1
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DeMarco AG, Dibble MG, Hall MC. Inducible degradation-coupled phosphoproteomics identifies PP2A Rts1 as a novel eisosome regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563668. [PMID: 37961087 PMCID: PMC10634780 DOI: 10.1101/2023.10.24.563668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Reversible protein phosphorylation is an abundant post-translational modification dynamically regulated by opposing kinases and phosphatases. Protein phosphorylation has been extensively studied in cell division, where waves of cyclin-dependent kinase activity, peaking in mitosis, drive the sequential stages of the cell cycle. Here we developed and employed a strategy to specifically probe kinase or phosphatase substrates at desired times or experimental conditions in the model organism Saccharomyces cerevisiae. We combined auxin-inducible degradation (AID) with mass spectrometry-based phosphoproteomics, which allowed us to arrest physiologically normal cultures in mitosis prior to rapid phosphatase degradation and phosphoproteome analysis. Our results revealed that protein phosphatase 2A coupled with its B56 regulatory subunit, Rts1 (PP2ARts1), is involved in dephosphorylation of numerous proteins in mitosis, highlighting the need for phosphatases to selectively maintain certain proteins in a hypophosphorylated state in the face of high mitotic kinase activity. Unexpectedly, we observed elevated phosphorylation at many sites on several subunits of the fungal eisosome complex following rapid Rts1 degradation. Eisosomes are dynamic polymeric assemblies that create furrows in the plasma membrane important in regulating nutrient import, lipid metabolism, and stress responses, among other things. We found that PP2ARts1-mediated dephosphorylation of eisosomes promotes their plasma membrane association and we provide evidence that this regulation impacts eisosome roles in metabolic homeostasis. The combination of rapid, inducible protein degradation with proteomic profiling offers several advantages over common protein disruption methods for characterizing substrates of regulatory enzymes involved in dynamic biological processes.
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Affiliation(s)
- Andrew G. DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
| | - Marcella G. Dibble
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
- Institute for Cancer Research, Purdue University, West Lafayette, IN, 47907
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2
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Kollath-Leiß K, Yang Q, Winter H, Kempken F. Complementation of an Eisosomal Yeast pil1 Mutant and Characteristics of Eisosomal Distribution in Hyphae of Neurospora crassa Germinating from Two Different Spore Types. J Fungi (Basel) 2023; 9:jof9020147. [PMID: 36836262 PMCID: PMC9964885 DOI: 10.3390/jof9020147] [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: 08/31/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/24/2023] Open
Abstract
Eisosomes are plasma-membrane-associated protein complexes of fungi and algae involved in various cellular processes. The eisosome composition of the budding yeast is well described, but there is a limited number of studies only about eisosomes in filamentous fungi. In our study, we examined the Neurospora crassa LSP-1 protein (NcLSP1). By complementing a Saccharomyces cerevisiae Δpil1 mutant strain with nclsp1, we show the functional homology of the NcLSP1 to yeast PIL1 rather than to yeast LSP1 and hereby confirm that the NcLSP1 is an eisosomal core protein and suitable eisosomal marker. The subsequent cloning and expression of the nclsp1::trfp reporter gene construct in N. crassa allowed for a systematical investigation of the characteristics of eisosome formation and distribution in different developmental stages. In N. crassa, the hyphae germinating from sexual and asexual spores are morphologically identical and have been historically recognized as the same type of cells. Here, we demonstrate the structural differences on the cellular level between the hyphae germinating from sexual and asexual spores.
