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Liu S, Su L, Li J, Zhang Y, Hu X, Wang P, Liu P, Ye J. Inhibition of miR-146b-5p alleviates isoprenaline-induced cardiac hypertrophy via regulating DFCP1. Mol Cell Endocrinol 2024; 589:112252. [PMID: 38649132 DOI: 10.1016/j.mce.2024.112252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Pathological cardiac hypertrophy often precedes heart failure due to various stimuli, yet effective clinical interventions remain limited. Recently, microRNAs (miRNAs) have been identified as critical regulators of cardiovascular development. In this study, we investigated the role of miR-146b-5p and its underlying mechanisms of action in cardiac hypertrophy. Isoprenaline (ISO) treatment induced significant hypertrophy and markedly enhanced the expression of miR-146b-5p in cultured neonatal rat cardiomyocytes and hearts of C57BL/6 mice. Transfection with the miR-146b-5p mimic led to cardiomyocyte hypertrophy accompanied by autophagy inhibition. Conversely, miR-146b-5p inhibition significantly alleviated ISO-induced autophagy depression, thereby mitigating cardiac hypertrophy both in vitro and in vivo. Our results showed that the autophagy-related mediator double FYVE domain-containing protein 1 (DFCP1) is a target of miR-146b-5p. MiR-146b-5p blocked autophagic flux in cardiomyocytes by suppressing DFCP1, thus contributing to hypertrophy. These findings revealed that miR-146b-5p is a potential regulator of autophagy associated with the onset of cardiac hypertrophy, suggesting a possible therapeutic strategy involving the inhibition of miR-146b-5p.
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Affiliation(s)
- Siling Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Linjie Su
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Jie Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Yuexin Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Xiaopei Hu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Pengcheng Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Peiqing Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China.
| | - Jiantao Ye
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China.
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2
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Nähse V, Stenmark H, Schink KO. Omegasomes control formation, expansion, and closure of autophagosomes. Bioessays 2024; 46:e2400038. [PMID: 38724256 DOI: 10.1002/bies.202400038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
Autophagy, an essential cellular process for maintaining cellular homeostasis and eliminating harmful cytoplasmic objects, involves the de novo formation of double-membraned autophagosomes that engulf and degrade cellular debris, protein aggregates, damaged organelles, and pathogens. Central to this process is the phagophore, which forms from donor membranes rich in lipids synthesized at various cellular sites, including the endoplasmic reticulum (ER), which has emerged as a primary source. The ER-associated omegasomes, characterized by their distinctive omega-shaped structure and accumulation of phosphatidylinositol 3-phosphate (PI3P), play a pivotal role in autophagosome formation. Omegasomes are thought to serve as platforms for phagophore assembly by recruiting essential proteins such as DFCP1/ZFYVE1 and facilitating lipid transfer to expand the phagophore. Despite the critical importance of phagophore biogenesis, many aspects remain poorly understood, particularly the complete range of proteins involved in omegasome dynamics, and the detailed mechanisms of lipid transfer and membrane contact site formation.
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Affiliation(s)
- Viola Nähse
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Harald Stenmark
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kay O Schink
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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3
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Kim DH, Lee J, Ko JK, Lee K. Melanophilin regulates dendritogenesis in melanocytes for feather pigmentation. Commun Biol 2024; 7:592. [PMID: 38760591 PMCID: PMC11101434 DOI: 10.1038/s42003-024-06284-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/03/2024] [Indexed: 05/19/2024] Open
Abstract
Limited studies using animal models with a few natural mutations in melanophilin (Mlph) provided partial functions of Mlph in melanosome trafficking. To investigate cellular functions of Mlph, especially ZnF motif of Mlph, we analyzed all three Mlph knockout (KO) quail lines, one and two base pair (bp) deletions as models for total KO, and three bp deletion causing deletion of one Cysteine (C84del) in the ZnF motif. All quail lines had diluted feather pigmentation with impaired dendritogenesis and melanosome transport in melanocytes. In vitro studies revealed capability of binding of the ZnF motif to PIP3, and impairment of PI3P binding and mislocalization of MLPH proteins with ZnF motif mutations. The shortened melanocyte dendrites by the C84del mutation were rescued by introducing WT Mlph in vitro. These results revealed the diluted feather pigmentation by Mlph mutations resulted from congregation of melanosomes in the cell bodies with impairment of the dendritogenesis and the transport of melanosomes to the cell periphery.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Joonbum Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Jae-Kyun Ko
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
- Pathology Advanced Translational Research Unit (PATRU), Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA.
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4
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Johnson LL, Abrahante JE, McLoon LK. Nystagmus in the B6(CG)Tyr(c-2J)/J Albino Mouse: A Functional and RNA-Seq Analysis. Invest Ophthalmol Vis Sci 2024; 65:26. [PMID: 38206276 PMCID: PMC10787582 DOI: 10.1167/iovs.65.1.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Purpose Infantile nystagmus syndrome (INS) is a gaze-holding disorder characterized by conjugate, uncontrolled eye oscillations that can result in significant visual acuity loss. INS is often associated with albinism, but the mechanism is unclear. Albino mice have nystagmus; however, a pigmented mouse with a tyr mutation making it phenotypically albino, the B6(CG)-Tyr(c-2J)/J (B6 albino), had not been tested. We tested optokinetic response (OKR) in B6 albino and control mice. RNA-Seq was performed on extraocular muscles (EOM), tibialis anterior (TA) muscle, abducens (CN6), and oculomotor (CN3) neurons to uncover molecular differences that may contribute to nystagmus. Methods OKR was measured using an ISCAN system. RNA was isolated from four tissues to identify differentially expressed genes and validated with qPCR and immunohistochemistry. Ingenuity pathway analyses identified top biological pathways. Results All B6 albino mice tested had nystagmus. Differential RNA expression analysis showed 383 genes differentially expressed in EOM, 70 in CN3, 20 in CN6, and 639 in the TA. Two genes were differentially expressed in all four tissues: wdfy1 and nnt. Differences were validated by qPCR and immunostaining. Conclusions The tyr mutation in B6 albino mice, genotypically pigmented and phenotypically albino, is sufficient to result in spontaneous nystagmus. The two genes with decreased expression in the B6 albino tissues examined, wdfy1 and nnt, have been implicated in mitochondrial dysfunction and stem cell maintenance in other systems. Their function in extraocular muscle is unknown. These studies suggest that this mouse model of nystagmus may allow molecular identification of candidate nystagmus-related genes.
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Affiliation(s)
- Laura L. Johnson
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States
- Graduate Program in Cellular, Molecular, Developmental Biology and Genetics, University of Minnesota, Minneapolis, Minnesota, United States
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, United States
| | - Linda K. McLoon
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States
- Graduate Program in Cellular, Molecular, Developmental Biology and Genetics, University of Minnesota, Minneapolis, Minnesota, United States
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5
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Buck TM, Quinn PMJ, Pellissier LP, Mulder AA, Jongejan A, Lu X, Boon N, Koot D, Almushattat H, Arendzen CH, Vos RM, Bradley EJ, Freund C, Mikkers HMM, Boon CJF, Moerland PD, Baas F, Koster AJ, Neefjes J, Berlin I, Jost CR, Wijnholds J. CRB1 is required for recycling by RAB11A+ vesicles in human retinal organoids. Stem Cell Reports 2023; 18:1793-1810. [PMID: 37541258 PMCID: PMC10545476 DOI: 10.1016/j.stemcr.2023.07.001] [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: 12/22/2021] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 08/06/2023] Open
Abstract
CRB1 gene mutations can cause early- or late-onset retinitis pigmentosa, Leber congenital amaurosis, or maculopathy. Recapitulating human CRB1 phenotypes in animal models has proven challenging, necessitating the development of alternatives. We generated human induced pluripotent stem cell (iPSC)-derived retinal organoids of patients with retinitis pigmentosa caused by biallelic CRB1 mutations and evaluated them against autologous gene-corrected hiPSCs and hiPSCs from healthy individuals. Patient organoids show decreased levels of CRB1 and NOTCH1 expression at the retinal outer limiting membrane. Proximity ligation assays show that human CRB1 and NOTCH1 can interact via their extracellular domains. CRB1 patient organoids feature increased levels of WDFY1+ vesicles, fewer RAB11A+ recycling endosomes, decreased VPS35 retromer complex components, and more degradative endolysosomal compartments relative to isogenic control organoids. Taken together, our data demonstrate that patient-derived retinal organoids enable modeling of retinal degeneration and highlight the importance of CRB1 in early endosome maturation receptor recycling in the retina.
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Affiliation(s)
- Thilo M Buck
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Peter M J Quinn
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Lucie P Pellissier
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands
| | - Aat A Mulder
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Epidemiology & Data Science, Amsterdam University Medical Centers, Amsterdam 1105 AZ, the Netherlands
| | - Xuefei Lu
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Nanda Boon
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Daniëlle Koot
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | - Hind Almushattat
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands
| | | | - Rogier M Vos
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands
| | - Edward J Bradley
- Department of Genome Analysis, Amsterdam University Medical Centers, Amsterdam 1105 AZ, the Netherlands
| | - Christian Freund
- Leiden University Medical Center hiPSC Hotel, Leiden 2333 ZA, the Netherlands
| | - Harald M M Mikkers
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands; Leiden University Medical Center hiPSC Hotel, Leiden 2333 ZA, the Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands; Department of Ophthalmology, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam 1000 AE, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Epidemiology & Data Science, Amsterdam University Medical Centers, Amsterdam 1105 AZ, the Netherlands
| | - Frank Baas
- Department of Genome Analysis, Amsterdam University Medical Centers, Amsterdam 1105 AZ, the Netherlands; Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Abraham J Koster
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Jacques Neefjes
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Ilana Berlin
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Carolina R Jost
- Department of Cell & Chemical Biology, Leiden University Medical Center (LUMC), Leiden 2300 RC, the Netherlands
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden 2333 ZA, the Netherlands; Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands.
