomolecular processes beyond the formation of membrane-less organelles.
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Affiliation(s)
- Eleonora Perego
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Sabrina Zappone
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi, University of Genoa, Genoa, Italy
| | - Francesco Castagnetti
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Davide Mariani
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Erika Vitiello
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Jakob Rupert
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Elsa Zacco
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Gian Gaetano Tartaglia
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Irene Bozzoni
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Eli Slenders
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy.
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44
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Yoo W, Song YW, Kim J, Ahn J, Kim J, Shin Y, Ryu JK, Kim KK. Molecular basis for SOX2-dependent regulation of super-enhancer activity. Nucleic Acids Res 2023; 51:11999-12019. [PMID: 37930832 PMCID: PMC10711550 DOI: 10.1093/nar/gkad908] [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: 08/16/2023] [Revised: 09/22/2023] [Accepted: 10/06/2023] [Indexed: 11/08/2023] Open
Abstract
Pioneer transcription factors (TFs) like SOX2 are vital for stemness and cancer through enhancing gene expression within transcriptional condensates formed with coactivators, RNAs and mediators on super-enhancers (SEs). Despite their importance, how these factors work together for transcriptional condensation and activation remains unclear. SOX2, a pioneer TF found in SEs of pluripotent and cancer stem cells, initiates SE-mediated transcription by binding to nucleosomes, though the mechanism isn't fully understood. To address SOX2's role in SEs, we identified mSE078 as a model SOX2-enriched SE and p300 as a coactivator through bioinformatic analysis. In vitro and cell assays showed SOX2 forms condensates with p300 and SOX2-binding motifs in mSE078. We further proved that SOX2 condensation is highly correlated with mSE078's enhancer activity in cells. Moreover, we successfully demonstrated that p300 not only elevated transcriptional activity but also triggered chromatin acetylation via its direct interaction with SOX2 within these transcriptional condensates. Finally, our validation of SOX2-enriched SEs showcased their contribution to target gene expression in both stem cells and cancer cells. In its entirety, this study imparts valuable mechanistic insights into the collaborative interplay of SOX2 and its coactivator p300, shedding light on the regulation of transcriptional condensation and activation within SOX2-enriched SEs.
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Affiliation(s)
- Wanki Yoo
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Yi Wei Song
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jihyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jihye Ahn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Je-Kyung Ryu
- Department of Physics & Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
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45
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Chang CC, Coyle SM. Regulatable assembly of synthetic microtubule architectures using engineered MAP-IDR condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532644. [PMID: 38105997 PMCID: PMC10723337 DOI: 10.1101/2023.03.14.532644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Microtubules filaments are assembled into higher-order structures and machines critical for cellular processes using microtubule-associated proteins (MAPs). However, the design of synthetic MAPs that direct the formation of new structures in cells is challenging, as nanoscale biochemical activities must be organized across micron length-scales. Here we develop synthetic MAP-IDR condensates (synMAPs) that provide tunable and regulatable assembly of higher-order microtubule structures in vitro and in mammalian cells. synMAPs harness a small microtubule-binding domain from oligodendrocytes (TPPP) whose activity can be synthetically rewired by interaction with condensate-forming IDR sequences. This combination allows synMAPs to self-organize multivalent structures that bind and bridge microtubules into synthetic architectures. Regulating the connection between the microtubule-binding and condensate-forming components allows synMAPs to act as nodes in more complex cytoskeletal circuits in which the formation and dynamics of the microtubule structure can be controlled by small molecules or cell-signaling inputs. By systematically testing a panel of synMAP circuit designs, we define a two-level control scheme for dynamic assembly of microtubule architectures at the nanoscale (via microtubule-binding) and microscale (via condensate formation). synMAPs provide a compact and rationally engineerable starting point for the design of more complex microtubule architectures and cellular machines.
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Affiliation(s)
- Chih-Chia Chang
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Scott M. Coyle
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
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46
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Zhou ZK, Narlikar GJ. Understanding how genetically encoded tags affect phase separation by Heterochromatin Protein HP1α. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569983. [PMID: 38106110 PMCID: PMC10723358 DOI: 10.1101/2023.12.04.569983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Liquid-liquid phase separation (LLPS) is driven by weak multi-valent interactions. Such interactions can result in the formation of puncta in cells and droplets in vitro . The heterochromatin protein HP1α forms droplets with chromatin in vitro and is found in puncta in cells. A common approach to visualize the dynamics of HP1α in cells is to genetically encode fluorescent tags on the protein. HP1α modified with tags such as GFP has been shown to localize to dynamic puncta in vivo . However, whether tagged HP1α retains its intrinsic phase separation properties has not been systematically studied. Here, using different C-terminal tags (AID-sfGFP, mEGFP, and UnaG), we assessed how tag size and linker length affected the phase separation ability of HP1α with DNA in vitro . We found that the AID-sfGFP tag (52 kDa) promoted HP1α phase-separation, possibly driven by the highly disordered AID degron. The mEGFP tag (27 kDa) inhibited phase-separation by HP1α, whereas an UnaG tag (13 kDa) with a 16 amino acid linker showed minimal perturbation. The UnaG tag can thus be used in cellular studies of HP1α to better correlate in vitro and in vivo studies. To test if cellular crowding overcomes the negative effects of large tags in vivo , we used polyethylene glycol (PEG) to mimic crowding in vitro . We found that addition of 10% PEG8000 or PEG4000 enables phase separation by GFP-tagged HP1α at comparable concentrations as untagged HP1α. However, these crowding agents also substantially dampened the differences in phase-separation between wild-type and mutant HP1α proteins. PEG further drove phase-separation of Maltose Binding Protein (MBP), a tag often used to solubilize other proteins. These results suggest that phase-separation of biological macromolecules with PEG should be interpreted with caution as PEG-based crowding agents may change the types of interactions made within the phases.
