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Overduin M, Kervin TA, Klarenbach Z, Adra TRC, Bhat RK. Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL. Biophys Chem 2023; 295:106971. [PMID: 36801589 DOI: 10.1016/j.bpc.2023.106971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Structures can now be predicted for any protein using programs like AlphaFold and Rosetta, which rely on a foundation of experimentally determined structures of architecturally diverse proteins. The accuracy of such artificial intelligence and machine learning (AI/ML) approaches benefits from the specification of restraints which assist in navigating the universe of folds to converge on models most representative of a given protein's physiological structure. This is especially pertinent for membrane proteins, with structures and functions that depend on their presence in lipid bilayers. Structures of proteins in their membrane environments could conceivably be predicted from AI/ML approaches with user-specificized parameters that describe each element of the architecture of a membrane protein accompanied by its lipid environment. We propose the Classification Of Membrane Proteins based On Structures Engaging Lipids (COMPOSEL), which builds on existing nomenclature types for monotopic, bitopic, polytopic and peripheral membrane proteins as well as lipids. Functional and regulatory elements are also defined in the scripts, as shown with membrane fusing synaptotagmins, multidomain PDZD8 and Protrudin proteins that recognize phosphoinositide (PI) lipids, the intrinsically disordered MARCKS protein, caveolins, the β barrel assembly machine (BAM), an adhesion G-protein coupled receptor (aGPCR) and two lipid modifying enzymes - diacylglycerol kinase DGKε and fatty aldehyde dehydrogenase FALDH. This demonstrates how COMPOSEL communicates lipid interactivity as well as signaling mechanisms and binding of metabolites, drug molecules, polypeptides or nucleic acids to describe the operations of any protein. Moreover COMPOSEL can be scaled to express how genomes encode membrane structures and how our organs are infiltrated by pathogens such as SARS-CoV-2.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Trixie Rae C Adra
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Rakesh K Bhat
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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2
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Troutman KK, Varlakhanova NV, Tornabene BA, Ramachandran R, Ford MGJ. Conserved Pib2 regions have distinct roles in TORC1 regulation at the vacuole. J Cell Sci 2022; 135:276418. [PMID: 36000409 PMCID: PMC9584352 DOI: 10.1242/jcs.259994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/15/2022] [Indexed: 12/27/2022] Open
Abstract
TORC1 is a critical controller of cell growth in eukaryotes. In yeast (Saccharomyces cerevisiae), the presence of nutrients is signaled to TORC1 by several upstream regulatory sensors that together coordinate TORC1 activity. TORC1 localizes to both vacuolar and endosomal membranes, where differential signaling occurs. This localization is mimicked by Pib2, a key upstream TORC1 regulator that is essential for TORC1 reactivation after nutrient starvation or pharmacological inhibition. Pib2 has both positive and negative effects on TORC1 activity, but the mechanisms remain poorly understood. Here, we pinpoint the Pib2 inhibitory function on TORC1 to residues within short, conserved N-terminal regions. We also show that the Pib2 C-terminal regions, helical region E and tail, are essential for TORC1 reactivation. Furthermore, the Pib2 FYVE domain plays a role in vacuolar localization, but it is surprisingly unnecessary for recovery from rapamycin exposure. Using chimeric Pib2 targeting constructs, we show that endosomal localization is not necessary for TORC1 reactivation and cell growth after rapamycin treatment. Thus, a comprehensive molecular dissection of Pib2 demonstrates that each of its conserved regions differentially contribute to Pib2-mediated regulation of TORC1 activity.
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Affiliation(s)
- Kayla K. Troutman
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Natalia V. Varlakhanova
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Bryan A. Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Rajesh Ramachandran
- Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Marijn G. J. Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA,Author for correspondence ()
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3
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Agaoua A, Rittener V, Troadec C, Desbiez C, Bendahmane A, Moquet F, Dogimont C. A single substitution in Vacuolar protein sorting 4 is responsible for resistance to Watermelon mosaic virus in melon. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4008-4021. [PMID: 35394500 DOI: 10.1093/jxb/erac135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
In plants, introgression of genetic resistance is a proven strategy for developing new resistant lines. While host proteins involved in genome replication and cell to cell movement are widely studied, other cell mechanisms responsible for virus infection remain under investigated. Endosomal sorting complexes required for transport (ESCRT) play a key role in membrane trafficking in plants and are involved in the replication of several plant RNA viruses. In this work, we describe the role of the ESCRT protein CmVPS4 as a new susceptibility factor to the Potyvirus Watermelon mosaic virus (WMV) in melon. Using a worldwide collection of melons, we identified three different alleles carrying non-synonymous substitutions in CmVps4. Two of these alleles were shown to be associated with WMV resistance. Using a complementation approach, we demonstrated that resistance is due to a single non-synonymous substitution in the allele CmVps4P30R. This work opens up new avenues of research on a new family of host factors required for virus infection and new targets for resistance.
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Affiliation(s)
- Aimeric Agaoua
- Genetics and Breeding of Fruit and Vegetables (GAFL-INRAE), 84000 Avignon, France
| | - Vincent Rittener
- Genetics and Breeding of Fruit and Vegetables (GAFL-INRAE), 84000 Avignon, France
| | - Christelle Troadec
- Institute of Plant Sciences-Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | | | | | | | - Catherine Dogimont
- Genetics and Breeding of Fruit and Vegetables (GAFL-INRAE), 84000 Avignon, France
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4
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Overduin M, Kervin TA. The phosphoinositide code is read by a plethora of protein domains. Expert Rev Proteomics 2021; 18:483-502. [PMID: 34351250 DOI: 10.1080/14789450.2021.1962302] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The proteins that decipher nucleic acid- and protein-based information are well known, however, those that read membrane-encoded information remain understudied. Here we report 70 different human, microbial and viral protein folds that recognize phosphoinositides (PIs), comprising the readers of a vast membrane code. AREAS COVERED Membrane recognition is best understood for FYVE, PH and PX domains, which exemplify hundreds of PI code readers. Comparable lipid interaction mechanisms may be mediated by kinases, adjacent C1 and C2 domains, trafficking arrestin, GAT and VHS modules, membrane-perturbing annexin, BAR, CHMP, ENTH, HEAT, syntaxin and Tubby helical bundles, multipurpose FERM, EH, MATH, PHD, PDZ, PROPPIN, PTB and SH2 domains, as well as systems that regulate receptors, GTPases and actin filaments, transfer lipids and assembled bacterial and viral particles. EXPERT OPINION The elucidation of how membranes are recognized has extended the genetic code to the PI code. Novel discoveries include PIP-stop and MET-stop residues to which phosphates and metabolites are attached to block phosphatidylinositol phosphate (PIP) recognition, memteins as functional membrane protein apparatuses, and lipidons as lipid "codons" recognized by membrane readers. At least 5% of the human proteome senses such membrane signals and allows eukaryotic organelles and pathogens to operate and replicate.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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5
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Walpole GFW, Grinstein S. Endocytosis and the internalization of pathogenic organisms: focus on phosphoinositides. F1000Res 2020; 9. [PMID: 32494357 PMCID: PMC7233180 DOI: 10.12688/f1000research.22393.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 12/18/2022] Open
Abstract
Despite their comparatively low abundance in biological membranes, phosphoinositides are key to the regulation of a diverse array of signaling pathways and direct membrane traffic. The role of phosphoinositides in the initiation and progression of endocytic pathways has been studied in considerable depth. Recent advances have revealed that distinct phosphoinositide species feature prominently in clathrin-dependent and -independent endocytosis as well as in phagocytosis and macropinocytosis. Moreover, a variety of intracellular and cell-associated pathogens have developed strategies to commandeer host cell phosphoinositide metabolism to gain entry and/or metabolic advantage, thereby promoting their survival and proliferation. Here, we briefly survey the current knowledge on the involvement of phosphoinositides in endocytosis, phagocytosis, and macropinocytosis and highlight several examples of molecular mimicry employed by pathogens to either “hitch a ride” on endocytic pathways endogenous to the host or create an entry path of their own.
