1
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Dai M, Liu X, Goldman GH, Lu L, Zhang S. The EH domain-containing protein, EdeA, is involved in endocytosis, cell wall integrity, and pathogenicity in Aspergillus fumigatus. mSphere 2024; 9:e0005724. [PMID: 38687129 PMCID: PMC11237632 DOI: 10.1128/msphere.00057-24] [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: 01/29/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
Endocytosis has been extensively studied in yeasts, where it plays crucial roles in growth, signaling regulation, and cell-surface receptor internalization. However, the biological functions of endocytosis in pathogenic filamentous fungi remain largely unexplored. In this study, we aimed to functionally characterize the roles of EdeA, an ortholog of the Saccharomyces cerevisiae endocytic protein Ede1, in Aspergillus fumigatus. EdeA was observed to be distributed as patches on the plasma membrane and concentrated in the subapical collar of hyphae, a localization characteristic of endocytic proteins. Loss of edeA caused defective hyphal polarity, reduced conidial production, and fewer sites of endocytosis initiations than that of the parental wild type. Notably, the edeA null mutant exhibited increased sensitivity to cell wall-disrupting agents, indicating a role for EdeA in maintaining cell wall integrity in A. fumigatus. This observation was further supported by the evidence showing that the thickness of the cell wall in the ΔedeA mutant increased, accompanied by abnormal activation of MpkA, a key component in the cell wall integrity pathway. Additionally, the ΔedeA mutant displayed increased pathogenicity in the Galleria mellonella wax moth infection model, possibly due to alterations in cell wall morphology. Site-directed mutagenesis identified the conserved residue E348 within the third EH (Eps15 homology) domain of EdeA as crucial for its subcellular localization and functions. In conclusion, our results highlight the involvement of EdeA in endocytosis, hyphal polarity, cell wall integrity, and pathogenicity in A. fumigatus. IMPORTANCE Aspergillus fumigatus is a significant human pathogenic fungus known to cause invasive aspergillosis, a disease with a high mortality rate. Understanding the basic principles of A. fumigatus pathogenicity is crucial for developing effective strategies against this pathogen. Previous research has underscored the importance of endocytosis in the infection capacity of pathogenic yeasts; however, its biological function in pathogenic mold remains largely unexplored. Our characterization of EdeA in A. fumigatus sheds light on the role of endocytosis in the development, stress response, and pathogenicity of pathogenic molds. These findings suggest that the components of the endocytosis process may serve as potential targets for antifungal therapy.
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Affiliation(s)
- Mengyao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xintian Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shizhu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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2
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Woodard TK, Rioux DJ, Prosser DC. Actin- and microtubule-based motors contribute to clathrin-independent endocytosis in yeast. Mol Biol Cell 2023; 34:ar117. [PMID: 37647159 PMCID: PMC10846617 DOI: 10.1091/mbc.e23-05-0164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023] Open
Abstract
Most eukaryotic cells utilize clathrin-mediated endocytosis as well as multiple clathrin-independent pathways to internalize proteins and membranes. Although clathrin-mediated endocytosis has been studied extensively and many machinery proteins have been identified, clathrin-independent pathways remain poorly characterized by comparison. We previously identified the first known yeast clathrin-independent endocytic pathway, which relies on the actin-modulating GTPase Rho1, the formin Bni1 and unbranched actin filaments, but does not require the clathrin coat or core clathrin machinery proteins. In this study, we sought to better understand clathrin-independent endocytosis in yeast by exploring the role of myosins as actin-based motors, because actin is required for endocytosis in yeast. We find that Myo2, which transports secretory vesicles, organelles and microtubules along actin cables to sites of polarized growth, participates in clathrin-independent endocytosis. Unexpectedly, the ability of Myo2 to transport microtubule plus ends to the cell cortex appears to be required for its role in clathrin-independent endocytosis. In addition, dynein, dynactin, and proteins involved in cortical microtubule capture are also required. Thus, our results suggest that interplay between actin and microtubules contributes to clathrin-independent internalization in yeast.
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Affiliation(s)
| | - Daniel J. Rioux
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284
- Life Sciences, Virginia Commonwealth University, Richmond, VA 23284
| | - Derek C. Prosser
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284
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3
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Prischich D, Camarero N, Encinar del Dedo J, Cambra-Pellejà M, Prat J, Nevola L, Martín-Quirós A, Rebollo E, Pastor L, Giralt E, Geli MI, Gorostiza P. Light-dependent inhibition of clathrin-mediated endocytosis in yeast unveils conserved functions of the AP2 complex. iScience 2023; 26:107899. [PMID: 37766990 PMCID: PMC10520943 DOI: 10.1016/j.isci.2023.107899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is an essential cellular process, conserved among eukaryotes. Yeast constitutes a powerful genetic model to dissect the complex endocytic machinery, yet there is a lack of specific pharmacological agents to interfere with CME in these organisms. TL2 is a light-regulated peptide inhibitor targeting the AP2-β-adaptin/β-arrestin interaction and that can photocontrol CME with high spatiotemporal precision in mammalian cells. Here, we study endocytic protein dynamics by live-cell imaging of the fluorescently tagged coat-associated protein Sla1-GFP, demonstrating that TL2 retains its inhibitory activity in S. cerevisiae spheroplasts. This is despite the β-adaptin/β-arrestin interaction not being conserved in yeast. Our data indicate that the AP2 α-adaptin is the functional target of activated TL2. We identified as interacting partners for the α-appendage, the Eps15 and epsin homologues Ede1 and Ent1. This demonstrates that endocytic cargo loading and sensing can be executed by conserved molecular interfaces, regardless of the proteins involved.
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Affiliation(s)
- Davia Prischich
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Núria Camarero
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Javier Encinar del Dedo
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Maria Cambra-Pellejà
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Judit Prat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrés Martín-Quirós
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elena Rebollo
- Molecular Imaging Platform, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Laura Pastor
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Inorganic and Organic Chemistry, University of Barcelona (UB), Barcelona, Spain
| | - María Isabel Geli
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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4
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Kozak M, Kaksonen M. Condensation of Ede1 promotes the initiation of endocytosis. eLife 2022; 11:72865. [PMID: 35412456 PMCID: PMC9064294 DOI: 10.7554/elife.72865] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 04/01/2022] [Indexed: 11/27/2022] Open
Abstract
Clathrin-mediated endocytosis is initiated by a network of weakly interacting proteins through a poorly understood mechanism. Ede1, the yeast homolog of mammalian Eps15, is an early-arriving endocytic protein and a key initiation factor. In the absence of Ede1, most other early endocytic proteins lose their punctate localization and endocytic uptake is decreased. We show that in yeast cells, cytosolic concentration of Ede1 is buffered at a critical level. Excess amounts of Ede1 form large condensates which recruit other endocytic proteins and exhibit properties of phase-separated liquid droplets. We demonstrate that the central region of Ede1, containing a coiled-coil and a prion-like region, is essential for both the condensate formation and the function of Ede1 in endocytosis. The functionality of Ede1 mutants lacking the central region can be partially rescued by an insertion of heterologous prion-like domains. Conversely, fusion of a heterologous lipid-binding domain with the central region of Ede1 can promote clustering into stable plasma membrane domains. We propose that the ability of Ede1 to form condensed networks supports the clustering of early endocytic proteins and promotes the initiation of endocytosis.
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Affiliation(s)
- Mateusz Kozak
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Marko Kaksonen
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
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5
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Pashkova N, Gakhar L, Yu L, Schnicker NJ, Minard AY, Winistorfer S, Johnson IE, Piper RC. ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals. eLife 2021; 10:72583. [PMID: 34821552 PMCID: PMC8648300 DOI: 10.7554/elife.72583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Attachment of ubiquitin (Ub) to cell surface proteins serves as a signal for internalization via clathrin-mediated endocytosis (CME). How ubiquitinated membrane proteins engage the internalization apparatus remains unclear. The internalization apparatus contains proteins such as Epsin and Eps15, which bind Ub, potentially acting as adaptors for Ub-based internalization signals. Here, we show that additional components of the endocytic machinery including CALM, HIP1R, and Sla2 bind Ub via their N-terminal ANTH domain, a domain belonging to the superfamily of ENTH and VHS domains. Structural studies revealed that Ub binds with µM affinity to a unique C-terminal region within the ANTH domain not found in ENTH domains. Functional studies showed that combined loss of Ub-binding by ANTH-domain proteins and other Ub-binding domains within the yeast internalization apparatus caused defects in the Ub-dependent internalization of the GPCR Ste2 that was engineered to rely exclusively on Ub as an internalization signal. In contrast, these mutations had no effect on the internalization of Ste2 engineered to use an alternate Ub-independent internalization signal. These studies define new components of the internalization machinery that work collectively with Epsin and Eps15 to specify recognition of Ub as an internalization signal.
