1
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Liang S, Zheng YY, Pan Y. Blood transcriptome analysis uncovered COVID-19-myocarditis crosstalk. Microb Pathog 2024; 189:106587. [PMID: 38373644 DOI: 10.1016/j.micpath.2024.106587] [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: 10/12/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND The condition of COVID-19-related myocarditis has emerged as a prominent contributor to COVID-19 mortality. As the epidemic persists, its incidence continues to rise. Despite ongoing efforts, the elucidation of COVID-19-related myocarditis underlying molecular mechanisms still requires further investigation. METHODS Hub genes for COVID-19-related myocarditis were screened by integrating gene expression profile analysis via differential expression in COVID-19 (GSE196822) and myocarditis (GSE148153 and GSE147517). After verification with independent datasets (GSE211979, GSE167028, GSE178491 and GSE215865), the hub genes were studied using a range of systems-biology approaches, such as ceRNA, TF-mRNA networks and PPI networks, as well as gene ontology, pathway enrichment, immune infiltration analysis and drug target identification. RESULTS TBKBP1 and ERGIC1 were identified as COVID-19-related myocarditis hub genes via integrated bioinformatics analysis. In addition, receiver operating characteristic curves constructed based on the expression levels of TBKBP1 and ERGIC1 could effectively distinguish healthy control individuals from patients with COVID-19. Functional enrichment analysis suggested several enriched biological pathways related to inflammation and immune response. Immune cell changes correlated with TBKBP1 and ERGIC1 levels in patients with COVID-19 or patients with COVID-19 and myocarditis. Tamibarotene, methotrexate and theophylline were identified as a potential drug targeting TBKBP1 and ERGIC1. CONCLUSION TBKBP1 and ERGIC1 were identified as crucial genes in the development of COVID-19-related myocarditis and have demonstrated a strong association with innate antiviral immunity. The present work may be helpful for further investigation of the molecular mechanisms and new therapeutic drug targets correlated with myocarditis in COVID-19.
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Affiliation(s)
- Shuang Liang
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China.
| | - Ying-Ying Zheng
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China
| | - Ying Pan
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China
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2
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Nordengen K, Cappelletti C, Bahrami S, Frei O, Pihlstrøm L, Henriksen SP, Geut H, Rozemuller AJM, van de Berg WDJ, Andreassen OA, Toft M. Pleiotropy with sex-specific traits reveals genetic aspects of sex differences in Parkinson's disease. Brain 2024; 147:858-870. [PMID: 37671566 PMCID: PMC10907091 DOI: 10.1093/brain/awad297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/01/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Parkinson's disease is an age-related neurodegenerative disorder with a higher incidence in males than females. The causes for this sex difference are unknown. Genome-wide association studies (GWAS) have identified 90 Parkinson's disease risk loci, but the genetic studies have not found sex-specific differences in allele frequency on autosomal chromosomes or sex chromosomes. Genetic variants, however, could exert sex-specific effects on gene function and regulation of gene expression. To identify genetic loci that might have sex-specific effects, we studied pleiotropy between Parkinson's disease and sex-specific traits. Summary statistics from GWASs were acquired from large-scale consortia for Parkinson's disease (n cases = 13 708; n controls = 95 282), age at menarche (n = 368 888 females) and age at menopause (n = 69 360 females). We applied the conditional/conjunctional false discovery rate (FDR) method to identify shared loci between Parkinson's disease and these sex-specific traits. Next, we investigated sex-specific gene expression differences in the superior frontal cortex of both neuropathologically healthy individuals and Parkinson's disease patients (n cases = 61; n controls = 23). To provide biological insights to the genetic pleiotropy, we performed sex-specific expression quantitative trait locus (eQTL) analysis and sex-specific age-related differential expression analysis for genes mapped to Parkinson's disease risk loci. Through conditional/conjunctional FDR analysis we found 11 loci shared between Parkinson's disease and the sex-specific traits age at menarche and age at menopause. Gene-set and pathway analysis of the genes mapped to these loci highlighted the importance of the immune response in determining an increased disease incidence in the male population. Moreover, we highlighted a total of nine genes whose expression or age-related expression in the human brain is influenced by genetic variants in a sex-specific manner. With these analyses we demonstrated that the lack of clear sex-specific differences in allele frequencies for Parkinson's disease loci does not exclude a genetic contribution to differences in disease incidence. Moreover, further studies are needed to elucidate the role that the candidate genes identified here could have in determining a higher incidence of Parkinson's disease in the male population.
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Affiliation(s)
- Kaja Nordengen
- Department of Neurology, Oslo University Hospital, 0424 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
| | - Chiara Cappelletti
- Department of Neurology, Oslo University Hospital, 0424 Oslo, Norway
- Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, OsloMet—Oslo Metropolitan University, 0130 Oslo, Norway
- Department of Research, Innovation and Education, Oslo University Hospital, 0424 Oslo, Norway
| | - Shahram Bahrami
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, 0450 Oslo, Norway
| | - Oleksandr Frei
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, 0450 Oslo, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, 0424 Oslo, Norway
| | | | - Hanneke Geut
- Section of Clinical Neuroanatomy and Biobanking, Department of Anatomy and Neurosciences, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 Amsterdam, The Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 Amsterdam, The Netherlands
| | - Wilma D J van de Berg
- Section of Clinical Neuroanatomy and Biobanking, Department of Anatomy and Neurosciences, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 Amsterdam, The Netherlands
| | - Ole A Andreassen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital, 0450 Oslo, Norway
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, 0424 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
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3
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Karousi P, Samiotaki M, Makridakis M, Zoidakis J, Sideris DC, Scorilas A, Carell T, Kontos CK. 3'-tRF-Cys GCA overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways. Funct Integr Genomics 2023; 23:341. [PMID: 37987851 PMCID: PMC10663186 DOI: 10.1007/s10142-023-01272-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
tRNA fragments (tRFs) are small non-coding RNAs generated through specific cleavage of tRNAs and involved in various biological processes. Among the different types of tRFs, the 3'-tRFs have attracted scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3'-tRF-CysGCA, a tRF deriving from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3'-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3'-tRF-CysGCA levels in human cells have not been investigated so far. To fill this gap, we stably overexpressed 3'-tRF-CysGCA in HEK-293 cells and performed transcriptomic and proteomic analyses. Moreover, we validated the interaction of this tRF with putative targets, the levels of which were found to be affected by 3'-tRF-CysGCA overexpression. Lastly, we investigated the implication of 3'-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3'-tRF-CysGCA overexpression led to changes in the global gene expression profile of HEK-293 cells and that multiple cellular pathways were affected by the deregulation of the levels of this tRF. Additionally, we demonstrated that 3'-tRF-CysGCA directly interacts with thymopoietin (TMPO) transcript variant 1 (also known as LAP2α), leading to modulation of its levels. In conclusion, our findings suggest that 3'-tRF-CysGCA plays a significant role in gene expression regulation and highlight the importance of this tRF in cellular processes.