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Affiliation(s)
- Glenn F W Walpole
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Sergio Grinstein
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
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6
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Butenko A, Kostygov AY, Sádlová J, Kleschenko Y, Bečvář T, Podešvová L, Macedo DH, Žihala D, Lukeš J, Bates PA, Volf P, Opperdoes FR, Yurchenko V. Comparative genomics of Leishmania (Mundinia). BMC Genomics 2019; 20:726. [PMID: 31601168 PMCID: PMC6787982 DOI: 10.1186/s12864-019-6126-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/20/2019] [Indexed: 12/31/2022] Open
Abstract
Background Trypanosomatids of the genus Leishmania are parasites of mammals or reptiles transmitted by bloodsucking dipterans. Many species of these flagellates cause important human diseases with clinical symptoms ranging from skin sores to life-threatening damage of visceral organs. The genus Leishmania contains four subgenera: Leishmania, Sauroleishmania, Viannia, and Mundinia. The last subgenus has been established recently and remains understudied, although Mundinia contains human-infecting species. In addition, it is interesting from the evolutionary viewpoint, representing the earliest branch within the genus and possibly with a different type of vector. Here we analyzed the genomes of L. (M.) martiniquensis, L. (M.) enriettii and L. (M.) macropodum to better understand the biology and evolution of these parasites. Results All three genomes analyzed were approximately of the same size (~ 30 Mb) and similar to that of L. (Sauroleishmania) tarentolae, but smaller than those of the members of subgenera Leishmania and Viannia, or the genus Endotrypanum (~ 32 Mb). This difference was explained by domination of gene losses over gains and contractions over expansions at the Mundinia node, although only a few of these genes could be identified. The analysis predicts significant changes in the Mundinia cell surface architecture, with the most important ones relating to losses of LPG-modifying side chain galactosyltransferases and arabinosyltransferases, as well as β-amastins. Among other important changes were gene family contractions for the oxygen-sensing adenylate cyclases and FYVE zinc finger-containing proteins. Conclusions We suggest that adaptation of Mundinia to different vectors and hosts has led to alternative host-parasite relationships and, thereby, made some proteins redundant. Thus, the evolution of genomes in the genus Leishmania and, in particular, in the subgenus Mundinia was mainly shaped by host (or vector) switches.
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Affiliation(s)
- Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budejovice (Budweis), Czech Republic
| | - Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia
| | - Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Yuliya Kleschenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Tomáš Bečvář
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Podešvová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Diego H Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - David Žihala
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budejovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budejovice (Budweis), Czech Republic
| | - Paul A Bates
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.
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7
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Liu K, Guo C, Lao Y, Yang J, Chen F, Zhao Y, Yang Y, Yang J, Yi J. A fine-tuning mechanism underlying self-control for autophagy: deSUMOylation of BECN1 by SENP3. Autophagy 2019; 16:975-990. [PMID: 31373534 DOI: 10.1080/15548627.2019.1647944] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The roles of SUMOylation and the related enzymes in autophagic regulation are unclear. Based on our previous studies that identified the SUMO2/3-specific peptidase SENP3 as an oxidative stress-responsive molecule, we investigated the correlation between SUMOylation and macroautophagy/autophagy. We found that Senp3± mice showed increased autophagy in the liver under basal and fasting conditions, compared to Senp3+/+ mice. We constructed a liver-specific senp3 knockout mouse; these Senp3-deficient liver tissues showed increased autophagy as well. Autophagic flux was accelerated in hepatic and other cell lines following knockdown of SENP3, both before and after the cells underwent starvation in the form of the serum and amino acid deprivation. We demonstrated that BECN1/beclin 1, the core molecule of the BECN1-PIK3C3 complex, could be SUMO3-conjugated by PIAS3 predominantly at K380 and deSUMOylated by SENP3. The basal SUMOylation of BECN1 was increased upon cellular starvation, which enhanced autophagosome formation by facilitating BECN1 interaction with other complex components UVRAG, PIK3C3 and ATG14, thus promoting PIK3C3 activity. In contrast, SENP3 deSUMOylated BECN1, which impaired BECN1-PIK3C3 complex formation or stability to suppress the PIK3C3 activity. DeSUMOylation of BECN1 restrained autophagy induction under basal conditions and especially upon starvation when SENP3 had accumulated in response to the increased generation of reactive oxygen species. Thus, while reversible SUMOylation regulated the degree of autophagy, SENP3 provided an intrinsic overflow valve for fine-tuning autophagy induction. ABBREVIATIONS AL: autolysosome; AP: autophagosome; ATG: autophagy related; ATG14: autophagy related 14; BECN1: beclin 1, autophagy related; cKO: conditional knockout; co-IP: co-immunoprecipitation; CQ: chloroquine; EBSS: Earle's balanced salt solution; GFP: green fluorescent protein; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; NAC: N-acetyl-L-cysteine; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PTM: post-translational modification; RFP: red fluorescent protein; ROS: reactive oxygen species; RUBCN/rubicon: RUN domain and cysteine-rich domain containing, BECN1-interacting protein; SENP3: SUMO specific peptidase 3; shRNA: small hairpin RNA; siRNA: small interfering RNA; SQSTM1: sequestosome 1; SUMO: small ubiquitin-like modifier; UVRAG: UV radiation resistance associated gene.
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Affiliation(s)
- Kejia Liu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Chu Guo
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Yimin Lao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Jie Yang
- Electron Microscopy Core Facilities, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Fei Chen
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology , Shanghai, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai, China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology , Shanghai, China.,CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Jie Yang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Jing Yi
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine , Shanghai, China
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8
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Li Y, Liao S, Li F, Zhu Z. Crystal Structure of the PX Domain of SNX27. BIOCHEMISTRY (MOSCOW) 2019; 84:147-152. [PMID: 31216973 DOI: 10.1134/s0006297919020056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
SNX27 is a component of the retromer complex essential for the recycling of transmembrane receptors. SNX27 contains the N-terminal Phox (PX) domain that binds inositol 1,3-diphosphate (Ins(1,3)P2) and is important for the SNX27 localization. Here, we determined the crystal structure of human SNX27 PX domain by X-ray crystallography. We found that the sulfate ion is located in the positively charged lipid-binding pocket of the PX domain, which mimics the phospholipid recognition. In addition, we modelled the SNX27-PX-Ins(1,3)P2 complex to better understand the mechanism of Ins(1,3)P2 recognition by the PX domain of SNX27.
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Affiliation(s)
- Y Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - S Liao
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - F Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - Z Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
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9
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Eitzen G, Smithers CC, Murray AG, Overduin M. Structure and function of the Fgd family of divergent FYVE domain proteins. Biochem Cell Biol 2019; 97:257-264. [DOI: 10.1139/bcb-2018-0185] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Gary Eitzen
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Cameron C. Smithers
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Allan G. Murray
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
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10
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Fang C, Manes TD, Liu L, Liu K, Qin L, Li G, Tobiasova Z, Kirkiles-Smith NC, Patel M, Merola J, Fu W, Liu R, Xie C, Tietjen GT, Nigrovic PA, Tellides G, Pober JS, Jane-Wit D. ZFYVE21 is a complement-induced Rab5 effector that activates non-canonical NF-κB via phosphoinosotide remodeling of endosomes. Nat Commun 2019; 10:2247. [PMID: 31113953 PMCID: PMC6529429 DOI: 10.1038/s41467-019-10041-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/09/2019] [Indexed: 12/28/2022] Open
Abstract
Complement promotes vascular inflammation in transplant organ rejection and connective tissue diseases. Here we identify ZFYVE21 as a complement-induced Rab5 effector that induces non-canonical NF-κB in endothelial cells (EC). In response to membrane attack complexes (MAC), ZFYVE21 is post-translationally stabilized on MAC+Rab5+ endosomes in a Rab5- and PI(3)P-dependent manner. ZFYVE21 promotes SMURF2-mediated polyubiquitinylation and proteasome-dependent degradation of endosome-associated PTEN to induce vesicular enrichment of PI(3,4,5)P3 and sequential recruitment of activated Akt and NF-κB-inducing kinase (NIK). Pharmacologic alteration of cellular phosphoinositide content with miltefosine reduces ZFYVE21 induction, EC activation, and allograft vasculopathy in a humanized mouse model. ZFYVE21 induction distinctly occurs in response to MAC and is detected in human renal and synovial tissues. Our data identifies ZFYVE21 as a Rab5 effector, defines a Rab5-ZFYVE21-SMURF2-pAkt axis by which it mediates EC activation, and demonstrates a role for this pathway in complement-mediated conditions. Complement activation contributes to vascular inflammation in the contexts of allograft rejection and connective tissue disease. Here Fang et al. identify ZFYVE21 as a novel effector of Rab5 and find it regulates pro-inflammatory NF-κB signaling in endothelial cells in response to complement activation.
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Affiliation(s)
- Caodi Fang
- Division of Cardiovascular Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Thomas D Manes
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Lufang Liu
- Division of Cardiovascular Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kevin Liu
- Division of Cardiovascular Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Lingfeng Qin
- Department of Surgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Guangxin Li
- Department of Surgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Zuzana Tobiasova
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Nancy C Kirkiles-Smith
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Manal Patel
- St. John's College, University of Cambridge, Cambridge, CB2 1TP, UK
| | - Jonathan Merola
- Department of Surgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Whitney Fu
- Division of Cardiovascular Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Rebecca Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Catherine Xie
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Gregory T Tietjen
- Department of Surgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Peter A Nigrovic
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Division of Immunology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - George Tellides
- Department of Surgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Jordan S Pober
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Dan Jane-Wit
- Division of Cardiovascular Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA.