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6
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Ismail VA, Naismith T, Kast DJ. The NTPase activity of the double FYVE domain-containing protein 1 regulates lipid droplet metabolism. J Biol Chem 2023; 299:102830. [PMID: 36574842 PMCID: PMC9881219 DOI: 10.1016/j.jbc.2022.102830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/26/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Lipid droplets (LDs) are transient lipid storage organelles that can be readily tapped to resupply cells with energy or lipid building blocks and therefore play a central role in cellular metabolism. However, the molecular factors and underlying mechanisms that regulate the growth and degradation of LDs are poorly understood. It has emerged that proteins that establish contacts between LDs and the endoplasmic reticulum play a critical role in regulating LD metabolism. Recently, the autophagy-related protein, double FYVE domain-containing protein 1 (DFCP1/ZFYVE1) was shown to reside at the interface of the endoplasmic reticulum and LDs, however, little is known about the involvement of DFCP1 in autophagy and LD metabolism. Here, we show that DFCP1 is a novel NTPase that regulates free fatty acid metabolism. Specifically, we show that DFPC1-knockdown, particularly during starvation, increases cellular free fatty acids and decreases the levels of cellular TAGs, resulting in accumulated small LDs. Using selective truncations, we demonstrate that DFCP1 accumulation on LDs in cells and in vitro is regulated by a previously unknown NTPase domain. Using spectroscopic approaches, we show that this NTPase domain can dimerize and can hydrolyze both ATP and GTP. Furthermore, mutations in DFCP1 that either impact nucleotide hydrolysis or dimerization result in changes in the accumulation of DFCP1 on LDs, changes in LD density and size, and colocalization of LDs to autophagosomes. Collectively, our findings suggest that DFCP1 is an NTPase that modulates the metabolism of LDs in cells.
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Affiliation(s)
- V A Ismail
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - T Naismith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - D J Kast
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA.
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7
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Teranishi H, Tabata K, Saeki M, Umemoto T, Hatta T, Otomo T, Yamamoto K, Natsume T, Yoshimori T, Hamasaki M. Identification of CUL4A-DDB1-WDFY1 as an E3 ubiquitin ligase complex involved in initiation of lysophagy. Cell Rep 2022; 40:111349. [PMID: 36103833 DOI: 10.1016/j.celrep.2022.111349] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 07/14/2022] [Accepted: 08/22/2022] [Indexed: 01/13/2023] Open
Abstract
Macroautophagy is a bulk degradation system in which double membrane-bound structures called autophagosomes to deliver cytosolic materials to lysosomes. Autophagy promotes cellular homeostasis by selectively recognizing and sequestering specific targets, such as damaged organelles, protein aggregates, and invading bacteria, termed selective autophagy. We previously reported a type of selective autophagy, lysophagy, which helps clear damaged lysosomes. Damaged lysosomes become ubiquitinated and recruit autophagic machinery. Proteomic studies using transfection reagent-coated beads and further evaluations reveal that a CUL4A-DDB1-WDFY1 E3 ubiquitin ligase complex is essential to initiate lysophagy and clear damaged lysosomes. Moreover, we show that LAMP2 is ubiquitinated by the CUL4A E3 ligase complex as a substrate on damaged lysosomes. These results reveal how cells selectively tag damaged lysosomes to initiate autophagy for the clearance of lysosomes.
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Affiliation(s)
- Hirofumi Teranishi
- JT Pharmaceutical Frontier Research Laboratory, Yokohama 236-0004, Japan
| | - Keisuke Tabata
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan; Department of Genetics, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan
| | - Marika Saeki
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan
| | - Tetsuo Umemoto
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery, AIST, Tokyo 135-0064, Japan
| | - Takanobu Otomo
- Department of Genetics, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan
| | - Kentaro Yamamoto
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan
| | - Toru Natsume
- Molecular Profiling Research Center for Drug Discovery, AIST, Tokyo 135-0064, Japan
| | - Tamotsu Yoshimori
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan; Department of Genetics, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan.
| | - Maho Hamasaki
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka 565-0871, Japan; Department of Genetics, Graduate School of Medicine Osaka University, Osaka 565-0871, Japan.
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8
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Ricciardi S, Guarino AM, Giaquinto L, Polishchuk EV, Santoro M, Di Tullio G, Wilson C, Panariello F, Soares VC, Dias SSG, Santos JC, Souza TML, Fusco G, Viscardi M, Brandi S, Bozza PT, Polishchuk RS, Venditti R, De Matteis MA. The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle. Nature 2022; 606:761-768. [PMID: 35551511 DOI: 10.1038/s41586-022-04835-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022]
Abstract
SARS-CoV-2, like other coronaviruses, builds a membrane-bound replication organelle (RO) to enable RNA replication1. The SARS-CoV-2 RO is composed of double membrane vesicles (DMVs) tethered to the endoplasmic reticulum (ER) by thin membrane connectors2, but the viral proteins and the host factors involved are currently unknown. Here we identify the viral non-structural proteins (NSPs) that generate the SARS-CoV-2 RO. NSP3 and NSP4 generate the DMVs while NSP6, through oligomerization and an amphipathic helix, zippers ER membranes and establishes the connectors. The NSP6ΔSGF mutant, which arose independently in the α, β, γ, η, ι, and λ variants of SARS-CoV-2, behaves as a gain-of-function mutant with a higher ER-zippering activity. We identified three main roles for NSP6: to act as a filter in RO-ER communication allowing lipid flow but restricting access of ER luminal proteins to the DMVs, to position and organize DMV clusters, and to mediate contact with lipid droplets (LDs) via the LD-tethering complex DFCP1-Rab18. NSP6 thus acts as an organizer of DMV clusters and can provide a selective track to refurbish them with LD-derived lipids. Importantly, both properly formed NSP6 connectors and LDs are required for SARS-CoV-2 replication. Our findings, uncovering the biological activity of NSP6 of SARS-CoV-2 and of other coronaviruses, have the potential to fuel the search for broad antiviral agents.
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Affiliation(s)
- Simona Ricciardi
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy.,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Elena V Polishchuk
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Michele Santoro
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Giuseppe Di Tullio
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | | | - Vinicius C Soares
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Programa de Imunologia e Inflamação, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Suelen S G Dias
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Julia C Santos
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Thiago M L Souza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde (CDTS) and National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), FIOCRUZ, Rio de Janeiro, Brazil
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Maurizio Viscardi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Sergio Brandi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Roman S Polishchuk
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy.
| | - Rossella Venditti
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy. .,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy. .,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
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9
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Rahman S, Vandewalle J, van Hamersveld PHP, Verseijden C, Welting O, Jongejan A, Casanova P, Meijer SL, Libert C, Hakvoort TBM, de Jonge WJ, Heinsbroek SEM. miR-511 Deficiency Protects Mice from Experimental Colitis by Reducing TLR3 and TLR4 Responses via WD Repeat and FYVE-Domain-Containing Protein 1. Cells 2021; 11:58. [PMID: 35011620 PMCID: PMC8750561 DOI: 10.3390/cells11010058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial responses play an important role in maintaining intestinal heath. Recently we reported that miR-511 may regulate TLR4 responses leading to enhanced intestinal inflammation. However, the exact mechanism remained unclear. In this study we investigated the effect of miR-511 deficiency on anti-microbial responses and DSS-induced intestinal inflammation. miR-511-deficient mice were protected from DSS-induced colitis as shown by significantly lower disease activity index, weight loss and histology scores in the miR-511-deficient group. Furthermore, reduced inflammatory cytokine responses were observed in colons of miR-511 deficient mice. In vitro studies with bone marrow-derived M2 macrophages showed reduced TLR3 and TLR4 responses in miR-511-deficient macrophages compared to WT macrophages. Subsequent RNA sequencing revealed Wdfy1 as the potential miR-511 target. WDFY1 deficiency is related to impaired TLR3/TLR4 immune responses and the expression was downregulated in miR-511-deficient macrophages and colons. Together, this study shows that miR-511 is involved in the regulation of intestinal inflammation through downstream regulation of TLR3 and TLR4 responses via Wdfy1.
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Affiliation(s)
- Shafaque Rahman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (C.V.); (O.W.); (P.C.); (T.B.M.H.); (S.E.M.H.)
| | - Jolien Vandewalle
- Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium; (J.V.); (C.L.)
- VIB Centre for Inflammation Research, VIB, 9052 Ghent, Belgium
| | - Patricia H. P. van Hamersveld
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (C.V.); (O.W.); (P.C.); (T.B.M.H.); (S.E.M.H.)
| | - Caroline Verseijden
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (C.V.); (O.W.); (P.C.); (T.B.M.H.); (S.E.M.H.)
| | - Olaf Welting
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (C.V.); (O.W.); (P.C.); (T.B.M.H.); (S.E.M.H.)
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Pierina Casanova
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (C.V.); (O.W.); (P.C.); (T.B.M.H.); (S.E.M.H.)
| | - Sybren L. Meijer
- Department of Pathology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Claude Libert
- Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium; (J.V.); (C.L.)