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Affiliation(s)
- Natalya Pashkova
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Lokesh Gakhar
- Carver College of Medicine Protein Crystallography Core, University of Iowa, Iowa City, United States.,Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, United States
| | - Liping Yu
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, United States.,Carver College of Medicine NMR Core, University of Iowa, Iowa City, United States
| | - Nicholas J Schnicker
- Carver College of Medicine Protein Crystallography Core, University of Iowa, Iowa City, United States
| | - Annabel Y Minard
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Stanley Winistorfer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Ivan E Johnson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
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6
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Laidlaw KME, Bisinski DD, Shashkova S, Paine KM, Veillon MA, Leake MC, MacDonald C. A glucose-starvation response governs endocytic trafficking and eisosomal retention of surface cargoes in budding yeast. J Cell Sci 2021; 134:224110. [PMID: 33443082 PMCID: PMC7860119 DOI: 10.1242/jcs.257733] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic cells adapt their metabolism to the extracellular environment. Downregulation of surface cargo proteins in response to nutrient stress reduces the burden of anabolic processes whilst elevating catabolic production in the lysosome. We show that glucose starvation in yeast triggers a transcriptional response that increases internalisation from the plasma membrane. Nuclear export of the Mig1 transcriptional repressor in response to glucose starvation increases levels of the Yap1801 and Yap1802 clathrin adaptors, which is sufficient to increase cargo internalisation. Beyond this, we show that glucose starvation results in Mig1-independent transcriptional upregulation of various eisosomal factors. These factors serve to sequester a portion of nutrient transporters at existing eisosomes, through the presence of Ygr130c and biochemical and biophysical changes in Pil1, allowing cells to persist throughout the starvation period and maximise nutrient uptake upon return to replete conditions. This provides a physiological benefit for cells to rapidly recover from glucose starvation. Collectively, this remodelling of the surface protein landscape during glucose starvation calibrates metabolism to available nutrients.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kamilla M E Laidlaw
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Daniel D Bisinski
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Sviatlana Shashkova
- York Biomedical Research Institute and Department of Biology, University of York, York, UK.,Department of Physics, University of York, York YO10 5DD, UK
| | - Katherine M Paine
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Malaury A Veillon
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Mark C Leake
- York Biomedical Research Institute and Department of Biology, University of York, York, UK.,Department of Physics, University of York, York YO10 5DD, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
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7
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Sen A, Hsieh WC, Hanna CB, Hsu CC, Pearson M, Tao WA, Aguilar RC. The Na + pump Ena1 is a yeast epsin-specific cargo requiring its ubiquitylation and phosphorylation sites for internalization. J Cell Sci 2020; 133:jcs245415. [PMID: 32694166 DOI: 10.1242/jcs.245415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/14/2020] [Indexed: 12/16/2022] Open
Abstract
It is well known that in addition to its classical role in protein turnover, ubiquitylation is required for a variety of membrane protein sorting events. However, and despite substantial progress in the field, a long-standing question remains: given that all ubiquitin units are identical, how do different elements of the sorting machinery recognize their specific cargoes? Our results indicate that the yeast Na+ pump Ena1 is an epsin (Ent1 and Ent2 in yeast)-specific cargo and that its internalization requires K1090, which likely undergoes Art3-dependent ubiquitylation. In addition, an Ena1 serine and threonine (ST)-rich patch, proposed to be targeted for phosphorylation by casein kinases, was also required for its uptake. Interestingly, our data suggest that this phosphorylation was not needed for cargo ubiquitylation. Furthermore, epsin-mediated internalization of Ena1 required a specific spatial organization of the ST patch with respect to K1090 within the cytoplasmic tail of the pump. We hypothesize that ubiquitylation and phosphorylation of Ena1 are required for epsin-mediated internalization.
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Affiliation(s)
- Arpita Sen
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Wen-Chieh Hsieh
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Claudia B Hanna
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - McKeith Pearson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - R Claudio Aguilar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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8
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Hoban K, Lux SY, Poprawski J, Zhang Y, Shepherdson J, Castiñeira PG, Pesari S, Yao T, Prosser DC, Norris C, Wendland B. ESCRT-dependent protein sorting is required for the viability of yeast clathrin-mediated endocytosis mutants. Traffic 2020; 21:430-450. [PMID: 32255230 DOI: 10.1111/tra.12731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022]
Abstract
Endocytosis regulates many processes, including signaling pathways, nutrient uptake, and protein turnover. During clathrin-mediated endocytosis (CME), adaptors bind to cytoplasmic regions of transmembrane cargo proteins, and many endocytic adaptors are also directly involved in the recruitment of clathrin. This clathrin-associated sorting protein family includes the yeast epsins, Ent1/2, and AP180/PICALM homologs, Yap1801/2. Mutant strains lacking these four adaptors, but expressing an epsin N-terminal homology (ENTH) domain necessary for viability (4Δ+ENTH), exhibit endocytic defects, such as cargo accumulation at the plasma membrane (PM). This CME-deficient strain provides a sensitized background ideal for revealing cellular components that interact with clathrin adaptors. We performed a mutagenic screen to identify alleles that are lethal in 4Δ+ENTH cells using a colony-sectoring reporter assay. After isolating candidate synthetic lethal genes by complementation, we confirmed that mutations in VPS4 led to inviability of a 4Δ+ENTH strain. Vps4 mediates the final step of endosomal sorting complex required for transport (ESCRT)-dependent trafficking, and we found that multiple ESCRTs are also essential in 4Δ+ENTH cells, including Snf7, Snf8 and Vps36. Deletion of VPS4 from an end3Δ strain, another CME mutant, similarly resulted in inviability, and upregulation of a clathrin-independent endocytosis pathway rescued 4Δ+ENTH vps4Δ cells. Loss of Vps4 from an otherwise wild-type background caused multiple cargoes to accumulate at the PM because of an increase in Rcy1-dependent recycling of internalized protein to the cell surface. Additionally, vps4Δ rcy1Δ mutants exhibited deleterious growth phenotypes. Together, our findings reveal previously unappreciated effects of disrupted ESCRT-dependent trafficking on endocytic recycling and the PM.
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Affiliation(s)
- Kyle Hoban
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Samantha Y Lux
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joanna Poprawski
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yorke Zhang
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - James Shepherdson
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pedro G Castiñeira
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sanjana Pesari
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Tony Yao
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Derek C Prosser
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Carolyn Norris
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Beverly Wendland
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
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9
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Tey HJ, Ng CH. Computational analysis of functional SNPs in Alzheimer's disease-associated endocytosis genes. PeerJ 2019; 7:e7667. [PMID: 31592138 PMCID: PMC6776068 DOI: 10.7717/peerj.7667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/13/2019] [Indexed: 01/10/2023] Open
Abstract
Background From genome wide association studies on Alzheimer’s disease (AD), it has been shown that many single nucleotide polymorphisms (SNPs) of genes of different pathways affect the disease risk. One of the pathways is endocytosis, and variants in these genes may affect their functions in amyloid precursor protein (APP) trafficking, amyloid-beta (Aβ) production as well as its clearance in the brain. This study uses computational methods to predict the effect of novel SNPs, including untranslated region (UTR) variants, splice site variants, synonymous SNPs (sSNPs) and non-synonymous SNPs (nsSNPs) in three endocytosis genes associated with AD, namely PICALM, SYNJ1 and SH3KBP1. Materials and Methods All the variants’ information was retrieved from the Ensembl genome database, and then different variation prediction analyses were performed. UTRScan was used to predict UTR variants while MaxEntScan was used to predict splice site variants. Meta-analysis by PredictSNP2 was used to predict sSNPs. Parallel prediction analyses by five different software packages including SIFT, PolyPhen-2, Mutation Assessor, I-Mutant2.0 and SNPs&GO were used to predict the effects of nsSNPs. The level of evolutionary conservation of deleterious nsSNPs was further analyzed using ConSurf server. Mutant protein structures of deleterious nsSNPs were modelled and refined using SPARKS-X and ModRefiner for structural comparison. Results A total of 56 deleterious variants were identified in this study, including 12 UTR variants, 18 splice site variants, eight sSNPs and 18 nsSNPs. Among these 56 deleterious variants, seven variants were also identified in the Alzheimer’s Disease Sequencing Project (ADSP), Alzheimer’s Disease Neuroimaging Initiative (ADNI) and Mount Sinai Brain Bank (MSBB) studies. Discussion The 56 deleterious variants were predicted to affect the regulation of gene expression, or have functional impacts on these three endocytosis genes and their gene products. The deleterious variants in these genes are expected to affect their cellular function in endocytosis and may be implicated in the pathogenesis of AD as well. The biological consequences of these deleterious variants and their potential impacts on the disease risks could be further validated experimentally and may be useful for gene-disease association study.
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Affiliation(s)
- Han Jieh Tey
- Faculty of Information Science and Technology, Multimedia University, Ayer Keroh, Melaka, Malaysia
| | - Chong Han Ng
- Faculty of Information Science and Technology, Multimedia University, Ayer Keroh, Melaka, Malaysia
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10
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Kaneda M, van Oostende-Triplet C, Chebli Y, Testerink C, Bednarek SY, Geitmann A. Plant AP180 N-Terminal Homolog Proteins Are Involved in Clathrin-Dependent Endocytosis during Pollen Tube Growth in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:1316-1330. [PMID: 30796435 DOI: 10.1093/pcp/pcz036] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 02/18/2019] [Indexed: 05/05/2023]
Abstract
Polarized cell growth in plants is maintained under the strict control and exquisitely choreographed balance of exocytic and endocytic membrane trafficking. The pollen tube has become a model system for rapid polar growth in which delivery of cell wall material and membrane recycling are controlled by membrane trafficking. Endocytosis plays an important role that is poorly understood. The plant AP180 N-Terminal Homolog (ANTH) proteins are putative homologs of Epsin 1 that recruits clathrin to phosphatidylinositol 4, 5-bisphosphate (PIP2) containing membranes to facilitate vesicle budding during endocytosis. Two Arabidopsis ANTH encoded by the genes AtAP180 and AtECA2 are highly expressed in pollen tubes. Pollen tubes from T-DNA inserted knockout mutant lines display significant morphological defects and unique pectin deposition. Fluorescent tagging reveals organization into dynamic foci located at the lateral flanks of the pollen tube. This precisely defined subapical domain coincides which clathrin-mediated endocytosis (CME) and PIP2 localization. Using a liposome-protein binding test, we showed that AtECA2 protein and ANTH domain recombinant proteins have strong affinity to PIP2 and phosphatidic acid containing liposomes in vitro. Taken together these data suggest that Arabidopsis ANTH proteins may play an important role in CME, proper cell wall assembly and morphogenesis.