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11
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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12
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Nomaguchi T, Maeda Y, Liang Y, Yoshino T, Asahi T, Tanaka T. Comprehensive analysis of triacylglycerol lipases in the oleaginous diatom Fistulifera solaris JPCC DA0580 with transcriptomics under lipid degradation. J Biosci Bioeng 2018; 126:258-265. [DOI: 10.1016/j.jbiosc.2018.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 12/17/2022]
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13
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Kluska K, Adamczyk J, Krężel A. Metal binding properties, stability and reactivity of zinc fingers. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Overton NLD, Brakhage AA, Thywißen A, Denning DW, Bowyer P. Mutations in EEA1 are associated with allergic bronchopulmonary aspergillosis and affect phagocytosis of Aspergillus fumigatus by human macrophages. PLoS One 2018; 13:e0185706. [PMID: 29547649 PMCID: PMC5856258 DOI: 10.1371/journal.pone.0185706] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/18/2017] [Indexed: 01/05/2023] Open
Abstract
Allergic bronchopulmonary aspergillosis (ABPA) in asthma is a severe, life-affecting disease that potentially affects over 4.8 million people globally. In the UK, ABPA is predominantly caused by the fungus Aspergillus fumigatus. Phagocytosis is important in clearance of this fungus, and Early Endosome Antigen 1 (EEA1) has been demonstrated to be involved in phagocytosis of fungi. We sought to investigate the role of EEA1 mutations and phagocytosis in ABPA. We used exome sequencing to identify variants in EEA1 associated with ABPA. We then cultured monocyte-derived macrophages (MDMs) from 17 ABPA subjects with A. fumigatus conidia, and analyzed phagocytosis and phagolysosome acidification in relation to the presence of these variants. We found that variants in EEA1 were associated with ABPA and with the rate of phagocytosis of A. fumigatus conidia and the acidification of phagolysosomes. MDMs from ABPA subjects carrying the disease associated genotype showed increased acidification and phagocytosis compared to those from ABPA subjects carrying the non-associated genotypes or healthy controls.The identification of ABPA-associated variants in EEA that have functional effects on MDM phagocytosis and phagolysosome acidification of A. fumigatus conidia revolutionizes our understanding of susceptibility to this disease, which may in future benefit patients by earlier identification or improved treatments. We suggest that the increased phagocytosis and acidification observed demonstrates an over-active MDM profile in these patients, resulting in an exaggerated cellular response to the presence of A. fumigatus in the airways.
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Affiliation(s)
- Nicola L. D. Overton
- Manchester Fungal Infection Group (MFIG), Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Andreas Thywißen
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - David W. Denning
- Manchester Fungal Infection Group (MFIG), Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- The National Aspergillosis Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Paul Bowyer
- Manchester Fungal Infection Group (MFIG), Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- * E-mail:
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15
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Wang Y, He T, Herman JG, Linghu E, Yang Y, Fuks F, Zhou F, Song L, Guo M. Methylation of ZNF331 is an independent prognostic marker of colorectal cancer and promotes colorectal cancer growth. Clin Epigenetics 2017; 9:115. [PMID: 29075358 PMCID: PMC5648453 DOI: 10.1186/s13148-017-0417-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/05/2017] [Indexed: 12/22/2022] Open
Abstract
Background ZNF331 was reported to be a transcriptional repressor. Methylation of the promoter region of ZNF331 has been found frequently in human esophageal and gastric cancers. The function and methylation status of ZNF331 remain to be elucidated in human colorectal cancer (CRC). Methods Six colorectal cancer cell lines, 146 cases of primary colorectal cancer samples, and 10 cases of noncancerous colorectal mucosa were analyzed in this study using the following techniques: methylation specific PCR (MSP), qRT-PCR, siRNA, flow cytometry, xenograft mice, MTT, colony formation, and transfection assays. Results Loss of ZNF331 expression was found in DLD1 and SW48 cells, reduced expression was found in SW480, SW620, and HCT116 cells, and high level expression was detected in DKO cells. Complete methylation of the ZNF331 in the promoter region was found in DLD1 and SW48 cells, partial methylation was found in SW480, SW620, and HCT116 cells, and unmethylation was detected in DKO cells. Loss of/reduced expression of ZNF331 is correlated with promoter region methylation. Restoration of ZNF331 expression was induced by 5-aza-2′-deoxycytidine (DAC) in DLD1 and SW48 cells. These results suggest that ZNF331 expression is regulated by promoter region methylation in CRC cells. ZNF331 was methylated in 67.1% (98/146) of human primary colorectal cancer samples. Methylation of ZNF331 was significantly associated with tumor size, overall survival (OS), and disease-free survival (DFS) (p < 0.01, p < 0.01, p < 0.05). Methylation of ZNF331 was an independent poor prognostic marker for 5-year OS and 5-year DFS (both p < 0.05). ZNF331 suppressed cell proliferation and colony formation in CRC cells and suppressed human CRC cell xenograft growth in mice. Conclusions ZNF331 is frequently methylated in human colorectal cancer, and the expression of ZNF331 is regulated by promoter region methylation. Methylation of ZNF331 is a poor prognostic marker of CRC.
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Affiliation(s)
- Yuzhu Wang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China.,Department of Geriatric Digestive System, Chinese PLA Navy General Hospital, 6 Fucheng Road, Beijing, 100048 China
| | - Tao He
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213 USA
| | - Enqiang Linghu
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - Yunsheng Yang
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - François Fuks
- Laboratory of Cancer Epigenetics, Free University of Brussels (U.L.B.), 1070 Brussels, Belgium
| | - Fuyou Zhou
- Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, 455000 China
| | - Linjie Song
- Department of General Surgery, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China.,Medical College of NanKai University, Tianjin, 300071 China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 China
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16
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Lai MY, Lau YL. Screening and identification of host proteins interacting with Toxoplasma gondii SAG2 by yeast two-hybrid assay. Parasit Vectors 2017; 10:456. [PMID: 28969712 PMCID: PMC5625703 DOI: 10.1186/s13071-017-2387-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/17/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The identification of receptors or binding partners of Toxoplasma gondii from humans is an essential activity. Many proteins involved in T. gondii invasion have been characterized, and their contribution for parasite entry has been proposed. However, their molecular interactions remain unclear. RESULTS Yeast two-hybrid (Y2H) experiment was used to identify the binding partners of surface antigens of T. gondii by using SAG2 as bait. Colony PCR was performed and positive clones were sent for sequencing to confirm their identity. The yeast plasmids for true positive clones were rescued by transformation into E. coli TOP 10F' cells. The interplay between bait and prey was confirmed by β-galactosidase assay and co-immunoprecipitation experiment. We detected 20 clones interacting with SAG2 based on a series of the selection procedures. Following the autoactivation and toxicity tests, SAG2 was proven to be a suitable candidate as a bait. Thirteen clones were further examined by small scale Y2H experiment. The results indicated that a strong interaction existed between Homo sapiens zinc finger protein and SAG2, which could activate the expressions of the reporter genes in diploid yeast. Co-immunoprecipitation experiment result indicated the binding between this prey and SAG2 protein was significant (Mann-Whitney U-test: Z = -1.964, P = 0.05). CONCLUSIONS Homo sapiens zinc finger protein was found to interact with SAG2. To improve the understanding of this prey protein's function, advanced investigations need to be carried out.
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Affiliation(s)
- Meng-Yee Lai
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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17
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Xu D, Zhang T, Xiao J, Zhu K, Wei R, Wu Z, Meng H, Li Y, Yuan J. Modification of BECN1 by ISG15 plays a crucial role in autophagy regulation by type I IFN/interferon. Autophagy 2016; 11:617-28. [PMID: 25906440 DOI: 10.1080/15548627.2015.1023982] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
ISG15 (ISG15 ubiquitin-like modifier), a ubiquitin-like protein, is one of the major type I IFN (interferon) effector systems. ISG15 can be conjugated to target proteins (ISGylation) via the stepwise action of E1, E2, and E3 enzymes. Conjugated ISG15 can be removed (deISGylated) from target proteins by USP18 (ubiquitin-specific peptidase 18). Here we investigated the role of deISGylation by USP18 in regulating autophagy and EGFR degradation in cells treated with type I IFNs. We show that type I IFN induced expression of ISG15 leads to ISGylation of BECN1 at Lys117, as well as Lys263, Lys265, and Lys266 which competes with Lys63 ubiquitination of BECN1. We demonstrate that ISGylation of BECN1 at Lys117, as well as Lys263, Lys265, and Lys266 serve an important role in negative regulation of intracellular processes including autophagy and EGFR degradation that are critically dependent upon the activity of class III PtdIns 3-kinase. Our studies provide fundamental new mechanistic insights into the innate immunity response implemented by type I IFNs.