- VIB Centre for Inflammation Research, VIB, 9052 Ghent, Belgium
| | - Theodorus B. M. Hakvoort
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (C.V.); (O.W.); (P.C.); (T.B.M.H.); (S.E.M.H.)
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (C.V.); (O.W.); (P.C.); (T.B.M.H.); (S.E.M.H.)
- Department of Surgery, University of Bonn, 53113 Bonn, Germany
| | - Sigrid E. M. Heinsbroek
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (S.R.); (P.H.P.v.H.); (C.V.); (O.W.); (P.C.); (T.B.M.H.); (S.E.M.H.)
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10
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Yang Y, Paul A, Bach TN, Huang ZJ, Zhang MQ. Single-cell alternative polyadenylation analysis delineates GABAergic neuron types. BMC Biol 2021; 19:144. [PMID: 34301239 PMCID: PMC8299648 DOI: 10.1186/s12915-021-01076-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/17/2021] [Indexed: 01/10/2023] Open
Abstract
Background Alternative polyadenylation (APA) is emerging as an important mechanism in the post-transcriptional regulation of gene expression across eukaryotic species. Recent studies have shown that APA plays key roles in biological processes, such as cell proliferation and differentiation. Single-cell RNA-seq technologies are widely used in gene expression heterogeneity studies; however, systematic studies of APA at the single-cell level are still lacking. Results Here, we described a novel computational framework, SAPAS, that utilizes 3′-tag-based scRNA-seq data to identify novel poly(A) sites and quantify APA at the single-cell level. Applying SAPAS to the scRNA-seq data of phenotype characterized GABAergic interneurons, we identified cell type-specific APA events for different GABAergic neuron types. Genes with cell type-specific APA events are enriched for synaptic architecture and communications. In further, we observed a strong enrichment of heritability for several psychiatric disorders and brain traits in altered 3′ UTRs and coding sequences of cell type-specific APA events. Finally, by exploring the modalities of APA, we discovered that the bimodal APA pattern of Pak3 could classify chandelier cells into different subpopulations that are from different laminar positions. Conclusions We established a method to characterize APA at the single-cell level. When applied to a scRNA-seq dataset of GABAergic interneurons, the single-cell APA analysis not only identified cell type-specific APA events but also revealed that the modality of APA could classify cell subpopulations. Thus, SAPAS will expand our understanding of cellular heterogeneity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01076-3.
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Affiliation(s)
- Yang Yang
- Present Address: Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.,Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Anirban Paul
- Cold Spring Harbor Laboratory, Harbor, Cold Spring, NY, 11724, USA.,Deparment of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Thao Nguyen Bach
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Harbor, Cold Spring, NY, 11724, USA.,Deparment of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Michael Q Zhang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA.
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11
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Wang G, Zheng C. Zinc finger proteins in the host-virus interplay: multifaceted functions based on their nucleic acid-binding property. FEMS Microbiol Rev 2021; 45:fuaa059. [PMID: 33175962 DOI: 10.1093/femsre/fuaa059] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/07/2020] [Indexed: 12/14/2022] Open
Abstract
Zinc finger proteins (ZFPs) are a huge family comprised of massive, structurally diverse proteins characterized by zinc ion coordinating. They engage in the host-virus interplay in-depth and occupy a significant portion of the host antiviral arsenal. Nucleic acid-binding is the basic property of certain ZFPs, which draws increasing attention due to their immense influence on viral infections. ZFPs exert multiple roles on the viral replications and host cell transcription profiles by recognizing viral genomes and host mRNAs. Their roles could be either antiviral or proviral and were separately discussed. Our review covers the recent research progress and provides a comprehensive understanding of ZFPs in antiviral immunity based on their DNA/RNA binding property.
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Affiliation(s)
- Guanming Wang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Dr NW, Calgary, Alberta, Canada, AB T2N 4N1
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12
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Yang Y, Hu YH, Liu Y. Wdfy1 deficiency impairs Tlr3-mediated immune responses in vivo. Cell Mol Immunol 2020; 17:1014-1016. [PMID: 32398807 PMCID: PMC7608371 DOI: 10.1038/s41423-020-0461-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Affiliation(s)
- Yang Yang
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yun-Hong Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yu Liu
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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13
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Gao G, Sheng Y, Yang H, Chua BT, Xu L. DFCP1 associates with lipid droplets. Cell Biol Int 2019; 43:1492-1504. [PMID: 31293035 DOI: 10.1002/cbin.11199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/07/2019] [Indexed: 01/24/2023]
Abstract
Double FYVE-containing protein 1 (DFCP1) is ubiquitously expressed, participates in intracellular membrane trafficking and labels omegasomes through specific interactions with phosphatidylinositol-3-phosphate (PI3P). Previous studies showed that subcellular DFCP1 proteins display multi-organelle localization, including in the endoplasmic reticulum (ER), Golgi apparatus and mitochondria. However, its localization and function on lipid droplets (LDs) remain unclear. Here, we demonstrate that DFCP1 localizes to the LD upon oleic acid incubation. The ER-targeted domain of DFCP1 is indispensable for its LD localization, which is further enhanced by double FYVE domains. Inhibition of PI3P binding at the FYVE domain through wortmannin treatment or double mutation at C654S and C770S have no effect on DFCP1's LD localization. These show that the mechanisms for DFCP1 targeting the omegasome and LDs are different. DFCP1 deficiency in MEF cells causes an increase in LD number and reduces LD size. Interestingly, DFCP1 interacts with GTP-bound Rab18, an LD-associated protein. Taken together, our work demonstrates the dynamic localization of DFCP1 is regulated by nutritional status in response to cellular metabolism.
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Affiliation(s)
- Guangang Gao
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yuanyuan Sheng
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 New South Wales, Sydney, Australia
| | - Boon Tin Chua
- The Institute of Metabolism and Integrative Biology, Fudan University, 200438, Shanghai, China
| | - Li Xu
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
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14
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Zhong X, Feng L, Xu WH, Wu X, Ding YD, Zhou Y, Lei CQ, Shu HB. The zinc-finger protein ZFYVE1 modulates TLR3-mediated signaling by facilitating TLR3 ligand binding. Cell Mol Immunol 2019; 17:741-752. [PMID: 31388100 DOI: 10.1038/s41423-019-0265-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
Recognition of viral dsRNA by Toll-like receptor 3 (TLR3) leads to the induction of downstream antiviral effectors and the innate antiviral immune response. Here, we identified the zinc-finger FYVE domain-containing protein ZFYVE1, a guanylate-binding protein (GBP), as a positive regulator of TLR3-mediated signaling. Overexpression of ZFYVE1 promoted the transcription of downstream antiviral genes upon stimulation with the synthetic TLR3 ligand poly(I:C). Conversely, ZFYVE1 deficiency had the opposite effect. Zfyve1-/- mice were less susceptible than wild-type mice to inflammatory death induced by poly(I:C) but not LPS. ZFYVE1 was associated with TLR3, and the FYVE domain of ZFYVE1 and the ectodomain of TLR3 were shown to be responsible for their interaction. ZFYVE1 was bound to poly(I:C) and increased the binding affinity of TLR3 to poly(I:C). These findings suggest that ZFYVE1 plays an important role in the TLR3-mediated innate immune and inflammatory responses by promoting the ligand binding of TLR3.
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Affiliation(s)
- Xuan Zhong
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, Wuhan University, Wuhan, 430072, China
| | - Lu Feng
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, Wuhan University, Wuhan, 430072, China
| | - Wen-Hua Xu
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, Wuhan University, Wuhan, 430072, China
| | - Xin Wu
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, Wuhan University, Wuhan, 430072, China
| | - Yi-Di Ding
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Zhou
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China.,Medical Research Institute, Wuhan University, Wuhan, 430072, China
| | - Cao-Qi Lei
- College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China. .,Medical Research Institute, Wuhan University, Wuhan, 430072, China.
| | - Hong-Bing Shu
- College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China. .,Medical Research Institute, Wuhan University, Wuhan, 430072, China.
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15
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Ning F, Li X, Yu L, Zhang B, Zhao Y, Liu Y, Zhao B, Shang Y, Hu X. Hes1 attenuates type I IFN responses via VEGF-C and WDFY1. J Exp Med 2019; 216:1396-1410. [PMID: 31015298 PMCID: PMC6547865 DOI: 10.1084/jem.20180861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/22/2018] [Accepted: 04/04/2019] [Indexed: 12/26/2022] Open
Abstract
Transcription factor Hes1 acts as a homeostatic negative regulator of type I interferon production to restrain interferon-mediated immune responses, including antiviral immunity and autoimmune conditions. Mechanistically, Hes1 suppresses interferon expression by targeting a regulatory circuit composed of WDFY1 and VEGF-C. Induction of type I interferons (IFNs) is critical for eliciting competent immune responses, especially antiviral immunity. However, uncontrolled IFN production contributes to pathogenesis of autoimmune and inflammatory diseases. We found that transcription factor Hes1 suppressed production of type I IFNs and expression of IFN-stimulated genes. Functionally, Hes1-deficient mice displayed a heightened IFN signature in vivo, mounted enhanced resistance against encephalomyocarditis virus infection, and showed signs of exacerbated experimental lupus nephritis. Mechanistically, Hes1 did not suppress IFNs via direct transcriptional repression of IFN-encoding genes. Instead, Hes1 attenuated activation of TLR upstream signaling by inhibition of an adaptor molecule, WDFY1. Genome-wide assessment of Hes1 occupancy revealed that suppression of WDFY1 was secondary to direct binding and thus enhancement of expression of VEGF-C by Hes1, making Vegfc a rare example of an Hes1 positively regulated gene. In summary, these results identified Hes1 as a homeostatic negative regulator of type I IFNs for the maintenance of immune balance in the context of antiviral immunity and autoimmune diseases.
