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Garcia-Parajo MF, Mayor S. The ubiquitous nanocluster: A molecular scale organizing principle that governs cellular information flow. Curr Opin Cell Biol 2024; 86:102285. [PMID: 38056142 DOI: 10.1016/j.ceb.2023.102285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023]
Abstract
The language of biology at the scale of the cell is constituted of alphabets represented by biomolecules. These are stitched together in a variety of ways to create meaning. We argue that the phrases of this language are nanoscale molecular assemblies or nano-hubs for the purpose of information flow. At the cell surface information is sensed and processed via membrane receptors, often configured as multimers. These nano-assemblies serve as receiver nano-hubs, which are flexibly configured with additional nano-hubs that we term modifiers and transducers. This framework serves to process information that is transmitted for execution inside the cell. Here, we explore some examples about how nano-hubs are built and how they may contribute to cellular information flow.
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Affiliation(s)
- Maria F Garcia-Parajo
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Satyajit Mayor
- National Centre for Biological Sciences, 560065 Bangalore, India.
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Brumbaugh-Reed EH, Aoki K, Toettcher JE. Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575860. [PMID: 38293146 PMCID: PMC10827175 DOI: 10.1101/2024.01.16.575860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Biomolecular condensates are broadly implicated in both normal cellular regulation and disease. Consequently, several chemical biology and optogenetic approaches have been developed to induce phase separation of a protein of interest. However, few tools are available to perform the converse function-dissolving a condensate of interest on demand. Such a tool would aid in testing whether the condensate plays specific functional roles, a major question in cell biology and drug development. Here we report an optogenetic approach to selectively dissolve a condensate of interest in a reversible and spatially controlled manner. We show that light-gated recruitment of maltose-binding protein (MBP), a commonly used solubilizing domain in protein purification, results in rapid and controlled dissolution of condensates formed from proteins of interest. Our optogenetic MBP-based dissolution strategy (OptoMBP) is rapid, reversible, and can be spatially controlled with subcellular precision. We also provide a proof-of-principle application of OptoMBP, showing that disrupting condensation of the oncogenic fusion protein FUS-CHOP results in reversion of FUS-CHOP driven transcriptional changes. We envision that the OptoMBP system could be broadly useful for disrupting constitutive protein condensates to probe their biological functions.
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Affiliation(s)
- Ellen H Brumbaugh-Reed
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton NJ 08544
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
| | - Kazuhiro Aoki
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8315, Japan
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton NJ 08544
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Lee HN, Lee SE, Inn KS, Seong J. Optical sensing and control of T cell signaling pathways. Front Physiol 2024; 14:1321996. [PMID: 38269062 PMCID: PMC10806162 DOI: 10.3389/fphys.2023.1321996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
T cells regulate adaptive immune responses through complex signaling pathways mediated by T cell receptor (TCR). The functional domains of the TCR are combined with specific antibodies for the development of chimeric antigen receptor (CAR) T cell therapy. In this review, we first overview current understanding on the T cell signaling pathways as well as traditional methods that have been widely used for the T cell study. These methods, however, are still limited to investigating dynamic molecular events with spatiotemporal resolutions. Therefore, genetically encoded biosensors and optogenetic tools have been developed to study dynamic T cell signaling pathways in live cells. We review these cutting-edge technologies that revealed dynamic and complex molecular mechanisms at each stage of T cell signaling pathways. They have been primarily applied to the study of dynamic molecular events in TCR signaling, and they will further aid in understanding the mechanisms of CAR activation and function. Therefore, genetically encoded biosensors and optogenetic tools offer powerful tools for enhancing our understanding of signaling mechanisms in T cells and CAR-T cells.
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Affiliation(s)
- Hae Nim Lee
- Brain Science Institute, Korea Institute of Science and Technoloy, Seoul, Republic of Korea
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Seung Eun Lee
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Soo Inn
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Jihye Seong
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Republic of Korea
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Pal AA, Benman W, Mumford TR, Huang Z, Chow BY, Bugaj LJ. Optogenetic clustering and membrane translocation of the BcLOV4 photoreceptor. Proc Natl Acad Sci U S A 2023; 120:e2221615120. [PMID: 37527339 PMCID: PMC10410727 DOI: 10.1073/pnas.2221615120] [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: 12/20/2022] [Accepted: 06/25/2023] [Indexed: 08/03/2023] Open
Abstract
Optogenetic tools respond to light through one of a small number of behaviors including allosteric changes, dimerization, clustering, or membrane translocation. Here, we describe a new class of optogenetic actuator that simultaneously clusters and translocates to the plasma membrane in response to blue light. We demonstrate that dual translocation and clustering of the BcLOV4 photoreceptor can be harnessed for novel single-component optogenetic tools, including for control of the entire family of epidermal growth factor receptor (ErbB1-4) tyrosine kinases. We further find that clustering and membrane translocation are mechanistically linked. Stronger clustering increased the magnitude of translocation and downstream signaling, increased sensitivity to light by ~threefold-to-fourfold, and decreased the expression levels needed for strong signal activation. Thus light-induced clustering of BcLOV4 provides a strategy to generate a new class of optogenetic tools and to enhance existing ones.