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Key Words
- AKT/PKB, v-akt murine thymoma viral oncogene homolog
- ATG, autophagy-related
- BECN1
- BECN1, Beclin 1, autophagy-related
- EGF, epidermal growth factor
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- HERC5, HECT, and RLD domain containing E3 ubiquitin protein ligase 5
- IFN, interferon
- ISG15
- ISG15, ISG15 ubiquitin-like modifier
- LC3, microtubule-associated protein 1 light chain 3
- MTOR, mechanistic target of rapamycin
- MX1, MX dynamin-like GTPase 1
- PIK3C3, phosphatidylinositol 3-kinase, catalytic subunit type 3
- RPS6KB, ribosomal protein S6 kinase, 70kDa, polypeptide
- SQSTM1/p62, sequestosome 1
- UBA7, ubiquitin-like modifier activating enzyme 7
- USP18
- USP18, ubiquitin specific peptidase 18
- Ub, ubiquitin
- autophagy
- type I IFN
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Affiliation(s)
- Daichao Xu
- a Interdisciplinary Research Center on Biology and Chemistry; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences ; Shanghai , China
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18
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Abstract
Eukaryotic cells have been confronted throughout their evolution with potentially lethal plasma membrane injuries, including those caused by osmotic stress, by infection from bacterial toxins and parasites, and by mechanical and ischemic stress. The wounded cell can survive if a rapid repair response is mounted that restores boundary integrity. Calcium has been identified as the key trigger to activate an effective membrane repair response that utilizes exocytosis and endocytosis to repair a membrane tear, or remove a membrane pore. We here review what is known about the cellular and molecular mechanisms of membrane repair, with particular emphasis on the relevance of repair as it relates to disease pathologies. Collective evidence reveals membrane repair employs primitive yet robust molecular machinery, such as vesicle fusion and contractile rings, processes evolutionarily honed for simplicity and success. Yet to be fully understood is whether core membrane repair machinery exists in all cells, or whether evolutionary adaptation has resulted in multiple compensatory repair pathways that specialize in different tissues and cells within our body.
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Affiliation(s)
- Sandra T Cooper
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia; Discipline of Paediatrics and Child Health, Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia; and Department of Cellular Biology and Anatomy, Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, Georgia
| | - Paul L McNeil
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia; Discipline of Paediatrics and Child Health, Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia; and Department of Cellular Biology and Anatomy, Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, Georgia
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Xhabija B, Vacratsis PO. Receptor-mediated Endocytosis 8 Utilizes an N-terminal Phosphoinositide-binding Motif to Regulate Endosomal Clathrin Dynamics. J Biol Chem 2015; 290:21676-89. [PMID: 26134565 DOI: 10.1074/jbc.m115.644757] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Indexed: 11/06/2022] Open
Abstract
Receptor-mediated endocytosis 8 (RME-8) is a DnaJ domain containing protein implicated in translocation of Hsc70 to early endosomes for clathrin removal during retrograde transport. Previously, we have demonstrated that RME-8 associates with early endosomes in a phosphatidylinositol 3-phosphate (PI(3)P)-dependent fashion. In this study, we have now identified amino acid determinants required for PI(3)P binding within a region predicted to adopt a pleckstrin homology-like fold in the N terminus of RME-8. The ability of RME-8 to associate with PI(3)P and early endosomes is largely abolished when residues Lys(17), Trp(20), Tyr(24), or Arg(26) are mutated resulting in diffuse cytoplasmic localization of RME-8 while maintaining the ability to interact with Hsc70. We also provide evidence that RME-8 PI(3)P binding regulates early endosomal clathrin dynamics and alters the steady state localization of the cation-independent mannose 6-phosphate receptor. Interestingly, RME-8 endosomal association is also regulated by the PI(3)P-binding protein SNX1, a member of the retromer complex. Wild type SNX1 restores endosomal localization of RME-8 W20A, whereas a SNX1 variant deficient in PI(3)P binding disrupts endosomal localization of wild type RME-8. These results further highlight the critical role for PI(3)P in the RME-8-mediated organizational control of various endosomal activities, including retrograde transport.
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Affiliation(s)
- Besa Xhabija
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Panayiotis O Vacratsis
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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20
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Daher W, Morlon-Guyot J, Sheiner L, Lentini G, Berry L, Tawk L, Dubremetz JF, Wengelnik K, Striepen B, Lebrun M. Lipid kinases are essential for apicoplast homeostasis in Toxoplasma gondii. Cell Microbiol 2014; 17:559-78. [PMID: 25329540 DOI: 10.1111/cmi.12383] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 09/26/2014] [Accepted: 10/10/2014] [Indexed: 12/25/2022]
Abstract
Phosphoinositides regulate numerous cellular processes by recruiting cytosolic effector proteins and acting as membrane signalling entities. The cellular metabolism and localization of phosphoinositides are tightly regulated by distinct lipid kinases and phosphatases. Here, we identify and characterize a unique phosphatidylinositol 3 kinase (PI3K) in Toxoplasma gondii, a protozoan parasite belonging to the phylum Apicomplexa. Conditional depletion of this enzyme and subsequently of its product, PI(3)P, drastically alters the morphology and inheritance of the apicoplast, an endosymbiotic organelle of algal origin that is a unique feature of many Apicomplexa. We searched the T. gondii genome for PI(3)P-binding proteins and identified in total six PX and FYVE domain-containing proteins including a PIKfyve lipid kinase, which phosphorylates PI(3)P into PI(3,5)P2 . Although depletion of putative PI(3)P-binding proteins shows that they are not essential for parasite growth and apicoplast biology, conditional disruption of PIKfyve induces enlarged apicoplasts, as observed upon loss of PI(3)P. A similar defect of apicoplast homeostasis was also observed by knocking down the PIKfyve regulatory protein ArPIKfyve, suggesting that in T. gondii, PI(3)P-related function for the apicoplast might mainly be to serve as a precursor for the synthesis of PI(3,5)P2 . Accordingly, PI3K is conserved in all apicomplexan parasites whereas PIKfyve and ArPIKfyve are absent in Cryptosporidium species that lack an apicoplast, supporting a direct role of PI(3,5)P2 in apicoplast homeostasis. This study enriches the already diverse functions attributed to PI(3,5)P2 in eukaryotic cells and highlights these parasite lipid kinases as potential drug targets.
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Affiliation(s)
- Wassim Daher
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR5235 CNRS, Université de Montpellier 1 et 2, Montpellier, France
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21
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Abstract
Membrane trafficking depends on transport vesicles and carriers docking and fusing with the target organelle for the delivery of cargo. Membrane tethers and small guanosine triphosphatases (GTPases) mediate the docking of transport vesicles/carriers to enhance the efficiency of the subsequent SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor)-mediated fusion event with the target membrane bilayer. Different classes of membrane tethers and their specific intracellular location throughout the endomembrane system are now well defined. Recent biochemical and structural studies have led to a deeper understanding of the mechanism by which membrane tethers mediate docking of membrane carriers as well as an appreciation of the role of tethers in coordinating the correct SNARE complex and in regulating the organization of membrane compartments. This review will summarize the properties and roles of membrane tethers of both secretory and endocytic systems.
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Affiliation(s)
- Pei Zhi Cheryl Chia
- National Institute of Dental and Craniofacial Research, National Institutes of Health30 Convent Drive, Bethesda, MD 20892-4340USA
| | - Paul A. Gleeson
- The Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute30 Flemington Road, The University of Melbourne, Victoria 3010Australia
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22
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Kümmel D, Ungermann C. Principles of membrane tethering and fusion in endosome and lysosome biogenesis. Curr Opin Cell Biol 2014; 29:61-6. [PMID: 24813801 DOI: 10.1016/j.ceb.2014.04.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/15/2014] [Accepted: 04/23/2014] [Indexed: 11/29/2022]
Abstract
Endosomes and lysosomes receive cargo via vesicular carriers that arrive along multiple trafficking routes. On both organelles, tethering proteins have been identified that interact specifically with Rab5 on endosomes and Rab7 on late endosomes/lysosomes and that facilitate the SNARE-driven membrane fusion. Even though the structure and stoichiometry of the involved proteins and protein complexes differ strongly, they may operate by similar principles. Within this review, we will provide insights into their common functions and discuss the open questions in the field.
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Affiliation(s)
- Daniel Kümmel
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry Section, Barbarastrasse 13, Osnabrück 49076, Germany.
| | - Christian Ungermann
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry Section, Barbarastrasse 13, Osnabrück 49076, Germany.
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23
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Mageswaran SK, Dixon MG, Curtiss M, Keener JP, Babst M. Binding to any ESCRT can mediate ubiquitin-independent cargo sorting. Traffic 2013; 15:212-29. [PMID: 24148098 DOI: 10.1111/tra.12135] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/18/2013] [Accepted: 10/18/2013] [Indexed: 11/28/2022]
Abstract
The ESCRT (endosomal sorting complex required for transport) machinery is known to sort ubiquitinated transmembrane proteins into vesicles that bud into the lumen of multivesicular bodies (MVBs). Although the ESCRTs themselves are ubiquitinated they are excluded from the intraluminal vesicles and recycle back to the cytoplasm for further rounds of sorting. To obtain insights into the rules that distinguish ESCRT machinery from cargo we analyzed the trafficking of artificial ESCRT-like protein fusions. These studies showed that lowering ESCRT-binding affinity converts a protein from behaving like ESCRT machinery into cargo of the MVB pathway, highlighting the close relationship between machinery and the cargoes they sort. Furthermore, our findings give insights into the targeting of soluble proteins into the MVB pathway and show that binding to any of the ESCRTs can mediate ubiquitin-independent MVB sorting.