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Affiliation(s)
- Fei Ning
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Xiaoyu Li
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Li Yu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Bin Zhang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China.,Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Yuna Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control & Prevention, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Yu Liu
- State Key Laboratory of Virology, Medical Research Institute, College of Life Sciences, Wuhan University, Wuhan, China
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Yingli Shang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control & Prevention, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Xiaoyu Hu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China .,Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
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16
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Brier LW, Ge L, Stjepanovic G, Thelen AM, Hurley JH, Schekman R. Regulation of LC3 lipidation by the autophagy-specific class III phosphatidylinositol-3 kinase complex. Mol Biol Cell 2019; 30:1098-1107. [PMID: 30811270 PMCID: PMC6724508 DOI: 10.1091/mbc.e18-11-0743] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Autophagy is a conserved eukaryotic pathway critical for cellular adaptation to changes in nutrition levels and stress. The class III phosphatidylinositol (PI)3-kinase complexes I and II (PI3KC3-C1 and -C2) are essential for autophagosome initiation and maturation, respectively, from highly curved vesicles. We used a cell-free reaction that reproduces a key autophagy initiation step, LC3 lipidation, as a biochemical readout to probe the role of autophagy-related gene (ATG)14, a PI3KC3-C1-specific subunit implicated in targeting the complex to autophagy initiation sites. We reconstituted LC3 lipidation with recombinant PI3KC3-C1, -C2, or various mutant derivatives added to extracts derived from a CRISPR/Cas9-generated ATG14-knockout cell line. Both complexes C1 and C2 require the C-terminal helix of VPS34 for activity on highly curved membranes. However, only complex C1 supports LC3 lipidation through the curvature-targeting amphipathic lipid packing sensor (ALPS) motif of ATG14. Furthermore, the ALPS motif and VPS34 catalytic activity are required for downstream recruitment of WD-repeat domain phosphoinositide-interacting protein (WIPI)2, a protein that binds phosphatidylinositol 3-phosphate and its product phosphatidylinositol 3, 5-bisphosphate, and a WIPI-binding protein, ATG2A, but do not affect membrane association of ATG3 and ATG16L1, enzymes contributing directly to LC3 lipidation. These data reveal the nuanced role of the ATG14 ALPS in membrane curvature sensing, suggesting that the ALPS has additional roles in supporting LC3 lipidation.
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Affiliation(s)
- Livia W Brier
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94270
| | - Liang Ge
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94270
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94270.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Ashley M Thelen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94270.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Randy Schekman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94270
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17
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miR-216b enhances the efficacy of vemurafenib by targeting Beclin-1, UVRAG and ATG5 in melanoma. Cell Signal 2017; 42:30-43. [PMID: 28982601 DOI: 10.1016/j.cellsig.2017.09.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/30/2017] [Accepted: 09/30/2017] [Indexed: 02/06/2023]
Abstract
Autophagy maintains cells survival in many stressful conditions including starvation, growth factor deprivation and misfolded protein accumulation. Additionally, autophagic survival mechanisms are used by transformed tumor cells to inhibit cell death, limit drug effectiveness and possibly generate drug resistance. However, the mechanism of how cells utilize autophagy during drug resistance is not fully understood. Here, we demonstrate that miR-216b plays an important role in alleviating drug resistance by regulating autophagy in melanoma. We show that miR-216b attenuates autophagy by directly targeting three key autophagy genes Beclin-1, UVRAG and ATG5. Overexpression of these genes from miRNA immune cDNA constructs rescue autophagic activity in the presence of miR-216b. Antagomir-mediated inactivation of endogenous miR-216b led to an increase of Beclin-1, UVRAG, ATG5, and subsequent autophagic activity. More importantly, we have discovered that BRAF(V600E) inhibitor vemurafenib suppresses miR-216b activity, which in turn activates autophagy to generate drug resistance in both BRAFi-sensitive and -resistant cells. Strikingly, ectopic expression of miR-216b increases the efficacy of vemurafenib both in vitro and in vivo. Taken together, these data indicate that miR-216b regulates autophagy by suppressing three key autophagy genes, and enhances the antitumor activity of vemurafenib in BRAF(V600E) melanoma cells.
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18
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Coutts AS, La Thangue NB. Regulation of actin nucleation and autophagosome formation. Cell Mol Life Sci 2016; 73:3249-63. [PMID: 27147468 PMCID: PMC4967107 DOI: 10.1007/s00018-016-2224-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/21/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
Abstract
Autophagy is a process of self-eating, whereby cytosolic constituents are enclosed by a double-membrane vesicle before delivery to the lysosome for degradation. This is an important process which allows for recycling of nutrients and cellular components and thus plays a critical role in normal cellular homeostasis as well as cell survival during stresses such as starvation or hypoxia. A large number of proteins regulate various stages of autophagy in a complex and still incompletely understood series of events. In this review, we will discuss recent studies which provide a growing body of evidence that actin dynamics and proteins that influence actin nucleation play an important role in the regulation of autophagosome formation and maturation.
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Affiliation(s)
- Amanda S Coutts
- Laboratory of Cancer Biology, Medical Sciences Division, Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Nicholas B La Thangue
- Laboratory of Cancer Biology, Medical Sciences Division, Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Off Roosevelt Drive, Oxford, OX3 7DQ, UK.
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19
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Thurston TL, Boyle KB, Allen M, Ravenhill BJ, Karpiyevich M, Bloor S, Kaul A, Noad J, Foeglein A, Matthews SA, Komander D, Bycroft M, Randow F. Recruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy. EMBO J 2016; 35:1779-92. [PMID: 27370208 PMCID: PMC5010046 DOI: 10.15252/embj.201694491] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/24/2016] [Indexed: 01/01/2023] Open
Abstract
Mammalian cells deploy autophagy to defend their cytosol against bacterial invaders. Anti‐bacterial autophagy relies on the core autophagy machinery, cargo receptors, and “eat‐me” signals such as galectin‐8 and ubiquitin that label bacteria as autophagy cargo. Anti‐bacterial autophagy also requires the kinase TBK1, whose role in autophagy has remained enigmatic. Here we show that recruitment of WIPI2, itself essential for anti‐bacterial autophagy, is dependent on the localization of catalytically active TBK1 to the vicinity of cytosolic bacteria. Experimental manipulation of TBK1 recruitment revealed that engagement of TBK1 with any of a variety of Salmonella‐associated “eat‐me” signals, including host‐derived glycans and K48‐ and K63‐linked ubiquitin chains, suffices to restrict bacterial proliferation. Promiscuity in recruiting TBK1 via independent signals may buffer TBK1 functionality from potential bacterial antagonism and thus be of evolutionary advantage to the host.
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Affiliation(s)
- Teresa Lm Thurston
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Keith B Boyle
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Mark Allen
- Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Benjamin J Ravenhill
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Maryia Karpiyevich
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Stuart Bloor
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Annie Kaul
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jessica Noad
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Agnes Foeglein
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Sophie A Matthews
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Mark Bycroft
- Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Felix Randow
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
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20
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Dutta S, Roy S, Polavaram NS, Baretton GB, Muders MH, Batra S, Datta K. NRP2 transcriptionally regulates its downstream effector WDFY1. Sci Rep 2016; 6:23588. [PMID: 27026195 PMCID: PMC4812299 DOI: 10.1038/srep23588] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/09/2016] [Indexed: 12/15/2022] Open
Abstract
Neuropilins (NRPs) are cell surface glycoproteins that often act as co-receptors for plexins and VEGF family receptors. Neuropilin-2 (NRP2), a family member of NRPs, was shown to regulate autophagy and endocytic trafficking in cancer cells, a function distinctly different from its role as a co-receptor. WD Repeat and FYVE domain containing 1 (WDFY1)–protein acts downstream of NRP2 for this function. Our results indicated that NRP2 maintains an optimum concentration of WDFY1 by negatively regulating its expression. Since increased expression of WDFY1 reduces the endocytic activity, maintenance of WDFY1 level is crucial in metastatic cancer cells to sustain high endocytic activity, essential for promotion of oncogenic activation and cancer cell survival. Here, we have delineated the underlying molecular mechanism of WDFY1 synthesis by NRP2. Our results indicated that NRP2 inhibits WDFY1 transcription by preventing the nuclear localization of a transcription factor, Fetal ALZ50-reactive clone 1 (FAC1). Our finding is novel as transcriptional regulation of a gene by NRP2 axis has not been reported previously. Regulation of WDFY1 transcription by NRP2 axis is a critical event in maintaining metastatic phenotype in cancer cells. Thus, inhibiting NRP2 or hyper-activating WDFY1 can be an effective strategy to induce cell death in metastatic cancer.
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Affiliation(s)
- Samikshan Dutta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, U.S.A
| | - Sohini Roy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, U.S.A
| | - Navatha S Polavaram
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, U.S.A
| | - Gustavo B Baretton
- Institute of Pathology, University Hospital Carl Gustav Carus, University of Technology of Dresden, Germany
| | - Michael H Muders
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, U.S.A.,Institute of Pathology, University Hospital Carl Gustav Carus, University of Technology of Dresden, Germany
| | - Surinder Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, U.S.A.,Fred &Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer, Omaha, Nebraska, U.S.A
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, U.S.A.,Fred &Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer, Omaha, Nebraska, U.S.A
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21
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Nanao T, Koike M, Yamaguchi J, Sasaki M, Uchiyama Y. Cellular localization and tissue distribution of endogenous DFCP1 protein. Biomed Res 2016; 36:121-33. [PMID: 25876663 DOI: 10.2220/biomedres.36.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Autophagy is essential for the maintenance of cellular metabolism. Once autophagy is induced in cells, the isolation membrane forms a so-called phagophore. The endoplasmic reticulum (ER) is one of several candidates for the membrane source for phagophores. Recently, LC3-positive isolation membranes were found to emerge from a DFCP1 (double FYVE domain-containing protein)-positive, ER-associated compartment called the omegasome. Although the GFP-tagged DFCP1 protein has been examined in cultured cells, little is known about the precise cellular and tissue distribution of this endogenous protein. To determine the expression of the endogenous DFCP1 protein, we produced antibodies specific to mouse DFCP1 protein. The antibody recognized both human and mouse DFCP1 proteins, both of which have molecular masses of approximately 87 kDa. In HeLa cells under normal conditions, immunoreactivity for DFCP1 was found dotted or tubular along Tom20-positive filamentous mitochondria and was only partially co-localized in the ER or Golgi apparatus. Moreover, under starved conditions, distinct DFCP1-positive structures became more dotted and scattered in the cytoplasm, while one part of the LC3-positive autophagosomes were immunopositive for DFCP1. These results indicate that an antibody raised against DFCP1 could be a useful tool in explaining the mechanism of phagophore formation from omegasome compartments.
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Affiliation(s)
- Tomohisa Nanao
- Departments of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine
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22
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Mohl BP, Bartlett C, Mankouri J, Harris M. Early events in the generation of autophagosomes are required for the formation of membrane structures involved in hepatitis C virus genome replication. J Gen Virol 2016; 97:680-693. [PMID: 26727924 DOI: 10.1099/jgv.0.000387] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infection has been shown to induce autophagy but the mechanisms underpinning this process remain to be elucidated. Induction of autophagy requires the class III phosphatidylinositol 3-kinase, Vps34, which produces phosphatidylinositol 3-phosphate (PI3P) within the endoplasmic reticulum (ER) membrane. This recruits proteins with PI3P binding domains such as the double-FYVE-containing protein 1 (DFCP1). DFCP1 generates cup-shaped protrusions from the ER membrane, termed omegasomes, which provide a platform for the production of autophagosomes. Here we present data demonstrating that both Vps34 and DFCP1 are required for HCV genome replication, in the context of both a subgenomic replicon and virus infection, but did not affect virus entry or initial translation. Using live cell fluorescence microscopy we demonstrated that early during HCV infection the nascent viral genome replication complexes (identified by using non-structural protein NS5A as a marker) transiently colocalize with DFCP1-positive punctae (omegasomes), before the two structures move apart from each other. This observation is reminiscent of the transient association of LC3 and DFCP1 during omegasome formation, and therefore we propose that omegasomes are utilized by HCV to generate the double-membrane vesicles which are the hallmark of HCV replication complexes.
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Affiliation(s)
- Bjorn-Patrick Mohl
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Christopher Bartlett
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Jamel Mankouri
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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23
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Dutta S, Roy S, Polavaram NS, Stanton MJ, Zhang H, Bhola T, Hönscheid P, Donohue TM, Band H, Batra SK, Muders MH, Datta K. Neuropilin-2 Regulates Endosome Maturation and EGFR Trafficking to Support Cancer Cell Pathobiology. Cancer Res 2015; 76:418-28. [PMID: 26560516 DOI: 10.1158/0008-5472.can-15-1488] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/23/2015] [Indexed: 12/16/2022]
Abstract
Neuropilin-2 (NRP2) is a non-tyrosine kinase receptor frequently overexpressed in various malignancies, where it has been implicated in promoting many protumorigenic behaviors, such as imparting therapeutic resistance to metastatic cancer cells. Here, we report a novel function of NRP2 as a regulator of endocytosis, which is enhanced in cancer cells and is often associated with increased metastatic potential and drug resistance. We found that NRP2 depletion in human prostate and pancreatic cancer cells resulted in the accumulation of EEA1/Rab5-positive early endosomes concomitant with a decrease in Rab7-positive late endosomes, suggesting a delay in early-to-late endosome maturation. NRP2 depletion also impaired the endocytic transport of cell surface EGFR, arresting functionally active EGFR in endocytic vesicles that consequently led to aberrant ERK activation and cell death. Mechanistic investigations revealed that WD-repeat- and FYVE-domain-containing protein 1 (WDFY1) functioned downstream of NRP2 to promote endosome maturation, thereby influencing the endosomal trafficking of EGFR and the formation of autolysosomes responsible for the degradation of internalized cargo. Overall, our results indicate that the NRP2/WDFY1 axis is required for maintaining endocytic activity in cancer cells, which supports their oncogenic activities and confers drug resistance. Therefore, therapeutically targeting endocytosis may represent an attractive strategy to selectively target cancer cells in multiple malignancies.
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Affiliation(s)
- Samikshan Dutta
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sohini Roy
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Navatha S Polavaram
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Marissa J Stanton
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Heyu Zhang
- Department of Urologic Research, Biochemistry, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Tanvi Bhola
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Pia Hönscheid
- Institute of Pathology, University Hospital Carl Gustav Carus, TU, Dresden, Germany
| | - Terrence M Donohue
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska. Omaha VA Medical Center, Omaha, Nebraska
| | - Hamid Band
- Buffett Cancer Center, Eppley Cancer Institute, University of Nebraska Medical Center, Omaha, Nebraska
| | - Surinder K Batra
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. Buffett Cancer Center, Eppley Cancer Institute, University of Nebraska Medical Center, Omaha, Nebraska
| | - Michael H Muders
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. Institute of Pathology, University Hospital Carl Gustav Carus, TU, Dresden, Germany
| | - Kaustubh Datta
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. Buffett Cancer Center, Eppley Cancer Institute, University of Nebraska Medical Center, Omaha, Nebraska.
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24
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Mi N, Chen Y, Wang S, Chen M, Zhao M, Yang G, Ma M, Su Q, Luo S, Shi J, Xu J, Guo Q, Gao N, Sun Y, Chen Z, Yu L. CapZ regulates autophagosomal membrane shaping by promoting actin assembly inside the isolation membrane. Nat Cell Biol 2015; 17:1112-23. [DOI: 10.1038/ncb3215] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 07/01/2015] [Indexed: 12/16/2022]
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25
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Heck MV, Azizov M, Stehning T, Walter M, Kedersha N, Auburger G. Dysregulated expression of lipid storage and membrane dynamics factors in Tia1 knockout mouse nervous tissue. Neurogenetics 2015; 15:135-44. [PMID: 24659297 PMCID: PMC3994287 DOI: 10.1007/s10048-014-0397-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/03/2014] [Indexed: 12/13/2022]
Abstract
During cell stress, the transcription and translation of immediate early genes are prioritized, while most other messenger RNAs (mRNAs) are stored away in stress granules or degraded in processing bodies (P-bodies). TIA-1 is an mRNA-binding protein that needs to translocate from the nucleus to seed the formation of stress granules in the cytoplasm. Because other stress granule components such as TDP-43, FUS, ATXN2, SMN, MAPT, HNRNPA2B1, and HNRNPA1 are crucial for the motor neuron diseases amyotrophic lateral sclerosis (ALS)/spinal muscular atrophy (SMA) and for the frontotemporal dementia (FTD), here we studied mouse nervous tissue to identify mRNAs with selective dependence on Tia1 deletion. Transcriptome profiling with oligonucleotide microarrays in comparison of spinal cord and cerebellum, together with independent validation in quantitative reverse transcriptase PCR and immunoblots demonstrated several strong and consistent dysregulations. In agreement with previously reported TIA1 knock down effects, cell cycle and apoptosis regulators were affected markedly with expression changes up to +2-fold, exhibiting increased levels for Cdkn1a, Ccnf, and Tprkb vs. decreased levels for Bid and Inca1 transcripts. Novel and surprisingly strong expression alterations were detected for fat storage and membrane trafficking factors, with prominent +3-fold upregulations of Plin4, Wdfy1, Tbc1d24, and Pnpla2 vs. a −2.4-fold downregulation of Cntn4 transcript, encoding an axonal membrane adhesion factor with established haploinsufficiency. In comparison, subtle effects on the RNA processing machinery included up to 1.2-fold upregulations of Dcp1b and Tial1. The effect on lipid dynamics factors is noteworthy, since also the gene deletion of Tardbp (encoding TDP-43) and Atxn2 led to fat metabolism phenotypes in mouse. In conclusion, genetic ablation of the stress granule nucleator TIA-1 has a novel major effect on mRNAs encoding lipid homeostasis factors in the brain, similar to the fasting effect.
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Affiliation(s)
- Melanie Vanessa Heck
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Mekhman Azizov
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Tanja Stehning
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Michael Walter
- Institute for Medical Genetics, Eberhard-Karls-University of Tuebingen, 72076 Tübingen, Germany
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Smith 652, One Jimmy Fund Way, Boston, MA 02115 USA
| | - Georg Auburger
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
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Hu YH, Zhang Y, Jiang LQ, Wang S, Lei CQ, Sun MS, Shu HB, Liu Y. WDFY1 mediates TLR3/4 signaling by recruiting TRIF. EMBO Rep 2015; 16:447-55. [PMID: 25736436 DOI: 10.15252/embr.201439637] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/09/2015] [Indexed: 12/19/2022] Open
Abstract
Toll-like receptors (TLRs) are pattern recognition receptors that sense a variety of pathogens, initiate innate immune responses, and direct adaptive immunity. All TLRs except TLR3 recruit the adaptor MyD88 to ultimately elicit inflammatory gene expression, whereas TLR3 and internalized TLR4 use TIR-domain-containing adaptor TRIF for the induction of type I interferon and inflammatory cytokines. Here, we identify the WD repeat and FYVE-domain-containing protein WDFY1 as a crucial adaptor protein in the TLR3/4 signaling pathway. Overexpression of WDFY1 potentiates TLR3- and TLR4-mediated activation of NF-κB, interferon regulatory factor 3 (IRF3), and production of type I interferons and inflammatory cytokines. WDFY1 depletion has the opposite effect. WDFY1 interacts with TLR3 and TLR4 and mediates the recruitment of TRIF to these receptors. Our findings suggest a crucial role for WDFY1 in bridging the TLR-TRIF interaction, which is necessary for TLR signaling.
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Affiliation(s)
- Yun-Hong Hu
- State Key Laboratory of Virology, Medical Research Institute College of Life Sciences Wuhan University, Wuhan, China
| | - Yu Zhang
- State Key Laboratory of Virology, Medical Research Institute College of Life Sciences Wuhan University, Wuhan, China
| | - Li-Qun Jiang
- State Key Laboratory of Virology, Medical Research Institute College of Life Sciences Wuhan University, Wuhan, China
| | - Shuai Wang
- State Key Laboratory of Virology, Medical Research Institute College of Life Sciences Wuhan University, Wuhan, China
| | - Cao-Qi Lei
- State Key Laboratory of Virology, Medical Research Institute College of Life Sciences Wuhan University, Wuhan, China
| | - Ming-Shun Sun
- State Key Laboratory of Virology, Medical Research Institute College of Life Sciences Wuhan University, Wuhan, China
| | - Hong-Bing Shu
- State Key Laboratory of Virology, Medical Research Institute College of Life Sciences Wuhan University, Wuhan, China
| | - Yu Liu
- State Key Laboratory of Virology, Medical Research Institute College of Life Sciences Wuhan University, Wuhan, China
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27
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Chandra V, Bhagyaraj E, Parkesh R, Gupta P. Transcription factors and cognate signalling cascades in the regulation of autophagy. Biol Rev Camb Philos Soc 2015; 91:429-51. [PMID: 25651938 DOI: 10.1111/brv.12177] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 01/04/2015] [Accepted: 01/11/2015] [Indexed: 12/11/2022]
Abstract
Autophagy is a process that maintains the equilibrium between biosynthesis and the recycling of cellular constituents; it is critical for avoiding the pathophysiology that results from imbalance in cellular homeostasis. Recent reports indicate the need for the design of high-throughput screening assays to identify targets and small molecules for autophagy modulation. For such screening, however, a better understanding of the regulation of autophagy is essential. In addition to regulation by various signalling cascades, regulation of gene expression by transcription factors is also critical. This review focuses on the various transcription factors as well as the corresponding signalling molecules that act together to translate the stimuli to effector molecules that up- or downregulate autophagy. This review rationalizes the importance of these transcription factors functioning in tandem with cognate signalling molecules and their interfaces as possible therapeutic targets for more specific pharmacological interventions.
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Affiliation(s)
- Vemika Chandra
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Ella Bhagyaraj
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Raman Parkesh
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Pawan Gupta
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
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28
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Merkestein M, McTaggart JS, Lee S, Kramer HB, McMurray F, Lafond M, Boutens L, Cox R, Ashcroft FM. Changes in gene expression associated with FTO overexpression in mice. PLoS One 2014; 9:e97162. [PMID: 24842286 PMCID: PMC4026227 DOI: 10.1371/journal.pone.0097162] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/14/2014] [Indexed: 01/24/2023] Open
Abstract
Single nucleotide polymorphisms in the first intron of the fat-mass-and-obesity-related gene FTO are associated with increased body weight and adiposity. Increased expression of FTO is likely underlying this obesity phenotype, as mice with two additional copies of Fto (FTO-4 mice) exhibit increased adiposity and are hyperphagic. FTO is a demethylase of single stranded DNA and RNA, and one of its targets is the m6A modification in RNA, which might play a role in the regulation of gene expression. In this study, we aimed to examine the changes in gene expression that occur in FTO-4 mice in order to gain more insight into the underlying mechanisms by which FTO influences body weight and adiposity. Our results indicate an upregulation of anabolic pathways and a downregulation of catabolic pathways in FTO-4 mice. Interestingly, although genes involved in methylation were differentially regulated in skeletal muscle of FTO-4 mice, no effect of FTO overexpression on m6A methylation of total mRNA was detected.
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Affiliation(s)
- Myrte Merkestein
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - James S. McTaggart
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Sheena Lee
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Holger B. Kramer
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Fiona McMurray
- Medical Research Council Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Harwell, Oxford, United Kingdom
| | - Mathilde Lafond
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Lily Boutens
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
| | - Roger Cox
- Medical Research Council Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Harwell, Oxford, United Kingdom
| | - Frances M. Ashcroft
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy; and Genetics, University of Oxford, Parks Road, Oxford, United Kingdom
- * E-mail:
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29
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Stahelin RV, Scott JL, Frick CT. Cellular and molecular interactions of phosphoinositides and peripheral proteins. Chem Phys Lipids 2014; 182:3-18. [PMID: 24556335 DOI: 10.1016/j.chemphyslip.2014.02.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 12/23/2022]
Abstract
Anionic lipids act as signals for the recruitment of proteins containing cationic clusters to biological membranes. A family of anionic lipids known as the phosphoinositides (PIPs) are low in abundance, yet play a critical role in recruitment of peripheral proteins to the membrane interface. PIPs are mono-, bis-, or trisphosphorylated derivatives of phosphatidylinositol (PI) yielding seven species with different structure and anionic charge. The differential spatial distribution and temporal appearance of PIPs is key to their role in communicating information to target proteins. Selective recognition of PIPs came into play with the discovery that the substrate of protein kinase C termed pleckstrin possessed the first PIP binding region termed the pleckstrin homology (PH) domain. Since the discovery of the PH domain, more than ten PIP binding domains have been identified including PH, ENTH, FYVE, PX, and C2 domains. Representative examples of each of these domains have been thoroughly characterized to understand how they coordinate PIP headgroups in membranes, translocate to specific membrane docking sites in the cell, and function to regulate the activity of their full-length proteins. In addition, a number of novel mechanisms of PIP-mediated membrane association have emerged, such as coincidence detection-specificity for two distinct lipid headgroups. Other PIP-binding domains may also harbor selectivity for a membrane physical property such as charge or membrane curvature. This review summarizes the current understanding of the cellular distribution of PIPs and their molecular interaction with peripheral proteins.
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Affiliation(s)
- Robert V Stahelin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States.
| | - Jordan L Scott
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States; Mike and Josie Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Cary T Frick
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
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30
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Takatori S, Mesman R, Fujimoto T. Microscopic methods to observe the distribution of lipids in the cellular membrane. Biochemistry 2014; 53:639-53. [PMID: 24460209 DOI: 10.1021/bi401598v] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane lipids not only provide the structural framework of cellular membranes but also influence protein functions in several different ways. In comparison to proteins, however, relatively little is known about distribution of membrane lipids because of the insufficiency of microscopic methods. The difficulty in studying lipid distribution results from several factors, including their unresponsiveness to chemical fixation, fast translational movement, small molecular size, and high packing density. In this Current Topic, we consider the major microscopic methods and discuss whether and to what degree of precision these methods can reveal membrane lipid distribution in situ. We highlight two fixation methods, chemical and physical, and compare the theoretical limitations to their spatial resolution. Recognizing the strengths and weaknesses of each method should help researchers interpret their microscopic results and increase our understanding of the physiological functions of lipids.
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Affiliation(s)
- Sho Takatori
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine , Nagoya 466-8550, Japan
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31
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Hernandez-Valladares M, Aran V, Prior IA. Quantitative proteomic analysis of compartmentalized signaling networks. Methods Enzymol 2014; 535:309-25. [PMID: 24377931 DOI: 10.1016/b978-0-12-397925-4.00018-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ras proteins operate predominantly from the plasma membrane; however, they have also been localized to most intracellular compartments. Various functions and signaling outputs have been ascribed to endomembranous Ras although systematic comparison and measurement of potential outputs have not yet been carried out. We describe the methodology for isolating and measuring compartment-specific signaling networks using quantitative proteomics. This approach reveals the potential of a subcellular platform for supporting specific outputs and will inform subsequent studies of endogenous isoform-specific Ras signaling.
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Affiliation(s)
- Maria Hernandez-Valladares
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Veronica Aran
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Ian A Prior
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.
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32
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Abstract
Autophagy is a conserved survival pathway, which cells and tissues will activate during times of stress. It is characterized by the formation of double-membrane vesicles called autophagosomes inside the cytoplasm. The molecular mechanisms and the signalling components involved require specific control to ensure correct activation. The present chapter describes the formation of autophagosomes from within omegasomes, newly identified membrane compartments enriched in PI3P (phosphatidylinositol 3-phosphate) that serve as platforms for the formation of at least some autophagosomes. We discuss the signalling events required to nucleate the formation of omegasomes as well as the protein complexes involved.
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33
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Karanasios E, Stapleton E, Manifava M, Kaizuka T, Mizushima N, Walker SA, Ktistakis NT. Dynamic association of the ULK1 complex with omegasomes during autophagy induction. J Cell Sci 2013; 126:5224-38. [PMID: 24013547 DOI: 10.1242/jcs.132415] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Induction of autophagy requires the ULK1 protein kinase complex and the Vps34 lipid kinase complex. PtdIns3P synthesised by Vps34 accumulates in omegasomes, membrane extensions of the ER within which some autophagosomes form. The ULK1 complex is thought to target autophagosomes independently of PtdIns3P, and its functional relationship to omegasomes is unclear. Here we show that the ULK1 complex colocalises with omegasomes in a PtdIns3P-dependent way. Live-cell imaging of Atg13 (a ULK1 complex component), omegasomes and LC3 establishes and annotates for the first time a complete sequence of steps leading to autophagosome formation, as follows. Upon starvation, the ULK1 complex forms puncta associated with the ER and sporadically with mitochondria. If PtdIns3P is available, these puncta become omegasomes. Subsequently, the ULK1 complex exits omegasomes and autophagosomes bud off. If PtdIns3P is unavailable, ULK1 puncta are greatly reduced in number and duration. Atg13 contains a region with affinity for acidic phospholipids, required for translocation to punctate structures and autophagy progression.
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34
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Ge L, Melville D, Zhang M, Schekman R. The ER-Golgi intermediate compartment is a key membrane source for the LC3 lipidation step of autophagosome biogenesis. eLife 2013; 2:e00947. [PMID: 23930225 PMCID: PMC3736544 DOI: 10.7554/elife.00947] [Citation(s) in RCA: 316] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/03/2013] [Indexed: 12/20/2022] Open
Abstract
Autophagy is a catabolic process for bulk degradation of cytosolic materials mediated by double-membraned autophagosomes. The membrane determinant to initiate the formation of autophagosomes remains elusive. Here, we establish a cell-free assay based on LC3 lipidation to define the organelle membrane supporting early autophagosome formation. In vitro LC3 lipidation requires energy and is subject to regulation by the pathways modulating autophagy in vivo. We developed a systematic membrane isolation scheme to identify the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) as a primary membrane source both necessary and sufficient to trigger LC3 lipidation in vitro. Functional studies demonstrate that the ERGIC is required for autophagosome biogenesis in vivo. Moreover, we find that the ERGIC acts by recruiting the early autophagosome marker ATG14, a critical step for the generation of preautophagosomal membranes. DOI:http://dx.doi.org/10.7554/eLife.00947.001.
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Affiliation(s)
- Liang Ge
- Department of Molecular and Cell Biology , Howard Hughes Medical Institute, University of California, Berkeley , Berkeley , United States
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35
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Compartmentalized Ras signaling differentially contributes to phenotypic outputs. Cell Signal 2013; 25:1748-53. [PMID: 23707528 PMCID: PMC3776226 DOI: 10.1016/j.cellsig.2013.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/07/2013] [Indexed: 12/30/2022]
Abstract
Ras isoforms are membrane bound proteins that differentially localize to the plasma membrane and subcellular compartments within the cell. Whilst the cell surface is the main site for Ras activity the extent to which intracellular pools contribute to Ras function is debated. We have generated Ras chimeras targeting Ras to the ER, Golgi, mitochondria and endosomes to compare the capacity of each of these locations to support activity equivalent to normal Ras function. We find that all locations are capable of regulating the MAP kinase and Akt pathways. Furthermore, whilst endomembranous Ras pools show location-specific competence to support proliferation and transformation, Golgi-Ras is as potent as N-Ras.
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Abstract
Over this past decade, macroautophagy has gained prominence in the field of adult-onset neurodegeneration: from sporadic disorders such as Alzheimer's and Parkinson's disease, to genetic disorders such as Huntington's disease and frontotemporal dementia, the influence of this fundamental pathway has become an important topic of discussion. While there has been particular emphasis on the potential benefits of macroautophagy, there is growing literature that also suggests that macroautophagy contributes towards neurotoxicity. In this review, we discuss the molecular mechanism of macroautophagy and the currently available pharmacological tools, with special emphasis on mammalian macroautophagy in adult brain. Studies indicate that neuronal context strongly influences the role macroautophagy plays in maintaining cellular health, reflecting an ongoing need for better understanding of how macroautophagic regulation is achieved in the heavily differentiated and polarized neurons if we are to effectively manipulate it to treat neurodegenerative disease.
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Chen X, Li M, Chen D, Gao W, Guan JL, Komatsu M, Yin XM. Autophagy induced by calcium phosphate precipitates involves endoplasmic reticulum membranes in autophagosome biogenesis. PLoS One 2012; 7:e52347. [PMID: 23285000 PMCID: PMC3528773 DOI: 10.1371/journal.pone.0052347] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 10/03/2012] [Indexed: 11/25/2022] Open
Abstract
Calcium can play an important role in the regulation of autophagy. We previously reported that exogenously introduced calcium in the form of calcium phosphate precipitates (CPP) induces autophagy. Here we showed that CPP-induced autophagy required the classical autophagic machinery, including the autophagosome initiating molecules FIP200 and Beclin 1, as well as molecules involved in the autophagosome membrane extension, Atg4, Atg5 and Atg3. On the other hand, Atg9 seemed to place a restriction on CPP-induced autophagy. Loss of Atg9 led to enhanced LC3 punctation and enhanced p62 degradation. CPP-induced autophagy was independent of mTOR and reactive oxygen species. It also did not affect MAP kinase activation and ER stress. DFCP1 is an ER-resident molecule that binds to phosphatidylinositol 3-phosphate. CPP activated DFCP1 punctation in a class III phosphatidylinositol-3-kinase and calcium dependent manner, and caused the association of DFCP1 puncta with the autophagosomes. Consistently, ER membranes, but not Golgi or mitochondrial membranes, colocalized with CPP-induced LC3 positive autophagosomes. These data suggest that CPP-induced autophagosome formation involves the interaction with the ER membrane.
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Affiliation(s)
- Xi Chen
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Min Li
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Daohong Chen
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Wentao Gao
- Department of Surgery, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jun-Lin Guan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Massaki Komatsu
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Xiao-Ming Yin
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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38
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Stanton MJ, Dutta S, Zhang H, Polavaram NS, Leontovich AA, Hönscheid P, Sinicrope FA, Tindall DJ, Muders MH, Datta K. Autophagy control by the VEGF-C/NRP-2 axis in cancer and its implication for treatment resistance. Cancer Res 2012; 73:160-71. [PMID: 23149913 DOI: 10.1158/0008-5472.can-11-3635] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A major contributor to cancer mortality is recurrence and subsequent metastatic transformation following therapeutic intervention. Therefore, in order to develop new treatment modalities and improve the efficacy of current ones, it is important to understand the molecular mechanisms that promote resistance to therapy in cancer cells. One pathway contributing to therapy resistance is autophagy, a self-digestive process that can eliminate unnecessary or damaged organelles to protect cancer cells from death. We have found that the VEGF-C/NRP-2 axis is involved in the activation of autophagy, which helps cancer cell survival following treatment. Inhibition of mTOR complex 1 activity by this axis is the underlying mechanism for the activation of autophagy. Furthermore, we identified two VEGF-C/NRP-2-regulated genes, LAMP-2 and WDFY-1, that have previously been suggested to participate in autophagy and vesicular trafficking. Upregulation of WDFY-1 following VEGF-C or NRP-2 depletion contributes to cytotoxic drug-mediated cell death. Together, these data suggest a link between the VEGF-C/NRP-2 axis and cancer cell survival despite the presence of chemotherapy-induced stress. Effective targeting of this pathway may lead to the development of new cancer therapies.
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Affiliation(s)
- Marissa J Stanton
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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39
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Gil JE, Kim E, Kim IS, Ku B, Park WS, Oh BH, Ryu SH, Cho W, Heo WD. Phosphoinositides differentially regulate protrudin localization through the FYVE domain. J Biol Chem 2012; 287:41268-76. [PMID: 23043110 DOI: 10.1074/jbc.m112.419127] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Protrudin is a FYVE (Fab 1, YOTB, Vac 1, and EEA1) domain-containing protein involved in transport of neuronal cargoes and implicated in the onset of hereditary spastic paraplegia. Our image-based screening of the lipid binding domain library revealed novel plasma membrane localization of the FYVE domain of protrudin unlike canonical FYVE domains that are localized to early endosomes. The membrane binding study by surface plasmon resonance analysis showed that this FYVE domain preferentially binds phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P(2)), phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P(2)), and phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P(3)) unlike canonical FYVE domains that specifically bind phosphatidylinositol 3-phosphate (PtdIns(3)P). Furthermore, we found that these phosphoinositides (PtdInsP) differentially regulate shuttling of protrudin between endosomes and plasma membrane via its FYVE domain. Protrudin mutants with reduced PtdInsP-binding affinity failed to promote neurite outgrowth in primary cultured hippocampal neurons. These results suggest that novel PtdInsP selectivity of the protrudin-FYVE domain is critical for its cellular localization and its role in neurite outgrowth.
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Affiliation(s)
- Jung-Eun Gil
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
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40
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Abstract
Diverse biological processes including cell growth and survival require transient association of proteins with cellular membranes. A large number of these proteins are drawn to a bilayer through binding of their modular domains to phosphoinositide (PI) lipids. Seven PI isoforms are found to concentrate in distinct pools of intracellular membranes, and this lipid compartmentalization provides an efficient way for recruiting PI-binding proteins to specific cellular organelles. The atomic-resolution structures and membrane docking mechanisms of a dozen PI effectors have been elucidated in the last decade, offering insight into the molecular basis for regulation of the PI-dependent signaling pathways. In this chapter, I summarize the mechanistic aspects of deciphering the 'PI code' by the most common PI-recognizing domains and discuss similarities and differences in the membrane anchoring mechanisms.
