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Koyama T, Iso N, Norizoe Y, Sakaue T, Yoshimura SH. Charge block-driven liquid-liquid phase separation - mechanism and biological roles. J Cell Sci 2024; 137:jcs261394. [PMID: 38855848 DOI: 10.1242/jcs.261394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.
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Affiliation(s)
- Tetsu Koyama
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Naoki Iso
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Yuki Norizoe
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies , Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for Living Systems Information Science (CeLiSIS) , Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto, 606-8501, Japan
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Walker C, Chandrasekaran A, Mansour D, Graham K, Torres A, Wang L, Lafer EM, Rangamani P, Stachowiak JC. Liquid-like condensates that bind actin drive filament polymerization and bundling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592527. [PMID: 38826190 PMCID: PMC11142076 DOI: 10.1101/2024.05.04.592527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Liquid-like protein condensates perform diverse physiological functions. Previous work showed that VASP, a processive actin polymerase, forms condensates that polymerize and bundle actin. To minimize their curvature, filaments accumulated at the inner condensate surface, ultimately deforming the condensate into a rod-like shape, filled with a bundle of parallel filaments. Here we show that this behavior does not require proteins with specific polymerase activity. Specifically, we found that condensates composed of Lamellipodin, a protein that binds actin but is not an actin polymerase, were also capable of polymerizing and bundling actin filaments. To probe the minimum requirements for condensate-mediated actin bundling, we developed an agent-based computational model. Guided by its predictions, we hypothesized that any condensate-forming protein that binds actin could bundle filaments through multivalent crosslinking. To test this idea, we added an actin-binding motif to Eps15, a condensate-forming protein that does not normally bind actin. The resulting chimera formed condensates that drove efficient actin polymerization and bundling. Collectively, these findings broaden the family of proteins that could organize cytoskeletal filaments to include any actin-binding protein that participates in protein condensation.
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Affiliation(s)
- Caleb Walker
- Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Aravind Chandrasekaran
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, United States
| | - Daniel Mansour
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, United States
| | - Kristin Graham
- Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Andrea Torres
- Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Liping Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Eileen M. Lafer
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, United States
| | - Jeanne C. Stachowiak
- Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
- Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
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Johnson DH, Kou OH, Bouzos N, Zeno WF. Protein-membrane interactions: sensing and generating curvature. Trends Biochem Sci 2024; 49:401-416. [PMID: 38508884 PMCID: PMC11069444 DOI: 10.1016/j.tibs.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024]
Abstract
Biological membranes are integral cellular structures that can be curved into various geometries. These curved structures are abundant in cells as they are essential for various physiological processes. However, curved membranes are inherently unstable, especially on nanometer length scales. To stabilize curved membranes, cells can utilize proteins that sense and generate membrane curvature. In this review, we summarize recent research that has advanced our understanding of interactions between proteins and curved membrane surfaces, as well as work that has expanded our ability to study curvature sensing and generation. Additionally, we look at specific examples of cellular processes that require membrane curvature, such as neurotransmission, clathrin-mediated endocytosis (CME), and organelle biogenesis.
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Affiliation(s)
- David H Johnson
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Orianna H Kou
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Nicoletta Bouzos
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Wade F Zeno
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA.