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Affiliation(s)
- Minako Kaneda
- Institut de recherche en biologie v�g�tale, Universit� de Montr�al, 4101 Rue Sherbrooke Est, Montr�al, QC, Canada
| | - Chloï van Oostende-Triplet
- Institut de recherche en biologie v�g�tale, Universit� de Montr�al, 4101 Rue Sherbrooke Est, Montr�al, QC, Canada
- Present address: Cell Biology and Image Acquisition Core Facility, Faculty of Medicine, University of Ottawa, RGN 3171, 451 Smyth Road, Ottawa, ON, Canada
| | - Youssef Chebli
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore, Ste-Anne-de-Bellevue, Qu�bec, Canada
| | - Christa Testerink
- Section of Plant Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands
- Present address: Laboratory of Plant Physiology, Wageningen University and Research, PB Wageningen, The Netherlands
| | | | - Anja Geitmann
- Institut de recherche en biologie v�g�tale, Universit� de Montr�al, 4101 Rue Sherbrooke Est, Montr�al, QC, Canada
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore, Ste-Anne-de-Bellevue, Qu�bec, Canada
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11
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A Flow Cytometry-Based Phenotypic Screen To Identify Novel Endocytic Factors in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018. [PMID: 29540444 PMCID: PMC5940143 DOI: 10.1534/g3.118.200102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Endocytosis is a fundamental process for internalizing material from the plasma membrane, including many transmembrane proteins that are selectively internalized depending on environmental conditions. In most cells, the main route of entry is clathrin-mediated endocytosis (CME), a process that involves the coordinated activity of over 60 proteins; however, there are likely as-yet unidentified proteins involved in cargo selection and/or regulation of endocytosis. We performed a mutagenic screen to identify novel endocytic genes in Saccharomyces cerevisiae expressing the methionine permease Mup1 tagged with pHluorin (pHl), a pH-sensitive GFP variant whose fluorescence is quenched upon delivery to the acidic vacuole lumen. We used fluorescence-activated cell sorting to isolate mutagenized cells with elevated fluorescence, resulting from failure to traffic Mup1-pHl cargo to the vacuole, and further assessed subcellular localization of Mup1-pHl to characterize the endocytic defects in 256 mutants. A subset of mutant strains was classified as having general endocytic defects based on mislocalization of additional cargo proteins. Within this group, we identified mutations in four genes encoding proteins with known roles in endocytosis: the endocytic coat components SLA2, SLA1, and EDE1, and the ARP3 gene, whose product is involved in nucleating actin filaments to form branched networks. All four mutants demonstrated aberrant dynamics of the endocytic machinery at sites of CME; moreover, the arp3R346H mutation showed reduced actin nucleation activity in vitro. Finally, whole genome sequencing of two general endocytic mutants identified mutations in conserved genes not previously implicated in endocytosis, KRE33 and IQG1, demonstrating that our screening approach can be used to identify new components involved in endocytosis.
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12
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Tolsma TO, Cuevas LM, Di Pietro SM. The Sla1 adaptor-clathrin interaction regulates coat formation and progression of endocytosis. Traffic 2018. [PMID: 29542219 DOI: 10.1111/tra.12563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Clathrin-mediated endocytosis is a fundamental transport pathway that depends on numerous protein-protein interactions. Testing the importance of the adaptor protein-clathrin interaction for coat formation and progression of endocytosis in vivo has been difficult due to experimental constrains. Here, we addressed this question using the yeast clathrin adaptor Sla1, which is unique in showing a cargo endocytosis defect upon substitution of 3 amino acids in its clathrin-binding motif (sla1AAA ) that disrupt clathrin binding. Live-cell imaging showed an impaired Sla1-clathrin interaction causes reduced clathrin levels but increased Sla1 levels at endocytic sites. Moreover, the rate of Sla1 recruitment was reduced indicating proper dynamics of both clathrin and Sla1 depend on their interaction. sla1AAA cells showed a delay in progression through the various stages of endocytosis. The Arp2/3-dependent actin polymerization machinery was present for significantly longer time before actin polymerization ensued, revealing a link between coat formation and activation of actin polymerization. Ultimately, in sla1AAA cells a larger than normal actin network was formed, dramatically higher levels of various machinery proteins other than clathrin were recruited, and the membrane profile of endocytic invaginations was longer. Thus, the Sla1-clathrin interaction is important for coat formation, regulation of endocytic progression and membrane bending.
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Affiliation(s)
- Thomas O Tolsma
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Lena M Cuevas
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Santiago M Di Pietro
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
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13
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Lu R, Drubin DG. Selection and stabilization of endocytic sites by Ede1, a yeast functional homologue of human Eps15. Mol Biol Cell 2017; 28:567-575. [PMID: 28057762 PMCID: PMC5328616 DOI: 10.1091/mbc.e16-06-0391] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 12/09/2016] [Accepted: 12/29/2016] [Indexed: 12/19/2022] Open
Abstract
During clathrin-mediated endocytosis (CME), endocytic-site maturation can be divided into two stages corresponding to the arrival of the early and late proteins at the plasma membrane. The early proteins are required to capture cargo and position the late machinery, which includes proteins involved in actin assembly and membrane scission. However, the mechanism by which early-arriving proteins select and stabilize endocytic sites is not known. Ede1, one of the earliest proteins recruited to endocytic sites, facilitates site initiation and stabilization. Deletion of EDE1 results in fewer CME initiations and defects in the timing of vesicle maturation. Here we made truncation mutants of Ede1 to better understand how different domains contribute to its recruitment to CME sites, site selection, and site maturation. We found that the minimal domains required for efficient Ede1 localization at CME sites are the third EH domain, the proline-rich region, and the coiled-coil region. We also found that many strains expressing ede1 truncations could support a normal rate of site initiation but still had defects in site-maturation timing, indicating separation of Ede1 functions. When expressed in yeast, human Eps15 localized to the plasma membrane, where it recruited late-phase CME proteins and supported productive endocytosis, identifying it as an Ede1 functional homologue.
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Affiliation(s)
- Rebecca Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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14
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Prosser DC, Wrasman K, Woodard TK, O'Donnell AF, Wendland B. Applications of pHluorin for Quantitative, Kinetic and High-throughput Analysis of Endocytosis in Budding Yeast. J Vis Exp 2016. [PMID: 27805610 DOI: 10.3791/54587] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Green fluorescent protein (GFP) and its variants are widely used tools for studying protein localization and dynamics of events such as cytoskeletal remodeling and vesicular trafficking in living cells. Quantitative methodologies using chimeric GFP fusions have been developed for many applications; however, GFP is somewhat resistant to proteolysis, thus its fluorescence persists in the lysosome/vacuole, which can impede quantification of cargo trafficking in the endocytic pathway. An alternative method for quantifying endocytosis and post-endocytic trafficking events makes use of superecliptic pHluorin, a pH-sensitive variant of GFP that is quenched in acidic environments. Chimeric fusion of pHluorin to the cytoplasmic tail of transmembrane cargo proteins results in a dampening of fluorescence upon incorporation of the cargo into multivesicular bodies (MVBs) and delivery to the lysosome/vacuole lumen. Thus, quenching of vacuolar fluorescence facilitates quantification of endocytosis and early events in the endocytic pathway. This paper describes methods using pHluorin-tagged cargos for quantification of endocytosis via fluorescence microscopy, as well as population-based assays using flow cytometry.
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15
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Hung CW, Duncan MC. Clathrin binding by the adaptor Ent5 promotes late stages of clathrin coat maturation. Mol Biol Cell 2016; 27:1143-53. [PMID: 26842894 PMCID: PMC4814221 DOI: 10.1091/mbc.e15-08-0588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/28/2016] [Indexed: 11/15/2022] Open
Abstract
Clathrin adaptors link cargo to the clathrin coat. The clathrin adaptor Ent5 is also required for the maturation of clathrin coats at the trans-Golgi network or endosome, suggesting that it plays a key mechanistic role in coat formation. This function requires only the Ent5 clathrin-binding sites and not its interaction with other endosomal adaptors. Clathrin is a ubiquitous protein that mediates membrane traffic at many locations. To function, clathrin requires clathrin adaptors that link it to transmembrane protein cargo. In addition to this cargo selection function, many adaptors also play mechanistic roles in the formation of the transport carrier. However, the full spectrum of these mechanistic roles is poorly understood. Here we report that Ent5, an endosomal clathrin adaptor in Saccharomyces cerevisiae, regulates the behavior of clathrin coats after the recruitment of clathrin. We show that loss of Ent5 disrupts clathrin-dependent traffic and prolongs the lifespan of endosomal structures that contain clathrin and other adaptors, suggesting a defect in coat maturation at a late stage. We find that the direct binding of Ent5 with clathrin is required for its role in coat behavior and cargo traffic. Surprisingly, the interaction of Ent5 with other adaptors is dispensable for coat behavior but not cargo traffic. These findings support a model in which Ent5 clathrin binding performs a mechanistic role in coat maturation, whereas Ent5 adaptor binding promotes cargo incorporation.