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Affiliation(s)
- Shrawan Kumar Mageswaran
- Center for Cell and Genome Science and Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
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24
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Abstract
Phosphoinositides (PIs) make up only a small fraction of cellular phospholipids, yet they control almost all aspects of a cell's life and death. These lipids gained tremendous research interest as plasma membrane signaling molecules when discovered in the 1970s and 1980s. Research in the last 15 years has added a wide range of biological processes regulated by PIs, turning these lipids into one of the most universal signaling entities in eukaryotic cells. PIs control organelle biology by regulating vesicular trafficking, but they also modulate lipid distribution and metabolism via their close relationship with lipid transfer proteins. PIs regulate ion channels, pumps, and transporters and control both endocytic and exocytic processes. The nuclear phosphoinositides have grown from being an epiphenomenon to a research area of its own. As expected from such pleiotropic regulators, derangements of phosphoinositide metabolism are responsible for a number of human diseases ranging from rare genetic disorders to the most common ones such as cancer, obesity, and diabetes. Moreover, it is increasingly evident that a number of infectious agents hijack the PI regulatory systems of host cells for their intracellular movements, replication, and assembly. As a result, PI converting enzymes began to be noticed by pharmaceutical companies as potential therapeutic targets. This review is an attempt to give an overview of this enormous research field focusing on major developments in diverse areas of basic science linked to cellular physiology and disease.
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Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
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25
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Ramanathan HN, Zhang G, Ye Y. Monoubiquitination of EEA1 regulates endosome fusion and trafficking. Cell Biosci 2013; 3:24. [PMID: 23701900 PMCID: PMC3673817 DOI: 10.1186/2045-3701-3-24] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 04/24/2013] [Indexed: 02/07/2023] Open
Abstract
Background Early endosomal autoantigen 1 (EEA1) is a membrane tethering factor required for the fusion and maturation of early endosomes in endocytosis. How the activity of EEA1 is regulated in cells is unclear. Results Here we show that endogenous EEA1 is prone to monoubiquitination at multiple sites, owing to an intrinsic affinity to ubiquitin conjugating enzymes (E2). The E2 interactions enable a ubiquitin ligase (E3) independent mechanism that decorate EEA1 with multiple mono-ubiquitin moieties. Expression of an ubiquitin-EEA1 chimera that mimics native mono-ubiquitinated EEA1 generates giant endosomes abutting the nucleus. Several lines of evidence suggest that this phenotype is due to increased endosome fusion and a simultaneous blockade on an endosome recycling pathway. The latter is likely caused by diminished endosome fission in cells expressing ubiquitin-EEA1. Conclusion Our results demonstrate that ubiquitination may dramatically affect the activity of an endosome fusion factor to alter endosome morphology and trafficking pattern, and thereby implicating an unexpected role of ubiquitin signaling in endocytosis.
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Affiliation(s)
- Harish N Ramanathan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 center drive, Bethesda, MD 20892, USA.
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26
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Petralia RS, Schwartz CM, Wang YX, Kawamoto EM, Mattson MP, Yao PJ. Sonic hedgehog promotes autophagy in hippocampal neurons. Biol Open 2013; 2:499-504. [PMID: 23789099 PMCID: PMC3654269 DOI: 10.1242/bio.20134275] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/20/2013] [Indexed: 01/07/2023] Open
Abstract
The Sonic hedgehog (Shh) signaling pathway is well known in patterning of the neural tube during embryonic development, but its emerging role in differentiated neurons is less understood. Here we report that Shh enhances autophagy in cultured hippocampal neurons. Microarray analysis reveals the upregulation of multiple autophagy-related genes in neurons in response to Shh application. Through analysis of the autophagy-marker LC3 by immunoblot analysis and immunocytochemistry, we confirm activation of the autophagy pathway in Shh-exposed neurons. Using electron microscopy, we find autophagosomes and associated structures with a wide range of morphologies in synaptic terminals of Shh-exposed neurons. Moreover, we show that Shh-triggered autophagy depends on class III Phosphatidylinositol 3-kinase complexes (PtdIns3K). These results identify a link between Shh and autophagy pathways and, importantly, provide a lead for further understanding the physiology of Shh signaling activity in neurons.
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27
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Catimel B, Kapp E, Yin MX, Gregory M, Wong LSM, Condron M, Church N, Kershaw N, Holmes AB, Burgess AW. The PI(3)P interactome from a colon cancer cell. J Proteomics 2013; 82:35-51. [DOI: 10.1016/j.jprot.2013.01.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/21/2012] [Accepted: 01/24/2013] [Indexed: 02/07/2023]
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28
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Yokogawa M, Kobashigawa Y, Yoshida N, Ogura K, Harada K, Inagaki F. NMR analyses of the interaction between the FYVE domain of early endosome antigen 1 (EEA1) and phosphoinositide embedded in a lipid bilayer. J Biol Chem 2012; 287:34936-34945. [PMID: 22915584 DOI: 10.1074/jbc.m112.398255] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphoinositides (PIs) are crucial lipid components of membranes and are involved in a number of cellular processes through interactions with their effector proteins. Recently, we have established a lipid-protein nanoscale bilayer (nanodisc) containing PIs, hereafter referred to as PI-nanodisc and demonstrated that it could be used for both qualitative and quantitative evaluations of protein-membrane interactions. Here, we report further NMR analyses for obtaining structural insights at the residue-specific level between PI-binding effector protein and PI-nanodisc, using the FYVE domain of early endosome antigen 1 (EEA1), denoted as EEA1 FYVE, and PI(3)P-nanodisc as a model system. We performed a combination of the NMR analyses including chemical shift perturbation, transferred cross-saturation, and paramagnetic relaxation enhancement experiments. These enabled an identification of the interaction surface, structural change, and relative orientation of EEA1 FYVE to the PI(3)P-incorporated lipid bilayer, substantiating that NMR analyses of protein-membrane interactions using nanodisc makes it possible to show the residue-specific interactions in the lipid bilayer environment.
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Affiliation(s)
- Mariko Yokogawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | | | - Naoki Yoshida
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenji Ogura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Kohsuke Harada
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Fuyuhiko Inagaki
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
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Abstract
Phosphoinositides are important regulators of cellular homoeostasis and numerous signal-transduction pathways. One of their major features is their ability to recruit signalling proteins to membranes by direct interaction with phosphoinositide-binding modules. The distribution and dynamics of membrane phosphoinositides are therefore major determinants in the spatiotemporal control of cell signalling and membrane trafficking. However, standard biochemical approaches cannot reveal the dynamics of phosphoinositides at the single-cell level. A major technical advance has been the development of genetically encoded fluorescent phosphoinositide probes on the basis of the phosphoinositide-binding domains found in signalling proteins, such as the PH (pleckstrin homology) domain. This review describes the diverse fluorescent phosphoinositide probes available for imaging specific phosphoinositide species and how their use has improved the understanding of phosphoinositide signalling at the single-cell level.
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Affiliation(s)
- Guillaume Halet
- Department of Physiology, University College London, Gower Street, London WC1E 6BT, UK.
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Schuh AL, Audhya A. Phosphoinositide signaling during membrane transport in Saccharomyces cerevisiae. Subcell Biochem 2012; 59:35-63. [PMID: 22374087 DOI: 10.1007/978-94-007-3015-1_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Phosphatidylinositol (PI) is distinct from other phospholipids, possessing a head group that can be modified by phosphorylation at multiple positions to generate unique signaling molecules collectively known as phosphoinositides. The set of kinases and phosphatases that regulate PI metabolism are conserved throughout eukaryotic evolution, and numerous studies have demonstrated that phosphoinositides regulate a diverse spectrum of cellular processes, including vesicle transport, cell proliferation, and cytoskeleton organization. Over the past two decades, nearly all PI derivatives have been shown to interact directly with cellular proteins to affect their localization and/or activity. Additionally, there is growing evidence, which suggests that phosphoinositides may also affect local membrane topology. Here, we focus on the role of phosphoinositides in membrane trafficking and underscore the significant role that yeast has played in the field.
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Affiliation(s)
- Amber L Schuh
- Department of Biomolecular Chemistry, University of Wisconsin-Madison Medical School, 1300 University Avenue, WI, 53706, Madison, USA
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31
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Slabbaert JR, Khuong TM, Verstreken P. Phosphoinositides at the Neuromuscular Junction of Drosophila melanogaster: A Genetic Approach. Methods Cell Biol 2012; 108:227-47. [DOI: 10.1016/b978-0-12-386487-1.00012-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
The endo-lysosomal system is an interconnected tubulo-vesicular network that acts as a sorting station to process and distribute internalised cargo. This network accepts cargoes from both the plasma membrane and the biosynthetic pathway, and directs these cargos either towards the lysosome for degradation, the peri-nuclear recycling endosome for return to the cell surface, or to the trans-Golgi network. These intracellular membranes are variously enriched in different phosphoinositides that help to shape compartmental identity. These lipids act to localise a number of phosphoinositide-binding proteins that function as sorting machineries to regulate endosomal cargo sorting. Herein we discuss regulation of these machineries by phosphoinositides and explore how phosphoinositide-switching contributes toward sorting decisions made at this platform.