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Leek AN, Quinn JA, Krapf D, Tamkun MM. GLT-1a glutamate transporter nanocluster localization is associated with astrocytic actin and neuronal Kv2 clusters at sites of neuron-astrocyte contact. Front Cell Dev Biol 2024; 12:1334861. [PMID: 38362041 PMCID: PMC10867268 DOI: 10.3389/fcell.2024.1334861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Introduction: Astrocytic GLT-1 glutamate transporters ensure the fidelity of glutamic neurotransmission by spatially and temporally limiting glutamate signals. The ability to limit neuronal hyperactivity relies on the localization and diffusion of GLT-1 on the astrocytic surface, however, little is known about the underlying mechanisms. We show that two isoforms of GLT-1, GLT-1a and GLT-1b, form nanoclusters on the surface of transfected astrocytes and HEK-293 cells. Methods: We used both fixed and live cell super-resolution imaging of fluorescent protein and epitope tagged proteins in co-cultures of rat astrocytes and neurons. Immunofluorescence techniques were also used. GLT1 diffusion was assessed via single particle tracking and fluorescence recovery after photobleach (FRAP). Results: We found GLT-1a, but not GLT-1b, nanoclusters concentrated adjacent to actin filaments which was maintained after addition of glutamate. GLT-1a nanocluster concentration near actin filaments was prevented by expression of a cytosolic GLT-1a C-terminus, suggesting the C-terminus is involved in the localization adjacent to cortical actin. Using super-resolution imaging, we show that astrocytic GLT-1a and actin co-localize in net-like structures around neuronal Kv2.1 clusters at points of neuron/astrocyte contact. Conclusion: Overall, these data describe a novel relationship between GLT-1a and cortical actin filaments, which localizes GLT-1a near neuronal structures responsive to ischemic insult.
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Affiliation(s)
- Ashley N. Leek
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
- Molecular, Cellular and Integrative Neuroscience Program, Colorado State University, Fort Collins, CO, United States
| | - Josiah A. Quinn
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO, United States
| | - Michael M. Tamkun
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
- Molecular, Cellular and Integrative Neuroscience Program, Colorado State University, Fort Collins, CO, United States
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
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Rioux DJ, Prosser DC. A CIE change in our understanding of endocytic mechanisms. Front Cell Dev Biol 2023; 11:1334798. [PMID: 38192364 PMCID: PMC10773762 DOI: 10.3389/fcell.2023.1334798] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
The past six decades have seen major advances in our understanding of endocytosis, ranging from descriptive studies based on electron microscopy to biochemical and genetic characterization of factors required for vesicle formation. Most studies focus on clathrin as the major coat protein; indeed, clathrin-mediated endocytosis (CME) is the primary pathway for internalization. Clathrin-independent (CIE) pathways also exist, although mechanistic understanding of these pathways remains comparatively elusive. Here, we discuss how early studies of CME shaped our understanding of endocytosis and describe recent advances in CIE, including pathways in model organisms that are poised to provide key insights into endocytic regulation.
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Affiliation(s)
- Daniel J. Rioux
- Life Sciences, Virginia Commonwealth University, Richmond, VA, United States
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - Derek C. Prosser
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
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Prado LG, Camara NOS, Barbosa AS. Cell lipid biology in infections: an overview. Front Cell Infect Microbiol 2023; 13:1148383. [PMID: 37868347 PMCID: PMC10587689 DOI: 10.3389/fcimb.2023.1148383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
Lipids are a big family of molecules with a vast number of functions in the cell membranes, within the cytoplasm, and extracellularly. Lipid droplets (LDs) are the most common storage organelles and are present in almost every tissue type in the body. They also have structural functions serving as building blocks of cellular membranes and may be precursors of other molecules such as hormones, and lipoproteins, and as messengers in signal transduction. Fatty acids (FAs), such as sterol esters and triacylglycerols, are stored in LDs and are used in β-oxidation as fuel for tricarboxylic acid cycle (TCA) and adenosine triphosphate (ATP) generation. FA uptake and entrance in the cytoplasm are mediated by membrane receptors. After a cytoplasmic round of α- and β-oxidation, FAs are guided into the mitochondrial matrix by the L-carnitine shuttle system, where they are fully metabolized, and enter the TCA cycle. Pathogen infections may lead to impaired lipid metabolism, usage of membrane phospholipids, and LD accumulation in the cytoplasm of infected cells. Otherwise, bacterial pathogens may use lipid metabolism as a carbon source, thus altering the reactions and leading to cellular and organelles malfunctioning. This review aims to describe cellular lipid metabolism and alterations that occur upon infections.
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Affiliation(s)
- Luan Gavião Prado
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Niels Olsen Saraiva Camara
- Laboratório de Imunobiologia de Transplantes, Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Disciplina de Nefrologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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