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Affiliation(s)
- Chao-Wei Hung
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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16
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Feliziani C, Valdez Taubas J, Moyano S, Quassollo G, Poprawski JE, Wendland B, Touz MC. Vestiges of Ent3p/Ent5p function in the giardial epsin homolog. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:749-59. [PMID: 26851076 DOI: 10.1016/j.bbamcr.2016.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/12/2016] [Accepted: 02/01/2016] [Indexed: 11/29/2022]
Abstract
An accurate way to characterize the functional potential of a protein is to analyze recognized protein domains encoded by the genes in a given group. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated trafficking. In this work, we investigate the function of the single ENTH-containing protein from the protist Giardia lamblia by testing its function in Saccharomyces cerevisiae. This protein, named GlENTHp (for G. lamblia ENTH protein), is involved in Giardia in endocytosis and in protein trafficking from the ER to the vacuoles, fulfilling the function of the ENTH proteins epsin and epsinR, respectively. There are two orthologs of epsin, Ent1p and Ent2p, and two orthologs of epsinR, Ent3p and Ent5p in S. cerevisiae. Although the expression of GlENTHp neither complemented growth in the ent1Δent2Δ mutant nor restored the GFP-Cps1 vacuolar trafficking defect in ent3Δent5Δ, it interfered with the normal function of Ent3/5 in the wild-type strain. The phenotype observed is linked to a defect in Cps1 localization and α-factor mating pheromone maturation. The finding that GlENTHp acts as dominant negative epsinR in yeast cells reinforces the phylogenetic data showing that GlENTHp belongs to the epsinR subfamily present in eukaryotes prior to their evolution into different taxa.
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Affiliation(s)
- Constanza Feliziani
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli, 2434, Córdoba, Argentina
| | - Javier Valdez Taubas
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC (UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Sofía Moyano
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli, 2434, Córdoba, Argentina
| | - Gonzalo Quassollo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli, 2434, Córdoba, Argentina
| | - Joanna E Poprawski
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Mudd Hall Room 35, Baltimore, USA
| | - Beverly Wendland
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Mudd Hall Room 35, Baltimore, USA
| | - Maria C Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli, 2434, Córdoba, Argentina.
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17
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Prosser DC, Pannunzio AE, Brodsky JL, Thorner J, Wendland B, O'Donnell AF. α-Arrestins participate in cargo selection for both clathrin-independent and clathrin-mediated endocytosis. J Cell Sci 2015; 128:4220-34. [PMID: 26459639 PMCID: PMC4712785 DOI: 10.1242/jcs.175372] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/05/2015] [Indexed: 12/24/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) is a well-studied mechanism to internalize plasma membrane proteins; however, to endocytose such cargo, most eukaryotic cells also use alternative clathrin-independent endocytic (CIE) pathways, which are less well characterized. The budding yeast Saccharomyces cerevisiae, a widely used model for studying CME, was recently shown to have a CIE pathway that requires the GTPase Rho1, the formin Bni1, and their regulators. Nevertheless, in both yeast and mammalian cells, the mechanisms underlying cargo selection in CME and CIE are only beginning to be understood. For CME in yeast, particular α-arrestins contribute to recognition of specific cargos and promote their ubiquitylation by recruiting the E3 ubiquitin protein ligase Rsp5. Here, we show that the same α-arrestin–cargo pairs promote internalization through the CIE pathway by interacting with CIE components. Notably, neither expression of Rsp5 nor its binding to α-arrestins is required for CIE. Thus, α-arrestins are important for cargo selection in both the CME and CIE pathways, but function by distinct mechanisms in each pathway. Summary: In yeast, α-arrestins bind the Rho1 GTPase and regulate internalization of selective cargo through the clathrin-independent endocytic pathway.
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Affiliation(s)
- Derek C Prosser
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Anthony E Pannunzio
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
| | - Beverly Wendland
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Allyson F O'Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
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18
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Manna PT, Gadelha C, Puttick AE, Field MC. ENTH and ANTH domain proteins participate in AP2-independent clathrin-mediated endocytosis. J Cell Sci 2015; 128:2130-42. [PMID: 25908855 PMCID: PMC4450294 DOI: 10.1242/jcs.167726] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/13/2015] [Indexed: 01/17/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is a major route of entry into eukaryotic cells. A core of evolutionarily ancient genes encodes many components of this system but much of our mechanistic understanding of CME is derived from a phylogenetically narrow sampling of a few model organisms. In the parasite Trypanosoma brucei, which is distantly related to the better characterised animals and fungi, exceptionally fast endocytic turnover aids its evasion of the host immune system. Although clathrin is absolutely essential for this process, the adaptor protein complex 2 (AP2) has been secondarily lost, suggesting mechanistic divergence. Here, we characterise two phosphoinositide-binding monomeric clathrin adaptors, T. brucei (Tb)EpsinR and TbCALM, which in trypanosomes are represented by single genes, unlike the expansions present in animals and fungi. Depletion of these gene products reveals essential, but partially redundant, activities in CME. Ultrastructural analysis of TbCALM and TbEpsinR double-knockdown cells demonstrated severe defects to clathrin-coated pit formation and morphology associated with a dramatic inhibition of endocytosis. Depletion of TbCALM alone, however, produced a distinct lysosomal segregation phenotype, indicating an additional non-redundant role for this protein. Therefore, TbEpsinR and TbCALM represent ancient phosphoinositide-binding proteins with distinct and vital roles in AP2-independent endocytosis.
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Affiliation(s)
- Paul T Manna
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Amy E Puttick
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Mark C Field
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
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19
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O’Brien KM, Lindsay EL, Starai VJ. The Legionella pneumophila effector protein, LegC7, alters yeast endosomal trafficking. PLoS One 2015; 10:e0116824. [PMID: 25643265 PMCID: PMC4314205 DOI: 10.1371/journal.pone.0116824] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/15/2014] [Indexed: 02/03/2023] Open
Abstract
The intracellular pathogen, Legionella pneumophila, relies on numerous secreted effector proteins to manipulate host endomembrane trafficking events during pathogenesis, thereby preventing fusion of the bacteria-laden phagosome with host endolysosomal compartments, and thus escaping degradation. Upon expression in the surrogate eukaryotic model Saccharomyces cerevisiae, we find that the L. pneumophila LegC7/YlfA effector protein disrupts the delivery of both biosynthetic and endocytic cargo to the yeast vacuole. We demonstrate that the effects of LegC7 are specific to the endosome:vacuole delivery pathways; LegC7 expression does not disrupt other known vacuole-directed pathways. Deletions of the ESCRT-0 complex member, VPS27, provide resistance to the LegC7 toxicity, providing a possible target for LegC7 function in vivo. Furthermore, a single amino acid substitution in LegC7 abrogates both its toxicity and ability to alter endosomal traffic in vivo, thereby identifying a critical functional domain. LegC7 likely inhibits endosomal trafficking during L. pneumophila pathogenesis to prevent entry of the phagosome into the endosomal maturation pathway and eventual fusion with the lysosome.
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Affiliation(s)
- Kevin M. O’Brien
- Department of Microbiology, University of Georgia, Athens, Georgia, Unites States of America
| | - Elizabeth L. Lindsay
- Department of Microbiology, University of Georgia, Athens, Georgia, Unites States of America
| | - Vincent J. Starai
- Department of Microbiology, University of Georgia, Athens, Georgia, Unites States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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20
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Abstract
Endocytosis, the process whereby the plasma membrane invaginates to form vesicles, is essential for bringing many substances into the cell and for membrane turnover. The mechanism driving clathrin-mediated endocytosis (CME) involves > 50 different protein components assembling at a single location on the plasma membrane in a temporally ordered and hierarchal pathway. These proteins perform precisely choreographed steps that promote receptor recognition and clustering, membrane remodeling, and force-generating actin-filament assembly and turnover to drive membrane invagination and vesicle scission. Many critical aspects of the CME mechanism are conserved from yeast to mammals and were first elucidated in yeast, demonstrating that it is a powerful system for studying endocytosis. In this review, we describe our current mechanistic understanding of each step in the process of yeast CME, and the essential roles played by actin polymerization at these sites, while providing a historical perspective of how the landscape has changed since the preceding version of the YeastBook was published 17 years ago (1997). Finally, we discuss the key unresolved issues and where future studies might be headed.
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Affiliation(s)
- Bruce L Goode
- Brandeis University, Department of Biology, Rosenstiel Center, Waltham, Massachusetts 02454
| | - Julian A Eskin
- Brandeis University, Department of Biology, Rosenstiel Center, Waltham, Massachusetts 02454
| | - Beverly Wendland
- The Johns Hopkins University, Department of Biology, Baltimore, Maryland 21218
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21
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Bradford MK, Whitworth K, Wendland B. Pan1 regulates transitions between stages of clathrin-mediated endocytosis. Mol Biol Cell 2015; 26:1371-85. [PMID: 25631817 PMCID: PMC4454182 DOI: 10.1091/mbc.e14-11-1510] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Saccharomyces cerevisiae endocytic protein Pan1 is critical for coat interactions during three transitions of the endocytic pathway. Pan1 depletion arrests endocytosis and causes actin misregulation, leading to actin flares that are connected to the coat but not the membrane. The Pan1 central region is critical for endocytic and essential functions. Endocytosis is a well-conserved process by which cells invaginate small portions of the plasma membrane to create vesicles containing extracellular and transmembrane cargo proteins. Dozens of proteins and hundreds of specific binding interactions are needed to coordinate and regulate these events. Saccharomyces cerevisiae is a powerful model system with which to study clathrin-mediated endocytosis (CME). Pan1 is believed to be a scaffolding protein due to its interactions with numerous proteins that act throughout the endocytic process. Previous research characterized many Pan1 binding interactions, but due to Pan1's essential nature, the exact mechanisms of Pan1's function in endocytosis have been difficult to define. We created a novel Pan1-degron allele, Pan1-AID, in which Pan1 can be specifically and efficiently degraded in <1 h upon addition of the plant hormone auxin. The loss of Pan1 caused a delay in endocytic progression and weakened connections between the coat/actin machinery and the membrane, leading to arrest in CME. In addition, we determined a critical role for the central region of Pan1 in endocytosis and viability. The regions important for endocytosis and viability can be separated, suggesting that Pan1 may have a distinct role in the cell that is essential for viability.
