151
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Kosno M, Currie SL, Kumar A, Xing C, Rosen MK. Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct. Sci Rep 2023; 13:11907. [PMID: 37488172 PMCID: PMC10366142 DOI: 10.1038/s41598-023-39102-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023] Open
Abstract
Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma. Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.
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Affiliation(s)
- Martyna Kosno
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Simon L Currie
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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152
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Galvanetto N, Ivanović MT, Chowdhury A, Sottini A, Nüesch MF, Nettels D, Best RB, Schuler B. Extreme dynamics in a biomolecular condensate. Nature 2023:10.1038/s41586-023-06329-5. [PMID: 37468629 DOI: 10.1038/s41586-023-06329-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
Abstract
Proteins and nucleic acids can phase-separate in the cell to form concentrated biomolecular condensates1-4. The functions of condensates span many length scales: they modulate interactions and chemical reactions at the molecular scale5, organize biochemical processes at the mesoscale6 and compartmentalize cells4. Understanding the underlying mechanisms of these processes will require detailed knowledge of the rich dynamics across these scales7. The mesoscopic dynamics of biomolecular condensates have been extensively characterized8, but their behaviour at the molecular scale has remained more elusive. Here, as an example of biomolecular phase separation, we study complex coacervates of two highly and oppositely charged disordered human proteins9. Their dense phase is 1,000 times more concentrated than the dilute phase, and the resulting percolated interaction network10 leads to a bulk viscosity 300 times greater than that of water. However, single-molecule spectroscopy optimized for measurements within individual droplets reveals that at the molecular scale, the disordered proteins remain exceedingly dynamic, with their chain configurations interconverting on submicrosecond timescales. Massive all-atom molecular dynamics simulations reproduce the experimental observations and explain this apparent discrepancy: the underlying interactions between individual charged side chains are short-lived and exchange on a pico- to nanosecond timescale. Our results indicate that, despite the high macroscopic viscosity of phase-separated systems, local biomolecular rearrangements required for efficient reactions at the molecular scale can remain rapid.
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Affiliation(s)
- Nicola Galvanetto
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
| | - Miloš T Ivanović
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Aritra Chowdhury
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Mark F Nüesch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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153
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Risso-Ballester J, Rameix-Welti MA. Spatial resolution of virus replication: RSV and cytoplasmic inclusion bodies. Adv Virus Res 2023; 116:1-43. [PMID: 37524479 DOI: 10.1016/bs.aivir.2023.06.001] [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] [Indexed: 08/02/2023]
Abstract
Respiratory Syncytial Virus (RSV) is a major cause of respiratory illness in young children, elderly and immunocompromised individuals worldwide representing a severe burden for health systems. The urgent development of vaccines or specific antivirals against RSV is impaired by the lack of knowledge regarding its replication mechanisms. RSV is a negative-sense single-stranded RNA (ssRNA) virus belonging to the Mononegavirales order (MNV) which includes other viruses pathogenic to humans as Rabies (RabV), Ebola (EBOV), or measles (MeV) viruses. Transcription and replication of viral genomes occur within cytoplasmatic virus-induced spherical inclusions, commonly referred as inclusion bodies (IBs). Recently IBs were shown to exhibit properties of membrane-less organelles (MLO) arising by liquid-liquid phase separation (LLPS). Compartmentalization of viral RNA synthesis steps in viral-induced MLO is indeed a common feature of MNV. Strikingly these key compartments still remain mysterious. Most of our current knowledge on IBs relies on the use of fluorescence microscopy. The ability to fluorescently label IBs in cells has been key to uncover their dynamics and nature. The generation of recombinant viruses expressing a fluorescently-labeled viral protein and the immunolabeling or the expression of viral fusion proteins known to be recruited in IBs are some of the tools used to visualize IBs in infected cells. In this chapter, microscope techniques and the most relevant studies that have shed light on RSV IBs fundamental aspects, including biogenesis, organization and dynamics are being discussed and brought to light with the investigations carried out on other MNV.
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Affiliation(s)
| | - Marie-Anne Rameix-Welti
- Institut Pasteur, Université Paris-Saclay, Université de Versailles St. Quentin, UMR 1173 (2I), INSERM, Paris, France; Assistance Publique des Hôpitaux de Paris, Hôpital Ambroise Paré, Laboratoire de Microbiologie, DMU15, Paris, France.
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154
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He C, Wu CY, Li W, Xu K. Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548239. [PMID: 37503034 PMCID: PMC10369965 DOI: 10.1101/2023.07.12.548239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remain unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here we uncover nanoscale heterogeneities in the aging process of FUS condensates. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SM d M), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating nanoscale structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems.
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155
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Schede HH, Natarajan P, Chakraborty AK, Shrinivas K. A model for organization and regulation of nuclear condensates by gene activity. Nat Commun 2023; 14:4152. [PMID: 37438363 DOI: 10.1038/s41467-023-39878-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
Condensation by phase separation has recently emerged as a mechanism underlying many nuclear compartments essential for cellular functions. Nuclear condensates enrich nucleic acids and proteins, localize to specific genomic regions, and often promote gene expression. How diverse properties of nuclear condensates are shaped by gene organization and activity is poorly understood. Here, we develop a physics-based model to interrogate how spatially-varying transcription activity impacts condensate properties and dynamics. Our model predicts that spatial clustering of active genes can enable precise localization and de novo nucleation of condensates. Strong clustering and high activity results in aspherical condensate morphologies. Condensates can flow towards distant gene clusters and competition between multiple clusters lead to stretched morphologies and activity-dependent repositioning. Overall, our model predicts and recapitulates morphological and dynamical features of diverse nuclear condensates and offers a unified mechanistic framework to study the interplay between non-equilibrium processes, spatially-varying transcription, and multicomponent condensates in cell biology.
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Affiliation(s)
- Halima H Schede
- School of Life Sciences, École Polytechnique Fédérale Lausanne, CH-1015, Lausanne, Switzerland
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pradeep Natarajan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Krishna Shrinivas
- NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, MA, USA.
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156
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Liu Y, Yao Z, Lian G, Yang P. Biomolecular phase separation in stress granule assembly and virus infection. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1099-1118. [PMID: 37401177 PMCID: PMC10415189 DOI: 10.3724/abbs.2023117] [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: 12/28/2022] [Accepted: 05/06/2023] [Indexed: 07/05/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a crucial mechanism for cellular compartmentalization. One prominent example of this is the stress granule. Found in various types of cells, stress granule is a biomolecular condensate formed through phase separation. It comprises numerous RNA and RNA-binding proteins. Over the past decades, substantial knowledge has been gained about the composition and dynamics of stress granules. SGs can regulate various signaling pathways and have been associated with numerous human diseases, such as neurodegenerative diseases, cancer, and infectious diseases. The threat of viral infections continues to loom over society. Both DNA and RNA viruses depend on host cells for replication. Intriguingly, many stages of the viral life cycle are closely tied to RNA metabolism in human cells. The field of biomolecular condensates has rapidly advanced in recent times. In this context, we aim to summarize research on stress granules and their link to viral infections. Notably, stress granules triggered by viral infections behave differently from the canonical stress granules triggered by sodium arsenite (SA) and heat shock. Studying stress granules in the context of viral infections could offer a valuable platform to link viral replication processes and host anti-viral responses. A deeper understanding of these biological processes could pave the way for innovative interventions and treatments for viral infectious diseases. They could potentially bridge the gap between basic biological processes and interactions between viruses and their hosts.
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Affiliation(s)
- Yi Liu
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Zhiying Yao
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Guiwei Lian
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Peiguo Yang
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
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157
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Hurtle BT, Xie L, Donnelly CJ. Disrupting pathologic phase transitions in neurodegeneration. J Clin Invest 2023; 133:e168549. [PMID: 37395272 DOI: 10.1172/jci168549] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Solid-like protein deposits found in aged and diseased human brains have revealed a relationship between insoluble protein accumulations and the resulting deficits in neurologic function. Clinically diverse neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis, exhibit unique and disease-specific biochemical protein signatures and abnormal protein depositions that often correlate with disease pathogenesis. Recent evidence indicates that many pathologic proteins assemble into liquid-like protein phases through the highly coordinated process of liquid-liquid phase separation. Over the last decade, biomolecular phase transitions have emerged as a fundamental mechanism of cellular organization. Liquid-like condensates organize functionally related biomolecules within the cell, and many neuropathology-associated proteins reside within these dynamic structures. Thus, examining biomolecular phase transitions enhances our understanding of the molecular mechanisms mediating toxicity across diverse neurodegenerative diseases. This Review explores the known mechanisms contributing to aberrant protein phase transitions in neurodegenerative diseases, focusing on tau and TDP-43 proteinopathies and outlining potential therapeutic strategies to regulate these pathologic events.