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3
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Feng MW, Delneri D, Millar CB, O'Keefe RT. Eisosome disruption by noncoding RNA deletion increases protein secretion in yeast. PNAS NEXUS 2022; 1:pgac241. [PMID: 36712349 PMCID: PMC9802208 DOI: 10.1093/pnasnexus/pgac241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Noncoding RNAs (ncRNAs) regulate many aspects of gene expression. We investigated how ncRNAs affected protein secretion in yeast by large-scale screening for improved endogenous invertase secretion in ncRNA deletion strains with deletion of stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs), tRNAs, or snRNAs. We identified three candidate ncRNAs, SUT418, SUT390, and SUT125, that improved endogenous invertase secretion when deleted. As SUTs can affect expression of nearby genes, we quantified adjacent gene transcription and found that the PIL1 gene was down-regulated in the SUT125 deletion strain. Pil1 is a core component of eisosomes, nonmobile invaginations found throughout the plasma membrane. PIL1 knockout alone, or in combination with eisosome components LSP1 or SUR7, resulted in further increased secretion of invertase. Secretion of heterologous GFP was also increased upon PIL1 deletion, but this increase was signal sequence dependent. To reveal the potential for increased biopharmaceutical production, secretion of monoclonal antibody Pexelizumab scFv peptide was increased by PIL1 deletion. Global analysis of secreted proteins revealed that approximately 20% of secreted proteins, especially serine-enriched secreted proteins, including invertase, were increased upon eisosome disruption. Eisosomes are enriched with APC transporters and sphingolipids, which are essential components for secretory vesicle formation and protein sorting. Sphingolipid and serine biosynthesis pathways were up-regulated upon PIL1 deletion. We propose that increased secretion of endogenous and heterologous proteins upon PIL1 deletion resulted from sphingolipid redistribution in the plasma membrane and up-regulated sphingolipid biosynthesis. Overall, a new pathway to improve protein secretion in yeast via eisosome disruption has been identified.
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Affiliation(s)
- Matthew Wenjie Feng
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Daniela Delneri
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK,Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, 131 Princess street, Manchester, M1 7DN, UK
| | - Catherine B Millar
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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4
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Correa Tedesco FG, Aguilar PS, Estrada L. Correlation analyses reveal differential diffusion behavior of eisosomal proteins between mother and daughter cells. Methods Appl Fluoresc 2022; 10. [PMID: 36067776 DOI: 10.1088/2050-6120/ac8fe1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/05/2022] [Indexed: 11/12/2022]
Abstract
Eisosomes are nanoscale plasma membrane domains shaped as furrow-like invaginations. In Saccharomyces cerevisiae these relatively immobile and uniform structures are mainly composed of two cytoplasmic proteins Pil1 and Lsp1. The present work uses fluctuation of fluorescence signals and analytical methods to determine Pil1 and Lsp1 dynamics at different subcellular locations. Using scanning techniques and autocorrelation analysis we determine that the cytoplasmic pools of Pil1 and Lsp1 behave mainly by passive diffusion. Single-point FCS experiments performed at several subcellular locations reveal that Pil1 mobility is faster in daughter cells. Furthermore, pair correlation function analysis indicates a rapid dynamic of Pil1 near the plasma membrane of growing yeast buds, where the membrane is expected to be actively assembling eisosomes.
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Affiliation(s)
- Francisco G Correa Tedesco
- Laboratorio de Biología Celular de Membranas, Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina, Campus Miguelete, Buenos Aires, 1650, ARGENTINA
| | - Pablo Sebastian Aguilar
- Laboratorio de Biología Celular de Membranas, Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina, Campus Miguelete, Buenos Aires, 1650, ARGENTINA
| | - Laura Estrada
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, UBA,, Intendente Guiraldes 2160, Pabellon 1, CABA, Buenos Aires, 1428, ARGENTINA
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5
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Jhaveri A, Maisuria D, Varga M, Mohammadyani D, Johnson ME. Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations. J Phys Chem B 2021; 125:3739-3751. [PMID: 33826319 DOI: 10.1021/acs.jpcb.0c10992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins with BAR domains function to bind to and remodel biological membranes, where the dimerization of BAR domains is a key step in this function. These domains can dimerize in solution or after localizing to the membrane surface. Here, we characterize the binding thermodynamics of homodimerization between the LSP1 BAR domain proteins in solution, using molecular dynamics (MD) simulations. By combining the MARTINI coarse-grained protein models with enhanced sampling through metadynamics, we construct a two-dimensional free energy surface quantifying the bound versus unbound ensembles as a function of two distance variables. With this methodology, our simulations can simultaneously characterize the structures and relative stabilities of a range of sampled dimers, portraying a heterogeneous and extraordinarily stable bound ensemble, where the proper crystal structure dimer is the most stable in a 100 mM NaCl solution. Nonspecific dimers that are sampled involve contacts that are consistent with experimental structures of higher-order oligomers formed by the LSP1 BAR domain. Because the BAR dimers and oligomers can assemble on membranes, we characterize the relative alignment of the known membrane binding patches, finding that only the specific dimer is aligned to form strong interactions with the membrane. Hence, we would predict a strong selection of the specific dimer in binding to or assembling when on the membrane. Establishing the pairwise stabilities of homodimer contacts is difficult experimentally when the proteins form stable oligomers, but through the method used here, we can isolate these contacts, providing a foundation to study the same interactions on the membrane.