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Affiliation(s)
| | - Karen Whitworth
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Beverly Wendland
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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22
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Boeke D, Trautmann S, Meurer M, Wachsmuth M, Godlee C, Knop M, Kaksonen M. Quantification of cytosolic interactions identifies Ede1 oligomers as key organizers of endocytosis. Mol Syst Biol 2014; 10:756. [PMID: 25366307 PMCID: PMC4299599 DOI: 10.15252/msb.20145422] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/11/2014] [Accepted: 10/01/2014] [Indexed: 01/08/2023] Open
Abstract
Clathrin-mediated endocytosis is a highly conserved intracellular trafficking pathway that depends on dynamic protein-protein interactions between up to 60 different proteins. However, little is known about the spatio-temporal regulation of these interactions. Using fluorescence (cross)-correlation spectroscopy in yeast, we tested 41 previously reported interactions in vivo and found 16 to exist in the cytoplasm. These detected cytoplasmic interactions included the self-interaction of Ede1, homolog of mammalian Eps15. Ede1 is the crucial scaffold for the organization of the early stages of endocytosis. We show that oligomerization of Ede1 through its central coiled coil domain is necessary for its localization to the endocytic site and we link the oligomerization of Ede1 to its function in locally concentrating endocytic adaptors and organizing the endocytic machinery. Our study sheds light on the importance of the regulation of protein-protein interactions in the cytoplasm for the assembly of the endocytic machinery in vivo.
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Affiliation(s)
- Dominik Boeke
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Deutsches Krebsforschungszentrum (DKFZ) DKFZ-ZMBH-Allianz, Heidelberg, Germany
| | - Susanne Trautmann
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Deutsches Krebsforschungszentrum (DKFZ) DKFZ-ZMBH-Allianz, Heidelberg, Germany
| | - Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Deutsches Krebsforschungszentrum (DKFZ) DKFZ-ZMBH-Allianz, Heidelberg, Germany
| | - Malte Wachsmuth
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Camilla Godlee
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) Deutsches Krebsforschungszentrum (DKFZ) DKFZ-ZMBH-Allianz, Heidelberg, Germany
| | - Marko Kaksonen
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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23
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Moshkanbaryans L, Chan LS, Graham ME. The Biochemical Properties and Functions of CALM and AP180 in Clathrin Mediated Endocytosis. MEMBRANES 2014; 4:388-413. [PMID: 25090048 PMCID: PMC4194041 DOI: 10.3390/membranes4030388] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/03/2014] [Accepted: 07/22/2014] [Indexed: 01/26/2023]
Abstract
Clathrin-mediated endocytosis (CME) is a fundamental process for the regulated internalization of transmembrane cargo and ligands via the formation of vesicles using a clathrin coat. A vesicle coat is initially created at the plasma membrane by clathrin assembly into a lattice, while a specific cargo sorting process selects and concentrates proteins for inclusion in the new vesicle. Vesicles formed via CME traffic to different parts of the cell and fuse with target membranes to deliver cargo. Both clathrin assembly and cargo sorting functions are features of the two gene family consisting of assembly protein 180 kDa (AP180) and clathrin assembly lymphoid myeloid leukemia protein (CALM). In this review, we compare the primary structure and domain organization of CALM and AP180 and relate these properties to known functions and roles in CME and disease.
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Affiliation(s)
- Lia Moshkanbaryans
- Children's Medical Research Institute, The University of Sydney, 214 Hawkesbury Road, Westmead, NSW 2145, Australia.
| | - Ling-Shan Chan
- Children's Medical Research Institute, The University of Sydney, 214 Hawkesbury Road, Westmead, NSW 2145, Australia.
| | - Mark E Graham
- Children's Medical Research Institute, The University of Sydney, 214 Hawkesbury Road, Westmead, NSW 2145, Australia.
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24
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Lang MJ, Martinez-Marquez JY, Prosser DC, Ganser LR, Buelto D, Wendland B, Duncan MC. Glucose starvation inhibits autophagy via vacuolar hydrolysis and induces plasma membrane internalization by down-regulating recycling. J Biol Chem 2014; 289:16736-47. [PMID: 24753258 DOI: 10.1074/jbc.m113.525782] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cellular energy influences all aspects of cellular function. Although cells can adapt to a gradual reduction in energy, acute energy depletion poses a unique challenge. Because acute depletion hampers the transport of new energy sources into the cell, the cell must use endogenous substrates to replenish energy after acute depletion. In the yeast Saccharomyces cerevisiae, glucose starvation causes an acute depletion of intracellular energy that recovers during continued glucose starvation. However, how the cell replenishes energy during the early phase of glucose starvation is unknown. In this study, we investigated the role of pathways that deliver proteins and lipids to the vacuole during glucose starvation. We report that in response to glucose starvation, plasma membrane proteins are directed to the vacuole through reduced recycling at the endosomes. Furthermore, we found that vacuolar hydrolysis inhibits macroautophagy in a target of rapamycin complex 1-dependent manner. Accordingly, we found that endocytosis and hydrolysis are required for survival in glucose starvation, whereas macroautophagy is dispensable. Together, these results suggest that hydrolysis of components delivered to the vacuole independent of autophagy is the cell survival mechanism used by S. cerevisiae in response to glucose starvation.
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Affiliation(s)
- Michael J Lang
- From the Department of Cell and Developmental Biology, the University of Michigan, Ann Arbor, Michigan 48109
| | - Jorge Y Martinez-Marquez
- From the Department of Cell and Developmental Biology, the University of Michigan, Ann Arbor, Michigan 48109
| | - Derek C Prosser
- the Department of Biology, the Johns Hopkins University, Baltimore, Maryland 21218, and
| | - Laura R Ganser
- the Department of Biology, the University of North Carolina, Chapel Hill, North Carolina 27599
| | - Destiney Buelto
- the Curriculum in Genetics and Molecular Biology, the University of North Carolina, Chapel Hill, North Carolina 27599
| | - Beverly Wendland
- the Department of Biology, the Johns Hopkins University, Baltimore, Maryland 21218, and
| | - Mara C Duncan
- From the Department of Cell and Developmental Biology, the University of Michigan, Ann Arbor, Michigan 48109, the Department of Biology, the University of North Carolina, Chapel Hill, North Carolina 27599, the Curriculum in Genetics and Molecular Biology, the University of North Carolina, Chapel Hill, North Carolina 27599
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25
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Shen D, Yuan H, Hutagalung A, Verma A, Kümmel D, Wu X, Reinisch K, McNew JA, Novick P. The synaptobrevin homologue Snc2p recruits the exocyst to secretory vesicles by binding to Sec6p. ACTA ACUST UNITED AC 2013; 202:509-26. [PMID: 23897890 PMCID: PMC3734085 DOI: 10.1083/jcb.201211148] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The exocyst is recruited to secretory vesicles by the combinatorial signals of Sec4-GTP and the Snc proteins to confer both specificity and directionality to vesicular traffic. A screen for mutations that affect the recruitment of the exocyst to secretory vesicles identified genes encoding clathrin and proteins that associate or colocalize with clathrin at sites of endocytosis. However, no significant colocalization of the exocyst with clathrin was seen, arguing against a direct role in exocyst recruitment. Rather, these components are needed to recycle the exocytic vesicle SNAREs Snc1p and Snc2p from the plasma membrane into new secretory vesicles where they act to recruit the exocyst. We observe a direct interaction between the exocyst subunit Sec6p and the latter half of the SNARE motif of Snc2p. An snc2 mutation that specifically disrupts this interaction led to exocyst mislocalization and a block in exocytosis in vivo without affecting liposome fusion in vitro. Overexpression of Sec4p partially suppressed the exocyst localization defects of mutations in clathrin and clathrin-associated components. We propose that the exocyst is recruited to secretory vesicles by the combinatorial signals of Sec4-GTP and the Snc proteins. This could help to confer both specificity and directionality to vesicular traffic.