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Affiliation(s)
- Peter J Cullen
- Henry Wellcome Integrated Signaling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, BS8 1TD, Bristol, United Kingdom,
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Bawolak MT, Lodge R, Morissette G, Marceau F. Bradykinin B2 receptor-mediated transport into intact cells: Anti-receptor antibody-based cargoes. Eur J Pharmacol 2011; 668:107-14. [DOI: 10.1016/j.ejphar.2011.06.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 06/09/2011] [Accepted: 06/23/2011] [Indexed: 12/26/2022]
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Nagano M, Hoshino D, Koshiba S, Shuo T, Koshikawa N, Tomizawa T, Hayashi F, Tochio N, Harada T, Akizawa T, Watanabe S, Handa N, Shirouzu M, Kigawa T, Yokoyama S, Seiki M. ZF21 protein, a regulator of the disassembly of focal adhesions and cancer metastasis, contains a novel noncanonical pleckstrin homology domain. J Biol Chem 2011; 286:31598-609. [PMID: 21768110 PMCID: PMC3173091 DOI: 10.1074/jbc.m110.199430] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 07/09/2011] [Indexed: 12/20/2022] Open
Abstract
Directional migration of adherent cells on an extracellular matrix requires repeated formation and disassembly of focal adhesions (FAs). Directional migration of adherent cells We have identified ZF21 as a regulator of disassembly of FAs and cell migration, and increased expression of the gene has been linked to metastatic colon cancer. ZF21 is a member of a protein family characterized by the presence of the FYVE domain, which is conserved among Fab1p, YOPB, Vps27p, and EEA1 proteins, and has been shown to mediate the binding of such proteins to phosphoinositides in the lipid layers of cell membranes. ZF21 binds multiple factors that promote disassembly of FAs such as FAK, β-tubulin, m-calpain, and SHP-2. ZF21 does not contain any other known protein motifs other than the FYVE domain, but a region of the protein C-terminal to the FYVE domain is sufficient to mediate binding to β-tubulin. In this study, we demonstrate that the C-terminal region is important for the ability of ZF21 to induce disassembly of FAs and cell migration, and to promote an early step of experimental metastasis to the lung in mice. In light of the importance of the C-terminal region, we analyzed its ternary structure using NMR spectroscopy. We demonstrate that this region exhibits a structure similar to that of a canonical pleckstrin homology domain, but that it lacks a positively charged interface to bind phosphatidylinositol phosphate. Thus, ZF21 contains a novel noncanonical PH-like domain that is a possible target to develop a therapeutic strategy to treat metastatic cancer.
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Affiliation(s)
- Makoto Nagano
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
- the Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotogecho, Hirakata Osaka, 573-0101
| | - Daisuke Hoshino
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Seizo Koshiba
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takuya Shuo
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Naohiko Koshikawa
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Tadashi Tomizawa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Fumiaki Hayashi
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Naoya Tochio
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takushi Harada
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Toshifumi Akizawa
- the Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotogecho, Hirakata Osaka, 573-0101
| | - Satoru Watanabe
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Noriko Handa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Mikako Shirouzu
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takanori Kigawa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuda-cho, Midori-ku, Yokohama 226-8502, and
| | - Shigeyuki Yokoyama
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motoharu Seiki
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
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Ramanathan HN, Ye Y. The p97 ATPase associates with EEA1 to regulate the size of early endosomes. Cell Res 2011; 22:346-59. [PMID: 21556036 DOI: 10.1038/cr.2011.80] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The AAA (ATPase-associated with various cellular activities) ATPase p97 acts on diverse substrate proteins to partake in various cellular processes such as membrane fusion and endoplasmic reticulum-associated degradation (ERAD). In membrane fusion, p97 is thought to function in analogy to the related ATPase NSF (N-ethylmaleimide-sensitive fusion protein), which promotes membrane fusion by disassembling a SNARE complex. In ERAD, p97 dislocates misfolded proteins from the ER membrane to facilitate their turnover by the proteasome. Here, we identify a novel function of p97 in endocytic trafficking by establishing the early endosomal autoantigen 1 (EEA1) as a new p97 substrate. We demonstrate that a fraction of p97 is localized to the early endosome membrane, where it binds EEA1 via the N-terminal C2H2 zinc finger domain. Inhibition of p97 either by siRNA or a pharmacological inhibitor results in clustering and enlargement of early endosomes, which is associated with an altered trafficking pattern for an endocytic cargo. Mechanistically, we show that p97 inhibition causes increased EEA1 self-association at the endosome membrane. We propose that p97 may regulate the size of early endosomes by governing the oligomeric state of EEA1.
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Affiliation(s)
- Harish N Ramanathan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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36
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Fernandes F, Chen K, Ehrlich LS, Jin J, Chen MH, Medina GN, Symons M, Montelaro R, Donaldson J, Tjandra N, Carter CA. Phosphoinositides direct equine infectious anemia virus gag trafficking and release. Traffic 2011; 12:438-51. [PMID: 21176037 PMCID: PMC3064743 DOI: 10.1111/j.1600-0854.2010.01153.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphatidylinositol 4,5-biphosphate [PI(4,5)P(2) ], the predominant phosphoinositide (PI) on the plasma membrane, binds the matrix (MA) protein of human immunodeficiency virus type 1 (HIV-1) and equine infectious anemia virus (EIAV) with similar affinities in vitro. Interaction with PI(4,5)P(2) is critical for HIV-1 assembly on the plasma membrane. EIAV has been shown to localize in internal compartments; hence, the significance of its interaction with PI(4,5)P(2) is unclear. We therefore investigated the binding in vitro of other PIs to EIAV MA and whether intracellular association with compartments bearing these PIs was important for assembly and release of virus-like particles (VLPs) formed by Gag. In vitro, EIAV MA bound phosphatidylinositol 3-phosphate [PI(3)P] with higher affinity than PI(4,5)P(2) as revealed by nuclear magnetic resonance (NMR) spectra upon lipid titration. Gag was detected on the plasma membrane and in compartments enriched in phosphatidylinositol 3,5-biphosphate [PI(3,5)P(2) ]. Treatment of cells with YM201636, a kinase inhibitor that blocks production of PI(3,5)P(2) from PI(3)P, caused Gag to colocalize with aberrant compartments and inhibited VLP release. In contrast to HIV-1, release of EIAV VLPs was not significantly diminished by coexpression with 5-phosphatase IV, an enzyme that specifically depletes PI(4,5)P(2) from the plasma membrane. However, coexpression with synaptojanin 2, a phosphatase with broader specificity, diminished VLP production. PI-binding pocket mutations caused striking budding defects, as revealed by electron microscopy. One of the mutations also modified Gag-Gag interaction, as suggested by altered bimolecular fluorescence complementation. We conclude that PI-mediated targeting to peripheral and internal membranes is a critical factor in EIAV assembly and release.
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Affiliation(s)
- Fiona Fernandes
- Dept. of Molecular Genetics & Microbiology, S.U.N.Y, Stony Brook, NY 11727, USA
| | - Kang Chen
- Laboratory of Molecular Biophysics, NHLBI-NIH, Bethesda, MD 20892, USA
| | - Lorna S. Ehrlich
- Dept. of Molecular Genetics & Microbiology, S.U.N.Y, Stony Brook, NY 11727, USA
| | - Jing Jin
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Min H. Chen
- Dept. of Molecular Genetics & Microbiology, S.U.N.Y, Stony Brook, NY 11727, USA
| | - Gisselle N. Medina
- Dept. of Molecular Genetics & Microbiology, S.U.N.Y, Stony Brook, NY 11727, USA
| | - Marc Symons
- Feinstein Institute, Manhasset, NY 11030, USA
| | - Ronald Montelaro
- Dept. of Microbiology and Molecular Genetics, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | - Julie Donaldson
- Laboratory of Cell Biology, NHLBI-NIH, Bethesda, MD 20892, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, NHLBI-NIH, Bethesda, MD 20892, USA
| | - Carol A. Carter
- Dept. of Molecular Genetics & Microbiology, S.U.N.Y, Stony Brook, NY 11727, USA
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Haughey NJ, Tovar-y-Romo LB, Bandaru VVR. Roles for biological membranes in regulating human immunodeficiency virus replication and progress in the development of HIV therapeutics that target lipid metabolism. J Neuroimmune Pharmacol 2011; 6:284-95. [PMID: 21445582 DOI: 10.1007/s11481-011-9274-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 03/08/2011] [Indexed: 01/14/2023]
Abstract
Infection by the human immunodeficiency virus (HIV) involves a number of important interactions with lipid components in host membranes that regulate binding, fusion, internalization, and viral assembly. Available data suggests that HIV actively modifies the sphingolipid content of cellular membranes to create focal environments that are favorable for infection. In this review, we summarize the roles that membrane lipids play in HIV infection and discuss the current status of therapeutics that attempt to modify biological membranes to inhibit HIV.