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Affiliation(s)
- Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center, "Alexander Fleming", Vari, Greece
| | - Manousos Makridakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jerome Zoidakis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Thomas Carell
- Department for Chemistry, Institute for Chemical Epigenetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
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4
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Damon LJ, Ocampo D, Sanford L, Jones T, Allen MA, Dowell RD, Palmer AE. Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567954. [PMID: 38045276 PMCID: PMC10690171 DOI: 10.1101/2023.11.20.567954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Zinc (Zn2+) is an essential metal required by approximately 2500 proteins. Nearly half of these proteins act on DNA, including > 850 human transcription factors, polymerases, DNA damage response factors, and proteins involved in chromatin architecture. How these proteins acquire their essential Zn2+ cofactor and whether they are sensitive to changes in the labile Zn2+ pool in cells remain open questions. Here, we examine how changes in the labile Zn2+ pool affect chromatin accessibility and transcription factor binding to DNA. We observed both increases and decreases in accessibility in different chromatin regions via ATAC-seq upon treating MCF10A cells with elevated Zn2+ or the Zn2+-specific chelator tris(2-pyridylmethyl)amine (TPA). Transcription factor enrichment analysis was used to correlate changes in chromatin accessibility with transcription factor motifs, revealing 477 transcription factor motifs that were differentially enriched upon Zn2+ perturbation. 186 of these transcription factor motifs were enriched in Zn2+ and depleted in TPA, and the majority correspond to Zn2+ finger transcription factors. We selected TP53 as a candidate to examine how changes in motif enrichment correlate with changes in transcription factor occupancy by ChIP-qPCR. Using publicly available ChIP-seq and nascent transcription datasets, we narrowed the 50,000+ ATAC-seq peaks to 2164 TP53 targets and subsequently selected 6 high-probability TP53 binding sites for testing. ChIP-qPCR revealed that for 5 of the 6 targets, TP53 binding correlates with the local accessibility determined by ATAC-seq. These results demonstrate that changes in labile zinc directly alter chromatin accessibility and transcription factor binding to DNA.
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Affiliation(s)
- Leah J. Damon
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Daniel Ocampo
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Lynn Sanford
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
| | - Taylor Jones
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
| | - Mary A. Allen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Robin D. Dowell
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
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5
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Polenghi M, Taverna E. Intracellular traffic and polarity in brain development. Front Neurosci 2023; 17:1172016. [PMID: 37859764 PMCID: PMC10583573 DOI: 10.3389/fnins.2023.1172016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/31/2023] [Indexed: 10/21/2023] Open
Abstract
Neurons forming the human brain are generated during embryonic development by neural stem and progenitor cells via a process called neurogenesis. A crucial feature contributing to neural stem cell morphological and functional heterogeneity is cell polarity, defined as asymmetric distribution of cellular components. Cell polarity is built and maintained thanks to the interplay between polarity proteins and polarity-generating organelles, such as the endoplasmic reticulum (ER) and the Golgi apparatus (GA). ER and GA affect the distribution of membrane components and work as a hub where glycans are added to nascent proteins and lipids. In the last decades our knowledge on the role of polarity in neural stem and progenitor cells have increased tremendously. However, the role of traffic and associated glycosylation in neural stem and progenitor cells is still relatively underexplored. In this review, we discuss the link between cell polarity, architecture, identity and intracellular traffic, and highlight how studies on neurons have shaped our knowledge and conceptual framework on traffic and polarity. We will then conclude by discussing how a group of rare diseases, called congenital disorders of glycosylation (CDG) offers the unique opportunity to study the contribution of traffic and glycosylation in the context of neurodevelopment.
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6
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Zhang L, Liang X, Takáč T, Komis G, Li X, Zhang Y, Ovečka M, Chen Y, Šamaj J. Spatial proteomics of vesicular trafficking: coupling mass spectrometry and imaging approaches in membrane biology. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:250-269. [PMID: 36204821 PMCID: PMC9884029 DOI: 10.1111/pbi.13929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
In plants, membrane compartmentalization requires vesicle trafficking for communication among distinct organelles. Membrane proteins involved in vesicle trafficking are highly dynamic and can respond rapidly to changes in the environment and to cellular signals. Capturing their localization and dynamics is thus essential for understanding the mechanisms underlying vesicular trafficking pathways. Quantitative mass spectrometry and imaging approaches allow a system-wide dissection of the vesicular proteome, the characterization of ligand-receptor pairs and the determination of secretory, endocytic, recycling and vacuolar trafficking pathways. In this review, we highlight major proteomics and imaging methods employed to determine the location, distribution and abundance of proteins within given trafficking routes. We focus in particular on methodologies for the elucidation of vesicle protein dynamics and interactions and their connections to downstream signalling outputs. Finally, we assess their biological applications in exploring different cellular and subcellular processes.
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Affiliation(s)
- Liang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
- College of Life ScienceHenan Normal UniversityXinxiangChina
| | - Xinlin Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Tomáš Takáč
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Xiaojuan Li
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuan Zhang
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
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7
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Roberts BS, Satpute-Krishnan P. The many hats of transmembrane emp24 domain protein TMED9 in secretory pathway homeostasis. Front Cell Dev Biol 2023; 10:1096899. [PMID: 36733337 PMCID: PMC9888432 DOI: 10.3389/fcell.2022.1096899] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
The secretory pathway is an intracellular highway for the vesicular transport of newly synthesized proteins that spans the endoplasmic reticulum (ER), Golgi, lysosomes and the cell surface. A variety of cargo receptors, chaperones, and quality control proteins maintain the smooth flow of cargo along this route. Among these is vesicular transport protein TMED9, which belongs to the p24/transmembrane emp24 domain (TMED) family of proteins, and is expressed across vertebrate species. The TMED family is comprised of structurally-related type I transmembrane proteins with a luminal N-terminal Golgi-dynamics domain, a luminal coiled-coil domain, a transmembrane domain and a short cytosolic C-terminal tail that binds COPI and COPII coat proteins. TMED9, like other members of the TMED family, was first identified as an abundant constituent of the COPI and COPII coated vesicles that mediate traffic between the ER and the Golgi. TMED9 is typically purified in hetero-oligomers together with TMED family members, suggesting that it may function as part of a complex. Recently, TMED family members have been discovered to play various roles in secretory pathway homeostasis including secreted protein processing, quality control and degradation of misfolded proteins, and post-Golgi trafficking. In particular, TMED9 has been implicated in autophagy, lysosomal sorting, viral replication and cancer, which we will discuss in this Mini-Review.