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Affiliation(s)
- Adip Jhaveri
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
| | - Dhruw Maisuria
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
| | - Matthew Varga
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
| | - Dariush Mohammadyani
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
| | - Margaret E Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
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6
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Tulha J, Amorim-Rodrigues M, Esquembre LA, Rauch S, Tamás MJ, Lucas C. Physical, genetic and functional interactions between the eisosome protein Pil1 and the MBOAT O-acyltransferase Gup1. FEMS Yeast Res 2020; 21:6045508. [PMID: 33355361 DOI: 10.1093/femsyr/foaa070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The Saccharomyces cerevisiae MBOAT O-acyltransferase Gup1 is involved in many processes, including cell wall and membrane composition and integrity, and acetic acid-induced cell death. Gup1 was previously shown to interact physically with the mitochondrial membrane VDAC (Voltage-Dependent Anion Channel) protein Por1 and the ammonium transceptor Mep2. By co-immunoprecipitation, the eisosome core component Pil1 was identified as a novel physical interaction partner of Gup1. The expression of PIL1 and Pil1 protein levels were found to be unaffected by GUP1 deletion. In ∆gup1 cells, Pil1 was distributed in dots (likely representing eisosomes) in the membrane, identically to wt cells. However, ∆gup1 cells presented 50% less Pil1-GFP dots/eisosomes, suggesting that Gup1 is important for eisosome formation. The two proteins also interact genetically in the maintenance of cell wall integrity, and during arsenite and acetic acid exposure. We show that Δgup1 Δpil1 cells take up more arsenite than wt and are extremely sensitive to arsenite and to acetic acid treatments. The latter causes a severe apoptotic wt-like cell death phenotype, epistatically reverting the ∆gup1 necrotic type of death. Gup1 and Pil1 are thus physically, genetically and functionally connected.
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Affiliation(s)
- Joana Tulha
- Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar 4710-057 Braga, Portugal
| | - Mariana Amorim-Rodrigues
- Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar 4710-057 Braga, Portugal
| | - Lidia Alejo Esquembre
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemihuset 412 96 Gothenburg, Sweden
| | - Sebastien Rauch
- Water Environment Technology, Department of Architecture and Civil and Environmental Engineering, Chalmers University of Technology, S-412 96 Gothenburg, Sweden
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemihuset 412 96 Gothenburg, Sweden
| | - Cândida Lucas
- Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar 4710-057 Braga, Portugal
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7
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Plasma Membrane MCC/Eisosome Domains Promote Stress Resistance in Fungi. Microbiol Mol Biol Rev 2020; 84:84/4/e00063-19. [PMID: 32938742 DOI: 10.1128/mmbr.00063-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is growing appreciation that the plasma membrane orchestrates a diverse array of functions by segregating different activities into specialized domains that vary in size, stability, and composition. Studies with the budding yeast Saccharomyces cerevisiae have identified a novel type of plasma membrane domain known as the MCC (membrane compartment of Can1)/eisosomes that correspond to stable furrows in the plasma membrane. MCC/eisosomes maintain proteins at the cell surface, such as nutrient transporters like the Can1 arginine symporter, by protecting them from endocytosis and degradation. Recent studies from several fungal species are now revealing new functional roles for MCC/eisosomes that enable cells to respond to a wide range of stressors, including changes in membrane tension, nutrition, cell wall integrity, oxidation, and copper toxicity. The different MCC/eisosome functions are often intertwined through the roles of these domains in lipid homeostasis, which is important for proper plasma membrane architecture and cell signaling. Therefore, this review will emphasize the emerging models that explain how MCC/eisosomes act as hubs to coordinate cellular responses to stress. The importance of MCC/eisosomes is underscored by their roles in virulence for fungal pathogens of plants, animals, and humans, which also highlights the potential of these domains to act as novel therapeutic targets.