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Affiliation(s)
- Norman J Haughey
- Department of Neurology, Richard T. Johnson Division of Neuroimmunology and Neurological Infections, The Johns Hopkins University School of Medicine, Meyer 6-109, 600N. Wolfe Street, Baltimore, MD 21287, USA.
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Samson RY, Obita T, Hodgson B, Shaw MK, Chong PLG, Williams RL, Bell SD. Molecular and structural basis of ESCRT-III recruitment to membranes during archaeal cell division. Mol Cell 2011; 41:186-96. [PMID: 21255729 DOI: 10.1016/j.molcel.2010.12.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/22/2010] [Accepted: 11/04/2010] [Indexed: 02/06/2023]
Abstract
Members of the crenarchaeal kingdom, such as Sulfolobus, divide by binary fission yet lack genes for the otherwise near-ubiquitous tubulin and actin superfamilies of cytoskeletal proteins. Recent work has established that Sulfolobus homologs of the eukaryotic ESCRT-III and Vps4 components of the ESCRT machinery play an important role in Sulfolobus cell division. In eukaryotes, several pathways recruit ESCRT-III proteins to their sites of action. However, the positioning determinants for archaeal ESCRT-III are not known. Here, we identify a protein, CdvA, that is responsible for recruiting Sulfolobus ESCRT-III to membranes. Overexpression of the isolated ESCRT-III domain that interacts with CdvA results in the generation of nucleoid-free cells. Furthermore, CdvA and ESCRT-III synergize to deform archaeal membranes in vitro. The structure of the CdvA/ESCRT-III interface gives insight into the evolution of the more complex and modular eukaryotic ESCRT complex.
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Affiliation(s)
- Rachel Y Samson
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
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Kano F, Arai T, Matsuto M, Hayashi H, Sato M, Murata M. Hydrogen peroxide depletes phosphatidylinositol-3-phosphate from endosomes in a p38 MAPK-dependent manner and perturbs endocytosis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:784-801. [PMID: 21277337 DOI: 10.1016/j.bbamcr.2011.01.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 01/14/2011] [Accepted: 01/20/2011] [Indexed: 01/08/2023]
Abstract
Phosphatidylinositol-3-phosphate (PI3P) is a lipid that is enriched specifically in early endosomes. Given that early endosomes containing PI3P act as a microdomain to recruit proteins that contain a PI3P-binding domain (FYVE domain), the equilibrium between the production and degradation of PI3P influences a variety of processes, including endocytosis and signal transduction via endosomes. In the study reported herein, we have developed a novel analytical method to quantify the amount of PI3P in endosomes by introducing a GST-2xFYVE protein probe into semi-intact cells. The GST-2xFYVE probe was targeted specifically to intracellular PI3P-containing endosomes, which retained their small punctate structure, and allowed the semi-quantitative measurement of intracellular PI3P. Using the method, we found that treatment of HeLa cells with H(2)O(2) decreased the amount of PI3P in endosomes in a p38 MAPK-dependent manner. In addition, H(2)O(2) treatment delayed transport through various endocytic pathways, especially post-early endosome transport; the retrograde transport of cholera toxin was especially dependent on the amount of PI3P in endosomes. This article is part of a Special Issue entitled: 11th European Symposium on Calcium.
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Affiliation(s)
- Fumi Kano
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan
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Kobashigawa Y, Harada K, Yoshida N, Ogura K, Inagaki F. Phosphoinositide-incorporated lipid-protein nanodiscs: A tool for studying protein-lipid interactions. Anal Biochem 2010; 410:77-83. [PMID: 21094116 DOI: 10.1016/j.ab.2010.11.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 11/10/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
Abstract
Phosphatidylinositol (PtdIns) is phosphorylated at D-3, D-4, and/or D-5 of the inositol ring to produce seven distinct lipid second messengers known as phosphoinositides (PIs). The PI level is temporally and spatially controlled at the cytosolic face of the cellular membrane. Effectors containing PI-binding domains (e.g., PH, PX, FYVE, ENTH, FERM) associate with specific PIs. This process is crucial for the localization of a variety of cell-signaling proteins, thereby regulating intracellular membrane trafficking, cell growth and survival, cytoskeletal organization, and so on. However, quantitative assessments of protein-PI interactions are generally difficult due to insolubility of PIs in aqueous solution. Here we incorporated PIs into a lipid-protein nanoscale bilayer (nanodisc), which is applied for studying the protein-PI interactions using pull-down binding assay, fluorescence polarization, and nuclear magnetic resonance studies, each facilitating fast, quantitative, and residue-specific evaluation of the protein-PI interactions. Therefore, the PI-incorporated nanodisc could be used as a versatile tool for studying the protein-lipid interactions by various biochemical and biophysical techniques.
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Affiliation(s)
- Yoshihiro Kobashigawa
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo 001-0021, Japan
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41
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Haughey NJ. Sphingolipids in neurodegeneration. Neuromolecular Med 2010; 12:301-5. [PMID: 20737248 DOI: 10.1007/s12017-010-8135-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 08/13/2010] [Indexed: 11/24/2022]
Abstract
Although the brain contains a high content of sphingolipids, we know relatively little about the roles that sphingolipids play in regulating neural functions. Once regarded only for their structural roles in maintaining the integrity of cellular and sub-cellular compartments, it is now apparent that many sphingolipid species are biologically active and play important roles in regulating signaling events. Recent technological and scientific advances are rapidly increasing our knowledge of the roles that sphingolipids play in regulating normal neural activity. Likewise, we are beginning to understand how perturbations in sphingolipid metabolism contribute to the pathogenesis of a variety of neurodegenerative conditions. In this special issue of NeuroMolecular Medicine, we present a series of review articles that summarize new and emerging technologies for the analysis of sphingolipids, sphingolipid metabolic pathways, and how dysfunctions in sphingolipid metabolism contribute to neurodegeneration in lysosomal storage disorders, Alzheimer's disease and Multiple Sclerosis.
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Affiliation(s)
- Norman J Haughey
- Department of Neurology, Richard T. Johnson Division of Neuroimmunology and Neurological Infections, The Johns Hopkins University School of Medicine, Meyer 6-109, 600 North Wolfe Street, Baltimore, MD 21287, USA.
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Wywial E, Singh SM. Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana. BMC PLANT BIOLOGY 2010; 10:157. [PMID: 20678208 PMCID: PMC3017826 DOI: 10.1186/1471-2229-10-157] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 08/02/2010] [Indexed: 05/02/2023]
Abstract
BACKGROUND FYVE domains have emerged as membrane-targeting domains highly specific for phosphatidylinositol 3-phosphate (PtdIns(3)P). They are predominantly found in proteins involved in various trafficking pathways. Although FYVE domains may function as individual modules, dimers or in partnership with other proteins, structurally, all FYVE domains share a fold comprising two small characteristic double-stranded beta-sheets, and a C-terminal alpha-helix, which houses eight conserved Zn2+ ion-binding cysteines. To date, the structural, biochemical, and biophysical mechanisms for subcellular targeting of FYVE domains for proteins from various model organisms have been worked out but plant FYVE domains remain noticeably under-investigated. RESULTS We carried out an extensive examination of all Arabidopsis FYVE domains, including their identification, classification, molecular modeling and biophysical characterization using computational approaches. Our classification of fifteen Arabidopsis FYVE proteins at the outset reveals unique domain architectures for FYVE containing proteins, which are not paralleled in other organisms. Detailed sequence analysis and biophysical characterization of the structural models are used to predict membrane interaction mechanisms previously described for other FYVE domains and their subtle variations as well as novel mechanisms that seem to be specific to plants. CONCLUSIONS Our study contributes to the understanding of the molecular basis of FYVE-based membrane targeting in plants on a genomic scale. The results show that FYVE domain containing proteins in plants have evolved to incorporate significant differences from those in other organisms implying that they play a unique role in plant signaling pathways and/or play similar/parallel roles in signaling to other organisms but use different protein players/signaling mechanisms.
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Affiliation(s)
- Ewa Wywial
- Department of Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| | - Shaneen M Singh
- Department of Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
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Abstract
The ESCRT machinery consists of the peripheral membrane protein complexes ESCRT-0, -I, -II, -III, and Vps4-Vta1, and the ALIX homodimer. The ESCRT system is required for degradation of unneeded or dangerous plasma membrane proteins; biogenesis of the lysosome and the yeast vacuole; the budding of most membrane enveloped viruses; the membrane abscission step in cytokinesis; macroautophagy; and several other processes. From their initial discovery in 2001-2002, the literature on ESCRTs has grown exponentially. This review will describe the structure and function of the six complexes noted above and summarize current knowledge of their mechanistic roles in cellular pathways and in disease.