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8
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de Los Ángeles Juricic Urzúa M, Gallardo Rojas J, Couve Correa A, Cerda M, Härtel Gründler S, González-Silva C. The Dendritic Ergic: Microtubule And Actin Cytoskeletons Participate In Stop-And-Go Movement Of Mobile Carriers Between Stable Structures. Traffic 2022; 23:174-187. [PMID: 35075729 DOI: 10.1111/tra.12832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/30/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022]
Abstract
The ER-to-Golgi intermediate compartment (ERGIC) is a membranous organelle that mediates protein transport between the endoplasmic reticulum (ER) and the Golgi apparatus. In neurons, clusters of these vesiculotubular structures are situated throughout the cell in proximity to the ER, passing cargo to the cis-Golgi cisternae, located mainly in the perinuclear region. Although ERGIC markers have been identified in neurons, the distribution and dynamics of neuronal ERGIC structures have not been characterized yet. Here, we show that long-distance ERGIC transport occurs via an intermittent mechanism in dendrites, with mobile elements moving between stationary structures. Slow and fast live-cell imaging have captured stable ERGIC structures remaining in place over long periods of time, as well as mobile ERGIC structures advancing very short distances along dendrites. These short distances have been consistent with the lengths between the stationary ERGIC structures. Kymography revealed ERGIC elements that moved intermittently, emerging from and fusing with stationary ERGIC structures. Interestingly, this movement apparently depends not only on the integrity of the microtubule cytoskeleton, as previously reported, but on the actin cytoskeleton as well. Our results indicate that the dendritic ERGIC has a dual nature, with both stationary and mobile structures. The neural ERGIC network transports proteins via a stop-and-go movement in which both the microtubule and the actin cytoskeletons participate. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- María de Los Ángeles Juricic Urzúa
- Neuroscience Department, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute (BNI), Santiago, Chile
| | - Javiera Gallardo Rojas
- Neuroscience Department, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute (BNI), Santiago, Chile
| | - Andrés Couve Correa
- Neuroscience Department, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute (BNI), Santiago, Chile
| | - Mauricio Cerda
- Biomedical Neuroscience Institute (BNI), Santiago, Chile.,Integrative Biology Program, Institute of Biomedical Sciences (ICBM), Center for Medical Informatics and Telemedicine (CIMT), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Steffen Härtel Gründler
- Biomedical Neuroscience Institute (BNI), Santiago, Chile.,Integrative Biology Program, Institute of Biomedical Sciences (ICBM), Center for Medical Informatics and Telemedicine (CIMT), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Carolina González-Silva
- Neuroscience Department, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute (BNI), Santiago, Chile
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9
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Guan L, Yang Y, Liang JJ, Miao Y, Shang AY, Wang B, Wang YC, Ding M. ERGIC2 and ERGIC3 regulate the ER-to-Golgi transport of gap junction proteins in metazoans. Traffic 2022; 23:140-157. [PMID: 34994051 DOI: 10.1111/tra.12830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/16/2021] [Accepted: 01/04/2022] [Indexed: 11/26/2022]
Abstract
The extremely dynamic life cycle of gap junction connections requires highly efficient intracellular trafficking system especially designed for gap junction proteins, but the underlying mechanisms are largely unknown. Here, we identified that the COPII-associated proteins ERGIC2 (ER-Golgi intermediate compartment) and ERGIC3 are specifically required for the efficient intracellular transport of gap junction proteins in both C. elegans and mice. In the absence of Ergic2 or Ergic3, gap junction proteins accumulate in the ER and Golgi apparatus and the size of endogenous gap junction plaques is reduced. Knocking out the Ergic2 or Ergic3 in mice results in heart enlargement and cardiac malfunction accompanied by reduced number and size of connexin 43 (Cx43) gap junctions. Invertebrates' gap junction protein innexins share no sequence similarity with vertebrates' connexins. However, ERGIC2 and ERGIC3 could bind to gap junction proteins in both worms and mice. Characterization of the highly specialized roles of ERGIC2 and ERGIC3 in metazoans reveals how the early secretory pathway could be adapted to facilitate the efficient transport for gap junction proteins in vivo. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Liying Guan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yongzhi Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Jing Liang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yue Miao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ang Yang Shang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Baolei Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying Chun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mei Ding
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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10
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Monticolo F, Chiusano ML. Computational Approaches for Cancer-Fighting: From Gene Expression to Functional Foods. Cancers (Basel) 2021; 13:4207. [PMID: 34439361 PMCID: PMC8393935 DOI: 10.3390/cancers13164207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 01/22/2023] Open
Abstract
It is today widely accepted that a healthy diet is very useful to prevent the risk for cancer or its deleterious effects. Nutrigenomics studies are therefore taking place with the aim to test the effects of nutrients at molecular level and contribute to the search for anti-cancer treatments. These efforts are expanding the precious source of information necessary for the selection of natural compounds useful for the design of novel drugs or functional foods. Here we present a computational study to select new candidate compounds that could play a role in cancer prevention and care. Starting from a dataset of genes that are co-expressed in programmed cell death experiments, we investigated on nutrigenomics treatments inducing apoptosis, and searched for compounds that determine the same expression pattern. Subsequently, we selected cancer types where the genes showed an opposite expression pattern and we confirmed that the apoptotic/nutrigenomics expression trend had a significant positive survival in cancer-affected patients. Furthermore, we considered the functional interactors of the genes as defined by public protein-protein interaction data, and inferred on their involvement in cancers and/or in programmed cell death. We identified 7 genes and, from available nutrigenomics experiments, 6 compounds effective on their expression. These 6 compounds were exploited to identify, by ligand-based virtual screening, additional molecules with similar structure. We checked for ADME criteria and selected 23 natural compounds representing suitable candidates for further testing their efficacy in apoptosis induction. Due to their presence in natural resources, novel drugs and/or the design of functional foods are conceivable from the presented results.
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Affiliation(s)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, Via Università 100, 80055 Portici, Italy;
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11
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Marconi C, Lemmens L, Masclaux F, Mattioli F, Fluss J, Extermann P, Mendez P, Leuchter RHV, Stathaki E, Laurent S, Hammar E, Vannier A, Varvagiannis K, Guipponi M, Sloan-Bena F, Blouin JL, Abramowicz M, Fokstuen S. Bi-allelic loss of ERGIC1 causes relatively mild arthrogryposis. Clin Genet 2021; 100:329-333. [PMID: 34037256 PMCID: PMC8453841 DOI: 10.1111/cge.14004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/29/2022]
Abstract
Arthrogryposis describes the presence of multiple joint-contractures. Clinical severity of this phenotype is variable, and more than 400 causative genes have been proposed. Among these, ERGIC1 is a recently reported candidate encoding a putative transmembrane protein of the ER-Golgi interface. Two homozygous missense variants have been reported in patients with relatively mild non-syndromic arthrogryposis. In a consanguineous family with two affected siblings presenting congenital arthrogryposis and some facial dysmorphism we performed prenatal array-CGH, postnatal targeted exome and genome sequencing. Genome sequencing identified a homozygous 22.6 Kb deletion encompassing the promoter and first exon of ERGIC1. mRNA quantification showed the complete absence of ERGIC1 expression in the two affected siblings and a decrease in heterozygous parents. Our observations validate the pathogenic role of ERGIC1 in congenital arthrogryposis and demonstrate that complete loss of function causes a relatively mild phenotype. These findings will contribute to improve genetic counseling of ERGIC1 mutations.