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Affiliation(s)
- David Shen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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26
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Prosser DC, Wendland B. Conserved roles for yeast Rho1 and mammalian RhoA GTPases in clathrin-independent endocytosis. Small GTPases 2013; 3:229-35. [PMID: 23238351 PMCID: PMC3520887 DOI: 10.4161/sgtp.21631] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic cells use numerous endocytic pathways for nutrient uptake, protein turnover and response to the extracellular environment. While clathrin-mediated endocytosis (CME) has been extensively studied in yeast and mammalian cells, recent studies in higher eukaryotes have described multiple clathrin-independent endocytic pathways that depend upon Rho family GTPases and their effector proteins. In contrast, yeast cells have been thought to rely solely on CME. In a recent study, we used CME-defective yeast cells lacking clathrin-binding endocytic adaptor proteins in a genetic screen to identify novel factors involved in endocytosis. This approach revealed the existence of a clathrin-independent endocytic pathway involving the GTPase Rho1, which is the yeast homolog of RhoA. Further characterization of the yeast Rho1-mediated endocytic pathway suggested that the Rho1 pathway requires additional proteins that appear to play conserved roles in RhoA-dependent, clathrin-independent endocytic pathways in mammalian cells. Here, we discuss the parallels between the yeast Rho1-dependent and mammalian RhoA-dependent endocytic pathways, as well as the applications of yeast as a model for studying clathrin-independent endocytosis in higher eukaryotes.
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Affiliation(s)
- Derek C Prosser
- Department of Biology, The John Hopkins University, Baltimore, MD, USA.
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27
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Chi RJ, Torres OT, Segarra VA, Lansley T, Chang JS, Newpher TM, Lemmon SK. Role of Scd5, a protein phosphatase-1 targeting protein, in phosphoregulation of Sla1 during endocytosis. J Cell Sci 2012; 125:4728-39. [PMID: 22825870 DOI: 10.1242/jcs.098871] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphorylation regulates assembly and disassembly of proteins during endocytosis. In yeast, Prk1 and Ark1 phosphorylate factors after vesicle internalization leading to coat disassembly. Scd5, a protein phosphatase-1 (PP1)-targeting subunit, is proposed to regulate dephosphorylation of Prk1/Ark1 substrates to promote new rounds of endocytosis. In this study we analyzed scd5-PP1Δ2, a mutation causing impaired PP1 binding. scd5-PP1Δ2 caused hyperphosphorylation of several Prk1 endocytic targets. Live-cell imaging of 15 endocytic components in scd5-PP1Δ2 revealed that most factors arriving before the invagination/actin phase of endocytosis had delayed lifetimes. Severely affected were early factors and Sla2 (Hip1R homolog), whose lifetime was extended nearly fourfold. In contrast, the lifetime of Sla1, a Prk1 target, was extended less than twofold, but its cortical recruitment was significantly reduced. Delayed Sla2 dynamics caused by scd5-PP1Δ2 were suppressed by SLA1 overexpression. This was dependent on the LxxQxTG repeats (SR) of Sla1, which are phosphorylated by Prk1 and bind Pan1, another Prk1 target, in the dephosphorylated state. Without the SR, Sla1ΔSR was still recruited to the cell surface, but was less concentrated in cortical patches than Pan1. sla1ΔSR severely impaired endocytic progression, but this was partially suppressed by overexpression of LAS17, suggesting that without the SR region the SH3 region of Sla1 causes constitutive negative regulation of Las17 (WASp). These results demonstrate that Scd5/PP1 is important for recycling Prk1 targets to initiate new rounds of endocytosis and provide new mechanistic information on the role of the Sla1 SR domain in regulating progression to the invagination/actin phase of endocytosis.
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Affiliation(s)
- Richard J Chi
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, FL 33136, USA
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28
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Tanner N, Prag G. Purification and crystallization of yeast Ent1 ENTH domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:820-3. [PMID: 22750874 PMCID: PMC3388931 DOI: 10.1107/s1744309112022488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 05/17/2012] [Indexed: 11/10/2022]
Abstract
Members of the Epsin protein family regulate the ubiquitin/clathrin-dependent trafficking of transmembrane proteins. The yeast Epsin-1 (ent1) gene was cloned and expressed in Escherichia coli. The protein product of a construct containing the ENTH-UIM modules was purified to homogeneity and subjected to crystallization screening using the sitting-drop vapour-diffusion method. Refined conditions containing polyethylene glycol 3350 and Tacsimate yielded thin rod-like crystals. X-ray analysis revealed that the crystallographic symmetry is primitive orthorhombic, space group P222, with unit-cell parameters a = 32.7, b = 35.5, c = 110.6 Å and a diffraction limit of 2.3 Å. Matthews coefficient calculations suggested that the crystal contained only the ENTH domain. This was corroborated by Coomassie Blue-stained SDS-PAGE analysis of dissolved crystals.
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Affiliation(s)
- Neta Tanner
- Department of Biochemistry and Molecular Biology, The Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gali Prag
- Department of Biochemistry and Molecular Biology, The Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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29
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Sen A, Madhivanan K, Mukherjee D, Aguilar RC. The epsin protein family: coordinators of endocytosis and signaling. Biomol Concepts 2012; 3:117-126. [PMID: 22942912 DOI: 10.1515/bmc-2011-0060] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The epsins are a conserved family of endocytic adaptors essential for cell viability in yeast and for embryo development in higher eukaryotes. Epsins function as adaptors by recognizing ubiquitinated cargo and as endocytic accessory proteins by contributing to endocytic network stability/regulation and membrane bending. Importantly, epsins play a critical role in signaling by contributing to epidermal growth factor receptor downregulation and the activation of notch and RhoGTPase pathways. In this review, we present an overview of the epsins and emphasize their functional importance as coordinators of endocytosis and signaling.
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Affiliation(s)
- Arpita Sen
- Department of Biological Sciences and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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30
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Abstract
Clathrin-mediated endocytosis (CME) is the major pathway for internalization of membrane proteins from the cell surface. Half a century of studies have uncovered tremendous insights into how a clathrin-coated vesicle is formed. More recently, the advent of live-cell imaging has provided a dynamic view of this process. As CME is highly conserved from yeast to humans, budding yeast provides an evolutionary template for this process and has been a valuable system for dissecting the underlying molecular mechanisms. In this review we trace the formation of a clathrin-coated vesicle from initiation to uncoating, focusing on key findings from the yeast system.
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31
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Carroll SY, Stimpson HEM, Weinberg J, Toret CP, Sun Y, Drubin DG. Analysis of yeast endocytic site formation and maturation through a regulatory transition point. Mol Biol Cell 2011; 23:657-68. [PMID: 22190733 PMCID: PMC3279393 DOI: 10.1091/mbc.e11-02-0108] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
ETOC: During yeast endocytic site formation, Ede1p (yeast Eps15), but not clathrin light chain, is important for the recruitment of most other early-arriving proteins to endocytic sites. Cargo and clathrin light chain may play roles in regulating the transition of endocytic sites out of the “intermediate coat” stage of endocytosis. The earliest stages of endocytic site formation and the regulation of endocytic site maturation are not well understood. Here we analyzed the order in which the earliest proteins are detectable at endocytic sites in budding yeast and found that an uncharacterized protein, Pal1p/Ydr348cp, is also present at the initial stages of endocytosis. Because Ede1p (homologue of Eps15) and clathrin are the early-arriving proteins most important for cargo uptake, their roles during the early stages of endocytosis were examined more comprehensively. Ede1p is necessary for efficient recruitment of most early-arriving proteins, but not for the recruitment of the adaptor protein Yap1802p, to endocytic sites. The early-arriving proteins, as well as the later-arriving proteins Sla2p and Ent1/2p (homologues of Hip1R and epsins), were found to have longer lifetimes in CLC1-knockout yeast, which indicates that clathrin light chain facilitates the transition from the intermediate to late coat stages. Cargo also arrives during the early stages of endocytosis, and therefore its effect on endocytic machinery dynamics was investigated. Our results are consistent with a role for cargo in regulating the transition of endocytic sites from the early stages of formation to the late stages during which vesicle formation occurs.
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Affiliation(s)
- Susheela Y Carroll
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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32
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Suzuki R, Toshima JY, Toshima J. Regulation of clathrin coat assembly by Eps15 homology domain-mediated interactions during endocytosis. Mol Biol Cell 2011; 23:687-700. [PMID: 22190739 PMCID: PMC3279396 DOI: 10.1091/mbc.e11-04-0380] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
ETOC: The EH domain is a highly conserved protein–protein interaction domain involved in endocytosis. The EH domains of yeast endocytic proteins, Pan1p, End3p, and Ede1p, have a redundant function and are required for efficient recruitment of several endocytic proteins to sites of endocytosis in order to facilitate clathrin coat assembly. Clathrin-mediated endocytosis involves a coordinated series of molecular events regulated by interactions among a variety of proteins and lipids through specific domains. One such domain is the Eps15 homology (EH) domain, a highly conserved protein–protein interaction domain present in a number of proteins distributed from yeast to mammals. Several lines of evidence suggest that the yeast EH domain–containing proteins Pan1p, End3p, and Ede1p play important roles during endocytosis. Although genetic and cell-biological studies of these proteins suggested a role for the EH domains in clathrin-mediated endocytosis, it was unclear how they regulate clathrin coat assembly. To explore the role of the EH domain in yeast endocytosis, we mutated those of Pan1p, End3p, or Ede1p, respectively, and examined the effects of single, double, or triple mutation on clathrin coat assembly. We found that mutations of the EH domain caused a defect of cargo internalization and a delay of clathrin coat assembly but had no effect on assembly of the actin patch. We also demonstrated functional redundancy among the EH domains of Pan1p, End3p, and Ede1p for endocytosis. Of interest, the dynamics of several endocytic proteins were differentially affected by various EH domain mutations, suggesting functional diversity of each EH domain.