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Affiliation(s)
- Bryan T Hurtle
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Longxin Xie
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Christopher J Donnelly
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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158
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Jevtic Z, Allram M, Grebien F, Schwaller J. Biomolecular Condensates in Myeloid Leukemia: What Do They Tell Us? Hemasphere 2023; 7:e923. [PMID: 37388925 PMCID: PMC10306439 DOI: 10.1097/hs9.0000000000000923] [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: 03/10/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Recent studies have suggested that several oncogenic and tumor-suppressive proteins carry out their functions in the context of specific membrane-less cellular compartments. As these compartments, generally referred to as onco-condensates, are specific to tumor cells and are tightly linked to disease development, the mechanisms of their formation and maintenance have been intensively studied. Here we review the proposed leukemogenic and tumor-suppressive activities of nuclear biomolecular condensates in acute myeloid leukemia (AML). We focus on condensates formed by oncogenic fusion proteins including nucleoporin 98 (NUP98), mixed-lineage leukemia 1 (MLL1, also known as KMT2A), mutated nucleophosmin (NPM1c) and others. We also discuss how altered condensate formation contributes to malignant transformation of hematopoietic cells, as described for promyelocytic leukemia protein (PML) in PML::RARA-driven acute promyelocytic leukemia (APL) and other myeloid malignancies. Finally, we discuss potential strategies for interfering with the molecular mechanisms related to AML-associated biomolecular condensates, as well as current limitations of the field.
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Affiliation(s)
- Zivojin Jevtic
- Department of Biomedicine (DBM), University Children’s Hospital Basel, University of Basel, Switzerland
| | - Melanie Allram
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Juerg Schwaller
- Department of Biomedicine (DBM), University Children’s Hospital Basel, University of Basel, Switzerland
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159
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Binder MJ, Pedley AM. The roles of molecular chaperones in regulating cell metabolism. FEBS Lett 2023; 597:1681-1701. [PMID: 37287189 PMCID: PMC10984649 DOI: 10.1002/1873-3468.14682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023]
Abstract
Fluctuations in nutrient and biomass availability, often as a result of disease, impart metabolic challenges that must be overcome in order to sustain cell survival and promote proliferation. Cells adapt to these environmental changes and stresses by adjusting their metabolic networks through a series of regulatory mechanisms. Our understanding of these rewiring events has largely been focused on those genetic transformations that alter protein expression and the biochemical mechanisms that change protein behavior, such as post-translational modifications and metabolite-based allosteric modulators. Mounting evidence suggests that a class of proteome surveillance proteins called molecular chaperones also can influence metabolic processes. Here, we summarize several ways the Hsp90 and Hsp70 chaperone families act on human metabolic enzymes and their supramolecular assemblies to change enzymatic activities and metabolite flux. We further highlight how these chaperones can assist in the translocation and degradation of metabolic enzymes. Collectively, these studies provide a new view for how metabolic processes are regulated to meet cellular demand and inspire new avenues for therapeutic intervention.
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160
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Ramm B, Schumacher D, Harms A, Heermann T, Klos P, Müller F, Schwille P, Søgaard-Andersen L. Biomolecular condensate drives polymerization and bundling of the bacterial tubulin FtsZ to regulate cell division. Nat Commun 2023; 14:3825. [PMID: 37380708 DOI: 10.1038/s41467-023-39513-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
Cell division is spatiotemporally precisely regulated, but the underlying mechanisms are incompletely understood. In the social bacterium Myxococcus xanthus, the PomX/PomY/PomZ proteins form a single megadalton-sized complex that directly positions and stimulates cytokinetic ring formation by the tubulin homolog FtsZ. Here, we study the structure and mechanism of this complex in vitro and in vivo. We demonstrate that PomY forms liquid-like biomolecular condensates by phase separation, while PomX self-assembles into filaments generating a single large cellular structure. The PomX structure enriches PomY, thereby guaranteeing the formation of precisely one PomY condensate per cell through surface-assisted condensation. In vitro, PomY condensates selectively enrich FtsZ and nucleate GTP-dependent FtsZ polymerization and bundle FtsZ filaments, suggesting a cell division site positioning mechanism in which the single PomY condensate enriches FtsZ to guide FtsZ-ring formation and division. This mechanism shares features with microtubule nucleation by biomolecular condensates in eukaryotes, supporting this mechanism's ancient origin.
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Affiliation(s)
- Beatrice Ramm
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
- Department of Physics, Princeton University, Princeton, NJ, 08544, USA.
| | - Dominik Schumacher
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
| | - Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Tamara Heermann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Philipp Klos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Franziska Müller
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
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161
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Xu J, Deng X, Gu A, Cai Y, Huang Y, Zhang W, Zhang Y, Wen W, Xie Y. Ccdc85c-Par3 condensates couple cell polarity with Notch to control neural progenitor proliferation. Cell Rep 2023; 42:112677. [PMID: 37352102 DOI: 10.1016/j.celrep.2023.112677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 05/15/2023] [Accepted: 06/06/2023] [Indexed: 06/25/2023] Open
Abstract
Polarity proteins regulate the proliferation and differentiation of neural progenitors to generate neurons during brain development through multiple signaling pathways. However, how cell polarity couples the signaling pathways remains unclear. Here, we show that coiled-coil domain-containing protein 85c (Ccdc85c) interacts with the polarity protein Par3 to regulate the proliferation of radial glial cells (RGCs) via phase separation coupled to percolation (PSCP). We find that the interaction with Ccdc85c relieves the intramolecular auto-inhibition of Par3, which leads to PSCP of Par3. Downregulation of Ccdc85c causes RGC differentiation. Importantly, the open conformation of Par3 facilitates the recruitment of the Notch regulator Numb to the Par3 condensates, which might prevent the attenuation of Notch activity to maintain RGC proliferation. Furthermore, ectopic activation of Notch signaling rescues RGC proliferation defects caused by the downregulation of Ccdc85c. These results suggest that Ccdc85c-mediated PSCP of Par3 regulates Notch signaling to control RGC proliferation during brain development.
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Affiliation(s)
- Jiawen Xu
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xin Deng
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Aihong Gu
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yuqun Cai
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yunyun Huang
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wen Zhang
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yiqing Zhang
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenyu Wen
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; The Shanghai Key Laboratory of Medical Epigenetics, National Center for Neurological Disorders, Fudan University, Shanghai 200032, China.
| | - Yunli Xie
- Department of Anesthesia, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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162
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Li Y, Xu M, Qi Z. Deciphering molecular mechanisms of phase separation in RNA biology by single-molecule biophysical technologies. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1034-1041. [PMID: 37337634 PMCID: PMC10415185 DOI: 10.3724/abbs.2023113] [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: 12/31/2022] [Accepted: 03/06/2023] [Indexed: 06/21/2023] Open
Abstract
Ribonucleic acid (RNA) biology has emerged as one of the most important areas in modern biology and biomedicine. RNA and RNA-binding proteins (RBPs) are involved in forming biomolecular condensates, which are crucial for RNA metabolism. To quantitively decipher the molecular mechanisms of RNP granules, researchers have turned to single-molecule biophysical techniques, such as single-molecule Förster resonance energy transfer (smFRET), in vivo single-molecule imaging technique with single particle tracking (SPT), DNA Curtains, optical tweezers, and atomic force microscopy (AFM). These methods are used to investigate the molecular biophysical properties within RNP granules, as well as the molecular interactions between RNA and RBPs and RBPs themselves, which are challenging to study using traditional experimental methods of the liquid-liquid phase separation (LLPS) field, such as fluorescence recovery after photobleaching (FRAP). In this work, we summarize the applications of single-molecule biophysical techniques in RNP granule studies and highlight how these methods can be used to reveal the molecular mechanisms of RNP granules.
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Affiliation(s)
- Yuchen Li
- Center for Quantitative Biology and Peking-Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
| | - Mengmeng Xu
- Tsinghua-Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Zhi Qi
- Center for Quantitative Biology and Peking-Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
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163
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Alghoul E, Basbous J, Constantinou A. Compartmentalization of the DNA damage response: Mechanisms and functions. DNA Repair (Amst) 2023; 128:103524. [PMID: 37320957 DOI: 10.1016/j.dnarep.2023.103524] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Cells have evolved an arsenal of molecular mechanisms to respond to continuous alterations in the primary structure of DNA. At the cellular level, DNA damage response proteins accumulate at sites of DNA damage and organize into nuclear foci. As recounted by Errol Friedberg, pioneering work on DNA repair in the 1930 s was stimulated by collaborations between physicists and geneticists. In recent years, the introduction of ideas from physics on self-organizing compartments has taken the field of cell biology by storm. Percolation and phase separation theories are increasingly used to model the self-assembly of compartments, called biomolecular condensates, that selectively concentrate molecules without a surrounding membrane. In this review, we discuss these concepts in the context of the DNA damage response. We discuss how studies of DNA repair foci as condensates can link molecular mechanisms with cell physiological functions, provide new insights into regulatory mechanisms, and open new perspectives for targeting DNA damage responses for therapeutic purposes.
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Affiliation(s)
- Emile Alghoul
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
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164
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Abstract
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase behavior of heterogeneous biomolecular mixtures are only beginning to be explored. Theory and simulation provide invaluable tools for probing the relationship between molecular determinants, such as protein and RNA sequences, and the emergence of phase-separated condensates in such complex environments. This review covers recent advances in the prediction and computational design of biomolecular mixtures that phase-separate into many coexisting phases. First, we review efforts to understand the phase behavior of mixtures with hundreds or thousands of species using theoretical models and statistical approaches. We then describe progress in developing analytical theories and coarse-grained simulation models to predict multiphase condensates with the molecular detail required to make contact with biophysical experiments. We conclude by summarizing the challenges ahead for modeling the inhomogeneous spatial organization of biomolecular mixtures in living cells.