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Affiliation(s)
- Caterina Marconi
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Laure Lemmens
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Frédéric Masclaux
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Francesca Mattioli
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Joël Fluss
- Pediatric Specialties division, Department of Women, Children and Adolescents, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | | | - Purificacion Mendez
- Obstetrics and Gynecology, Centre Médical Eaux-Vives, Genève (CH), Switzerland
| | - Russia Ha-Vinh Leuchter
- Pediatric Specialties division, Department of Women, Children and Adolescents, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Elissavet Stathaki
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Sacha Laurent
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Eva Hammar
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Anne Vannier
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Konstantinos Varvagiannis
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland
| | - Michel Guipponi
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland.,Department of Genetic Medicine and Development, School of Medicine, University of Geneva, Genève (CH), Switzerland
| | - Frédérique Sloan-Bena
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland.,Department of Genetic Medicine and Development, School of Medicine, University of Geneva, Genève (CH), Switzerland
| | - Jean-Louis Blouin
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland.,Department of Genetic Medicine and Development, School of Medicine, University of Geneva, Genève (CH), Switzerland
| | - Marc Abramowicz
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland.,Department of Genetic Medicine and Development, School of Medicine, University of Geneva, Genève (CH), Switzerland
| | - Siv Fokstuen
- Genetic Medicine division, Diagnostic Department, Hôpitaux Universitaires de Genève, Genève (CH), Switzerland.,Department of Genetic Medicine and Development, School of Medicine, University of Geneva, Genève (CH), Switzerland
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12
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Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS OMEGA 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
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13
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Quistgaard EM. BAP31: Physiological functions and roles in disease. Biochimie 2021; 186:105-129. [PMID: 33930507 DOI: 10.1016/j.biochi.2021.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/22/2022]
Abstract
B-cell receptor-associated protein 31 (BAP31 or BCAP31) is a ubiquitously expressed transmembrane protein found mainly in the endoplasmic reticulum (ER), including in mitochondria-associated membranes (MAMs). It acts as a broad-specificity membrane protein chaperone and quality control factor, which can promote different fates for its clients, including ER retention, ER export, ER-associated degradation (ERAD), or evasion of degradation, and it also acts as a MAM tetherer and regulatory protein. It is involved in several cellular processes - it supports ER and mitochondrial homeostasis, promotes proliferation and migration, plays several roles in metabolism and the immune system, and regulates autophagy and apoptosis. Full-length BAP31 can be anti-apoptotic, but can also mediate activation of caspase-8, and itself be cleaved by caspase-8 into p20-BAP31, which promotes apoptosis by mobilizing ER calcium stores at MAMs. BAP31 loss-of-function mutations is the cause of 'deafness, dystonia, and central hypomyelination' (DDCH) syndrome, characterized by severe neurological symptoms and early death. BAP31 is furthermore implicated in a growing number of cancers and other diseases, and several viruses have been found to target it to promote their survival or life cycle progression. The purpose of this review is to provide an overview and examination of the basic properties, functions, mechanisms, and roles in disease of BAP31.
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Affiliation(s)
- Esben M Quistgaard
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark.
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14
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Meng Z, Zhao Y, Liu L, Du X. Genome-wide characterization of the PDI gene family in Medicago truncatula and their roles in response to endoplasmic reticulum stress. Genome 2020; 64:599-614. [PMID: 33306442 DOI: 10.1139/gen-2020-0064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein disulfide isomerases (PDIs) are pivotal protein folding catalysts in the endoplasmic reticulum (ER) through formation of disulfide bond, isomerization, and inhibition of misfolded protein aggregation. When protein folding capacity is overwhelmed by the demands during transitions between growth phases or under environmental changes, the accumulation of unfolded or misfolded proteins in the ER triggers ER stress. However, little is known about the PDI gene family in the model legume Medicago truncatula, especially the responses to ER stress. Therefore, we identified 17 putative PDI genes from the genome of M. truncatula and present their gene and protein structures, phylogenetic relationships, chromosomal distributions, and synteny analysis with the orthologs in four other eudicot species, including Arabidopsis thaliana, Glycine max, Brassica rapa, and Vitis vinifera. Moreover, expression profiles derived from transcriptome data showed distinct expression patterns of MtPDI genes among plant organs, while real-time quantitative PCR analysis and data from the proteome revealed the potential roles of MtPDI genes in response to ER stress. Our study provides a foundation for further investigations of the biological roles of PDI genes in Medicago, especially their roles in response to ER stress.
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Affiliation(s)
- Zhe Meng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yuwei Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Lijie Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xihua Du
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
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15
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Tempio T, Anelli T. The pivotal role of ERp44 in patrolling protein secretion. J Cell Sci 2020; 133:133/21/jcs240366. [PMID: 33173013 DOI: 10.1242/jcs.240366] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Interactions between protein ligands and receptors are the main language of intercellular communication; hence, how cells select proteins to be secreted or presented on the plasma membrane is a central concern in cell biology. A series of checkpoints are located along the secretory pathway, which ensure the fidelity of such protein signals (quality control). Proteins that pass the checkpoints operated in the endoplasmic reticulum (ER) by the binding immunoglobulin protein (BiP; also known as HSPA5 and GRP78) and the calnexin-calreticulin systems, must still overcome additional scrutiny in the ER-Golgi intermediate compartment (ERGIC) and the Golgi. One of the main players of this process in all metazoans is the ER-resident protein 44 (ERp44); by cycling between the ER and the Golgi, ERp44 controls the localization of key enzymes designed to act in the ER but that are devoid of suitable localization motifs. ERp44 also patrols the secretion of correctly assembled disulfide-linked oligomeric proteins. Here, we discuss the mechanisms driving ERp44 substrate recognition, with important consequences on the definition of 'thiol-mediated quality control'. We also describe how pH and zinc gradients regulate the functional cycle of ERp44, coupling quality control and membrane trafficking along the early secretory compartment.
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Affiliation(s)
- Tiziana Tempio
- Division of Genetics and Cell Biology, Vita-Salute San Raffaele University, Milan 20132, Italy.,IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Tiziana Anelli
- Division of Genetics and Cell Biology, Vita-Salute San Raffaele University, Milan 20132, Italy .,IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
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16
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Scarpin MR, Leiboff S, Brunkard JO. Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation. eLife 2020; 9:e58795. [PMID: 33054972 PMCID: PMC7584452 DOI: 10.7554/elife.58795] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Target of rapamycin (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein (RP) mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5' oligopyrimidine tract motifs (5'TOPs) found in mammalian RP mRNAs. We then show that the TOR-LARP1-5'TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5'TOP mRNAs, as well as new, plant-specific 5'TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5'TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1.