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Affiliation(s)
- Ryohei Suzuki
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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33
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Prosser DC, Drivas TG, Maldonado-Báez L, Wendland B. Existence of a novel clathrin-independent endocytic pathway in yeast that depends on Rho1 and formin. ACTA ACUST UNITED AC 2011; 195:657-71. [PMID: 22065638 PMCID: PMC3257529 DOI: 10.1083/jcb.201104045] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Much like mammalian cells, yeast contain a Rho-dependent pathway for endocytosis in addition to canonical clathrin-dependent endocytosis. Yeast is a powerful model organism for dissecting the temporal stages and choreography of the complex protein machinery during endocytosis. The only known mechanism for endocytosis in yeast is clathrin-mediated endocytosis, even though clathrin-independent endocytic pathways have been described in other eukaryotes. Here, we provide evidence for a clathrin-independent endocytic pathway in yeast. In cells lacking the clathrin-binding adaptor proteins Ent1, Ent2, Yap1801, and Yap1802, we identify a second endocytic pathway that depends on the GTPase Rho1, the downstream formin Bni1, and the Bni1 cofactors Bud6 and Spa2. This second pathway does not require components of the better-studied endocytic pathway, including clathrin and Arp2/3 complex activators. Thus, our results reveal the existence of a second pathway for endocytosis in yeast, which suggests similarities with the RhoA-dependent endocytic pathways of mammalian cells.
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Affiliation(s)
- Derek C Prosser
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
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34
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Reider A, Wendland B. Endocytic adaptors--social networking at the plasma membrane. J Cell Sci 2011; 124:1613-22. [PMID: 21536832 DOI: 10.1242/jcs.073395] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Receptor-mediated endocytosis is a dynamic process that is crucial for maintaining plasma membrane composition and controlling cell-signaling pathways. A variety of entry routes have evolved to ensure that the vast array of molecules on the cell surface can be differentially internalized by endocytosis. This diversity has extended to include a growing list of endocytic adaptor proteins, which are thought to initiate the internalization process. The key function of adaptors is to select the proteins that should be removed from the cell surface. Thus, they have a central role in defining the physiology of a cell. This has made the study of adaptor proteins a very active area of research that is ripe for exciting future discoveries. Here, we review recent work on how adaptors mediate endocytosis and address the following questions: what characteristics define an endocytic adaptor protein? What roles do these proteins fulfill in addition to selecting cargo and how might adaptors function in clathrin-independent endocytic pathways? Through the findings discussed in this Commentary, we hope to stimulate further characterization of known adaptors and expansion of the known repertoire by identification of new adaptors.
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Affiliation(s)
- Amanda Reider
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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35
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Treusch S, Hamamichi S, Goodman JL, Matlack KES, Chung CY, Baru V, Shulman JM, Parrado A, Bevis BJ, Valastyan JS, Han H, Lindhagen-Persson M, Reiman EM, Evans DA, Bennett DA, Olofsson A, DeJager PL, Tanzi RE, Caldwell KA, Caldwell GA, Lindquist S. Functional links between Aβ toxicity, endocytic trafficking, and Alzheimer's disease risk factors in yeast. Science 2011; 334:1241-5. [PMID: 22033521 PMCID: PMC3281757 DOI: 10.1126/science.1213210] [Citation(s) in RCA: 274] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aβ (beta-amyloid peptide) is an important contributor to Alzheimer's disease (AD). We modeled Aβ toxicity in yeast by directing the peptide to the secretory pathway. A genome-wide screen for toxicity modifiers identified the yeast homolog of phosphatidylinositol binding clathrin assembly protein (PICALM) and other endocytic factors connected to AD whose relationship to Aβ was previously unknown. The factors identified in yeast modified Aβ toxicity in glutamatergic neurons of Caenorhabditis elegans and in primary rat cortical neurons. In yeast, Aβ impaired the endocytic trafficking of a plasma membrane receptor, which was ameliorated by endocytic pathway factors identified in the yeast screen. Thus, links between Aβ, endocytosis, and human AD risk factors can be ascertained with yeast as a model system.
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Affiliation(s)
- Sebastian Treusch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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36
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Weinberg J, Drubin DG. Clathrin-mediated endocytosis in budding yeast. Trends Cell Biol 2011; 22:1-13. [PMID: 22018597 DOI: 10.1016/j.tcb.2011.09.001] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/26/2011] [Accepted: 09/01/2011] [Indexed: 02/04/2023]
Abstract
Clathrin-mediated endocytosis in the budding yeast Saccharomyces cerevisiae involves the ordered recruitment, activity and disassembly of nearly 60 proteins at distinct sites on the plasma membrane. Two-color live-cell fluorescence microscopy has proven to be invaluable for in vivo analysis of endocytic proteins: identifying new components, determining the order of protein arrival and dissociation, and revealing even very subtle mutant phenotypes. Yeast genetics and functional genomics facilitate identification of complex interaction networks between endocytic proteins and their regulators. Quantitative datasets produced by these various analyses have made theoretical modeling possible. Here, we discuss recent findings on budding yeast endocytosis that have advanced our knowledge of how -60 endocytic proteins are recruited, perform their functions, are regulated by lipid and protein modifications, and are disassembled, all with remarkable regularity.
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Affiliation(s)
- Jasper Weinberg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
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37
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Goulart L, Rosa e Silva LK, Chiapello L, Silveira C, Crestani J, Masih D, Vainstein MH. Cryptococcus neoformans and Cryptococcus gattii genes preferentially expressed during rat macrophage infection. Med Mycol 2011; 48:932-41. [PMID: 20302549 DOI: 10.3109/13693781003677494] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii are encapsulated yeast agents of cryptococcosis and facultative intracellular pathogens. The interaction of these yeasts with macrophages is essential for containing the infection. However, Cryptococcus spp. overcome this initial host defense barrier using a unique pathogenic strategy involving intracellular replication and cytoplasmic accumulation of polysaccharide-containing vesicles. Here, we employed representational difference analysis (RDA) to identify C. neoformans and C. gattii genes differentially expressed during intracellular growth in rat peritoneal macrophages. The upregulated transcripts of C. neoformans during macrophage interaction were related to ATP-binding cassette (ABC) transporters, intra-golgi transport, chaperone activity, ribosomal maintenance, NAD metabolism, histone methylation, stress response, and monosaccharide metabolism. In contrast, with C. gattii, upregulated genes were associated with cell growth, aerobic respiration, protein binding, microtubule nucleation, monosaccharides and nitrogen metabolism, inositol or phosphatidylinositol phosphatase activity, cellular signaling, and stress response. Our findings reveal new genes that may be necessary for the intracellular parasitism of C. neoformans and C. gattii.
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Affiliation(s)
- Letícia Goulart
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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38
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Smaczynska-de Rooij II, Allwood EG, Aghamohammadzadeh S, Hettema EH, Goldberg MW, Ayscough KR. A role for the dynamin-like protein Vps1 during endocytosis in yeast. J Cell Sci 2010; 123:3496-506. [PMID: 20841380 DOI: 10.1242/jcs.070508] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Dynamins are a conserved family of proteins involved in membrane fusion and fission. Although mammalian dynamins are known to be involved in several membrane-trafficking events, the role of dynamin-1 in endocytosis is the best-characterised role of this protein family. Despite many similarities between endocytosis in yeast and mammalian cells, a comparable role for dynamins in yeast has not previously been demonstrated. The reported lack of involvement of dynamins in yeast endocytosis has raised questions over the general applicability of the current yeast model of endocytosis, and has also precluded studies using well-developed methods in yeast, to further our understanding of the mechanism of dynamin function during endocytosis. Here, we investigate the yeast dynamin-like protein Vps1 and demonstrate a transient burst of localisation to sites of endocytosis. Using live-cell imaging of endocytic reporters in strains lacking vps1, and also electron microscopy and biochemical approaches, we demonstrate a role for Vps1 in facilitating endocytic invagination. Vps1 mutants were generated, and analysis in several assays reveals a role for the C-terminal self-assembly domain in endocytosis but not in other membrane fission events with which Vps1 has previously been associated.
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Affiliation(s)
- Iwona I Smaczynska-de Rooij
- Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, Sheffield S102TN, UK
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39
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Prosser DC, Whitworth K, Wendland B. Quantitative analysis of endocytosis with cytoplasmic pHluorin chimeras. Traffic 2010; 11:1141-50. [PMID: 20626707 DOI: 10.1111/j.1600-0854.2010.01088.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The pH-sensitive green fluorescent protein (GFP) variant pHluorin is typically fused to the extracellular domain of transmembrane proteins to monitor endocytosis. Here, we have turned pHluorin inside-out, and show that cytoplasmic fusions of pHluorin are effective quantitative reporters for endocytosis and multivesicular body (MVB) sorting. In yeast in particular, fusion of GFP and its variants on the extracellular side of transmembrane proteins can result in perturbed trafficking. In contrast, cytoplasmic fusions are well tolerated, allowing for the quantitative assessment of trafficking of virtually any transmembrane protein. Quenching of degradation-resistant pHluorin in the acidic vacuole permits quantification of extravacuolar cargo proteins at steady-state levels and is compatible with kinetic analysis of endocytosis in live cells.