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8
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Athanasopoulos A, André B, Sophianopoulou V, Gournas C. Fungal plasma membrane domains. FEMS Microbiol Rev 2020; 43:642-673. [PMID: 31504467 DOI: 10.1093/femsre/fuz022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/25/2019] [Indexed: 12/11/2022] Open
Abstract
The plasma membrane (PM) performs a plethora of physiological processes, the coordination of which requires spatial and temporal organization into specialized domains of different sizes, stability, protein/lipid composition and overall architecture. Compartmentalization of the PM has been particularly well studied in the yeast Saccharomyces cerevisiae, where five non-overlapping domains have been described: The Membrane Compartments containing the arginine permease Can1 (MCC), the H+-ATPase Pma1 (MCP), the TORC2 kinase (MCT), the sterol transporters Ltc3/4 (MCL), and the cell wall stress mechanosensor Wsc1 (MCW). Additional cortical foci at the fungal PM are the sites where clathrin-dependent endocytosis occurs, the sites where the external pH sensing complex PAL/Rim localizes, and sterol-rich domains found in apically grown regions of fungal membranes. In this review, we summarize knowledge from several fungal species regarding the organization of the lateral PM segregation. We discuss the mechanisms of formation of these domains, and the mechanisms of partitioning of proteins there. Finally, we discuss the physiological roles of the best-known membrane compartments, including the regulation of membrane and cell wall homeostasis, apical growth of fungal cells and the newly emerging role of MCCs as starvation-protective membrane domains.
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Affiliation(s)
- Alexandros Athanasopoulos
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research 'Demokritos,' Patr. Grigoriou E & 27 Neapoleos St. 15341, Agia Paraskevi, Greece
| | - Bruno André
- Molecular Physiology of the Cell laboratory, Université Libre de Bruxelles (ULB), Institut de Biologie et de Médecine Moléculaires, rue des Pr Jeener et Brachet 12, 6041, Gosselies, Belgium
| | - Vicky Sophianopoulou
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research 'Demokritos,' Patr. Grigoriou E & 27 Neapoleos St. 15341, Agia Paraskevi, Greece
| | - Christos Gournas
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research 'Demokritos,' Patr. Grigoriou E & 27 Neapoleos St. 15341, Agia Paraskevi, Greece
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9
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Amen T, Kaganovich D. Stress granules sense metabolic stress at the plasma membrane and potentiate recovery by storing active Pkc1. Sci Signal 2020; 13:13/623/eaaz6339. [DOI: 10.1126/scisignal.aaz6339] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As the physical barrier between the cell and the outside environment, the plasma membrane is well-positioned to be the first responder to stress. The membrane is also highly vulnerable to many types of perturbation, including heat, force, osmotic pressure, lipid shortage, and starvation. To determine whether the structural changes in the plasma membrane of Saccharomyces cerevisiae brought about by nutrient stress can be communicated to regulatory networks within the cell, we identified proteins that interact with stress granules (SGs), subcellular structures composed of proteins, and nontranslated RNAs that form when cells are stressed. We found that SG proteins interacted with components of eisosomes, which are subcortical membrane structures with a distinct lipid and protein composition. In response to starvation-triggered phosphorylation of eisosome proteins, eisosomes clustered and recruited SG components, including active Pkc1. The absence of eisosomes impaired SG formation, resulting in delayed recovery from nutrient deprivation. Thus, eisosome clustering is an example of interdomain communication in response to stress and identifies a previously unknown mechanism of SG regulation.