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Affiliation(s)
- M Regina Scarpin
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
| | - Samuel Leiboff
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Laboratory of Genetics, University of Wisconsin—MadisonMadisonUnited States
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17
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Chen L, Zheng S. Understand variability of COVID-19 through population and tissue variations in expression of SARS-CoV-2 host genes. INFORMATICS IN MEDICINE UNLOCKED 2020; 21:100443. [PMID: 33072849 PMCID: PMC7550072 DOI: 10.1016/j.imu.2020.100443] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/28/2020] [Accepted: 10/04/2020] [Indexed: 12/25/2022] Open
Abstract
An urgent question of coronavirus disease 2019 (COVID-19) is population variation in susceptibility to SARS-CoV-2 infection and symptom severity. We explore the expression profiles of SARS-CoV-2 host genes, their population variations, associated genetic variants, age- and sex-dependency in normal individuals. SARS-CoV-2 host genes are provisionally defined as the human genes that are experimentally validated or bioinformatically predicted to interact with SARS-CoV-2 proteins. Genes exhibiting most variable expression include ACE2, CLEC4G, CLEC4M, CD209 (interact with the SARS-CoV-2 spike protein); REEP6 (a receptor accessory protein expressed in the olfactory epithelium); SLC27A2 and PKP2 (inhibit virus replication); and PTGS2 (mediates fever response). SNP rs4804803, associated with SARS severity, affects expression of CLEC4G and CD209. Genetic variants of proteases associated with SARS-CoV-2 entry (TMPRSS2, CTSB, and CTSL) are strongly associated with their expression variation, suggesting a genetic contribution to phenotypic variations in multiple organs upon virus attack. The most significant age-dependent gene is ACE2, the cellular receptor of SARS-CoV-2. Others include TGF-β family member GDF15, mediating inflammation, and VKORC1, possibly explaining vitamin K deficiency in COVID-19. TIMM10 and ERGIC1 exhibit significant sex differences. In summary, our results show genetic and multiple biological variables may underlie the population variation in SARS-CoV-2 infection and symptom severity.
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Affiliation(s)
- Liang Chen
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, United States
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Ave, Riverside, CA, 92521, United States
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18
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Nakamura R, Misawa K, Tohnai G, Nakatochi M, Furuhashi S, Atsuta N, Hayashi N, Yokoi D, Watanabe H, Watanabe H, Katsuno M, Izumi Y, Kanai K, Hattori N, Morita M, Taniguchi A, Kano O, Oda M, Shibuya K, Kuwabara S, Suzuki N, Aoki M, Ohta Y, Yamashita T, Abe K, Hashimoto R, Aiba I, Okamoto K, Mizoguchi K, Hasegawa K, Okada Y, Ishihara T, Onodera O, Nakashima K, Kaji R, Kamatani Y, Ikegawa S, Momozawa Y, Kubo M, Ishida N, Minegishi N, Nagasaki M, Sobue G. A multi-ethnic meta-analysis identifies novel genes, including ACSL5, associated with amyotrophic lateral sclerosis. Commun Biol 2020; 3:526. [PMID: 32968195 PMCID: PMC7511394 DOI: 10.1038/s42003-020-01251-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating progressive motor neuron disease that affects people of all ethnicities. Approximately 90% of ALS cases are sporadic and thought to have multifactorial pathogenesis. To understand the genetics of sporadic ALS, we conducted a genome-wide association study using 1,173 sporadic ALS cases and 8,925 controls in a Japanese population. A combined meta-analysis of our Japanese cohort with individuals of European ancestry revealed a significant association at the ACSL5 locus (top SNP p = 2.97 × 10−8). We validated the association with ACSL5 in a replication study with a Chinese population and an independent Japanese population (1941 ALS cases, 3821 controls; top SNP p = 1.82 × 10−4). In the combined meta-analysis, the intronic ACSL5 SNP rs3736947 showed the strongest association (p = 7.81 × 10−11). Using a gene-based analysis of the full multi-ethnic dataset, we uncovered additional genes significantly associated with ALS: ERGIC1, RAPGEF5, FNBP1, and ATXN3. These results advance our understanding of the genetic basis of sporadic ALS. Gen Sobue, Masao Nagasaki and colleagues report a genome-wide association study for amyotrophic lateral sclerosis (ALS) in a large, multi-ethnic cohort comprising Japanese, Chinese, and European ancestry populations. They find a significant association to variants within the ACSL5 gene and identify novel associations with 4 additional genes using a gene-based approach.
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Affiliation(s)
- Ryoichi Nakamura
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kazuharu Misawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan.,Department of Molecular Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka, Japan
| | - Genki Tohnai
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masahiro Nakatochi
- Division of Data Science, Department of Nursing, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Sho Furuhashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Naoki Atsuta
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Naoki Hayashi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Daichi Yokoi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,Department of Neurology, Kakeyu-Misayama Rehabilitation Center Kakeyu Hospital, Ueda, Nagano, Japan
| | - Hazuki Watanabe
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,Department of Neurology, Japanese Red Cross Nagoya Daiichi Hospital, Nagoya, Aichi, Japan
| | - Hirohisa Watanabe
- Brain and Mind Research Center, Nagoya University, Nagoya, Aichi, Japan.,Department of Neurology, Fujita Health University, Toyoake, Aichi, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yuishin Izumi
- Department of Neurology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Kazuaki Kanai
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Department of Neurology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mitsuya Morita
- Division of Neurology, Department of Internal Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Akira Taniguchi
- Department of Neurology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Osamu Kano
- Division of Neurology, Department of Internal Medicine, Toho University Faculty of Medicine, Tokyo, Japan
| | - Masaya Oda
- Department of Neurology, Vihara Hananosato Hospital, Miyoshi, Hiroshima, Japan
| | - Kazumoto Shibuya
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Kuwabara
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoki Suzuki
- Department of Neurology, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Yasuyuki Ohta
- Department of Neurology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Toru Yamashita
- Department of Neurology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Koji Abe
- Department of Neurology, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Rina Hashimoto
- Department of Neurology, National Hospital Organization Higashinagoya National Hospital, Nagoya, Aichi, Japan
| | - Ikuko Aiba
- Department of Neurology, National Hospital Organization Higashinagoya National Hospital, Nagoya, Aichi, Japan
| | - Koichi Okamoto
- Department of Neurology, Geriatrics Research Institute and Hospital, Maebashi, Gunma, Japan
| | - Kouichi Mizoguchi
- Department of Neurology, National Hospital Organization Shizuoka Medical Center, Shizuoka, Japan
| | - Kazuko Hasegawa
- Division of Neurology, National Hospital Organization, Sagamihara National Hospital, Sagamihara, Kanagawa, Japan
| | - Yohei Okada
- Department of Neurology, Aichi Medical University, Nagakute, Aichi, Japan
| | - Tomohiko Ishihara
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kenji Nakashima
- Department of Neurology, National Hospital Organization, Matsue Medical Center, Matsue, Shimane, Japan
| | - Ryuji Kaji
- Department of Neurology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Noriko Ishida
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan. .,Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Sakyo-ku, Kyoto, Japan. .,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Japan.
| | - Gen Sobue
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan. .,Brain and Mind Research Center, Nagoya University, Nagoya, Aichi, Japan. .,Aichi Medical University, Nagakute, Aichi, Japan.