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Affiliation(s)
- James H Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, USA.
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Negative regulation of Vps34 by Cdk mediated phosphorylation. Mol Cell 2010; 38:500-11. [PMID: 20513426 DOI: 10.1016/j.molcel.2010.05.009] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/30/2009] [Accepted: 04/01/2010] [Indexed: 11/20/2022]
Abstract
Vacuolar protein sorting 34 (Vps34) complexes, the class III PtdIns3 kinase, specifically phosphorylate the D3 position of PtdIns to produce PtdIns3P. Vps34 is involved in the control of multiple key intracellular membrane trafficking pathways including endocytic sorting and autophagy. In mammalian cells, Vps34 interacts with Beclin 1, an ortholog of Atg6 in yeast, to regulate the production of PtdIns3P and autophagy. We show that Vps34 is phosphorylated on Thr159 by Cdk1, which negatively regulates its interaction with Beclin 1 during mitosis. Cdk5/p25, a neuronal Cdk shown to play a role in Alzheimer's disease, can also phosphorylate Thr159 of Vps34. Phosphorylation of Vps34 on Thr159 inhibits its interaction with Beclin 1. We propose that phosphorylation of Thr159 in Vps34 is a key regulatory mechanism that controls the class III PtdIns3 kinase activity in cell-cycle progression, development, and human diseases including neurodegeneration and cancers.
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Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1). Proc Natl Acad Sci U S A 2010; 107:10866-71. [PMID: 20534488 DOI: 10.1073/pnas.1000843107] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Regulation of endosomal trafficking by Rab GTPases depends on selective interactions with multivalent effectors, including EEA1 and Rabenosyn-5, which facilitate endosome tethering, sorting, and fusion. Both EEA1 and Rabenosyn-5 contain a distinctive N-terminal C(2)H(2) zinc finger that binds Rab5. How these C(2)H(2) zinc fingers recognize Rab GTPases remains unknown. Here, we report the crystal structure of Rab5A in complex with the EEA1 C(2)H(2) zinc finger. The binding interface involves all elements of the zinc finger as well as a short N-terminal extension but is restricted to the switch and interswitch regions of Rab5. High selectivity for Rab5 and, to a lesser extent Rab22, is observed in quantitative profiles of binding to Rab family GTPases. Although critical determinants are identified in both switch regions, Rab4-to-Rab5 conversion-of-specificity mutants reveal an essential requirement for additional substitutions in the proximal protein core that are predicted to indirectly influence recognition through affects on the structure and conformational stability of the switch regions.
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HOPS prevents the disassembly of trans-SNARE complexes by Sec17p/Sec18p during membrane fusion. EMBO J 2010; 29:1948-60. [PMID: 20473271 DOI: 10.1038/emboj.2010.97] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 04/20/2010] [Indexed: 01/16/2023] Open
Abstract
SNARE-dependent membrane fusion requires the disassembly of cis-SNARE complexes (formed by SNAREs anchored to one membrane) followed by the assembly of trans-SNARE complexes (SNAREs anchored to two apposed membranes). Although SNARE complex disassembly and assembly might be thought to be opposing reactions, the proteins promoting disassembly (Sec17p/Sec18p) and assembly (the HOPS complex) work synergistically to support fusion. We now report that trans-SNARE complexes formed during vacuole fusion are largely associated with Sec17p. Using a reconstituted proteoliposome fusion system, we show that trans-SNARE complex, like cis-SNARE complex, is sensitive to Sec17p/Sec18p mediated disassembly. Strikingly, HOPS inhibits the disassembly of SNARE complexes in the trans-, but not in the cis-, configuration. This selective HOPS preservation of trans-SNARE complexes requires HOPS:SNARE recognition and is lost when the apposed bilayers are dissolved in Triton X-100; it is also observed during fusion of isolated vacuoles. HOPS thus directs the Sec17p/Sec18p chaperone system to maximize functional trans-SNARE complex for membrane fusion, a new role of tethering factors during membrane traffic.
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47
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PfPI3K, a phosphatidylinositol-3 kinase from Plasmodium falciparum, is exported to the host erythrocyte and is involved in hemoglobin trafficking. Blood 2010; 115:2500-7. [PMID: 20093402 DOI: 10.1182/blood-2009-08-238972] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Polyphosphorylated phosphoinositides (PIPs) are potent second messengers, which trigger a wide variety of signaling and trafficking events in most eukaryotic cells. However, the role and metabolism of PIPs in malaria parasite Plasmodium have remained largely unexplored. Our present studies suggest that PfPI3K, a novel phosphatidylinositol-3-kinase (PI3K) in Plasmodium falciparum, is exported to the host erythrocyte by the parasite in an active form. PfPI3K is a versatile enzyme as it can generate various 3'-phosphorylated PIPs. In the parasite, PfPI3K was localized in vesicular compartments near the membrane and in its food vacuole. PI3K inhibitors wortmannin and LY294002 were effective against PfPI3K and were used to study PfPI3K function. We found that PfPI3K is involved in endocytosis from the host and trafficking of hemoglobin in the parasite. The inhibition of PfPI3K resulted in entrapment of hemoglobin in vesicles in the parasite cytoplasm, which prevented its transport to the food vacuole, the site of hemoglobin catabolism. As a result, hemoglobin digestion, which is a source of amino acids necessary for parasite growth, was attenuated and caused the inhibition of parasite growth.
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He J, Vora M, Haney RM, Filonov GS, Musselman CA, Burd CG, Kutateladze AG, Verkhusha VV, Stahelin RV, Kutateladze TG. Membrane insertion of the FYVE domain is modulated by pH. Proteins 2009; 76:852-60. [PMID: 19296456 DOI: 10.1002/prot.22392] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The FYVE domain associates with phosphatidylinositol 3-phosphate [PtdIns(3)P] in membranes of early endosomes and penetrates bilayers. Here, we detail principles of membrane anchoring and show that the FYVE domain insertion into PtdIns(3)P-enriched membranes and membrane-mimetics is substantially increased in acidic conditions. The EEA1 FYVE domain binds to POPC/POPE/PtdIns(3)P vesicles with a Kd of 49 nM at pH 6.0, however associates approximately 24 fold weaker at pH 8.0. The decrease in the affinity is primarily due to much faster dissociation of the protein from the bilayers in basic media. Lowering the pH enhances the interaction of the Hrs, RUFY1, Vps27p and WDFY1 FYVE domains with PtdIns(3)P-containing membranes in vitro and in vivo, indicating that pH-dependency is a general function of the FYVE finger family. The PtdIns(3)P binding and membrane insertion of the FYVE domain is modulated by the two adjacent His residues of the R(R/K)HHCRXCG signature motif. Mutation of either His residue abolishes the pH-sensitivity. Both protonation of the His residues and nonspecific electrostatic contacts stabilize the FYVE domain in the lipid-bound form, promoting its penetration and increasing the membrane residence time.
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Affiliation(s)
- Ju He
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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49
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Balla T. Green light to illuminate signal transduction events. Trends Cell Biol 2009; 19:575-86. [PMID: 19818623 DOI: 10.1016/j.tcb.2009.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 08/03/2009] [Accepted: 08/11/2009] [Indexed: 11/17/2022]
Abstract
When cells are exposed to hormones that act on cell surface receptors, information is processed through the plasma membrane into the cell interior via second messengers generated in the inner leaflet of the plasma membrane. Individual biochemical steps along this cascade have been characterized from ligand binding to receptors through to activation of guanine nucleotide binding proteins and their downstream effectors such as adenylate cyclase or phospholipase C. However, the complexity of temporal and spatial integration of these molecular events requires that they are studied in intact cells. The great expansion of fluorescent techniques and improved imaging technologies such as confocal and TIRF microscopy combined with genetically-engineered protein modules has provided a completely new approach to signal transduction research. Spatial definition of biochemical events followed with real-time temporal resolution has become a standard goal, and several new techniques are now breaking the resolution barrier of light microscopy.
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Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Program on Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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50
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Samson RY, Bell SD. Ancient ESCRTs and the evolution of binary fission. Trends Microbiol 2009; 17:507-13. [PMID: 19783442 DOI: 10.1016/j.tim.2009.08.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 08/11/2009] [Accepted: 08/18/2009] [Indexed: 10/20/2022]
Abstract
Eukaryotic and prokaryotic orthologs of tubulin play key roles in DNA segregation and cell division processes. Remarkably, recent studies have revealed that cell division can occur in the absence of this highly conserved protein. Members of the hyperthermophilic crenarchaea, that lack tubulin-like proteins, undergo division by binary fission. Here we review how this process is dependent on archaeal homologs of the eukaryotic 'endosomal sorting complex required for transport' (ESCRT) system - an apparatus that plays a pivotal role in a wide range of membrane manipulation processes. Thus, two distinct machineries to drive binary fission have evolved in prokaryotes - one dependent on tubulin-like proteins and one dependent on the ESCRT system.
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Affiliation(s)
- Rachel Y Samson
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
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