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Affiliation(s)
- William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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165
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Park SH, Lee SE, Jeon JH, Lee JH, Itakura E, Chang S, Choi WH, Lee MJ. Formation of aggresomes with hydrogel-like characteristics by proteasome inhibition. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194932. [PMID: 36997115 DOI: 10.1016/j.bbagrm.2023.194932] [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: 09/30/2022] [Revised: 02/08/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
The spatiotemporal sequestration of misfolded proteins is a mechanism by which cells counterbalance proteome homeostasis upon exposure to various stress stimuli. Chronic inhibition of proteasomes results in a large, juxtanuclear, membrane-less inclusion, known as the aggresome. Although the molecular mechanisms driving its formation, clearance, and pathophysiological implications are continuously being uncovered, the biophysical aspects of aggresomes remain largely uncharacterized. Using fluorescence recovery after photobleaching and liquid droplet disruption assays, we found that the aggresomes are a homogeneously blended condensates with liquid-like properties similar to droplets formed via liquid-liquid phase separation. However, unlike fluidic liquid droplets, aggresomes have more viscosity and hydrogel-like characteristics. We also observed that the inhibition of aggresome formation using microtubule-disrupting agents resulted in less soluble and smaller cytoplasmic speckles, which was associated with marked cytotoxicity. Therefore, the aggresome appears to be cytoprotective and serves as a temporal reservoir for dysfunctional proteasomes and substrates that need to be degraded. Our results suggest that the aggresome assembles through distinct and potentially sequential processes of energy-dependent retrograde transportation and spontaneous condensation into a hydrogel.
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Affiliation(s)
- Seo Hyeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea
| | - Sang-Eun Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jun Hyoung Jeon
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Seegene, Inc., Seoul 05548, Republic of Korea
| | - Jung Hoon Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cellular Degradation Biology Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Eisuke Itakura
- Department of Biology, Graduate School of Science, Chiba University, Inage-ku, Chiba 263-8522, Japan
| | - Sunghoe Chang
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea; Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
| | - Won Hoon Choi
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cellular Degradation Biology Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Republic of Korea; Ischemic/Hypoxic Disease Institute, Convergence Research Center for Dementia, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Cellular Degradation Biology Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
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166
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Shelby SA, Castello-Serrano I, Wisser KC, Levental I, Veatch SL. Membrane phase separation drives responsive assembly of receptor signaling domains. Nat Chem Biol 2023; 19:750-758. [PMID: 36997644 PMCID: PMC10771812 DOI: 10.1038/s41589-023-01268-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/17/2023] [Indexed: 04/01/2023]
Abstract
Plasma membrane heterogeneity has been tied to a litany of cellular functions and is often explained by analogy to membrane phase separation; however, models based on phase separation alone fall short of describing the rich organization available within cell membranes. Here we present comprehensive experimental evidence motivating an updated model of plasma membrane heterogeneity in which membrane domains assemble in response to protein scaffolds. Quantitative super-resolution nanoscopy measurements in live B lymphocytes detect membrane domains that emerge upon clustering B cell receptors (BCRs). These domains enrich and retain membrane proteins based on their preference for the liquid-ordered phase. Unlike phase-separated membranes that consist of binary phases with defined compositions, membrane composition at BCR clusters is modulated through the protein constituents in clusters and the composition of the membrane overall. This tunable domain structure is detected through the variable sorting of membrane probes and impacts the magnitude of BCR activation.
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Affiliation(s)
- Sarah A Shelby
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Ivan Castello-Serrano
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.
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167
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Chattaraj A, Nalagandla I, Loew LM, Blinov ML. MolClustPy: a Python package to characterize multivalent biomolecular clusters. Bioinformatics 2023; 39:btad385. [PMID: 37326981 PMCID: PMC10290549 DOI: 10.1093/bioinformatics/btad385] [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: 02/15/2023] [Revised: 05/14/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023] Open
Abstract
SUMMARY Low-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become supply-limited large clusters. In stochastic simulations, such clusters display a wide range of sizes and compositions. We have developed a Python package, MolClustPy, which performs multiple stochastic simulation runs using NFsim (Network-Free stochastic simulator); MolClustPy characterizes and visualizes the distribution of cluster sizes, molecular composition, and bonds across molecular clusters. The statistical analysis offered by MolClustPy is readily applicable to other stochastic simulation software, such as SpringSaLaD and ReaDDy. AVAILABILITY AND IMPLEMENTATION The software is implemented in Python. A detailed Jupyter notebook is provided to enable convenient running. Code, user guide, and examples are freely available at https://molclustpy.github.io/.
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Affiliation(s)
- Aniruddha Chattaraj
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, United States
| | - Indivar Nalagandla
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, United States
| | - Leslie M Loew
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, United States
| | - Michael L Blinov
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, United States
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168
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Stitzinger SH, Sohrabi-Jahromi S, Söding J. Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains. NAR Genom Bioinform 2023; 5:lqad057. [PMID: 37305168 PMCID: PMC10251633 DOI: 10.1093/nargab/lqad057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/24/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
Numerous cellular processes rely on the binding of proteins with high affinity to specific sets of RNAs. Yet most RNA-binding domains display low specificity and affinity in comparison to DNA-binding domains. The best binding motif is typically only enriched by less than a factor 10 in high-throughput RNA SELEX or RNA bind-n-seq measurements. Here, we provide insight into how cooperative binding of multiple domains in RNA-binding proteins (RBPs) can boost their effective affinity and specificity orders of magnitude higher than their individual domains. We present a thermodynamic model to calculate the effective binding affinity (avidity) for idealized, sequence-specific RBPs with any number of RBDs given the affinities of their isolated domains. For seven proteins in which affinities for individual domains have been measured, the model predictions are in good agreement with measurements. The model also explains how a two-fold difference in binding site density on RNA can increase protein occupancy 10-fold. It is therefore rationalized that local clusters of binding motifs are the physiological binding targets of multi-domain RBPs.
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Affiliation(s)
- Simon H Stitzinger
- Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Salma Sohrabi-Jahromi
- Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Johannes Söding
- To whom correspondence should be addressed. Tel: +49 551 201 2890;
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169
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Zheng H, Wen W. Protein phase separation: new insights into cell division. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1042-1051. [PMID: 37249333 PMCID: PMC10415187 DOI: 10.3724/abbs.2023093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/15/2023] [Indexed: 05/31/2023] Open
Abstract
As the foundation for the development of multicellular organisms and the self-renewal of single cells, cell division is a highly organized event which segregates cellular components into two daughter cells equally or unequally, thus producing daughters with identical or distinct fates. Liquid-liquid phase separation (LLPS), an emerging biophysical concept, provides a new perspective for us to understand the mechanisms of a wide range of cellular events, including the organization of membrane-less organelles. Recent studies have shown that several key organelles in the cell division process are assembled into membrane-free structures via LLPS of specific proteins. Here, we summarize the regulatory functions of protein phase separation in centrosome maturation, spindle assembly and polarity establishment during cell division.
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Affiliation(s)
- Hongdan Zheng
- />Department of NeurosurgeryHuashan Hospitalthe Shanghai Key Laboratory of Medical EpigeneticsState Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceNational Center for Neurological DisordersInstitutes of Biomedical SciencesSchool of Basic Medical SciencesFudan UniversityShanghai200032China
| | - Wenyu Wen
- />Department of NeurosurgeryHuashan Hospitalthe Shanghai Key Laboratory of Medical EpigeneticsState Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceNational Center for Neurological DisordersInstitutes of Biomedical SciencesSchool of Basic Medical SciencesFudan UniversityShanghai200032China
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170
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Maltseva D, Chatterjee S, Yu CC, Brzezinski M, Nagata Y, Gonella G, Murthy AC, Stachowiak JC, Fawzi NL, Parekh SH, Bonn M. Fibril formation and ordering of disordered FUS LC driven by hydrophobic interactions. Nat Chem 2023:10.1038/s41557-023-01221-1. [PMID: 37231298 PMCID: PMC10396963 DOI: 10.1038/s41557-023-01221-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Biomolecular condensates, protein-rich and dynamic membrane-less organelles, play critical roles in a range of subcellular processes, including membrane trafficking and transcriptional regulation. However, aberrant phase transitions of intrinsically disordered proteins in biomolecular condensates can lead to the formation of irreversible fibrils and aggregates that are linked to neurodegenerative diseases. Despite the implications, the interactions underlying such transitions remain obscure. Here we investigate the role of hydrophobic interactions by studying the low-complexity domain of the disordered 'fused in sarcoma' (FUS) protein at the air/water interface. Using surface-specific microscopic and spectroscopic techniques, we find that a hydrophobic interface drives fibril formation and molecular ordering of FUS, resulting in solid-like film formation. This phase transition occurs at 600-fold lower FUS concentration than required for the canonical FUS low-complexity liquid droplet formation in bulk. These observations highlight the importance of hydrophobic effects for protein phase separation and suggest that interfacial properties drive distinct protein phase-separated structures.
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Affiliation(s)
- Daria Maltseva
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Sayantan Chatterjee
- Max Planck Institute for Polymer Research, Mainz, Germany
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Chun-Chieh Yu
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Mateusz Brzezinski
- Max Planck Institute for Polymer Research, Mainz, Germany
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Mainz, Germany
- Institute of Biochemistry and Bringing Materials to Life Initiative, ETH Zurich, Zürich, Switzerland
| | - Anastasia C Murthy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Sapun H Parekh
- Max Planck Institute for Polymer Research, Mainz, Germany.
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Mainz, Germany.
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171
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Labat-de-Hoz L, Rubio-Ramos A, Correas I, Alonso MA. The MAL Family of Proteins: Normal Function, Expression in Cancer, and Potential Use as Cancer Biomarkers. Cancers (Basel) 2023; 15:2801. [PMID: 37345137 DOI: 10.3390/cancers15102801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/06/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
The MAL family of integral membrane proteins consists of MAL, MAL2, MALL, PLLP, CMTM8, MYADM, and MYADML2. The best characterized members are elements of the machinery that controls specialized pathways of membrane traffic and cell signaling. This review aims to help answer the following questions about the MAL-family genes: (i) is their expression regulated in cancer and, if so, how? (ii) What role do they play in cancer? (iii) Might they have biomedical applications? Analysis of large-scale gene expression datasets indicated altered levels of MAL-family transcripts in specific cancer types. A comprehensive literature search provides evidence of MAL-family gene dysregulation and protein function repurposing in cancer. For MAL, and probably for other genes of the family, dysregulation is primarily a consequence of gene methylation, although copy number alterations also contribute to varying degrees. The scrutiny of the two sources of information, datasets and published studies, reveals potential prognostic applications of MAL-family members as cancer biomarkers-for instance, MAL2 in breast cancer, MAL2 and MALL in pancreatic cancer, and MAL and MYADM in lung cancer-and other biomedical uses. The availability of validated antibodies to some MAL-family proteins sanctions their use as cancer biomarkers in routine clinical practice.
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Affiliation(s)
- Leticia Labat-de-Hoz
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Armando Rubio-Ramos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Isabel Correas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Miguel A Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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172
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Otsuka K, Murakami S, Okajima K, Shibata K, Kubo Y, Gubin DG, Beaty LA, Cornelissen G. Appropriate Circadian-Circasemidian Coupling Protects Blood Pressure from Morning Surge and Promotes Human Resilience and Wellbeing. Clin Interv Aging 2023; 18:755-769. [PMID: 37193339 PMCID: PMC10183193 DOI: 10.2147/cia.s398957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
Background Blood pressure (BP) variability is involved in the appraisal of threat and safety, and can serve as a potential marker of psychological resilience against stress. The relationship between biological rhythms of BP and resilience was cross-sectionally assessed by 7-day/24-hour chronobiologic screening in a rural Japanese community (Tosa), with focus on the 12-hour component and the "circadian-circasemidian coupling" of systolic (S) BP. Subjects and Methods Tosa residents (N = 239, 147 women, 23-74 years), free of anti-hypertensive medication, completed 7-day/24-hour ambulatory BP monitoring. The circadian-circasemidian coupling was determined individually by computing the difference between the circadian phase and the circasemidian morning-phase of SBP. Participants were classified into three groups: those with a short coupling interval of about 4.5 hours (Group A), those with an intermediate coupling interval of about 6.0 hours (Group B), and those with a long coupling interval of about 8.0 hours (Group C). Results Residents of Group B who showed optimal circadian-circasemidian coordination had less pronounced morning and evening SBP surges, as compared to residents of Group A (10.82 vs 14.29 mmHg, P < 0.0001) and Group C (11.86 vs 15.21 mmHg, P < 0.0001), respectively. The incidence of morning or evening SBP surge was less in Group B than in Group A (P < 0.0001) or Group C (P < 0.0001). Group B residents showed highest measures of wellbeing and psychological resilience, assessed by good relation with friends (P < 0.05), life satisfaction (P < 0.05), and subjective happiness (P < 0.05). A disturbed circadian-circasemidian coupling was associated with elevated BP, dyslipidemia, arteriosclerosis and a depressive mood. Conclusion The circadian-circasemidian coupling of SBP could serve as a new biomarker in clinical practice to guide precision medicine interventions aimed at achieving properly timed rhythms, and thereby resilience and wellbeing.
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Affiliation(s)
- Kuniaki Otsuka
- Tokyo Women’s Medical University, Tokyo, Japan
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA
| | - Shougo Murakami
- Department of Cardiovascular Medicine, Soseikai General Hospital, Kyoto, Japan
| | - Kiyotaka Okajima
- Cardiovascular Internal Medicine, Higashi Omiya General Hospital, Saitama, Japan
| | | | - Yutaka Kubo
- Department of Medicine, Machida Keisen Hospital, Tokyo, Japan
| | - Denis G Gubin
- Laboratory for Chronobiology and Chronomedicine, Research Institute of Biomedicine and Biomedical Technologies, Medical University, Tyumen, 625023, Russia
- Department of Biology, Medical University, Tyumen, 625023, Russia
- Tyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia
| | - Larry A Beaty
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA
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173
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Modi N, Chen S, Adjei INA, Franco BL, Bishop KJM, Obermeyer AC. Designing negative feedback loops in enzymatic coacervate droplets. Chem Sci 2023; 14:4735-4744. [PMID: 37181760 PMCID: PMC10171067 DOI: 10.1039/d2sc03838b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/13/2023] [Indexed: 05/16/2023] Open
Abstract
Membraneless organelles within the living cell use phase separation of biomolecules coupled with enzymatic reactions to regulate cellular processes. The diverse functions of these biomolecular condensates motivate the pursuit of simpler in vitro models that exhibit primitive forms of self-regulation based on internal feedback mechanisms. Here, we investigate one such model based on complex coacervation of the enzyme catalase with an oppositely charge polyelectrolyte DEAE-dextran to form pH-responsive catalytic droplets. Upon addition of hydrogen peroxide "fuel", enzyme activity localized within the droplets causes a rapid increase in the pH. Under appropriate conditions, this reaction-induced pH change triggers coacervate dissolution owing to its pH-responsive phase behavior. Notably, this destabilizing effect of the enzymatic reaction on phase separation depends on droplet size owing to the diffusive delivery and removal of reaction components. Reaction-diffusion models informed by the experimental data show that larger drops support larger changes in the local pH thereby enhancing their dissolution relative to smaller droplets. Together, these results provide a basis for achieving droplet size control based on negative feedback between pH-dependent phase separation and pH-changing enzymatic reactions.
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Affiliation(s)
- Nisha Modi
- Department of Chemical Engineering, Columbia University New York USA
| | - Siwei Chen
- Department of Chemical Engineering, Columbia University New York USA
| | - Imelda N A Adjei
- Department of Biomedical Engineering, Columbia University New York USA
| | - Briana L Franco
- Department of Chemical Engineering, Columbia University New York USA
| | - Kyle J M Bishop
- Department of Chemical Engineering, Columbia University New York USA
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University New York USA
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174
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Guseva S, Schnapka V, Adamski W, Maurin D, Ruigrok RWH, Salvi N, Blackledge M. Liquid-Liquid Phase Separation Modifies the Dynamic Properties of Intrinsically Disordered Proteins. J Am Chem Soc 2023; 145:10548-10563. [PMID: 37146977 DOI: 10.1021/jacs.2c13647] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Liquid-liquid phase separation of flexible biomolecules has been identified as a ubiquitous phenomenon underlying the formation of membraneless organelles that harbor a multitude of essential cellular processes. We use nuclear magnetic resonance (NMR) spectroscopy to compare the dynamic properties of an intrinsically disordered protein (measles virus NTAIL) in the dilute and dense phases at atomic resolution. By measuring 15N NMR relaxation at different magnetic field strengths, we are able to characterize the dynamics of the protein in dilute and crowded conditions and to compare the amplitude and timescale of the different motional modes to those present in the membraneless organelle. Although the local backbone conformational sampling appears to be largely retained, dynamics occurring on all detectable timescales, including librational, backbone dihedral angle dynamics and segmental, chainlike motions, are considerably slowed down. Their relative amplitudes are also drastically modified, with slower, chain-like motions dominating the dynamic profile. In order to provide additional mechanistic insight, we performed extensive molecular dynamics simulations of the protein under self-crowding conditions at concentrations comparable to those found in the dense liquid phase. Simulation broadly reproduces the impact of formation of the condensed phase on both the free energy landscape and the kinetic interconversion between states. In particular, the experimentally observed reduction in the amplitude of the fastest component of backbone dynamics correlates with higher levels of intermolecular contacts or entanglement observed in simulations, reducing the conformational space available to this mode under strongly self-crowding conditions.
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Affiliation(s)
- Serafima Guseva
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Vincent Schnapka
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Wiktor Adamski
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Damien Maurin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Rob W H Ruigrok
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Nicola Salvi
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
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175
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Pappu R, Farag M, Borcherds W, Bremer A, Mittag T. Phase Separation in Mixtures of Prion-Like Low Complexity Domains is Driven by the Interplay of Homotypic and Heterotypic Interactions. RESEARCH SQUARE 2023:rs.3.rs-2870258. [PMID: 37205474 PMCID: PMC10187436 DOI: 10.21203/rs.3.rs-2870258/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Prion-like low-complexity domains (PLCDs) are involved in the formation and regulation of distinct biomolecular condensates that form via coupled associative and segregative phase transitions. We previously deciphered how evolutionarily conserved sequence features drive phase separation of PLCDs through homotypic interactions. However, condensates typically encompass a diverse mixture of proteins with PLCDs. Here, we combine simulations and experiments to study mixtures of PLCDs from two RNA binding proteins namely, hnRNPA1 and FUS. We find that 1:1 mixtures of the A1-LCD and FUS-LCD undergo phase separation more readily than either of the PLCDs on their own. The enhanced driving forces for phase separation of mixtures of A1-LCD and FUS-LCD arise partly from complementary electrostatic interactions between the two proteins. This complex coacervation-like mechanism adds to complementary interactions among aromatic residues. Further, tie line analysis shows that stoichiometric ratios of different components and their sequence-encoded interactions jointly contribute to the driving forces for condensate formation. These results highlight how expression levels might be tuned to regulate the driving forces for condensate formation in vivo . Simulations also show that the organization of PLCDs within condensates deviates from expectations based on random mixture models. Instead, spatial organization within condensates will reflect the relative strengths of homotypic versus heterotypic interactions. We also uncover rules for how interaction strengths and sequence lengths modulate conformational preferences of molecules at interfaces of condensates formed by mixtures of proteins. Overall, our findings emphasize the network-like organization of molecules within multicomponent condensates, and the distinctive, composition-specific conformational features of condensate interfaces.
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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177
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Bao H, Cao J, Chen M, Chen M, Chen W, Chen X, Chen Y, Chen Y, Chen Y, Chen Z, Chhetri JK, Ding Y, Feng J, Guo J, Guo M, He C, Jia Y, Jiang H, Jing Y, Li D, Li J, Li J, Liang Q, Liang R, Liu F, Liu X, Liu Z, Luo OJ, Lv J, Ma J, Mao K, Nie J, Qiao X, Sun X, Tang X, Wang J, Wang Q, Wang S, Wang X, Wang Y, Wang Y, Wu R, Xia K, Xiao FH, Xu L, Xu Y, Yan H, Yang L, Yang R, Yang Y, Ying Y, Zhang L, Zhang W, Zhang W, Zhang X, Zhang Z, Zhou M, Zhou R, Zhu Q, Zhu Z, Cao F, Cao Z, Chan P, Chen C, Chen G, Chen HZ, Chen J, Ci W, Ding BS, Ding Q, Gao F, Han JDJ, Huang K, Ju Z, Kong QP, Li J, Li J, Li X, Liu B, Liu F, Liu L, Liu Q, Liu Q, Liu X, Liu Y, Luo X, Ma S, Ma X, Mao Z, Nie J, Peng Y, Qu J, Ren J, Ren R, Song M, Songyang Z, Sun YE, Sun Y, Tian M, Wang S, Wang S, Wang X, Wang X, Wang YJ, Wang Y, Wong CCL, Xiang AP, Xiao Y, Xie Z, Xu D, Ye J, Yue R, Zhang C, Zhang H, Zhang L, Zhang W, Zhang Y, Zhang YW, Zhang Z, Zhao T, Zhao Y, Zhu D, Zou W, Pei G, Liu GH. Biomarkers of aging. SCIENCE CHINA. LIFE SCIENCES 2023; 66:893-1066. [PMID: 37076725 PMCID: PMC10115486 DOI: 10.1007/s11427-023-2305-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/27/2023] [Indexed: 04/21/2023]
Abstract
Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.
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Affiliation(s)
- Hainan Bao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengting Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Min Chen
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wei Chen
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xiao Chen
- Department of Nuclear Medicine, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Yanhao Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yutian Chen
- The Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhiyang Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China
| | - Jagadish K Chhetri
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Yingjie Ding
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junlin Feng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jun Guo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Mengmeng Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Chuting He
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Yujuan Jia
- Department of Neurology, First Affiliated Hospital, Shanxi Medical University, Taiyuan, 030001, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Ying Jing
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Dingfeng Li
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyi Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Qinhao Liang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Liang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China
| | - Feng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Zuojun Liu
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Jianwei Lv
- School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jingyi Ma
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Kehang Mao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China
| | - Jiawei Nie
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinpei Sun
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China
| | - Xiaoqiang Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianfang Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyuan Wang
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Xuan Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yuhan Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Rimo Wu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Kai Xia
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Fu-Hui Xiao
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yingying Xu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Haoteng Yan
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Liang Yang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Ruici Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuanxin Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yilin Ying
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China
| | - Le Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Weiwei Zhang
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China
| | - Wenwan Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xing Zhang
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Min Zhou
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Rui Zhou
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Qingchen Zhu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhengmao Zhu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Feng Cao
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China.
| | - Zhongwei Cao
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Piu Chan
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guobing Chen
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou, 510000, China.
| | - Hou-Zao Chen
- Department of Biochemistryand Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
| | - Jun Chen
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
| | - Bi-Sen Ding
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qiurong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Feng Gao
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Kai Huang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China.
| | - Qing-Peng Kong
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China.
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Baohua Liu
- School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518060, China.
| | - Feng Liu
- Metabolic Syndrome Research Center, The Second Xiangya Hospital, Central South Unversity, Changsha, 410011, China.
| | - Lin Liu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China.
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Institute of Translational Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, 300000, China.
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, China.
| | - Qiang Liu
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China.
| | - Qiang Liu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
- Tianjin Institute of Immunology, Tianjin Medical University, Tianjin, 300070, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
| | - Yong Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
| | - Xianghang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China.
| | - Shuai Ma
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Jing Nie
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Yaojin Peng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Center for Aging and Cancer, Hainan Medical University, Haikou, 571199, China.
| | - Moshi Song
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China.
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Yi Eve Sun
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| | - Yu Sun
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA, 98195, USA.
| | - Mei Tian
- Human Phenome Institute, Fudan University, Shanghai, 201203, China.
| | - Shusen Wang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China.
| | - Si Wang
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
| | - Xia Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Xiaoning Wang
- Institute of Geriatrics, The second Medical Center, Beijing Key Laboratory of Aging and Geriatrics, National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Yan-Jiang Wang
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Yunfang Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China.
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China.
| | - Andy Peng Xiang
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Yichuan Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Zhengwei Xie
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China.
- Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, 100101, China.
| | - Daichao Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Jing Ye
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China.
| | - Rui Yue
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Cuntai Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China.
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Liang Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yong Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Yun-Wu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Zhuohua Zhang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical Genetics, Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, 410078, China.
- Department of Neurosciences, Hengyang Medical School, University of South China, Hengyang, 421001, China.
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Dahai Zhu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Gang Pei
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-Based Biomedicine, The Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, 200070, China.
| | - Guang-Hui Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
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178
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Li Z, Huang X, Li M, Chen YE, Wang Z, Liu L. A ubiquitination-mediated degradation system to target 14-3-3-binding phosphoproteins. Heliyon 2023; 9:e16318. [PMID: 37251884 PMCID: PMC10213371 DOI: 10.1016/j.heliyon.2023.e16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
The phosphorylation of 14-3-3 binding motif is involved in many cellular processes. A strategy that enables targeted degradation of 14-3-3-binding phosphoproteins (14-3-3-BPPs) for studying their functions is highly desirable for basic research. Here, we report a phosphorylation-induced, ubiquitin-proteasome-system-mediated targeted protein degradation (TPD) strategy that allows specific degradation of 14-3-3-BPPs. Specifically, by ligating a modified von Hippel-Lindau E3-ligase with an engineered 14-3-3 bait, we generated a protein chimera referred to as Targeted Degradation of 14-3-3-binding PhosphoProtein (TDPP). TDPP can serve as a universal degrader for 14-3-3-BPPs based on the specific recognition of the phosphorylation in 14-3-3 binding motifs. TDPP shows high efficiency and specificity to a difopein-EGFP reporter, general and specific 14-3-3-BPPs. TDPP can also be applied for the validation of 14-3-3-BPPs. These results strongly support TDPP as a powerful tool for 14-3-3 related research.
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Affiliation(s)
- Zhaokai Li
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Emergency Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaoqiang Huang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mohan Li
- Department of Geriatrics, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing 100730, China
| | - Y. Eugene Chen
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhong Wang
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liu Liu
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
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179
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Zhang H, Zhao C, Zhang Y, Lu L, Shi W, Zhou Q, Pu Y, Wang S, Liu R, Yin L. Multi-omics analysis revealed NMBA induced esophageal carcinoma tumorigenesis via regulating PPARα signaling pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 324:121369. [PMID: 36858103 DOI: 10.1016/j.envpol.2023.121369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/13/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
As widespread environmental carcinogens causing esophageal carcinoma (EC), the effects of N-nitrosamines on human health hazards and accurate toxicity mechanisms have not been well-elucidated. In this study, we explored the tumorigenic mechanism of N-nitrosomethylbenzylamine (NMBA) exposure using both cell and rat models. It was found that NMBA (2 μM) exposure for 26 weeks induced malignant transformation of normal esophageal epithelial (Het-1A) cells. After then proteomics analysis showed that lipid metabolism disorder predominantly participated in the process of NMBA-induced cell malignant transformation. Further the integrated proteomics and lipidomics analysis revealed that the enhancement of fatty acid metabolism promoted the EC tumorigenesis induced by NMBA through facilitating the fatty acid-associated PPARα signaling pathway. The animal studies also revealed that accelerated fatty acid decomposition in the progression of NMBA-induced EC models of rats was accompanied by the activation of the PPARα pathway. Overall, our findings depicted the key dynamic molecular alteration triggered by N-nitrosamines, and provided comprehensive biological perspectives into the carcinogenic risk assessment of N-nitrosamines.
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Affiliation(s)
- Hu Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, People's Republic of China
| | - Chao Zhao
- School of Nursing & School of Public Health, Yangzhou University, Yangzhou, 225000, China
| | - Ying Zhang
- School of Nursing & School of Public Health, Yangzhou University, Yangzhou, 225000, China
| | - Lu Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, People's Republic of China
| | - Wei Shi
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, People's Republic of China
| | - Qian Zhou
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, People's Republic of China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, People's Republic of China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, People's Republic of China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, People's Republic of China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, People's Republic of China.
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180
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Swasthi HM, Basalla JL, Dudley CE, Vecchiarelli AG, Chapman MR. Cell surface-localized CsgF condensate is a gatekeeper in bacterial curli subunit secretion. Nat Commun 2023; 14:2392. [PMID: 37100792 PMCID: PMC10133297 DOI: 10.1038/s41467-023-38089-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/14/2023] [Indexed: 04/28/2023] Open
Abstract
Curli are functional amyloids present on the outer membrane of E. coli. CsgF is required for the proper assembly of curli. Here, we found that the CsgF phase separates in vitro and that the ability of CsgF variants to phase-separate is tightly correlated with CsgF function during curli biogenesis. Substitution of phenylalanine residues in the CsgF N-terminus both reduced the propensity of CsgF to phase-separate and impaired curli assembly. Exogenous addition of purified CsgF complemented csgF - cells. This exogenous addition assay was used to assess the ability of CsgF variants to complement csgF ‒ cells. CsgF on the cell surface modulated the secretion of CsgA, the curli major subunit, to the cell surface. We also found that the CsgB nucleator protein can form SDS-insoluble aggregates within the dynamic CsgF condensate. We propose that these multicomponent CsgF-B condensates form a nucleation-competent complex that templates CsgA amyloid formation on the cell surface.
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Affiliation(s)
- Hema M Swasthi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Joseph L Basalla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Claire E Dudley
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
| | - Matthew R Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA.
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181
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Wang B, Ji L, Bian Q. SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites. Cell Rep 2023; 42:112323. [PMID: 37000624 DOI: 10.1016/j.celrep.2023.112323] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in spatial genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells leads to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple levels, including compartments, topologically associating domains, and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 leads to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical regulators of T cell activation. The loss of SATB1 does not affect CTCF occupancy but significantly reduces the retention of CTCF in the nuclear matrix. Collectively, our data show that SATB1 contributes to 3D genome organization by constraining chromatin topology surrounding CTCF-binding sites.
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Affiliation(s)
- Bao Wang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Luzhang Ji
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Qian Bian
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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182
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Liu S, Wang C, Latham A, Ding X, Zhang B. OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537533. [PMID: 37131742 PMCID: PMC10153273 DOI: 10.1101/2023.04.19.537533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performances on a single GPU that rival the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that Open-ABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates. Open-ABC is available at https://github.com/ZhangGroup-MITChemistry/OpenABC.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cong Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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183
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Dai Y, You L, Chilkoti A. Engineering synthetic biomolecular condensates. NATURE REVIEWS BIOENGINEERING 2023; 1:1-15. [PMID: 37359769 PMCID: PMC10107566 DOI: 10.1038/s44222-023-00052-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 06/28/2023]
Abstract
The concept of phase-separation-mediated formation of biomolecular condensates provides a new framework to understand cellular organization and cooperativity-dependent cellular functions. With growing understanding of how biological systems drive phase separation and how cellular functions are encoded by biomolecular condensates, opportunities have emerged for cellular control through engineering of synthetic biomolecular condensates. In this Review, we discuss how to construct synthetic biomolecular condensates and how they can regulate cellular functions. We first describe the fundamental principles by which biomolecular components can drive phase separation. Next, we discuss the relationship between the properties of condensates and their cellular functions, which informs the design of components to create programmable synthetic condensates. Finally, we describe recent applications of synthetic biomolecular condensates for cellular control and discuss some of the design considerations and prospective applications.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC USA
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184
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Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535055. [PMID: 37066338 PMCID: PMC10103940 DOI: 10.1101/2023.03.31.535055] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport of specific macromolecules while impeding the exchange of unsolicited material. However, key aspects of this gating mechanism remain controversial. To address this issue, we determined the nanoscopic behavior of the permeability barrier directly within yeast S. cerevisiae NPCs at transport-relevant timescales. We show that the large intrinsically disordered domains of phenylalanine-glycine repeat nucleoporins (FG Nups) exhibit highly dynamic fluctuations to create transient voids in the permeability barrier that continuously shape-shift and reseal, resembling a radial polymer brush. Together with cargo-carrying transport factors the FG domains form a feature called the central plug, which is also highly dynamic. Remarkably, NPC mutants with longer FG domains show interweaving meshwork-like behavior that attenuates nucleocytoplasmic transport in vivo. Importantly, the bona fide nanoscale NPC behaviors and morphologies are not recapitulated by in vitro FG domain hydrogels. NPCs also exclude self-assembling FG domain condensates in vivo, thereby indicating that the permeability barrier is not generated by a self-assembling phase condensate, but rather is largely a polymer brush, organized by the NPC scaffold, whose dynamic gating selectivity is strongly enhanced by the presence of transport factors.
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Affiliation(s)
- Toshiya Kozai
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | | | - Adam Mazur
- Biozentrum, University of Basel, Switzerland
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Jeremy Tempkin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | - Barak Raveh
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
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185
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Duan C, Wang R. Electrostatics-Induced Nucleated Conformational Transition of Protein Aggregation. PHYSICAL REVIEW LETTERS 2023; 130:158401. [PMID: 37115902 DOI: 10.1103/physrevlett.130.158401] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Despite the wide existence of protein aggregation in nature and its intimate connection to many human diseases, the underlying mechanism remains unclear. Here, we develop a molecular theory by systematically incorporating the self-consistent field theory for charged macromolecules into the dilute solution thermodynamics. The kinetic pathway is tracked without any restriction on the morphology of the aggregates. We find that protein aggregation at low salt concentrations is via a two-step nucleated process involving a conformational transition from metastable spherical oligomer to elongated fibril. The scaling analysis elucidates the electrostatic origin of the conformational transition: the fibril enters the screening region much earlier than the spherical aggregate. As salt concentration increases, the classical mode of one-step nucleation corresponding to macroscopic liquid-liquid phase separation is recovered. Our results reveal that the screened electrostatic interaction is essential for the existence of the metastable oligomer and its subsequent conformational transition to fibril. The theoretical predictions of the kinetic pathway and the morphology of the aggregates are in good agreement with the experimental observations of real proteins.
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Affiliation(s)
- Chao Duan
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, California 94720, USA
| | - Rui Wang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, California 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
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186
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Farshad M, DelloStritto MJ, Suma A, Carnevale V. Detecting Liquid-Liquid Phase Separations Using Molecular Dynamics Simulations and Spectral Clustering. J Phys Chem B 2023; 127:3682-3689. [PMID: 37053472 DOI: 10.1021/acs.jpcb.3c00805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
A stringent test of the accuracy of empirical force fields is reproducing the phase diagram of bulk phases and mixtures. Exploring the phase diagram of mixtures requires the detection of phase boundaries and critical points. In contrast to most solid-liquid transitions, in which a global order parameter (average density) can be used to discriminate between two phases, some demixing transitions entail relatively subtle changes in the local environment of each molecule. In such cases, finite sampling errors and finite-size effects make the identification of trends in local order parameters extremely challenging. Here we analyze one such example, namely a methanol/hexane mixture, and compute several local and global structural properties. We simulate the system at various temperatures and study the structural changes associated with demixing. We show that despite a seemingly continuous transformation between mixed and demixed states, the topological properties of the H-bond network change abruptly as the system crosses the demixing line. In particular, by using spectral clustering, we show that the distribution of cluster sizes develops a fat tail (as expected from percolation theory) in the vicinity of the critical point. We illustrate a simple criterion to identify this behavior, which results from the emergence of large system-spanning clusters from a collection of aggregates. We further tested the spectral clustering analysis on a Lennard-Jones system as a standard example of a system with no H-bonds, and also, in this case, we were able to detect the demixing transition.
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Affiliation(s)
- Mohsen Farshad
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Mark J DelloStritto
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Antonio Suma
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
- Dipartimento di Fisica, Università di Bari, 70121 Bari, Italy
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania 19122, United States
- Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
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187
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Liu Z, Yethiraj A, Cui Q. Sensitive and selective polymer condensation at membrane surface driven by positive co-operativity. Proc Natl Acad Sci U S A 2023; 120:e2212516120. [PMID: 37018196 PMCID: PMC10104518 DOI: 10.1073/pnas.2212516120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Biomolecular phase separation has emerged as an essential mechanism for cellular organization. How cells respond to environmental stimuli in a robust and sensitive manner to build functional condensates at the proper time and location is only starting to be understood. Recently, lipid membranes have been recognized as an important regulatory center for biomolecular condensation. However, how the interplay between the phase behaviors of cellular membranes and surface biopolymers may contribute to the regulation of surface condensation remains to be elucidated. Using simulations and a mean-field theoretical model, we show that two key factors are the membrane's tendency to phase-separate and the surface polymer's ability to reorganize local membrane composition. Surface condensate forms with high sensitivity and selectivity in response to features of biopolymer when positive co-operativity is established between coupled growth of the condensate and local lipid domains. This effect relating the degree of membrane-surface polymer co-operativity and condensate property regulation is shown to be robust by different ways of tuning the co-operativity, such as varying membrane protein obstacle concentration, lipid composition, and the affinity between lipid and polymer. The general physical principle emerged from the current analysis may have implications in other biological processes and beyond.
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Affiliation(s)
- Zhuang Liu
- Department of Physics, Boston University, Boston, MA02215
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, WI53706
| | - Qiang Cui
- Department of Physics, Boston University, Boston, MA02215
- Department of Chemistry, Boston University, Boston, MA02215
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188
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Vecchiarelli A, Hoang Y, Azaldegui C, Ghalmi M, Biteen J. An experimental framework to assess biomolecular condensates in bacteria. RESEARCH SQUARE 2023:rs.3.rs-2725220. [PMID: 37066349 PMCID: PMC10104261 DOI: 10.21203/rs.3.rs-2725220/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
High-resolution imaging of biomolecular condensates in living cells is essential for correlating their properties to those observed through in vitro assays. However, such experiments are limited in bacteria due to resolution limitations. Here we present an experimental framework that probes the formation, reversibility, and dynamics of condensate-forming proteins in Escherichia coli as a means to determine the nature of biomolecular condensates in bacteria. We demonstrate that condensates form after passing a threshold concentration, maintain a soluble fraction, dissolve upon shifts in temperature and concentration, and exhibit dynamics consistent with internal rearrangement and exchange between condensed and soluble fractions. We also discovered that an established marker for insoluble protein aggregates, IbpA, has different colocalization patterns with bacterial condensates and aggregates, demonstrating its applicability as a reporter to differentiate the two in vivo. Overall, this framework provides a generalizable, accessible, and rigorous set of experiments to probe the nature of biomolecular condensates on the sub-micron scale in bacterial cells.
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189
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Di Nunzio F, Uversky VN, Mouland AJ. Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle. Retrovirology 2023; 20:4. [PMID: 37029379 PMCID: PMC10081342 DOI: 10.1186/s12977-023-00619-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023] Open
Abstract
A rapidly evolving understanding of phase separation in the biological and physical sciences has led to the redefining of virus-engineered replication compartments in many viruses with RNA genomes. Condensation of viral, host and genomic and subgenomic RNAs can take place to evade the innate immunity response and to help viral replication. Divergent viruses prompt liquid-liquid phase separation (LLPS) to invade the host cell. During HIV replication there are several steps involving LLPS. In this review, we characterize the ability of individual viral and host partners that assemble into biomolecular condensates (BMCs). Of note, bioinformatic analyses predict models of phase separation in line with several published observations. Importantly, viral BMCs contribute to function in key steps retroviral replication. For example, reverse transcription takes place within nuclear BMCs, called HIV-MLOs while during late replication steps, retroviral nucleocapsid acts as a driver or scaffold to recruit client viral components to aid the assembly of progeny virions. Overall, LLPS during viral infections represents a newly described biological event now appreciated in the virology field, that can also be considered as an alternative pharmacological target to current drug therapies especially when viruses become resistant to antiviral treatment.
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Affiliation(s)
- Francesca Di Nunzio
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Andrew J Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC, H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
- Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
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190
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Dao TP, Castañeda CA. We con-dense if we want to; We can't leave AZUL outside. Structure 2023; 31:369-371. [PMID: 37028393 DOI: 10.1016/j.str.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 04/09/2023]
Abstract
In this issue of Structure, Buel et al. (2023) combined NMR data with AlphaFold2 to map out the interaction between the AZUL domain of ubiquitin ligase E6AP and UBQLN1/2 UBA. The authors demonstrated that this interaction enhances the self-association of the helix neighboring UBA and enables E6AP to localize to UBQLN2 droplets.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA; Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA; Program in Neuroscience, Syracuse University, Syracuse, NY 13244, USA.
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191
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Alghoul E, Paloni M, Takedachi A, Urbach S, Barducci A, Gaillard PH, Basbous J, Constantinou A. Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair. Mol Cell 2023; 83:1640-1658.e9. [PMID: 37059091 DOI: 10.1016/j.molcel.2023.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/06/2023] [Accepted: 03/21/2023] [Indexed: 04/16/2023]
Abstract
SLX4, disabled in the Fanconi anemia group P, is a scaffolding protein that coordinates the action of structure-specific endonucleases and other proteins involved in the replication-coupled repair of DNA interstrand cross-links. Here, we show that SLX4 dimerization and SUMO-SIM interactions drive the assembly of SLX4 membraneless compartments in the nucleus called condensates. Super-resolution microscopy reveals that SLX4 forms chromatin-bound clusters of nanocondensates. We report that SLX4 compartmentalizes the SUMO-RNF4 signaling pathway. SENP6 and RNF4 regulate the assembly and disassembly of SLX4 condensates, respectively. SLX4 condensation per se triggers the selective modification of proteins by SUMO and ubiquitin. Specifically, SLX4 condensation induces ubiquitylation and chromatin extraction of topoisomerase 1 DNA-protein cross-links. SLX4 condensation also induces the nucleolytic degradation of newly replicated DNA. We propose that the compartmentalization of proteins by SLX4 through site-specific interactions ensures the spatiotemporal control of protein modifications and nucleolytic reactions during DNA repair.
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Affiliation(s)
- Emile Alghoul
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Matteo Paloni
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Arato Takedachi
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France; Montpellier RIO Imaging, Montpellier, France
| | - Alessandro Barducci
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Jihane Basbous
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
| | - Angelos Constantinou
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
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192
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Dai Y, Farag M, Lee D, Zeng X, Kim K, Son HI, Guo X, Su J, Peterson N, Mohammed J, Ney M, Shapiro DM, Pappu RV, Chilkoti A, You L. Programmable synthetic biomolecular condensates for cellular control. Nat Chem Biol 2023; 19:518-528. [PMID: 36747054 PMCID: PMC10786170 DOI: 10.1038/s41589-022-01252-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 12/21/2022] [Indexed: 02/08/2023]
Abstract
The formation of biomolecular condensates mediated by a coupling of associative and segregative phase transitions plays a critical role in controlling diverse cellular functions in nature. This has inspired the use of phase transitions to design synthetic systems. While design rules of phase transitions have been established for many synthetic intrinsically disordered proteins, most efforts have focused on investigating their phase behaviors in a test tube. Here, we present a rational engineering approach to program the formation and physical properties of synthetic condensates to achieve intended cellular functions. We demonstrate this approach through targeted plasmid sequestration and transcription regulation in bacteria and modulation of a protein circuit in mammalian cells. Our approach lays the foundation for engineering designer condensates for synthetic biology applications.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Dongheon Lee
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Xiangze Zeng
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Hye-In Son
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Xiao Guo
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Jonathan Su
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Nikhil Peterson
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Javid Mohammed
- Department of Immunology, Duke University, Durham, NC, USA
| | - Max Ney
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Daniel Mark Shapiro
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
| | - Lingchong You
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
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193
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Demarchi L, Goychuk A, Maryshev I, Frey E. Enzyme-Enriched Condensates Show Self-Propulsion, Positioning, and Coexistence. PHYSICAL REVIEW LETTERS 2023; 130:128401. [PMID: 37027840 DOI: 10.1103/physrevlett.130.128401] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/03/2023] [Indexed: 06/19/2023]
Abstract
Enzyme-enriched condensates can organize the spatial distribution of their substrates by catalyzing nonequilibrium reactions. Conversely, an inhomogeneous substrate distribution induces enzyme fluxes through substrate-enzyme interactions. We find that condensates move toward the center of a confining domain when this feedback is weak. Above a feedback threshold, they exhibit self-propulsion, leading to oscillatory dynamics. Moreover, catalysis-driven enzyme fluxes can lead to interrupted coarsening, resulting in equidistant condensate positioning, and to condensate division.
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Affiliation(s)
- Leonardo Demarchi
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Andriy Goychuk
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Ivan Maryshev
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539 München, Germany
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194
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Nam J, Gwon Y. Neuronal biomolecular condensates and their implications in neurodegenerative diseases. Front Aging Neurosci 2023; 15:1145420. [PMID: 37065458 PMCID: PMC10102667 DOI: 10.3389/fnagi.2023.1145420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/01/2023] [Indexed: 04/03/2023] Open
Abstract
Biomolecular condensates are subcellular organizations where functionally related proteins and nucleic acids are assembled through liquid-liquid phase separation, allowing them to develop on a larger scale without a membrane. However, biomolecular condensates are highly vulnerable to disruptions from genetic risks and various factors inside and outside the cell and are strongly implicated in the pathogenesis of many neurodegenerative diseases. In addition to the classical view of the nucleation-polymerization process that triggers the protein aggregation from the misfolded seed, the pathologic transition of biomolecular condensates can also promote the aggregation of proteins found in the deposits of neurodegenerative diseases. Furthermore, it has been suggested that several protein or protein-RNA complexes located in the synapse and along the neuronal process are neuron-specific condensates displaying liquid-like properties. As their compositional and functional modifications play a crucial role in the context of neurodegeneration, further research is needed to fully understand the role of neuronal biomolecular condensates. In this article, we will discuss recent findings that explore the pivotal role of biomolecular condensates in the development of neuronal defects and neurodegeneration.
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Affiliation(s)
| | - Youngdae Gwon
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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195
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Hoang Y, Azaldegui CA, Ghalmi M, Biteen JS, Vecchiarelli AG. An experimental framework to assess biomolecular condensates in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533878. [PMID: 36993636 PMCID: PMC10055370 DOI: 10.1101/2023.03.22.533878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
High-resolution imaging of biomolecular condensates in living cells is essential for correlating their properties to those observed through in vitro assays. However, such experiments are limited in bacteria due to resolution limitations. Here we present an experimental framework that probes the formation, reversibility, and dynamics of condensate-forming proteins in Escherichia coli as a means to determine the nature of biomolecular condensates in bacteria. We demonstrate that condensates form after passing a threshold concentration, maintain a soluble fraction, dissolve upon shifts in temperature and concentration, and exhibit dynamics consistent with internal rearrangement and exchange between condensed and soluble fractions. We also discovered that an established marker for insoluble protein aggregates, IbpA, has different colocalization patterns with bacterial condensates and aggregates, demonstrating its applicability as a reporter to differentiate the two in vivo. Overall, this framework provides a generalizable, accessible, and rigorous set of experiments to probe the nature of biomolecular condensates on the sub-micron scale in bacterial cells.
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Affiliation(s)
- Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Equal contribution
| | - Christopher A. Azaldegui
- Doctoral Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Equal contribution
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Julie S. Biteen
- Doctoral Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
| | - Anthony G. Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA
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196
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Gupta A, Joshi A, Arora K, Mukhopadhyay S, Guptasarma P. The bacterial nucleoid-associated proteins, HU, and Dps, condense DNA into context-dependent biphasic or multiphasic complex coacervates. J Biol Chem 2023; 299:104637. [PMID: 36963493 PMCID: PMC10141540 DOI: 10.1016/j.jbc.2023.104637] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
The bacterial chromosome, known as its nucleoid, is an amorphous assemblage of globular nucleoprotein domains. It exists in a state of phase separation from the cell's cytoplasm, as an irregularly-shaped, membrane-less, intracellular compartment. This state (the nature of which remains largely unknown) is maintained through bacterial generations ad infinitum. Here, we show that HU, and Dps, two of the most abundant nucleoid-associated proteins (NAPs) of Escherichia coli, undergo spontaneous complex coacervation with different forms of DNA/RNA, both individually and in each other's presence, to cause accretion and compaction of DNA/RNA into liquid-liquid phase separated (LLPS) condensates in vitro. Upon mixing with nucleic acids, HU-A and HU-B form (a) bi-phasic heterotypic mixed condensates in which HU-B helps to lower the Csat of HU-A; and also (b) multi-phasic heterotypic condensates, with Dps, in which de-mixed domains display different contents of HU and Dps. We believe that these modes of complex coacervation that are seen in vitro can serve as models for the in vivo relationships amongst NAPs in nucleoids, involving local and global variations in the relative abundances of the different NAPs, especially in de-mixed sub-domains that are characterized by differing grades of phase separation. Our results clearly demonstrate some quantitative, and some qualitative, differences in the coacervating abilities of different NAPs with DNA, potentially explaining (i) why E. coli has two isoforms of HU, and (ii) why changes in the abundances of HU and Dps facilitate the lag, logarithmic and stationary phases of E. coli growth.
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Affiliation(s)
- Archit Gupta
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India.
| | - Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Kanika Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Purnananda Guptasarma
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India.
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197
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Farag M, Borcherds WM, Bremer A, Mittag T, Pappu RV. Phase Separation in Mixtures of Prion-Like Low Complexity Domains is Driven by the Interplay of Homotypic and Heterotypic Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532828. [PMID: 36993212 PMCID: PMC10055064 DOI: 10.1101/2023.03.15.532828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Prion-like low-complexity domains (PLCDs) are involved in the formation and regulation of distinct biomolecular condensates that form via coupled associative and segregative phase transitions. We previously deciphered how evolutionarily conserved sequence features drive phase separation of PLCDs through homotypic interactions. However, condensates typically encompass a diverse mixture of proteins with PLCDs. Here, we combine simulations and experiments to study mixtures of PLCDs from two RNA binding proteins namely, hnRNPA1 and FUS. We find that 1:1 mixtures of the A1-LCD and FUS-LCD undergo phase separation more readily than either of the PLCDs on their own. The enhanced driving forces for phase separation of mixtures of A1-LCD and FUS-LCD arise partly from complementary electrostatic interactions between the two proteins. This complex coacervation-like mechanism adds to complementary interactions among aromatic residues. Further, tie line analysis shows that stoichiometric ratios of different components and their sequence-encoded interactions jointly contribute to the driving forces for condensate formation. These results highlight how expression levels might be tuned to regulate the driving forces for condensate formation in vivo . Simulations also show that the organization of PLCDs within condensates deviates from expectations based on random mixture models. Instead, spatial organization within condensates will reflect the relative strengths of homotypic versus heterotypic interactions. We also uncover rules for how interaction strengths and sequence lengths modulate conformational preferences of molecules at interfaces of condensates formed by mixtures of proteins. Overall, our findings emphasize the network-like organization of molecules within multicomponent condensates, and the distinctive, composition-specific conformational features of condensate interfaces. Significance Statement Biomolecular condensates are mixtures of different protein and nucleic acid molecules that organize biochemical reactions in cells. Much of what we know about how condensates form comes from studies of phase transitions of individual components of condensates. Here, we report results from studies of phase transitions of mixtures of archetypal protein domains that feature in distinct condensates. Our investigations, aided by a blend of computations and experiments, show that the phase transitions of mixtures are governed by a complex interplay of homotypic and heterotypic interactions. The results point to how expression levels of different protein components can be tuned in cells to modulate internal structures, compositions, and interfaces of condensates, thus affording distinct ways to control the functions of condensates.
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198
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Membraneless Compartmentalization of Nuclear Assembly Sites during Murine Cytomegalovirus Infection. Viruses 2023; 15:v15030766. [PMID: 36992475 PMCID: PMC10053344 DOI: 10.3390/v15030766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/28/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Extensive reorganization of infected cells and the formation of large structures known as the nuclear replication compartment (RC) and cytoplasmic assembly compartment (AC) is a hallmark of beta-herpesvirus infection. These restructurings rely on extensive compartmentalization of the processes that make up the virus manufacturing chain. Compartmentalization of the nuclear processes during murine cytomegalovirus (MCMV) infection is not well described. In this study, we visualized five viral proteins (pIE1, pE1, pM25, pm48.2, and pM57) and replicated viral DNA to reveal the nuclear events during MCMV infection. As expected, these events can be matched with those described for other beta and alpha herpesviruses and contribute to the overall picture of herpesvirus assembly. Imaging showed that four viral proteins (pE1, pM25, pm48.2, and pM57) and replicated viral DNA condense in the nucleus into membraneless assemblies (MLAs) that undergo a maturation sequence to form the RC. One of these proteins (pM25), which is also expressed in a cytoplasmic form (pM25l), showed similar MLAs in the AC. Bioinformatics tools for predicting biomolecular condensates showed that four of the five proteins had a high propensity for liquid–liquid phase separation (LLPS), suggesting that LLPS may be a mechanism for compartmentalization within RC and AC. Examination of the physical properties of MLAs formed during the early phase of infection by 1,6-hexanediol treatment in vivo revealed liquid-like properties of pE1 MLAs and more solid-like properties of pM25 MLAs, indicating heterogeneity of mechanisms in the formation of virus-induced MLAs. Analysis of the five viral proteins and replicated viral DNA shows that the maturation sequence of RC and AC is not completed in many cells, suggesting that virus production and release is carried out by a rather limited number of cells. This study thus lays the groundwork for further investigation of the replication cycle of beta-herpesviruses, and the results should be incorporated into plans for high-throughput and single-cell analytic approaches.
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199
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Chattaraj A, Nalagandla I, Loew LM, Blinov ML. MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532640. [PMID: 36993613 PMCID: PMC10055112 DOI: 10.1101/2023.03.14.532640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
S ummary Low-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become extra-large clusters. Characterizing the physical properties of these clusters is important in recent biophysical research. Due to weak interactions such clusters are highly stochastic, demonstrating a wide range of sizes and compositions. We have developed a Python package to perform multiple stochastic simulation runs using NFsim (Network-Free stochastic simulator), characterize and visualize the distribution of cluster sizes, molecular composition, and bonds across molecular clusters and individual molecules of different types. A vailability and implementation The software is implemented in Python. A detailed Jupyter notebook is provided to enable convenient running. Code, user guide and examples are freely available at https://molclustpy.github.io/. C ontact achattaraj007@gmail.com , blinov@uchc.edu. S upplementary information Available at https://molclustpy.github.io/.
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Affiliation(s)
- Aniruddha Chattaraj
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Indivar Nalagandla
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Leslie M Loew
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Michael L Blinov
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA
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200
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Phase separation properties of RPA combine high-affinity ssDNA binding with dynamic condensate functions at telomeres. Nat Struct Mol Biol 2023; 30:451-462. [PMID: 36894693 PMCID: PMC10113159 DOI: 10.1038/s41594-023-00932-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/27/2023] [Indexed: 03/11/2023]
Abstract
RPA has been shown to protect single-stranded DNA (ssDNA) intermediates from instability and breakage. RPA binds ssDNA with sub-nanomolar affinity, yet dynamic turnover is required for downstream ssDNA transactions. How ultrahigh-affinity binding and dynamic turnover are achieved simultaneously is not well understood. Here we reveal that RPA has a strong propensity to assemble into dynamic condensates. In solution, purified RPA phase separates into liquid droplets with fusion and surface wetting behavior. Phase separation is stimulated by sub-stoichiometric amounts of ssDNA, but not RNA or double-stranded DNA, and ssDNA gets selectively enriched in RPA condensates. We find the RPA2 subunit required for condensation and multi-site phosphorylation of the RPA2 N-terminal intrinsically disordered region to regulate RPA self-interaction. Functionally, quantitative proximity proteomics links RPA condensation to telomere clustering and integrity in cancer cells. Collectively, our results suggest that RPA-coated ssDNA is contained in dynamic RPA condensates whose properties are important for genome organization and stability.
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