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Affiliation(s)
- Ayush Aditya Pal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - Thomas R. Mumford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - Zikang Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - Brian Y. Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
| | - Lukasz J. Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA19104
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA19104
- Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA19104
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López-Palacios TP, Andersen JL. Kinase regulation by liquid–liquid phase separation. Trends Cell Biol 2022:S0962-8924(22)00260-4. [DOI: 10.1016/j.tcb.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
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Li R, Li T, Lu G, Cao Z, Chen B, Wang Y, Du J, Li P. Programming cell-surface signaling by phase-separation-controlled compartmentalization. Nat Chem Biol 2022; 18:1351-1360. [DOI: 10.1038/s41589-022-01192-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 09/30/2022] [Indexed: 11/18/2022]
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Gangopadhyay K, Roy S, Sen Gupta S, Chandradasan A, Chowdhury S, Das R. Regulating the discriminatory response to antigen by T-cell receptor. Biosci Rep 2022; 42:BSR20212012. [PMID: 35260878 PMCID: PMC8965820 DOI: 10.1042/bsr20212012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
The cell-mediated immune response constitutes a robust host defense mechanism to eliminate pathogens and oncogenic cells. T cells play a central role in such a defense mechanism and creating memories to prevent any potential infection. T cell recognizes foreign antigen by its surface receptors when presented through antigen-presenting cells (APCs) and calibrates its cellular response by a network of intracellular signaling events. Activation of T-cell receptor (TCR) leads to changes in gene expression and metabolic networks regulating cell development, proliferation, and migration. TCR does not possess any catalytic activity, and the signaling initiates with the colocalization of several enzymes and scaffold proteins. Deregulation of T cell signaling is often linked to autoimmune disorders like severe combined immunodeficiency (SCID), rheumatoid arthritis, and multiple sclerosis. The TCR remarkably distinguishes the minor difference between self and non-self antigen through a kinetic proofreading mechanism. The output of TCR signaling is determined by the half-life of the receptor antigen complex and the time taken to recruit and activate the downstream enzymes. A longer half-life of a non-self antigen receptor complex could initiate downstream signaling by activating associated enzymes. Whereas, the short-lived, self-peptide receptor complex disassembles before the downstream enzymes are activated. Activation of TCR rewires the cellular metabolic response to aerobic glycolysis from oxidative phosphorylation. How does the early event in the TCR signaling cross-talk with the cellular metabolism is an open question. In this review, we have discussed the recent developments in understanding the regulation of TCR signaling, and then we reviewed the emerging role of metabolism in regulating T cell function.
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Affiliation(s)
- Kaustav Gangopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Swarnendu Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Soumee Sen Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Athira C. Chandradasan
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Subhankar Chowdhury
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Rahul Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
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Banana Lectin from Musa paradisiaca Is Mitogenic for Cow and Pig PBMC via IL-2 Pathway and ELF1. IMMUNO 2021. [DOI: 10.3390/immuno1030018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aim of the study was to gain deeper insights in the potential of polyclonal stimulation of PBMC with banana lectin (BanLec) from Musa paradisiaca. BanLec induced a marked proliferative response in cow and pig PBMC, but was strongest in pigs, where it induced an even higher proliferation rate than Concanavalin A. Molecular processes associated with respective responses in porcine PBMC were examined with differential proteome analyses. Discovery proteomic experiments was applied to BanLec stimulated PBMC and cellular and secretome responses were analyzed with label free LC-MS/MS. In PBMC, 3955 proteins were identified. After polyclonal stimulation with BanLec, 459 proteins showed significantly changed abundance in PBMC. In respective PBMC secretomes, 2867 proteins were identified with 231 differentially expressed candidates as reaction to BanLec stimulation. The transcription factor “E74 like ETS transcription factor 1 (ELF1)” was solely enriched in BanLec stimulated PBMC. BanLec induced secretion of several immune regulators, amongst them positive regulators of activated T cell proliferation and Jak-STAT signaling pathway. Top changed immune proteins were CD226, CD27, IFNG, IL18, IL2, CXCL10, LAT, ICOS, IL2RA, LAG3, and CD300C. BanLec stimulates PBMC of cows and pigs polyclonally and induces IL2 pathway and further proinflammatory cytokines. Proteomics data are available via ProteomeXchange with identifier PXD027505.
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