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Affiliation(s)
- Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
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41
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Mah LY, O'Prey J, Baudot AD, Hoekstra A, Ryan KM. DRAM-1 encodes multiple isoforms that regulate autophagy. Autophagy 2012; 8:18-28. [PMID: 22082963 PMCID: PMC3335989 DOI: 10.4161/auto.8.1.18077] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/01/2011] [Accepted: 09/13/2011] [Indexed: 12/12/2022] Open
Abstract
Macro(autophagy) is a cellular mechanism which delivers cytoplasmic constituents to lysosomes for degradation. Due to its role in maintaining cellular integrity, autophagy protects against various diseases including cancer. p53 is a major tumor suppressor gene which can modulate autophagy both positively and negatively. p53 induces autophagy via transcriptional activation of Damage-Regulated Autophagy Modulator (DRAM-1). We report here that DRAM-1 encodes not just one mRNA, but a series of p53-inducible splice variants which are expressed at varying levels in multiple human and mouse cell lines. Two of these new splice variants, termed SV4 and SV5, result in mature mRNA species. Different to 'full-length' DRAM-1 (SV1), SV4 and SV5 do not localise to lysosomes or endosomes, but instead partially localise to peroxisomes and autophagosomes respectively. In addition, SV4 and SV5 can also be found co-localised with certain markers of the endoplasmic reticulum. Similar to SV1, SV4 and SV5 do not appear to be inducers of programmed cell death, but they do modulate autophagy. In summary, these findings identify new autophagy regulators that provide insight into the control of autophagy downstream of p53.
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Affiliation(s)
- Li Yen Mah
- Tumour Cell Death Laboratory, Beatson Institute for Cancer Research, Glasgow, Scotland, UK
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42
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Pantakani DVK, Czyzewska MM, Sikorska A, Bodda C, Mannan AU. Oligomerization of ZFYVE27 (Protrudin) is necessary to promote neurite extension. PLoS One 2011; 6:e29584. [PMID: 22216323 PMCID: PMC3247280 DOI: 10.1371/journal.pone.0029584] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 12/01/2011] [Indexed: 11/20/2022] Open
Abstract
ZFYVE27 (Protrudin) was originally identified as an interacting partner of spastin, which is most frequently mutated in hereditary spastic paraplegia. ZFYVE27 is a novel member of FYVE family, which is implicated in the formation of neurite extensions by promoting directional membrane trafficking in neurons. Now, through a yeast two-hybrid screen, we have identified that ZFYVE27 interacts with itself and the core interaction region resides within the third hydrophobic region (HR3) of the protein. We confirmed the ZFYVE27's self-interaction in the mammalian cells by co-immunoprecipitation and co-localization studies. To decipher the oligomeric nature of ZFYVE27, we performed sucrose gradient centrifugation and showed that ZFYVE27 oligomerizes into dimer/tetramer forms. Sub-cellular fractionation and Triton X-114 membrane phase separation analysis indicated that ZFYVE27 is a peripheral membrane protein. Furthermore, ZFYVE27 also binds to phosphatidylinositol 3-phosphate lipid moiety. Interestingly, cells expressing ZFYVE27ΔHR3 failed to produce protrusions instead caused swelling of cell soma. When ZFYVE27ΔHR3 was co-expressed with wild-type ZFYVE27 (ZFYVE27WT), it exerted a dominant negative effect on ZFYVE27WT as the cells co-expressing both proteins were also unable to induce protrusions and showed cytoplasmic swelling. Altogether, it is evident that a functionally active form of oligomer is crucial for ZFYVE27 ability to promote neurite extensions.
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Affiliation(s)
| | - Marta M. Czyzewska
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Anna Sikorska
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Chiranjeevi Bodda
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
| | - Ashraf U. Mannan
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany
- * E-mail:
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43
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44
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Regulation of membrane biogenesis in autophagy via PI3P dynamics. Semin Cell Dev Biol 2010; 21:671-6. [DOI: 10.1016/j.semcdb.2010.04.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 04/07/2010] [Accepted: 04/08/2010] [Indexed: 12/20/2022]
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45
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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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46
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Abstract
Phosphoinositide (PI) lipids are essential components of eukaryotic cell membranes. They are produced by mono-, bis- and trisphosphorylation of the inositol headgroup of phosphatidylinositol (PtdIns) and are concentrated in separate pools of cytosolic membranes. PIs serve as markers of the cell compartments and form unique docking sites for protein effectors. Collectively, seven known PIs, the protein effectors that bind them and enzymes that generate or modify PIs compose a remarkably complex protein-lipid signaling network. A number of cytosolic proteins contain one or several effector modules capable of recognizing individual PIs and recruiting the host proteins to distinct intracellular compartment. The recently determined atomic-resolution structures and membrane-targeting mechanisms of a dozen PI effectors have provided insights into the molecular basis for regulation of endocytic membrane trafficking and signaling. In this review, I highlight the structural aspects of the deciphering of the 'PI code' by the most common PI-recognizing effectors and discuss the mechanistic details of their membrane anchoring.
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47
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A novel HPLC-based approach makes possible the spatial characterization of cellular PtdIns5P and other phosphoinositides. Biochem J 2010; 428:375-84. [PMID: 20370717 DOI: 10.1042/bj20100129] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PtdIns5P was discovered in 1997 [Rameh, Tolias, Duckworth and Cantley (1997) Nature 390, 192-196], but still very little is known about its regulation and function. Hitherto, studies of PtdIns5P regulation have been hindered by the inability to measure cellular PtdIns5P using conventional HPLC, owing to poor separation from PtdIns4P. In the present paper we describe a new HPLC method for resolving PtdIns5P from PtdIns4P, which makes possible accurate measurements of basal and inducible levels of cellular PtdIns5P in the context of other phosphoinositides. Using this new method, we found that PtdIns5P is constitutively present in all cells examined (epithelial cells, fibroblasts and myoblasts, among others) at levels typically 1-2% of PtdIns4P levels. In the beta-pancreatic cell line BTC6, which is specialized in insulin secretion, PtdIns5P levels were higher than in most cells (2.5-4% of PtdIns4P). Using subcellular fractionation, we found that the majority of the basal PtdIns5P is present in the plasma membrane, but it is also enriched in intracellular membrane compartments, especially in SER (smooth endoplasmic reticulum) and/or Golgi, where high levels of PtdIns3P were also detected. Unlike PtdIns3P, PtdIns5P was also found in fractions containing very-low-density vesicles. Knockdown of PIP4K (PtdIns5P 4-kinase) leads to accumulation of PtdIns5P in light fractions and fractions enriched in SER/Golgi, whereas treatment with Brefeldin A results in a subtle, but reproducible, change in PtdIns5P distribution. These results indicate that basal PtdIns5P and the PtdIns5P pathway for PtdIns(4,5)P(2) synthesis may play a role in Golgi-mediated vesicle trafficking.
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Abstract
Autophagy, a process by which cells degrade their own components within lysosomes, is a major homeostatic mechanism that favors adaptation and survival under nutrient-deficient conditions. Starvation increases the number and size of autophagosomes in many tissues, suggesting that autophagy is a critical component of the body's response to nutrient deprivation and amino acid/fuel homeostasis. In addition, autophagy has been shown to play a critical role in maintaining amino acid and energy homeostasis in neonates during the transitional hours immediately following birth. The recent identification of functional mammalian orthologues of Atg14 and Atg17 has completed the identification of mammalian orthologues of all of the core yeast autophagy genes. In addition, the recent placement of the Atg1*Atg13*Atg17 complex downstream of mTORC1 has provided at least one pathway by which changes in nutrient availability regulate autophagy.
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Affiliation(s)
- Martha H Stipanuk
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA.
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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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50
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Conway SJ, Gardiner J, Grove SJA, Johns MK, Lim ZY, Painter GF, Robinson DEJE, Schieber C, Thuring JW, Wong LSM, Yin MX, Burgess AW, Catimel B, Hawkins PT, Ktistakis NT, Stephens LR, Holmes AB. Synthesis and biological evaluation of phosphatidylinositol phosphate affinity probes. Org Biomol Chem 2009; 8:66-76. [PMID: 20024134 DOI: 10.1039/b913399b] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The synthesis of the complete family of phosphatidylinositol phosphate analogues (PIPs) from five key core intermediates A-E is described. These core compounds were obtained from myo-inositol orthoformate 1 via regioselective DIBAL-H and trimethylaluminium-mediated cleavages and a resolution-protection process using camphor acetals 10. Coupling of cores A-E with phosphoramidites 34 and 38, derived from the requisite protected lipid side chains, afforded the fully-protected PIPs. Removal of the remaining protecting groups was achieved via hydrogenolysis using palladium black or palladium hydroxide on carbon in the presence of sodium bicarbonate to afford the complete family of dipalmitoyl- and amino-PIP analogues 42, 45, 50, 51, 58, 59, 67, 68, 76, 77, 82, 83, 92, 93, 99 and 100. Investigations using affinity probes incorporating these compounds have identified novel proteins involved in the PI3K intracellular signalling network and have allowed a comprehensive proteomic analysis of phosphoinositide interacting proteins.
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Affiliation(s)
- Stuart J Conway
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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