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19
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Steinmetz TD, Schlötzer-Schrehardt U, Hearne A, Schuh W, Wittner J, Schulz SR, Winkler TH, Jäck HM, Mielenz D. TFG is required for autophagy flux and to prevent endoplasmic reticulum stress in CH12 B lymphoma cells. Autophagy 2020; 17:2238-2256. [PMID: 32910713 DOI: 10.1080/15548627.2020.1821546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plasma cells depend on quality control of newly synthesized antibodies in the endoplasmic reticulum (ER) via macroautophagy/autophagy and proteasomal degradation. The cytosolic adaptor protein TFG (Trk-fused gene) regulates ER-Golgi transport, the secretory pathway and proteasome activity in non-immune cells. We show here that TFG is upregulated during lipopolysaccharide- and CpG-induced differentiation of B1 and B2 B cells into plasmablasts, with the highest expression of TFG in mature plasma cells. CRISPR-CAS9-mediated gene disruption of tfg in the B lymphoma cell line CH12 revealed increased apoptosis, which was reverted by BCL2 but even more by ectopic TFG expression. Loss of TFG disrupted ER structure, leading to an expanded ER and increased expression of ER stress genes. When compared to wild-type CH12 cells, tfg KO CH12 cells were more sensitive toward ER stress induced by tunicamycin, monensin and proteasome inhibition or by expression of an ER-bound immunoglobulin (Ig) μ heavy (µH) chain. CH12 tfg KO B cells displayed more total LC3, lower LC3-II turnover and increased numbers and size of autophagosomes. Tandem-fluorescent-LC3 revealed less accumulation of GFP-LC3 in starved and chloroquine-treated CH12 tfg KO B cells. The GFP:RFP ratio of tandem-fluorescent-LC3 was higher in tunicamycin-treated CH12 tfg KO B cells, suggesting less autophagy flux during induced ER stress. Based on these data, we suggest that TFG controls autophagy flux in CH12 B cells and propose that TFG is a survival factor that alleviates ER stress through the support of autophagy flux in activated B cells and mature plasma cells.Abbreviations: Ab, antibody; Ag, antigen; ASC, antibody-secreting cells; ATG, autophagy-related; BCR, B cell receptor; COPII, coat protein complex II; CpG, non-methylated CpG oligonucleotide; ER, endoplasmic reticulum; ERAD, ER-associated degradation; FO, follicular; GFP, green fluorescent protein; HC, heavy chain; Ig, immunoglobulin; IRES, internal ribosomal entry site; LC, light chain; MZ, marginal zone; NFKB, nuclear factor of kappa light polypeptide gene enhancer in B cells; TLR, toll-like receptor; UPR, unfolded protein response.
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Affiliation(s)
- Tobit D Steinmetz
- Division of Molecular Immunology, Department of Internal Medicine 3, Nikolaus-Fiebiger-Zentrum, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | | | - Abigail Hearne
- Division of Molecular Immunology, Department of Internal Medicine 3, Nikolaus-Fiebiger-Zentrum, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Wolfgang Schuh
- Division of Molecular Immunology, Department of Internal Medicine 3, Nikolaus-Fiebiger-Zentrum, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Jens Wittner
- Division of Molecular Immunology, Department of Internal Medicine 3, Nikolaus-Fiebiger-Zentrum, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Nikolaus-Fiebiger-Zentrum, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Chair of Genetics, Nikolaus-Fiebiger-Zentrum, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Nikolaus-Fiebiger-Zentrum, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Department of Internal Medicine 3, Nikolaus-Fiebiger-Zentrum, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
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20
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Pérez-Rodriguez S, de Jesús Ramírez-Lira M, Wulff T, Voldbor BG, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Enrichment of microsomes from Chinese hamster ovary cells by subcellular fractionation for its use in proteomic analysis. PLoS One 2020; 15:e0237930. [PMID: 32841274 PMCID: PMC7447005 DOI: 10.1371/journal.pone.0237930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/06/2020] [Indexed: 11/19/2022] Open
Abstract
Chinese hamster ovary cells have been the workhorse for the production of recombinant proteins in mammalian cells. Since biochemical, cellular and omics studies are usually affected by the lack of suitable fractionation procedures to isolate compartments from these cells, differential and isopycnic centrifugation based techniques were characterized and developed specially for them. Enriched fractions in intact nuclei, mitochondria, peroxisomes, cis-Golgi, trans-Golgi and endoplasmic reticulum (ER) were obtained in differential centrifugation steps and subsequently separated in discontinuous sucrose gradients. Nuclei, mitochondria, cis-Golgi, peroxisomes and smooth ER fractions were obtained as defined bands in 30-60% gradients. Despite the low percentage represented by the microsomes of the total cell homogenate (1.7%), their separation in a novel sucrose gradient (10-60%) showed enough resolution and efficiency to quantitatively separate their components into enriched fractions in trans-Golgi, cis-Golgi and ER. The identity of these organelles belonging to the classical secretion pathway that came from 10-60% gradients was confirmed by proteomics. Data are available via ProteomeXchange with identifier PXD019778. Components from ER and plasma membrane were the most frequent contaminants in almost all obtained fractions. The improved sucrose gradient for microsomal samples proved being successful in obtaining enriched fractions of low abundance organelles, such as Golgi apparatus and ER components, for biochemical and molecular studies, and suitable for proteomic research, which makes it a useful tool for future studies of this and other mammalian cell lines.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - María de Jesús Ramírez-Lira
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bjørn Gunnar Voldbor
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Octavio T. Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Mauricio A. Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - Norma A. Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
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21
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Kwiatek JM, Han GS, Carman GM. Phosphatidate-mediated regulation of lipid synthesis at the nuclear/endoplasmic reticulum membrane. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158434. [PMID: 30910690 PMCID: PMC6755077 DOI: 10.1016/j.bbalip.2019.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/14/2019] [Indexed: 12/11/2022]
Abstract
In yeast and higher eukaryotes, phospholipids and triacylglycerol are derived from phosphatidate at the nuclear/endoplasmic reticulum membrane. In de novo biosynthetic pathways, phosphatidate is channeled into membrane phospholipids via its conversion to CDP-diacylglycerol. Its dephosphorylation to diacylglycerol is required for the synthesis of triacylglycerol as well as for the synthesis of phosphatidylcholine and phosphatidylethanolamine via the Kennedy pathway. In addition to the role of phosphatidate as a precursor, it is a regulatory molecule in the transcriptional control of phospholipid synthesis genes via the Henry regulatory circuit. Pah1 phosphatidate phosphatase and Dgk1 diacylglycerol kinase are key players that function counteractively in the control of the phosphatidate level at the nuclear/endoplasmic reticulum membrane. Loss of Pah1 phosphatidate phosphatase activity not only affects triacylglycerol synthesis but also disturbs the balance of the phosphatidate level, resulting in the alteration of lipid synthesis and related cellular defects. The pah1Δ phenotypes requiring Dgk1 diacylglycerol kinase exemplify the importance of the phosphatidate level in the misregulation of cellular processes. The catalytic function of Pah1 requires its translocation from the cytoplasm to the nuclear/endoplasmic reticulum membrane, which is regulated through its phosphorylation in the cytoplasm by multiple protein kinases as well as through its dephosphorylation by the membrane-associated Nem1-Spo7 protein phosphatase complex. This article is part of a Special Issue entitled Endoplasmic reticulum platforms for lipid dynamics edited by Shamshad Cockcroft and Christopher Stefan.
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Affiliation(s)
- Joanna M Kwiatek
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA.
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22
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Lee Y, Sun D, Ori AP, Lu AT, Seeboth A, Harris SE, Deary IJ, Marioni RE, Soerensen M, Mengel-From J, Hjelmborg J, Christensen K, Wilson JG, Levy D, Reiner AP, Chen W, Li S, Harris JR, Magnus P, Aviv A, Jugessur A, Horvath S. Epigenome-wide association study of leukocyte telomere length. Aging (Albany NY) 2019; 11:5876-5894. [PMID: 31461406 PMCID: PMC6738430 DOI: 10.18632/aging.102230] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/18/2019] [Indexed: 12/24/2022]
Abstract
Telomere length is associated with age-related diseases and is highly heritable. It is unclear, however, to what extent epigenetic modifications are associated with leukocyte telomere length (LTL). In this study, we conducted a large-scale epigenome-wide association study (EWAS) of LTL using seven large cohorts (n=5,713) - the Framingham Heart Study, the Jackson Heart Study, the Women's Health Initiative, the Bogalusa Heart Study, the Lothian Birth Cohorts of 1921 and 1936, and the Longitudinal Study of Aging Danish Twins. Our stratified analysis suggests that EWAS findings for women of African ancestry may be distinct from those of three other groups: males of African ancestry, and males and females of European ancestry. Using a meta-analysis framework, we identified DNA methylation (DNAm) levels at 823 CpG sites to be significantly associated (P<1E-7) with LTL after adjusting for age, sex, ethnicity, and imputed white blood cell counts. Functional enrichment analyses revealed that these CpG sites are near genes that play a role in circadian rhythm, blood coagulation, and wound healing. Weighted correlation network analysis identified four co-methylation modules associated with LTL, age, and blood cell counts. Overall, this study reveals highly significant relationships between two hallmarks of aging: telomere biology and epigenetic changes.
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Affiliation(s)
- Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- Department of Epidemiology, Tulane University, New Orleans, LA 70118, USA
| | - Anil P.S. Ori
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Anne Seeboth
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
- Center for Individualized Medicine in Arterial Diseases, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Jacob Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA 20892, USA
| | - Daniel Levy
- The Framingham Heart Study, Framingham, MA 01702, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Seattle, MD 20892, USA
| | - Alex P. Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Wei Chen
- Department of Epidemiology, Tulane University, New Orleans, LA 70118, USA
| | - Shengxu Li
- Children’s Minnesota Research Institute, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404, USA
| | - Jennifer R. Harris
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Abraham Aviv
- Center of Development and Aging, New Jersey Medical School, Rutgers State University of New Jersey, Newark, NJ 07103, USA
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
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23
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Pehlivan D, Bayram Y, Gunes N, Coban Akdemir Z, Shukla A, Bierhals T, Tabakci B, Sahin Y, Gezdirici A, Fatih JM, Gulec EY, Yesil G, Punetha J, Ocak Z, Grochowski CM, Karaca E, Albayrak HM, Radhakrishnan P, Erdem HB, Sahin I, Yildirim T, Bayhan IA, Bursali A, Elmas M, Yuksel Z, Ozdemir O, Silan F, Yildiz O, Yesilbas O, Isikay S, Balta B, Gu S, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Boerwinkle E, Gibbs RA, Tsiakas K, Hempel M, Girisha KM, Gul D, Posey JE, Elcioglu NH, Tuysuz B, Lupski JR. The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance. Am J Hum Genet 2019; 105:132-150. [PMID: 31230720 PMCID: PMC6612529 DOI: 10.1016/j.ajhg.2019.05.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/21/2019] [Indexed: 01/29/2023] Open
Abstract
Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members.
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Affiliation(s)
- Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nilay Gunes
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Burcu Tabakci
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey
| | - Yavuz Sahin
- Department of Medical Genetics, Necip Fazıl City Hospital, Kahramanmaras 46050, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul 34093, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Ocak
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hatice Mutlu Albayrak
- Department of Pediatrics, Division of Pediatric Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun 55270, Turkey
| | - Periyasamy Radhakrishnan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Ibrahim Sahin
- Department of Medical Genetics, University of Erzurum, School of Medicine, Erzurum 25240, Turkey
| | - Timur Yildirim
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Ilhan A Bayhan
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Aysegul Bursali
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Zafer Yuksel
- Medical Genetics Clinic, Mersin Women and Children Hospital, Mersin 33330, Turkey
| | - Ozturk Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Fatma Silan
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Onur Yildiz
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, University of Health Sciences, Van Training and Research Hospital, Van 65130, Turkey
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep 27000, Turkey
| | - Burhan Balta
- Department of Medical Genetics, Kayseri Training and Research Hospital, Kayseri 38080, Turkey
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Konstantinos Tsiakas
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey; Eastern Mediterranean University School of Medicine, Cyprus, Mersin 10, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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24
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Yoo W, Cho EB, Kim S, Yoon JB. The E3 ubiquitin ligase MARCH2 regulates ERGIC3-dependent trafficking of secretory proteins. J Biol Chem 2019; 294:10900-10912. [PMID: 31142615 DOI: 10.1074/jbc.ra119.007435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/17/2019] [Indexed: 11/06/2022] Open
Abstract
The E3 ubiquitin ligase membrane-associated ring-CH-type finger 2 (MARCH2) is known to be involved in intracellular vesicular trafficking, but its role in the early secretory pathway between the endoplasmic reticulum (ER) and Golgi compartments is largely unknown. Human ER-Golgi intermediate compartment protein 2 (ERGIC2) and ERGIC3 are orthologs of Erv41 and Erv46 in yeast, proteins that form a heteromeric complex, cycle between the ER and Golgi, and function as cargo receptors in both anterograde and retrograde protein trafficking. Here, we report that MARCH2 directs ubiquitination and subsequent degradation of ERGIC3 and that MARCH2 depletion increases endogenous ERGIC3 levels. We provide evidence that the lysine residues at positions 6 and 8 of ERGIC3 are the major sites of MARCH2-mediated ubiquitination. Of note, MARCH2 did not significantly decrease the levels of an ERGIC3 variant with lysine-to-arginine substitutions at residues 6 and 8. We also show that ERGIC3 binds to itself or to ERGIC2, whereas ERGIC2 is unable to interact with itself. Our results indicate that α1-antitrypsin and haptoglobin are likely to be cargo proteins of ERGIC3. We further observed that α1-antitrypsin and haptoglobin specifically bind to ERGIC3 and that ERGIC3 depletion decreases their secretion. Moreover, MARCH2 reduced secretion of α1-antitrypsin and haptoglobin, and coexpression of the ubiquitination-resistant ERGIC3 variant largely restored their secretion, suggesting that MARCH2-mediated ERGIC3 ubiquitination is the major cause of the decrease in trafficking of ERGIC3-binding secretory proteins. Our findings provide detailed insights into the regulation of the early secretory pathway by MARCH2 and into ERGIC3 function.
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Affiliation(s)
- Wonjin Yoo
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea and
| | - Eun-Bee Cho
- Department of Medical Lifesciences, Catholic University of Korea, Seoul 06591, Korea
| | - Sungjoo Kim
- Department of Medical Lifesciences, Catholic University of Korea, Seoul 06591, Korea
| | - Jong-Bok Yoon
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea and.
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25
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Papillomaviruses and Endocytic Trafficking. Int J Mol Sci 2018; 19:ijms19092619. [PMID: 30181457 PMCID: PMC6163501 DOI: 10.3390/ijms19092619] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022] Open
Abstract
Endocytic trafficking plays a major role in transport of incoming human papillomavirus (HPVs) from plasma membrane to the trans Golgi network (TGN) and ultimately into the nucleus. During this infectious entry, several cellular sorting factors are recruited by the viral capsid protein L2, which plays a critical role in ensuring successful transport of the L2/viral DNA complex to the nucleus. Later in the infection cycle, two viral oncoproteins, E5 and E6, have also been shown to modulate different aspects of endocytic transport pathways. In this review, we highlight how HPV makes use of and perturbs normal endocytic transport pathways, firstly to achieve infectious virus entry, secondly to produce productive infection and the completion of the viral life cycle and, finally, on rare occasions, to bring about the development of malignancy.
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26
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Saraste J, Marie M. Intermediate compartment (IC): from pre-Golgi vacuoles to a semi-autonomous membrane system. Histochem Cell Biol 2018; 150:407-430. [PMID: 30173361 PMCID: PMC6182704 DOI: 10.1007/s00418-018-1717-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2018] [Indexed: 12/19/2022]
Abstract
Despite its discovery more than three decades ago and well-established role in protein sorting and trafficking in the early secretory pathway, the intermediate compartment (IC) has remained enigmatic. The prevailing view is that the IC evolved as a specialized organelle to mediate long-distance endoplasmic reticulum (ER)–Golgi communication in metazoan cells, but is lacking in other eukaryotes, such as plants and fungi. However, this distinction is difficult to reconcile with the high conservation of the core machineries that regulate early secretory trafficking from yeast to man. Also, it has remained unclear whether the pleiomorphic IC components—vacuoles, tubules and vesicles—represent transient transport carriers or building blocks of a permanent pre-Golgi organelle. Interestingly, recent studies have revealed that the IC maintains its compositional, structural and spatial properties throughout the cell cycle, supporting a model that combines the dynamic and stable aspects of the organelle. Moreover, the IC has been assigned novel functions, such as cell signaling, Golgi-independent trafficking and autophagy. The emerging permanent nature of the IC and its connections with the centrosome and the endocytic recycling system encourage reconsideration of its relationship with the Golgi ribbon, role in Golgi biogenesis and ubiquitous presence in eukaryotic cells.
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Affiliation(s)
- Jaakko Saraste
- Department of Biomedicine and Molecular Imaging Center (MIC), University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway.
| | - Michaël Marie
- Department of Biomedicine and Molecular Imaging Center (MIC), University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
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27
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Wang F, Guan X, Yang J, He W, Wei Y, Chen H, Li Y. Differential Expression and Significance of Endoplasmic Reticulum Golgi Intermediate Compartment 1 in Precancerous Gastric Lesions and Gastric Cancer. Am J Med Sci 2018; 355:228-234. [DOI: 10.1016/j.amjms.2017.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 10/18/2017] [Accepted: 11/06/2017] [Indexed: 02/06/2023]
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28
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Wang FR, Wei YC, Han ZJ, He WT, Guan XY, Chen H, Li YM. Aberrant DNA-PKcs and ERGIC1 expression may be involved in initiation of gastric cancer. World J Gastroenterol 2017; 23:6119-6127. [PMID: 28970727 PMCID: PMC5597503 DOI: 10.3748/wjg.v23.i33.6119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/14/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the molecular mechanisms of gastric carcinogenesis.
METHODS We used label-free quantification technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify differentially expressed proteins in 160 specimens of normal gastric mucosa, gastric mucosa with mild dysplasia, moderate dysplasia, severe dysplasia, and early mucosal gastric cancer (GC) collected at the Second Hospital of Lanzhou University from 2010 to 2015. Immunohistochemistry was used to verify the differentially expressed proteins detected by LC-MS/MS.
RESULTS With a threshold of a 1.2-fold change and a P-value < 0.05 between mild dysplasia, moderate dysplasia, severe dysplasia or early mucosal GC and matched normal gastric mucosa tissues, proteomic analysis identified 365 significantly differentially expressed proteins. ERGIC1 expression decreased, while DNA-PKcs expression increased gradually along with different stages of GC initiation based on the tendency of fold change. The expression patterns of ERGIC1 and DNA-PKcs revealed by immunohistochemistry were consistent with the LC-MS/MS results.
CONCLUSION The results suggest that aberrant ERGIC1 and DNA-PKcs expression may be involved in GC initiation.
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Affiliation(s)
- Fu-Rong Wang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu Province, China
- Department of Pathology, Second Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Yu-Cai Wei
- Department of General Surgery, Second Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Zhi-Jian Han
- The Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Wen-Ting He
- The Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Xiao-Ying Guan
- Department of Pathology, Second Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Hao Chen
- Department of General Surgery, Second Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Yu-Min Li
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu Province, China
- Department of General Surgery, Second Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
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29
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Sirkis DW, Aparicio RE, Schekman R. Neurodegeneration-associated mutant TREM2 proteins abortively cycle between the ER and ER-Golgi intermediate compartment. Mol Biol Cell 2017; 28:2723-2733. [PMID: 28768830 PMCID: PMC5620379 DOI: 10.1091/mbc.e17-06-0423] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 07/28/2017] [Accepted: 07/28/2017] [Indexed: 11/21/2022] Open
Abstract
Mutations in the microglial cell surface receptor TREM2 are associated with multiple forms of neurodegeneration. Several of these mutant forms of TREM2 were thought to be retained in the endoplasmic reticulum (ER), but careful analysis reveals that they engage in an abortive cycling pathway between the ER and ER–Golgi intermediate compartment. Triggering receptor expressed on myeloid cells 2 (TREM2) is a transmembrane protein expressed on microglia within the brain. Several rare mutations in TREM2 cause an early-onset form of neurodegeneration when inherited homozygously. Here we investigate how these mutations affect the intracellular transport of TREM2. We find that most pathogenic TREM2 mutant proteins fail to undergo normal maturation in the Golgi complex and show markedly reduced cell-surface expression. Prior research has suggested that two such mutants are retained in the endoplasmic reticulum (ER), but we find, using a cell-free coat protein complex II (COPII) vesicle budding reaction, that mutant TREM2 is exported efficiently from the ER. In addition, mutant TREM2 becomes sensitive to cleavage by endoglycosidase D under conditions that inhibit recycling to the ER, indicating that it normally reaches a post-ER compartment. Maturation-defective TREM2 mutants are also efficiently bound by a lectin that recognizes O-glycans added in the ER–Golgi intermediate compartment (ERGIC) and cis-Golgi cisterna. Finally, mutant TREM2 accumulates in the ERGIC in cells depleted of COPI. These results indicate that efficient ER export is not sufficient to enable normal cell-surface expression of TREM2. Moreover, our findings suggest that the ERGIC may play an underappreciated role as a quality-control center for mutant and/or malformed membrane proteins.
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Affiliation(s)
- Daniel W Sirkis
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720
| | - Renan E Aparicio
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720
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30
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Reinstein E, Drasinover V, Lotan R, Gal-Tanamy M, Bolocan Nachman I, