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Kay RR, Lutton JE, King JS, Bretschneider T. Making cups and rings: the 'stalled-wave' model for macropinocytosis. Biochem Soc Trans 2024; 52:1785-1794. [PMID: 38934501 DOI: 10.1042/bst20231426] [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: 03/13/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Macropinocytosis is a broadly conserved endocytic process discovered nearly 100 years ago, yet still poorly understood. It is prominent in cancer cell feeding, immune surveillance, uptake of RNA vaccines and as an invasion route for pathogens. Macropinocytic cells extend large cups or flaps from their plasma membrane to engulf droplets of medium and trap them in micron-sized vesicles. Here they are digested and the products absorbed. A major problem - discussed here - is to understand how cups are shaped and closed. Recently, lattice light-sheet microscopy has given a detailed description of this process in Dictyostelium amoebae, leading to the 'stalled-wave' model for cup formation and closure. This is based on membrane domains of PIP3 and active Ras and Rac that occupy the inner face of macropinocytic cups and are readily visible with suitable reporters. These domains attract activators of dendritic actin polymerization to their periphery, creating a ring of protrusive F-actin around themselves, thus shaping the walls of the cup. As domains grow, they drive a wave of actin polymerization across the plasma membrane that expands the cup. When domains stall, continued actin polymerization under the membrane, combined with increasing membrane tension in the cup, drives closure at lip or base. Modelling supports the feasibility of this scheme. No specialist coat proteins or contractile activities are required to shape and close cups: rings of actin polymerization formed around PIP3 domains that expand and stall seem sufficient. This scheme may be widely applicable and begs many biochemical questions.
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Affiliation(s)
- Robert R Kay
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, U.K
| | - Judith E Lutton
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, U.K
| | - Jason S King
- Department of Biomedical Sciences, Western Bank, Sheffield S10 2TN, U.K
| | - Till Bretschneider
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, U.K
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2
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Lutton JE, Coker HLE, Paschke P, Munn CJ, King JS, Bretschneider T, Kay RR. Formation and closure of macropinocytic cups in Dictyostelium. Curr Biol 2023; 33:3083-3096.e6. [PMID: 37379843 PMCID: PMC7614961 DOI: 10.1016/j.cub.2023.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
Macropinocytosis is a conserved endocytic process by which cells engulf droplets of medium into micron-sized vesicles. We use light-sheet microscopy to define an underlying set of principles by which macropinocytic cups are shaped and closed in Dictyostelium amoebae. Cups form around domains of PIP3 stretching almost to their lip and are supported by a specialized F-actin scaffold from lip to base. They are shaped by a ring of actin polymerization created by recruiting Scar/WAVE and Arp2/3 around PIP3 domains, but how cups evolve over time to close and form a vesicle is unknown. Custom 3D analysis shows that PIP3 domains expand from small origins, capturing new membrane into the cup, and crucially, that cups close when domain expansion stalls. We show that cups can close in two ways: either at the lip, by inwardly directed actin polymerization, or the base, by stretching and delamination of the membrane. This provides the basis for a conceptual mechanism whereby closure is brought about by a combination of stalled cup expansion, continued actin polymerization at the lip, and membrane tension. We test this through the use of a biophysical model, which can recapitulate both forms of cup closure and explain how 3D cup structures evolve over time to mediate engulfment.
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Affiliation(s)
- Judith E Lutton
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, UK
| | - Helena L E Coker
- CAMDU, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Peggy Paschke
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Jason S King
- School of Biosciences, Western Bank, Sheffield S10 2TN, UK.
| | - Till Bretschneider
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, UK.
| | - Robert R Kay
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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3
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Schaf J, Shinhmar S, Zeng Q, Pardo OE, Beesley P, Syed N, Williams RSB. Enhanced Sestrin expression through Tanshinone 2A treatment improves PI3K-dependent inhibition of glioma growth. Cell Death Discov 2023; 9:172. [PMID: 37202382 DOI: 10.1038/s41420-023-01462-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/20/2023] Open
Abstract
Glioblastomas are a highly aggressive cancer type which respond poorly to current pharmaceutical treatments, thus novel therapeutic approaches need to be investigated. One such approach involves the use of the bioactive natural product Tanshinone IIA (T2A) derived from the Chinese herb Danshen, where mechanistic insight for this anti-cancer agent is needed to validate its use. Here, we employ a tractable model system, Dictyostelium discoideum, to provide this insight. T2A potently inhibits cellular proliferation of Dictyostelium, suggesting molecular targets in this model. We show that T2A rapidly reduces phosphoinositide 3 kinase (PI3K) and protein kinase B (PKB) activity, but surprisingly, the downstream complex mechanistic target of rapamycin complex 1 (mTORC1) is only inhibited following chronic treatment. Investigating regulators of mTORC1, including PKB, tuberous sclerosis complex (TSC), and AMP-activated protein kinase (AMPK), suggests these enzymes were not responsible for this effect, implicating an additional molecular mechanism of T2A. We identify this mechanism as the increased expression of sestrin, a negative regulator of mTORC1. We further show that combinatory treatment using a PI3K inhibitor and T2A gives rise to a synergistic inhibition of cell proliferation. We then translate our findings to human and mouse-derived glioblastoma cell lines, where both a PI3K inhibitor (Paxalisib) and T2A reduces glioblastoma proliferation in monolayer cultures and in spheroid expansion, with combinatory treatment significantly enhancing this effect. Thus, we propose a new approach for cancer treatment, including glioblastomas, through combinatory treatment with PI3K inhibitors and T2A.
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Affiliation(s)
- Judith Schaf
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Sonia Shinhmar
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Qingyu Zeng
- John Fulcher Neuro-Oncology Laboratory, Imperial College London, Hammersmith Hospital, London, UK
| | - Olivier E Pardo
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Philip Beesley
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Nelofer Syed
- John Fulcher Neuro-Oncology Laboratory, Imperial College London, Hammersmith Hospital, London, UK
| | - Robin S B Williams
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK.
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4
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Salloum G, Bresnick AR, Backer JM. Macropinocytosis: mechanisms and regulation. Biochem J 2023; 480:335-362. [PMID: 36920093 DOI: 10.1042/bcj20210584] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/16/2023]
Abstract
Macropinocytosis is defined as an actin-dependent but coat- and dynamin-independent endocytic uptake process, which generates large intracellular vesicles (macropinosomes) containing a non-selective sampling of extracellular fluid. Macropinocytosis provides an important mechanism of immune surveillance by dendritic cells and macrophages, but also serves as an essential nutrient uptake pathway for unicellular organisms and tumor cells. This review examines the cell biological mechanisms that drive macropinocytosis, as well as the complex signaling pathways - GTPases, lipid and protein kinases and phosphatases, and actin regulatory proteins - that regulate macropinosome formation, internalization, and disposition.
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Affiliation(s)
- Gilbert Salloum
- Department of Molecular Pharamacology, Albert Einstein College of Medicine, Bronx, NY, U.S.A
| | - Anne R Bresnick
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, U.S.A
| | - Jonathan M Backer
- Department of Molecular Pharamacology, Albert Einstein College of Medicine, Bronx, NY, U.S.A
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, U.S.A
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5
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Banerjee T, Matsuoka S, Biswas D, Miao Y, Pal DS, Kamimura Y, Ueda M, Devreotes PN, Iglesias PA. A dynamic partitioning mechanism polarizes membrane protein distribution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522496. [PMID: 36712016 PMCID: PMC9881856 DOI: 10.1101/2023.01.03.522496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The plasma membrane is widely regarded as the hub of the signal transduction network activities that drives numerous physiological responses, including cell polarity and migration. Yet, the symmetry breaking process in the membrane, that leads to dynamic compartmentalization of different proteins, remains poorly understood. Using multimodal live-cell imaging, here we first show that multiple endogenous and synthetic lipid-anchored proteins, despite maintaining stable tight association with the inner leaflet of the plasma membrane, were unexpectedly depleted from the membrane domains where the signaling network was spontaneously activated such as in the new protrusions as well as within the propagating ventral waves. Although their asymmetric patterns resembled those of standard peripheral "back" proteins such as PTEN, unlike the latter, these lipidated proteins did not dissociate from the membrane upon global receptor activation. Our experiments not only discounted the possibility of recurrent reversible translocation from membrane to cytosol as it occurs for weakly bound peripheral membrane proteins, but also ruled out the necessity of directed vesicular trafficking and cytoskeletal supramolecular structure-based restrictions in driving these dynamic symmetry breaking events. Selective photoconversion-based protein tracking assays suggested that these asymmetric patterns instead originate from the inherent ability of these membrane proteins to "dynamically partition" into distinct domains within the plane of the membrane. Consistently, single-molecule measurements showed that these lipid-anchored molecules have substantially dissimilar diffusion profiles in different regions of the membrane. When these profiles were incorporated into an excitable network-based stochastic reaction-diffusion model of the system, simulations revealed that our proposed "dynamic partitioning" mechanism is sufficient to give rise to familiar asymmetric propagating wave patterns. Moreover, we demonstrated that normally uniform integral and lipid-anchored membrane proteins in Dictyostelium and mammalian neutrophil cells can be induced to partition spatiotemporally to form polarized patterns, by optogenetically recruiting membrane domain-specific peptides to these proteins. Together, our results indicate "dynamic partitioning" as a new mechanism of plasma membrane organization, that can account for large-scale compartmentalization of a wide array of lipid-anchored and integral membrane proteins in different physiological processes.
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6
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Xu X, Pots H, Gilsbach BK, Parsons D, Veltman DM, Ramachandra SG, Li H, Kortholt A, Jin T. C2GAP2 is a common regulator of Ras signaling for chemotaxis, phagocytosis, and macropinocytosis. Front Immunol 2022; 13:1075386. [PMID: 36524124 PMCID: PMC9745196 DOI: 10.3389/fimmu.2022.1075386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022] Open
Abstract
Phagocytosis, macropinocytosis, and G protein coupled receptor-mediated chemotaxis are Ras-regulated and actin-driven processes. The common regulator for Ras activity in these three processes remains unknown. Here, we show that C2GAP2, a Ras GTPase activating protein, highly expressed in the vegetative growth state in model organism Dictyostelium. C2GAP2 localizes at the leading edge of chemotaxing cells, phagosomes during phagocytosis, and macropinosomes during micropinocytosis. c2gapB- cells lacking C2GAP2 displayed increased Ras activation upon folic acid stimulation and subsequent impaired chemotaxis in the folic acid gradient. In addition, c2gaB- cells have elevated phagocytosis and macropinocytosis, which subsequently results in faster cell growth. C2GAP2 binds multiple phospholipids on the plasma membrane and the membrane recruitment of C2GAP2 requires calcium. Taken together, we show a shared negative regulator of Ras signaling that mediates Ras signaling for chemotaxis, phagocytosis, and macropinocytosis.
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Affiliation(s)
- Xuehua Xu
- Chemotaxis Signaling Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States,*Correspondence: Xuehua Xu,
| | - Henderikus Pots
- Department of Cell Biochemistry, University of Groningen, Groningen, Netherlands
| | - Bernd K. Gilsbach
- Functional Neuroproteomics and Translational Biomarkers in Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Dustin Parsons
- Chemotaxis Signaling Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Douwe M. Veltman
- Department of Cell Biochemistry, University of Groningen, Groningen, Netherlands
| | - Sharmila G. Ramachandra
- Chemotaxis Signaling Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Haoran Li
- Chemotaxis Signaling Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen, Netherlands
| | - Tian Jin
- Chemotaxis Signaling Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
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7
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Actin dynamics in protein homeostasis. Biosci Rep 2022; 42:231720. [PMID: 36043949 PMCID: PMC9469105 DOI: 10.1042/bsr20210848] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cell homeostasis is maintained in all organisms by the constant adjustment of cell constituents and organisation to account for environmental context. Fine-tuning of the optimal balance of proteins for the conditions, or protein homeostasis, is critical to maintaining cell homeostasis. Actin, a major constituent of the cytoskeleton, forms many different structures which are acutely sensitive to the cell environment. Furthermore, actin structures interact with and are critically important for the function and regulation of multiple factors involved with mRNA and protein production and degradation, and protein regulation. Altogether, actin is a key, if often overlooked, regulator of protein homeostasis across eukaryotes. In this review, we highlight these roles and how they are altered following cell stress, from mRNA transcription to protein degradation.
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8
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Singh SP, Paschke P, Tweedy L, Insall RH. AKT and SGK kinases regulate cell migration by altering Scar/WAVE complex activation and Arp2/3 complex recruitment. Front Mol Biosci 2022; 9:965921. [PMID: 36106016 PMCID: PMC9466652 DOI: 10.3389/fmolb.2022.965921] [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: 06/10/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022] Open
Abstract
Cell polarity and cell migration both depend on pseudopodia and lamellipodia formation. These are regulated by coordinated signaling acting through G-protein coupled receptors and kinases such as PKB/AKT and SGK, as well as the actin cytoskeletal machinery. Here we show that both Dictyostelium PKB and SGK kinases (encoded by pkbA and pkgB) are dispensable for chemotaxis towards folate. However, both are involved in the regulation of pseudopod formation and thus cell motility. Cells lacking pkbA and pkgB showed a substantial drop in cell speed. Actin polymerization is perturbed in pkbA- and reduced in pkgB- and pkbA-/pkgB- mutants. The Scar/WAVE complex, key catalyst of pseudopod formation, is recruited normally to the fronts of all mutant cells (pkbA-, pkgB- and pkbA-/pkgB-), but is unexpectedly unable to recruit the Arp2/3 complex in cells lacking SGK. Consequently, loss of SGK causes a near-complete loss of normal actin pseudopodia, though this can be rescued by overexpression of PKB. Hence both PKB and SGK are required for correct assembly of F-actin and recruitment of the Arp2/3 complex by the Scar/WAVE complex during pseudopodia formation.
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Affiliation(s)
- Shashi Prakash Singh
- CRUK Beatson Institute, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
- *Correspondence: Shashi Prakash Singh,
| | | | - Luke Tweedy
- CRUK Beatson Institute, Glasgow, United Kingdom
| | - Robert H. Insall
- CRUK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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9
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Mendel ZI, Reynolds MB, Abuaita BH, O'Riordan MX, Swanson JA. Amino acids suppress macropinocytosis and promote release of CSF1 receptor in macrophages. J Cell Sci 2022; 135:jcs259284. [PMID: 35107133 PMCID: PMC8919328 DOI: 10.1242/jcs.259284] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/31/2021] [Indexed: 01/12/2023] Open
Abstract
The internalization of solutes by macropinocytosis provides an essential route for nutrient uptake in many cells. Macrophages increase macropinocytosis in response to growth factors and other stimuli. To test the hypothesis that nutrient environments modulate solute uptake by macropinocytosis, this study analyzed the effects of extracellular amino acids on the accumulation of fluorescent fluid-phase probes in murine macrophages. Nine amino acids, added individually or together, were capable of suppressing macropinocytosis in murine bone marrow-derived macrophages stimulated with the growth factors colony stimulating factor 1 (CSF1) or interleukin 34, both ligands of the CSF1 receptor (CSF1R). The suppressive amino acids did not inhibit macropinocytosis in response to lipopolysaccharide, the chemokine CXCL12, or the tumor promoter phorbol myristate acetate. Suppressive amino acids promoted release of CSF1R from cells and resulted in the formation of smaller macropinosomes in response to CSF1. This suppression of growth factor-stimulated macropinocytosis indicates that different nutrient environments modulate CSF1R levels and bulk ingestion by macropinocytosis, with likely consequences for macrophage growth and function.
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Affiliation(s)
- Zachary I. Mendel
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109,USA
| | - Mack B. Reynolds
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109,USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109,USA
| | - Basel H. Abuaita
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109,USA
| | - Mary X. O'Riordan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109,USA
| | - Joel A. Swanson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109,USA
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10
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Kay RR, Lutton J, Coker H, Paschke P, King JS, Bretschneider T. The Amoebal Model for Macropinocytosis. Subcell Biochem 2022; 98:41-59. [PMID: 35378702 DOI: 10.1007/978-3-030-94004-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macropinocytosis is a relatively unexplored form of large-scale endocytosis driven by the actin cytoskeleton. Dictyostelium amoebae form macropinosomes from cups extended from the plasma membrane, then digest their contents and absorb the nutrients in the endo-lysosomal system. They use macropinocytosis for feeding, maintaining a high rate of fluid uptake that makes assay and experimentation easy. Mutants collected over the years identify cytoskeletal and signalling proteins required for macropinocytosis. Cups are organized around plasma membrane domains of intense PIP3, Ras and Rac signalling, proper formation of which also depends on the RasGAPs NF1 and RGBARG, PTEN, the PIP3-regulated protein kinases Akt and SGK and their activators PDK1 and TORC2, Rho proteins, plus other components yet to be identified. This PIP3 domain directs dendritic actin polymerization to the extending lip of macropinocytic cups by recruiting a ring of the SCAR/WAVE complex around itself and thus activating the Arp2/3 complex. The dynamics of PIP3 domains are proposed to shape macropinocytic cups from start to finish. The role of the Ras-PI3-kinase module in organizing feeding structures in unicellular organisms most likely predates its adoption into growth factor signalling, suggesting an evolutionary origin for growth factor signalling.
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Affiliation(s)
- Robert R Kay
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Josiah Lutton
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Helena Coker
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Peggy Paschke
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, UK
| | - Jason S King
- School of Biomedical Sciences, University of Sheffield, Sheffield, UK
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11
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Saito N, Sawai S. Three-dimensional morphodynamic simulations of macropinocytic cups. iScience 2021; 24:103087. [PMID: 34755081 PMCID: PMC8560551 DOI: 10.1016/j.isci.2021.103087] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/13/2021] [Accepted: 09/01/2021] [Indexed: 12/02/2022] Open
Abstract
Macropinocytosis refers to the non-specific uptake of extracellular fluid, which plays ubiquitous roles in cell growth, immune surveillance, and virus entry. Despite its widespread occurrence, it remains unclear how its initial cup-shaped plasma membrane extensions form without any external solid support, as opposed to the process of particle uptake during phagocytosis. Here, by developing a computational framework that describes the coupling between the bistable reaction-diffusion processes of active signaling patches and membrane deformation, we demonstrated that the protrusive force localized to the edge of the patches can give rise to a self-enclosing cup structure, without further assumptions of local bending or contraction. Efficient uptake requires a balance among the patch size, magnitude of protrusive force, and cortical tension. Furthermore, our model exhibits cyclic cup formation, coexistence of multiple cups, and cup-splitting, indicating that these complex morphologies self-organize via a common mutually-dependent process of reaction-diffusion and membrane deformation.
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Affiliation(s)
- Nen Saito
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Satoshi Sawai
- Department of Basic Science, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
- Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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12
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Gruenheit N, Baldwin A, Stewart B, Jaques S, Keller T, Parkinson K, Salvidge W, Baines R, Brimson C, Wolf JB, Chisholm R, Harwood AJ, Thompson CRL. Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology. BMC Biol 2021; 19:172. [PMID: 34429112 PMCID: PMC8386026 DOI: 10.1186/s12915-021-01108-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/22/2021] [Indexed: 01/26/2023] Open
Abstract
Background Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in the cell, developmental and evolutionary biology. Results We describe REMI-seq, an adaptation of Tn-seq, which allows high throughput, en masse, and quantitative identification of the genomic site of insertion of a drug resistance marker after restriction enzyme-mediated integration. We use REMI-seq to develop tools which greatly enhance the efficiency with which the sequence, transcriptome or proteome variation can be linked to phenotype in D. discoideum. These comprise (1) a near genome-wide resource of individual mutants and (2) a defined pool of ‘barcoded’ mutants to allow large-scale parallel phenotypic analyses. These resources are freely available and easily accessible through the REMI-seq website that also provides comprehensive guidance and pipelines for data analysis. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Conclusions We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01108-y.
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Affiliation(s)
- Nicole Gruenheit
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Amy Baldwin
- Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Balint Stewart
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Sarah Jaques
- Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Thomas Keller
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Katie Parkinson
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - William Salvidge
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Robert Baines
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Chris Brimson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Jason B Wolf
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Rex Chisholm
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
| | - Adrian J Harwood
- Cardiff School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
| | - Christopher R L Thompson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.
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13
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Quinn SE, Huang L, Kerkvliet JG, Swanson JA, Smith S, Hoppe AD, Anderson RB, Thiex NW, Scott BL. The structural dynamics of macropinosome formation and PI3-kinase-mediated sealing revealed by lattice light sheet microscopy. Nat Commun 2021. [PMID: 34376698 DOI: 10.1101/2020.12.01.390195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
Abstract
Macropinosomes are formed by shaping actin-rich plasma membrane ruffles into large intracellular organelles in a phosphatidylinositol 3-kinase (PI3K)-coordinated manner. Here, we utilize lattice lightsheet microscopy and image visualization methods to map the three-dimensional structure and dynamics of macropinosome formation relative to PI3K activity. We show that multiple ruffling morphologies produce macropinosomes and that the majority form through collisions of adjacent PI3K-rich ruffles. By combining multiple volumetric representations of the plasma membrane structure and PI3K products, we show that PI3K activity begins early throughout the entire ruffle volume and continues to increase until peak activity concentrates at the base of the ruffle after the macropinosome closes. Additionally, areas of the plasma membrane rich in ruffling had increased PI3K activity and produced many macropinosomes of various sizes. Pharmacologic inhibition of PI3K activity had little effect on the rate and morphology of membrane ruffling, demonstrating that early production of 3'-phosphoinositides within ruffles plays a minor role in regulating their morphology. However, 3'-phosphoinositides are critical for the fusogenic activity that seals ruffles into macropinosomes. Taken together, these data indicate that local PI3K activity is amplified in ruffles and serves as a priming mechanism for closure and sealing of ruffles into macropinosomes.
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Affiliation(s)
- Shayne E Quinn
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA
- BioSNTR, South Dakota Mines, Rapid City, SD, USA
| | - Lu Huang
- Department of Biology and Microbiology, South Dakota State University (SDSU), Brookings, SD, USA
- BioSNTR, SDSU, Brookings, SD, USA
| | - Jason G Kerkvliet
- BioSNTR, SDSU, Brookings, SD, USA
- Department of Chemistry and Biochemistry, SDSU, Brookings, SD, USA
| | - Joel A Swanson
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Steve Smith
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA
- BioSNTR, South Dakota Mines, Rapid City, SD, USA
| | - Adam D Hoppe
- BioSNTR, SDSU, Brookings, SD, USA
- Department of Chemistry and Biochemistry, SDSU, Brookings, SD, USA
| | - Robert B Anderson
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA.
- BioSNTR, South Dakota Mines, Rapid City, SD, USA.
| | - Natalie W Thiex
- Department of Biology and Microbiology, South Dakota State University (SDSU), Brookings, SD, USA.
- BioSNTR, SDSU, Brookings, SD, USA.
| | - Brandon L Scott
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA.
- BioSNTR, South Dakota Mines, Rapid City, SD, USA.
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14
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Quinn SE, Huang L, Kerkvliet JG, Swanson JA, Smith S, Hoppe AD, Anderson RB, Thiex NW, Scott BL. The structural dynamics of macropinosome formation and PI3-kinase-mediated sealing revealed by lattice light sheet microscopy. Nat Commun 2021; 12:4838. [PMID: 34376698 PMCID: PMC8355319 DOI: 10.1038/s41467-021-25187-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
Macropinosomes are formed by shaping actin-rich plasma membrane ruffles into large intracellular organelles in a phosphatidylinositol 3-kinase (PI3K)-coordinated manner. Here, we utilize lattice lightsheet microscopy and image visualization methods to map the three-dimensional structure and dynamics of macropinosome formation relative to PI3K activity. We show that multiple ruffling morphologies produce macropinosomes and that the majority form through collisions of adjacent PI3K-rich ruffles. By combining multiple volumetric representations of the plasma membrane structure and PI3K products, we show that PI3K activity begins early throughout the entire ruffle volume and continues to increase until peak activity concentrates at the base of the ruffle after the macropinosome closes. Additionally, areas of the plasma membrane rich in ruffling had increased PI3K activity and produced many macropinosomes of various sizes. Pharmacologic inhibition of PI3K activity had little effect on the rate and morphology of membrane ruffling, demonstrating that early production of 3'-phosphoinositides within ruffles plays a minor role in regulating their morphology. However, 3'-phosphoinositides are critical for the fusogenic activity that seals ruffles into macropinosomes. Taken together, these data indicate that local PI3K activity is amplified in ruffles and serves as a priming mechanism for closure and sealing of ruffles into macropinosomes.
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Affiliation(s)
- Shayne E Quinn
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA
- BioSNTR, South Dakota Mines, Rapid City, SD, USA
| | - Lu Huang
- Department of Biology and Microbiology, South Dakota State University (SDSU), Brookings, SD, USA
- BioSNTR, SDSU, Brookings, SD, USA
| | - Jason G Kerkvliet
- BioSNTR, SDSU, Brookings, SD, USA
- Department of Chemistry and Biochemistry, SDSU, Brookings, SD, USA
| | - Joel A Swanson
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Steve Smith
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA
- BioSNTR, South Dakota Mines, Rapid City, SD, USA
| | - Adam D Hoppe
- BioSNTR, SDSU, Brookings, SD, USA
- Department of Chemistry and Biochemistry, SDSU, Brookings, SD, USA
| | - Robert B Anderson
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA.
- BioSNTR, South Dakota Mines, Rapid City, SD, USA.
| | - Natalie W Thiex
- Department of Biology and Microbiology, South Dakota State University (SDSU), Brookings, SD, USA.
- BioSNTR, SDSU, Brookings, SD, USA.
| | - Brandon L Scott
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA.
- BioSNTR, South Dakota Mines, Rapid City, SD, USA.
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15
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Mathavarajah S, VanIderstine C, Dellaire G, Huber RJ. Cancer and the breakdown of multicellularity: What Dictyostelium discoideum, a social amoeba, can teach us. Bioessays 2021; 43:e2000156. [PMID: 33448043 DOI: 10.1002/bies.202000156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 01/01/2023]
Abstract
Ancient pathways promoting unicellularity and multicellularity are associated with cancer, the former being pro-oncogenic and the latter acting to suppress oncogenesis. However, there are only a limited number of non-vertebrate models for studying these pathways. Here, we review Dictyostelium discoideum and describe how it can be used to understand these gene networks. D. discoideum has a unicellular and multicellular life cycle, making it possible to study orthologs of cancer-associated genes in both phases. During development, differentiated amoebae form a fruiting body composed of a mass of spores that are supported atop a stalk. A portion of the cells sacrifice themselves to become non-reproductive stalk cells. Cheating disrupts the principles of multicellularity, as cheater cells alter their cell fate to preferentially become spores. Importantly, D. discoideum has gene networks and several strategies for maintaining multicellularity. Therefore, D. discoideum can help us better understand how conserved genes and pathways involved in multicellularity also influence cancer development, potentially identifying new therapeutic avenues.
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Affiliation(s)
- Sabateeshan Mathavarajah
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Carter VanIderstine
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada
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16
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Stévenin V, Chang YY, Le Toquin Y, Duchateau M, Gianetto QG, Luk CH, Salles A, Sohst V, Matondo M, Reiling N, Enninga J. Dynamic Growth and Shrinkage of the Salmonella-Containing Vacuole Determines the Intracellular Pathogen Niche. Cell Rep 2020; 29:3958-3973.e7. [PMID: 31851926 PMCID: PMC6931108 DOI: 10.1016/j.celrep.2019.11.049] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/23/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
Salmonella is a human and animal pathogen that causes gastro-enteric diseases. The key to Salmonella infection is its entry into intestinal epithelial cells, where the bacterium resides within a Salmonella-containing vacuole (SCV). Salmonella entry also induces the formation of empty macropinosomes, distinct from the SCV, in the vicinity of the entering bacteria. A few minutes after its formation, the SCV increases in size through fusions with the surrounding macropinosomes. Salmonella also induces membrane tubules that emanate from the SCV and lead to SCV shrinkage. Here, we show that these antipodal events are utilized by Salmonella to either establish a vacuolar niche or to be released into the cytosol by SCV rupture. We identify the molecular machinery underlying dynamic SCV growth and shrinkage. In particular, the SNARE proteins SNAP25 and STX4 participate in SCV inflation by fusion with macropinosomes. Thus, host compartment size control emerges as a pathogen strategy for intracellular niche regulation. The early SCV simultaneously grows and shrinks through fusion and tubule formation SCV shrinkage promotes vacuolar rupture and cytosolic release IAMs are enriched in the host SNAREs SNAP25 and STX4, enabling IAM-SCV fusion Promoting SNX1-mediated tubule formation, SopB fosters SCV ruptures
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Affiliation(s)
- Virginie Stévenin
- Institut Pasteur, Dynamics of Host-Pathogen Interactions Unit, 25 Rue du Dr. Roux, Paris, France
| | - Yuen-Yan Chang
- Institut Pasteur, Dynamics of Host-Pathogen Interactions Unit, 25 Rue du Dr. Roux, Paris, France
| | - Yoann Le Toquin
- Institut Pasteur, Dynamics of Host-Pathogen Interactions Unit, 25 Rue du Dr. Roux, Paris, France
| | - Magalie Duchateau
- Institut Pasteur, Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie, C2RT, USR 2000 CNRS, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie, C2RT, USR 2000 CNRS, Paris, France; Institut Pasteur, Bioinformatics and Biostatistics HUB, C3BI, USR CNRS 3756, Paris, France
| | - Chak Hon Luk
- Institut Pasteur, Dynamics of Host-Pathogen Interactions Unit, 25 Rue du Dr. Roux, Paris, France
| | - Audrey Salles
- Institut Pasteur, UtechS Photonic BioImaging PBI (Imagopole), Centre de Recherche et de Ressources Technologiques C2RT, Paris, France
| | - Victoria Sohst
- Research Center Borstel, Leibniz Lung Center, RG Microbial Interface Biology, Parkallee 22, 23845 Borstel, Germany
| | - Mariette Matondo
- Institut Pasteur, Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie, C2RT, USR 2000 CNRS, Paris, France
| | - Norbert Reiling
- Research Center Borstel, Leibniz Lung Center, RG Microbial Interface Biology, Parkallee 22, 23845 Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Jost Enninga
- Institut Pasteur, Dynamics of Host-Pathogen Interactions Unit, 25 Rue du Dr. Roux, Paris, France.
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17
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Decanoic acid inhibits mTORC1 activity independent of glucose and insulin signaling. Proc Natl Acad Sci U S A 2020; 117:23617-23625. [PMID: 32879008 PMCID: PMC7519326 DOI: 10.1073/pnas.2008980117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The mTORC1 complex provides a critical role in cell function, regulating a variety of processes including growth and autophagy. mTORC1 signaling is hyperactivated in a range of common diseases including cancer, epilepsy, and neurodegenerative disorders. Hence, mTORC1 signaling provides an important target for regulation in many contexts. Here, we show that decanoic acid, a key component of a widely used medicinal diet, reduces mTORC1 activity. We identify this in a tractable model system, and validate it in ex vivo rat brain tissue and in human iPSC-derived astrocytes from patients with a clinically relevant disease. Thus, we provide insight into an easily accessible therapeutic approach for a range of diseases. Low-glucose and -insulin conditions, associated with ketogenic diets, can reduce the activity of the mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway, potentially leading to a range of positive medical and health-related effects. Here, we determined whether mTORC1 signaling is also a target for decanoic acid, a key component of the medium-chain triglyceride (MCT) ketogenic diet. Using a tractable model system, Dictyostelium, we show that decanoic acid can decrease mTORC1 activity, under conditions of constant glucose and in the absence of insulin, measured by phosphorylation of eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1). We determine that this effect of decanoic acid is dependent on a ubiquitin regulatory X domain-containing protein, mediating inhibition of a conserved Dictyostelium AAA ATPase, p97, a homolog of the human transitional endoplasmic reticulum ATPase (VCP/p97) protein. We then demonstrate that decanoic acid decreases mTORC1 activity in the absence of insulin and under high-glucose conditions in ex vivo rat hippocampus and in tuberous sclerosis complex (TSC) patient-derived astrocytes. Our data therefore indicate that dietary decanoic acid may provide a new therapeutic approach to down-regulate mTORC1 signaling.
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18
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Buckley CM, Pots H, Gueho A, Vines JH, Munn CJ, Phillips BA, Gilsbach B, Traynor D, Nikolaev A, Soldati T, Parnell AJ, Kortholt A, King JS. Coordinated Ras and Rac Activity Shapes Macropinocytic Cups and Enables Phagocytosis of Geometrically Diverse Bacteria. Curr Biol 2020; 30:2912-2926.e5. [PMID: 32531280 PMCID: PMC7416115 DOI: 10.1016/j.cub.2020.05.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/20/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022]
Abstract
Engulfment of extracellular material by phagocytosis or macropinocytosis depends on the ability of cells to generate specialized cup-shaped protrusions. To effectively capture and internalize their targets, these cups are organized into a ring or ruffle of actin-driven protrusion encircling a non-protrusive interior domain. These functional domains depend on the combined activities of multiple Ras and Rho family small GTPases, but how their activities are integrated and differentially regulated over space and time is unknown. Here, we show that the amoeba Dictyostelium discoideum coordinates Ras and Rac activity using the multidomain protein RGBARG (RCC1, RhoGEF, BAR, and RasGAP-containing protein). We find RGBARG uses a tripartite mechanism of Ras, Rac, and phospholipid interactions to localize at the protruding edge and interface with the interior of both macropinocytic and phagocytic cups. There, we propose RGBARG shapes the protrusion by expanding Rac activation at the rim while suppressing expansion of the active Ras interior domain. Consequently, cells lacking RGBARG form enlarged, flat interior domains unable to generate large macropinosomes. During phagocytosis, we find that disruption of RGBARG causes a geometry-specific defect in engulfing rod-shaped bacteria and ellipsoidal beads. This demonstrates the importance of coordinating small GTPase activities during engulfment of more complex shapes and thus the full physiological range of microbes, and how this is achieved in a model professional phagocyte. We identify a new regulator that shapes macropinocytic and phagocytic cups Shaping protrusions into cups requires differential regulation of Ras and Rac Cups are organized by integrating interactions with phospholipids and multiple GTPases Defective cup formation causes a target shape-specific defect in phagocytosis
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Affiliation(s)
- Catherine M Buckley
- Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TT, UK
| | - Henderikus Pots
- Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, Netherlands
| | - Aurelie Gueho
- Department of Biochemistry, Faculty of Sciences, Sciences II, University of Geneva, CH-1211-Geneva-4, Switzerland
| | - James H Vines
- Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TT, UK
| | - Christopher J Munn
- Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TT, UK
| | - Ben A Phillips
- Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TT, UK
| | - Bernd Gilsbach
- German Centre for Neurodegenerative Diseases, Tübingen 72076, Germany
| | - David Traynor
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Anton Nikolaev
- Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TT, UK
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Sciences, Sciences II, University of Geneva, CH-1211-Geneva-4, Switzerland
| | - Andrew J Parnell
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, Netherlands
| | - Jason S King
- Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TT, UK.
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19
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Nichols JME, Antolović V, Reich JD, Brameyer S, Paschke P, Chubb JR. Cell and molecular transitions during efficient dedifferentiation. eLife 2020; 9:e55435. [PMID: 32255425 PMCID: PMC7190356 DOI: 10.7554/elife.55435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/06/2020] [Indexed: 01/16/2023] Open
Abstract
Dedifferentiation is a critical response to tissue damage, yet is not well understood, even at a basic phenomenological level. Developing Dictyostelium cells undergo highly efficient dedifferentiation, completed by most cells within 24 hr. We use this rapid response to investigate the control features of dedifferentiation, combining single cell imaging with high temporal resolution transcriptomics. Gene expression during dedifferentiation was predominantly a simple reversal of developmental changes, with expression changes not following this pattern primarily associated with ribosome biogenesis. Mutation of genes induced early in dedifferentiation did not strongly perturb the reversal of development. This apparent robustness may arise from adaptability of cells: the relative temporal ordering of cell and molecular events was not absolute, suggesting cell programmes reach the same end using different mechanisms. In addition, although cells start from different fates, they rapidly converged on a single expression trajectory. These regulatory features may contribute to dedifferentiation responses during regeneration.
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Affiliation(s)
- John ME Nichols
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Vlatka Antolović
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Jacob D Reich
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | | | - Peggy Paschke
- CRUK Beatson Institute, Garscube Estate, Switchback Road, BearsdenGlasgowUnited Kingdom
| | - Jonathan R Chubb
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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20
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Fabrice TN, Fiedler T, Studer V, Vinet A, Brogna F, Schmidt A, Pieters J. Interactome and F-Actin Interaction Analysis of Dictyostelium discoideum Coronin A. Int J Mol Sci 2020; 21:E1469. [PMID: 32098122 PMCID: PMC7073074 DOI: 10.3390/ijms21041469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/17/2022] Open
Abstract
Coronin proteins are evolutionary conserved WD repeat containing proteins that have been proposed to carry out different functions. In Dictyostelium, the short coronin isoform, coronin A, has been implicated in cytoskeletal reorganization, chemotaxis, phagocytosis and the initiation of multicellular development. Generally thought of as modulators of F-actin, coronin A and its mammalian homologs have also been shown to mediate cellular processes in an F-actin-independent manner. Therefore, it remains unclear whether or not coronin A carries out its functions through its capacity to interact with F-actin. Moreover, the interacting partners of coronin A are not known. Here, we analyzed the interactome of coronin A as well as its interaction with F-actin within cells and in vitro. Interactome analysis showed the association with a diverse set of interaction partners, including fimbrin, talin and myosin subunits, with only a transient interaction with the minor actin10 isoform, but not the major form of actin, actin8, which was consistent with the absence of a coronin A-actin interaction as analyzed by co-sedimentation from cells and lysates. In vitro, however, purified coronin A co-precipitated with rabbit muscle F-actin in a coiled-coil-dependent manner. Our results suggest that an in vitro interaction of coronin A and rabbit muscle actin may not reflect the cellular interaction state of coronin A with actin, and that coronin A interacts with diverse proteins in a time-dependent manner.
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Affiliation(s)
| | | | | | | | | | | | - Jean Pieters
- Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (T.N.F.); (T.F.); (V.S.); (A.V.); (F.B.); (A.S.)
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21
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Nichols JME, Paschke P, Peak-Chew S, Williams TD, Tweedy L, Skehel M, Stephens E, Chubb JR, Kay RR. The Atypical MAP Kinase ErkB Transmits Distinct Chemotactic Signals through a Core Signaling Module. Dev Cell 2019; 48:491-505.e9. [PMID: 30612939 PMCID: PMC6397043 DOI: 10.1016/j.devcel.2018.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/15/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022]
Abstract
Signaling from chemoattractant receptors activates the cytoskeleton of crawling cells for chemotaxis. We show using phosphoproteomics that different chemoattractants cause phosphorylation of the same core set of around 80 proteins in Dictyostelium cells. Strikingly, the majority of these are phosphorylated at an [S/T]PR motif by the atypical MAP kinase ErkB. Unlike most chemotactic responses, ErkB phosphorylations are persistent and do not adapt to sustained stimulation with chemoattractant. ErkB integrates dynamic autophosphorylation with chemotactic signaling through G-protein-coupled receptors. Downstream, our phosphoproteomics data define a broad panel of regulators of chemotaxis. Surprisingly, targets are almost exclusively other signaling proteins, rather than cytoskeletal components, revealing ErkB as a regulator of regulators rather than acting directly on the motility machinery. ErkB null cells migrate slowly and orientate poorly over broad dynamic ranges of chemoattractant. Our data indicate a central role for ErkB and its substrates in directing chemotaxis.
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Affiliation(s)
- John M E Nichols
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Peggy Paschke
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Cancer Research UK (CRUK) Beatson Institute, University of Glasgow, Bearsden, Glasgow G61 1BD, UK.
| | - Sew Peak-Chew
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas D Williams
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Luke Tweedy
- Cancer Research UK (CRUK) Beatson Institute, University of Glasgow, Bearsden, Glasgow G61 1BD, UK
| | - Mark Skehel
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elaine Stephens
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Pfizer Inc, 1 Burtt Road, Andover, MA 01810, USA
| | - Jonathan R Chubb
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower St., London WC1E 6BT, UK
| | - Robert R Kay
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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