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Affiliation(s)
- Derek C Prosser
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
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40
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Dores MR, Schnell JD, Maldonado-Baez L, Wendland B, Hicke L. The function of yeast epsin and Ede1 ubiquitin-binding domains during receptor internalization. Traffic 2010; 11:151-60. [PMID: 19903324 DOI: 10.1111/j.1600-0854.2009.01003.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The formation of a primary endocytic vesicle is a dynamic process involving the transient organization of adaptor and scaffold proteins at the plasma membrane. Epsins and Eps15-like proteins are ubiquitin-binding proteins that act early in this process. The yeast epsins, Ent1 and Ent2, carry functional ubiquitin-interacting motifs (UIMs), whereas the yeast Eps15-like protein, Ede1, has a C-terminal ubiquitin-associated (UBA) domain. Analysis of mutants lacking early endocytic adaptors reveals that the ubiquitin-binding domains (UBDs) of Ent2 and Ede1 are likely to function primarily to mediate protein-protein interactions between components of the early endocytic machinery. Cells that lack epsin and Ede1 UBDs are able to internalize activated, ubiquitinated receptors. Furthermore, under conditions in which epsin UIMs are important for receptor internalization, receptors internalized via both ubiquitin-dependent and ubiquitin-independent signals require the UIMs, indicating that UIM function is not restricted to ubiquitinated receptors. Epsin UIMs share function with non-UBD protein-protein interaction motifs in Ent2 and Ede1, and the Ede1 UBA domain appears to negatively regulate interactions between endocytic proteins. Together, our results suggest that the ubiquitin-binding domains within the yeast epsin Ent2 and Ede1 are involved in the formation and regulation of the endocytic network.
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Affiliation(s)
- Michael R Dores
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Campus Drive, Evanston, IL 60208, USA
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41
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Sims JJ, Haririnia A, Dickinson BC, Fushman D, Cohen RE. Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains. Nat Struct Mol Biol 2009; 16:883-9. [PMID: 19620964 PMCID: PMC2744598 DOI: 10.1038/nsmb.1637] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 06/11/2009] [Indexed: 11/09/2022]
Abstract
Ubiquitin (denoted Ub) receptor proteins as a group must contain a diverse set of binding specificities to distinguish the many forms of polyubiquitin (polyUb) signals. Previous studies suggested that the large class of ubiquitin-associated (UBA) domains contains members with intrinsic specificity for Lys63-linked polyUb or Lys48-linked polyUb, thus explaining how UBA-containing proteins can mediate diverse signaling events. Here we show that previously observed Lys63-polyUb selectivity in UBA domains is the result of an artifact in which the dimeric fusion partner, glutathione S-transferase (GST), positions two UBAs for higher affinity, avid interactions with Lys63-polyUb, but not with Lys48-polyUb. Freed from GST, these UBAs are either nonselective or prefer Lys48-polyUb. Accordingly, NMR experiments reveal no Lys63-polyUb-specific binding epitopes for these UBAs. We reexamine previous conclusions based on GST-UBAs and present an alternative model for how UBAs achieve a diverse range of linkage specificities.
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Affiliation(s)
- Joshua J Sims
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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42
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Mukherjee D, Coon BG, Edwards DF, Hanna CB, Longhi SA, McCaffery JM, Wendland B, Retegui LA, Bi E, Aguilar RC. The yeast endocytic protein Epsin 2 functions in a cell-division signaling pathway. J Cell Sci 2009; 122:2453-63. [PMID: 19531587 DOI: 10.1242/jcs.041137] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The epsins are a family of adaptors involved in recruiting other endocytic proteins, binding of ubiquitylated cargo and induction of membrane curvature. These molecules bear a characteristic epsin N-terminal homology (ENTH) domain and multiple peptide motifs that mediate protein-protein interactions. We have previously demonstrated that the ENTH domain of epsin is involved in Cdc42 signaling regulation. Here, we present evidence that yeast epsin 2 (Ent2) plays a signaling role during cell division. We observed that overexpression of the ENTH domain of Ent2 (ENTH2), but not Ent1, promoted the formation of chains of cells and aberrant septa. This dominant-negative effect resulted from ENTH2-mediated interference with septin assembly pathways. We mapped the ENTH2 determinants responsible for induction of the phenotype and found them to be important for efficient binding to the septin regulatory protein, Bem3. Supporting a physiological role for epsin 2 in cell division, the protein localized to sites of polarized growth and cytokinesis and rescued a defect in cell division induced by Bem3 misregulation. Collectively, our findings provide a potential molecular mechanism linking endocytosis (via epsin 2) with signaling pathways regulating cell division.
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Affiliation(s)
- Debarati Mukherjee
- Department of Biological Sciences, Purdue Cancer Center, Purdue University, West Lafayette, IN 47907, USA
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Burston HE, Maldonado-Báez L, Davey M, Montpetit B, Schluter C, Wendland B, Conibear E. Regulators of yeast endocytosis identified by systematic quantitative analysis. J Cell Biol 2009; 185:1097-110. [PMID: 19506040 PMCID: PMC2711619 DOI: 10.1083/jcb.200811116] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 05/12/2009] [Indexed: 11/22/2022] Open
Abstract
Endocytosis of receptors at the plasma membrane is controlled by a complex mechanism that includes clathrin, adaptors, and actin regulators. Many of these proteins are conserved in yeast yet lack observable mutant phenotypes, which suggests that yeast endocytosis may be subject to different regulatory mechanisms. Here, we have systematically defined genes required for internalization using a quantitative genome-wide screen that monitors localization of the yeast vesicle-associated membrane protein (VAMP)/synaptobrevin homologue Snc1. Genetic interaction mapping was used to place these genes into functional modules containing known and novel endocytic regulators, and cargo selectivity was evaluated by an array-based comparative analysis. We demonstrate that clathrin and the yeast AP180 clathrin adaptor proteins have a cargo-specific role in Snc1 internalization. We additionally identify low dye binding 17 (LDB17) as a novel conserved component of the endocytic machinery. Ldb17 is recruited to cortical actin patches before actin polymerization and regulates normal coat dynamics and actin assembly. Our findings highlight the conserved machinery and reveal novel mechanisms that underlie endocytic internalization.
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Affiliation(s)
- Helen E. Burston
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, and Department of Medical Genetics, University of British Columbia, Vancouver V5Z 4H4, British Columbia, Canada
| | | | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, and Department of Medical Genetics, University of British Columbia, Vancouver V5Z 4H4, British Columbia, Canada
| | - Benjamen Montpetit
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, and Department of Medical Genetics, University of British Columbia, Vancouver V5Z 4H4, British Columbia, Canada
| | - Cayetana Schluter
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, and Department of Medical Genetics, University of British Columbia, Vancouver V5Z 4H4, British Columbia, Canada
| | - Beverly Wendland
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, and Department of Medical Genetics, University of British Columbia, Vancouver V5Z 4H4, British Columbia, Canada
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Collette JR, Chi RJ, Boettner DR, Fernandez-Golbano IM, Plemel R, Merz AJ, Geli MI, Traub LM, Lemmon SK. Clathrin functions in the absence of the terminal domain binding site for adaptor-associated clathrin-box motifs. Mol Biol Cell 2009; 20:3401-13. [PMID: 19458198 DOI: 10.1091/mbc.e08-10-1082] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Clathrin is involved in vesicle formation in the trans-Golgi network (TGN)/endosomal system and during endocytosis. Clathrin recruitment to membranes is mediated by the clathrin heavy chain (HC) N-terminal domain (TD), which forms a seven-bladed beta-propeller. TD binds membrane-associated adaptors, which have short peptide motifs, either the clathrin-box (CBM) and/or the W-box; however, the importance of the TD binding sites for these motifs has not been tested in vivo. We investigated the importance of the TD in clathrin function by generating 1) mutations in the yeast HC gene (CHC1) to disrupt the binding sites for the CBM and W-box (chc1-box), and 2) four TD-specific temperature-sensitive alleles of CHC1. We found that TD is important for the retention of resident TGN enzymes and endocytosis of alpha-factor; however, the known adaptor binding sites are not necessary, because chc1-box caused little to no effect on trafficking pathways involving clathrin. The Chc1-box TD was able to interact with the endocytic adaptor Ent2 in a CBM-dependent manner, and HCs encoded by chc1-box formed clathrin-coated vesicles. These data suggest that additional or alternative binding sites exist on the TD propeller to help facilitate the recruitment of clathrin to sites of vesicle formation.
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Affiliation(s)
- John R Collette
- Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33101, USA
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Gabernet-Castello C, Dacks JB, Field MC. The single ENTH-domain protein of trypanosomes; endocytic functions and evolutionary relationship with epsin. Traffic 2009; 10:894-911. [PMID: 19416477 DOI: 10.1111/j.1600-0854.2009.00910.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Epsin N-terminal homology (ENTH) domains occur in proteins of either the epsin or epsin-related (epsinR) form. They principally function in clathrin-mediated trafficking and membrane deformation. Both epsin and epsinR possess clathrin-binding motifs, but only epsin incorporates a ubiquitin-interaction motif (UIM). To better understand the origins of ENTH-domain proteins and their functions, we performed detailed comparative genomics and phylogenetics on the epsin family. The epsin ENTH-UIM configuration is an architecture restricted to yeast and animals. Further, we undertook functional analysis in Trypanosoma brucei (T. brucei), a divergent organism possessing a single ENTH-domain protein (TbEpsinR). TbEpsinR has a cellular location similar to both epsin and epsinR at plasma membrane clathrin budding sites and endosomal compartments, and associates with clathrin, as demonstrated by coimmunoprecipitation. Knockdown of TbEpsinR leads to a significant decrease in the intracellular pools of multiple surface antigens, without affecting bulk membrane internalization. Therefore, despite lacking the UIM, TbEpsinR maintains a similar role to metazoan epsin in endocytosis and participates as a clathrin-associated adaptor. We suggest that recruitment of a UIM to the ENTH-domain proteins was not essential for participation in endocytosis of ubiquitylated molecules, and is presumably a specific innovation restricted to higher eukaryotes.
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