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Holt LJ, Delarue M. Macromolecular crowding: Sensing without a sensor. Curr Opin Cell Biol 2023; 85:102269. [PMID: 37897928 DOI: 10.1016/j.ceb.2023.102269] [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: 08/23/2023] [Revised: 09/28/2023] [Accepted: 10/01/2023] [Indexed: 10/30/2023]
Abstract
All living cells are crowded with macromolecules. Crowding can directly modulate biochemical reactions to various degrees depending on the sizes, shapes, and binding affinities of the reactants. Here, we explore the possibility that cells can sense and adapt to changes in crowding through the widespread modulation of biochemical reactions without the need for a dedicated sensor. Additionally, we explore phase separation as a general physicochemical response to changes in crowding, and a mechanism to both transduce information and physically restore crowding homeostasis.
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Affiliation(s)
- Liam J Holt
- New York University Grossman School of Medicine, Institute for Systems Genetics, New York, NY, USA
| | - Morgan Delarue
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.
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48
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Li Q, Song Q, Guo W, Cao Y, Cui X, Chen D, Shum HC. Synthetic Membraneless Droplets for Synaptic-Like Clustering of Lipid Vesicles. Angew Chem Int Ed Engl 2023; 62:e202313096. [PMID: 37728515 DOI: 10.1002/anie.202313096] [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: 09/05/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/21/2023]
Abstract
In eukaryotic cells, the membraneless organelles (MLOs) formed via liquid-liquid phase separation (LLPS) are found to interact intimately with membranous organelles (MOs). One major mode is the clustering of MOs by MLOs, such as the formation of clusters of synaptic vesicles at nerve terminals mediated by the synapsin-rich MLOs. Aqueous droplets, including complex coacervates and aqueous two-phase systems, have been plausible MLO-mimics to emulate or elucidate biological processes. However, neither of them can cluster lipid vesicles (LVs) like MLOs. In this work, we develop a synthetic droplet assembled from a combination of two different interactions underlying the formation of these two droplets, namely, associative and segregative interactions, which we call segregative-associative (SA) droplets. The SA droplets cluster and disperse LVs recapitulating the key functional features of synapsin condensates, which can be attributed to the weak electrostatic interaction environment provided by SA droplets. This work suggests LLPS with combined segregative and associative interactions as a possible route for synaptic clustering of lipid vesicles and highlights SA droplets as plausible MLO-mimics and models for studying and mimicking related cellular dynamics.
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Affiliation(s)
- Qingchuan Li
- School of Chemistry & Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong, P.R.China
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
| | - Qingchun Song
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Wei Guo
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
| | - Yang Cao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xinyu Cui
- Department of Public Health, Mudanjiang Medical University, Mudanjiang, 157000, P. R. China
| | - Dairong Chen
- School of Chemistry & Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong, P.R.China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China
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49
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Posey AE, Ross KA, Bagheri M, Lanum EN, Khan MA, Jennings CE, Harwig MC, Kennedy NW, Hilser VJ, Harden JL, Hill RB. The variable domain from dynamin-related protein 1 promotes liquid-liquid phase separation that enhances its interaction with cardiolipin-containing membranes. Protein Sci 2023; 32:e4787. [PMID: 37743569 PMCID: PMC10578129 DOI: 10.1002/pro.4787] [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: 06/12/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" important for regulation. For the mitochondrial fission dynamin, dynamin-related protein 1, a regulatory role for the variable domain (VD) is demonstrated by gain- and loss-of-function mutations, yet the basis for this is unclear. Here, the isolated VD is shown to be intrinsically disordered and undergo a cooperative transition in the stabilizing osmolyte trimethylamine N-oxide. However, the osmolyte-induced state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, which appears to promote phase separation. Since dynamin-related protein 1 is found assembled into discrete punctate structures on the mitochondrial surface, the inference from the present work is that these structures might arise from a condensed state involving the VD that may enable rapid tuning of mechanoenzyme assembly necessary for fission.
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Affiliation(s)
- Ammon E. Posey
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
- Present address:
Department of Biomedical EngineeringWashington UniversitySt. LouisMissouriUSA
| | - Kyle A. Ross
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Mehran Bagheri
- Department of PhysicsUniversity of OttawaOttawaOntarioUSA
| | - Elizabeth N. Lanum
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Misha A. Khan
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | | | - Megan C. Harwig
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Nolan W. Kennedy
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Vincent J. Hilser
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | | | - R. Blake Hill
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
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50
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Ripin N, Parker R. Formation, function, and pathology of RNP granules. Cell 2023; 186:4737-4756. [PMID: 37890457 PMCID: PMC10617657 DOI: 10.1016/j.cell.2023.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/28/2023] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
Ribonucleoprotein (RNP) granules are diverse membrane-less organelles that form through multivalent RNA-RNA, RNA-protein, and protein-protein interactions between RNPs. RNP granules are implicated in many aspects of RNA physiology, but in most cases their functions are poorly understood. RNP granules can be described through four key principles. First, RNP granules often arise because of the large size, high localized concentrations, and multivalent interactions of RNPs. Second, cells regulate RNP granule formation by multiple mechanisms including posttranslational modifications, protein chaperones, and RNA chaperones. Third, RNP granules impact cell physiology in multiple manners. Finally, dysregulation of RNP granules contributes to human diseases. Outstanding issues in the field remain, including determining the scale and molecular mechanisms of RNP granule function and how granule dysfunction contributes to human disease.
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Affiliation(s)
- Nina Ripin
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Roy Parker
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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