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Affiliation(s)
- Triana Amen
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Daniel Kaganovich
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- 1Base Pharmaceuticals, Boston, MA 02129, USA
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10
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Cutrale F, Rodriguez D, Hortigüela V, Chiu CL, Otterstrom J, Mieruszynski S, Seriola A, Larrañaga E, Raya A, Lakadamyali M, Fraser SE, Martinez E, Ojosnegros S. Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. Nat Protoc 2019; 14:616-638. [DOI: 10.1038/s41596-018-0111-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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Zamai M, Trullo A, Giordano M, Corti V, Arza Cuesta E, Francavilla C, Cavallaro U, Caiolfa VR. Number and brightness analysis reveals that NCAM and FGF2 elicit different assembly and dynamics of FGFR1 in live cells. J Cell Sci 2019; 132:jcs.220624. [PMID: 30478195 DOI: 10.1242/jcs.220624] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/15/2018] [Indexed: 12/31/2022] Open
Abstract
Both fibroblast growth factor-2 (FGF2) and neural cell adhesion molecule (NCAM) trigger FGF receptor 1 (FGFR1) signaling; however, they induce remarkably distinct receptor trafficking and cellular responses. The molecular basis of such a dichotomy and the role of distinct types of ligand-receptor interaction remain elusive. Number of molecules and brightness (N&B) analysis revealed that FGF2 and NCAM promote different FGFR1 assembly and dynamics at the plasma membrane. NCAM stimulation elicits long-lasting cycles of short-lived FGFR1 monomers and multimers, a behavior that might reflect a rapid FGFR1 internalization and recycling. FGF2, instead, induces stable dimerization at the dose that stimulates cell proliferation. Reducing the occupancy of FGFR1 in response to low FGF2 doses causes a switch towards cyclically exposed and unstable receptor dimers, consistently with previously reported biphasic response to FGF2 and with the divergent signaling elicited by different ligand concentrations. Similar instability was observed upon altering the endocytic pathway. Thus, FGF2 and NCAM induce differential FGFR1 clustering at the cell surface, which might account for the distinct intracellular fate of the receptor and, hence, for the different signaling cascades and cellular responses.
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Affiliation(s)
- Moreno Zamai
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy.,Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Antonio Trullo
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy
| | - Marco Giordano
- Unit of Gynecological Oncology Research, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Valeria Corti
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy
| | - Elvira Arza Cuesta
- Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Chiara Francavilla
- Division of Molecular and Cellular Functions, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Ugo Cavallaro
- Unit of Gynecological Oncology Research, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Valeria R Caiolfa
- Centro di Imaging Sperimentale (CIS), Ospedale San Raffaele, IRCCS, Milan 20132, Italy .,Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
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12
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Bharat TAM, Hoffmann PC, Kukulski W. Correlative Microscopy of Vitreous Sections Provides Insights into BAR-Domain Organization In Situ. Structure 2018; 26:879-886.e3. [PMID: 29681471 PMCID: PMC5992340 DOI: 10.1016/j.str.2018.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/22/2018] [Accepted: 03/22/2018] [Indexed: 12/15/2022]
Abstract
Electron microscopy imaging of macromolecular complexes in their native cellular context is limited by the inherent difficulty to acquire high-resolution tomographic data from thick cells and to specifically identify elusive structures within crowded cellular environments. Here, we combined cryo-fluorescence microscopy with electron cryo-tomography of vitreous sections into a coherent correlative microscopy workflow, ideal for detection and structural analysis of elusive protein assemblies in situ. We used this workflow to address an open question on BAR-domain coating of yeast plasma membrane compartments known as eisosomes. BAR domains can sense or induce membrane curvature, and form scaffold-like membrane coats in vitro. Our results demonstrate that in cells, the BAR protein Pil1 localizes to eisosomes of varying membrane curvature. Sub-tomogram analysis revealed a dense protein coat on curved eisosomes, which was not present on shallow eisosomes, indicating that while BAR domains can assemble at shallow membranes in vivo, scaffold formation is tightly coupled to curvature generation. Cryo-fluorescence microscopy eases electron cryo-tomography of vitreous sections Elusive protein assemblies are localized in situ by correlative microscopy Yeast BAR-domain protein Pil1 binds to plasma membrane with varying curvature Scaffold-like coats are only seen when Pil1 is bound to high curvature membranes
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Affiliation(s)
- Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Central Oxford Structural and Molecular Imaging Centre, South Parks Road, Oxford OX1 3RE, UK; Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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13
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MCC/Eisosomes Regulate Cell Wall Synthesis and Stress Responses in Fungi. J Fungi (Basel) 2017; 3:jof3040061. [PMID: 29371577 PMCID: PMC5753163 DOI: 10.3390/jof3040061] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/26/2017] [Accepted: 10/31/2017] [Indexed: 12/20/2022] Open
Abstract
The fungal plasma membrane is critical for cell wall synthesis and other important processes including nutrient uptake, secretion, endocytosis, morphogenesis, and response to stress. To coordinate these diverse functions, the plasma membrane is organized into specialized compartments that vary in size, stability, and composition. One recently identified domain known as the Membrane Compartment of Can1 (MCC)/eisosome is distinctive in that it corresponds to a furrow-like invagination in the plasma membrane. MCC/eisosomes have been shown to be formed by the Bin/Amphiphysin/Rvs (BAR) domain proteins Lsp1 and Pil1 in a range of fungi. MCC/eisosome domains influence multiple cellular functions; but a very pronounced defect in cell wall synthesis has been observed for mutants with defects in MCC/eisosomes in some yeast species. For example, Candida albicans MCC/eisosome mutants display abnormal spatial regulation of cell wall synthesis, including large invaginations and altered chemical composition of the walls. Recent studies indicate that MCC/eisosomes affect cell wall synthesis in part by regulating the levels of the key regulatory lipid phosphatidylinositol 4,5-bisphosphate (PI4,5P2) in the plasma membrane. One general way MCC/eisosomes function is by acting as protected islands in the plasma membrane, since these domains are very stable. They also act as scaffolds to recruit >20 proteins. Genetic studies aimed at defining the function of the MCC/eisosome proteins have identified important roles in resistance to stress, such as resistance to oxidative stress mediated by the flavodoxin-like proteins Pst1, Pst2, Pst3 and Ycp4. Thus, MCC/eisosomes play multiple roles in plasma membrane organization that protect fungal cells from the environment.
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14
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Lacy MM, Baddeley D, Berro J. Single-molecule imaging of the BAR-domain protein Pil1p reveals filament-end dynamics. Mol Biol Cell 2017; 28:2251-2259. [PMID: 28659415 PMCID: PMC5555653 DOI: 10.1091/mbc.e17-04-0238] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/22/2017] [Indexed: 12/21/2022] Open
Abstract
Molecular assemblies can have highly heterogeneous dynamics within the cell, but the limitations of conventional fluorescence microscopy can mask nanometer-scale features. Here we adapt a single-molecule strategy to perform single-molecule recovery after photobleaching (SRAP) within dense macromolecular assemblies to reveal and characterize binding and unbinding dynamics within such assemblies. We applied this method to study the eisosome, a stable assembly of BAR-domain proteins on the cytoplasmic face of the plasma membrane in fungi. By fluorescently labeling only a small fraction of cellular Pil1p, the main eisosome BAR-domain protein in fission yeast, we visualized whole eisosomes and, after photobleaching, localized recruitment of new Pil1p molecules with ∼30-nm precision. Comparing our data to computer simulations, we show that Pil1p exchange occurs specifically at eisosome ends and not along their core, supporting a new model of the eisosome as a dynamic filament. This result is the first direct observation of any BAR-domain protein dynamics in vivo under physiological conditions consistent with the oligomeric filaments reported from in vitro experiments.
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Affiliation(s)
- Michael M Lacy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520.,Nanobiology Institute, Yale University, West Haven, CT 06516.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520
| | - David Baddeley
- Nanobiology Institute, Yale University, West Haven, CT 06516.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520.,Department of Cell Biology, Yale University, New Haven, CT 06520
| | - Julien Berro
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 .,Nanobiology Institute, Yale University, West Haven, CT 06516.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520
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15
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Zhang LB, Tang L, Ying SH, Feng MG. Two eisosome proteins play opposite roles in autophagic control and sustain cell integrity, function and pathogenicity in Beauveria bassiana. Environ Microbiol 2017; 19:2037-2052. [DOI: 10.1111/1462-2920.13727] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Long-Bin Zhang
- Institute of Microbiology, College of Life Sciences; Zhejiang University; Hangzhou Zhejiang 310058 People's Republic of China
| | - Li Tang
- Institute of Microbiology, College of Life Sciences; Zhejiang University; Hangzhou Zhejiang 310058 People's Republic of China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences; Zhejiang University; Hangzhou Zhejiang 310058 People's Republic of China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences; Zhejiang University; Hangzhou Zhejiang 310058 People's Republic of China
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16
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Pudake RN, Srivastava R, Mukherjee PK, Sharma A. Heat stress-induced activation of a Trichoderma harzianum PIL superfamily gene. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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New Insight Into the Roles of Membrane Microdomains in Physiological Activities of Fungal Cells. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:119-80. [PMID: 27241220 DOI: 10.1016/bs.ircmb.2016.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The organization of biological membranes into structurally and functionally distinct lateral microdomains is generally accepted. From bacteria to mammals, laterally compartmentalized membranes seem to be a vital attribute of life. The crucial fraction of our current knowledge about the membrane microdomains has been gained from studies on fungi. In this review we summarize the evidence of the microdomain organization of membranes from fungal cells, with accent on their enormous diversity in composition, temporal dynamics, modes of formation, and recognized engagement in the cell physiology. A special emphasis is laid on the fact that in addition to their other biological functions, membrane microdomains also mediate the communication among different membranes within a eukaryotic cell and coordinate their functions. Involvement of fungal membrane microdomains in stress sensing, regulation of lipid homeostasis, and cell differentiation is discussed more in detail.
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18
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Eisosome Ultrastructure and Evolution in Fungi, Microalgae, and Lichens. EUKARYOTIC CELL 2015; 14:1017-42. [PMID: 26253157 DOI: 10.1128/ec.00106-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/30/2015] [Indexed: 01/01/2023]
Abstract
Eisosomes are among the few remaining eukaryotic cellular differentations that lack a defined function(s). These trough-shaped invaginations of the plasma membrane have largely been studied in Saccharomyces cerevisiae, in which their associated proteins, including two BAR domain proteins, have been identified, and homologues have been found throughout the fungal radiation. Using quick-freeze deep-etch electron microscopy to generate high-resolution replicas of membrane fracture faces without the use of chemical fixation, we report that eisosomes are also present in a subset of red and green microalgae as well as in the cysts of the ciliate Euplotes. Eisosome assembly is closely correlated with both the presence and the nature of cell walls. Microalgal eisosomes vary extensively in topology and internal organization. Unlike fungi, their convex fracture faces can carry lineage-specific arrays of intramembranous particles, and their concave fracture faces usually display fine striations, also seen in fungi, that are pitched at lineage-specific angles and, in some cases, adopt a broad-banded patterning. The conserved genes that encode fungal eisosome-associated proteins are not found in sequenced algal genomes, but we identified genes encoding two algal lineage-specific families of predicted BAR domain proteins, called Green-BAR and Red-BAR, that are candidate eisosome organizers. We propose a model for eisosome formation wherein (i) positively charged recognition patches first establish contact with target membrane regions and (ii) a (partial) unwinding of the coiled-coil conformation of the BAR domains then allows interactions between the hydrophobic faces of their amphipathic helices and the lipid phase of the inner membrane leaflet, generating the striated patterns.
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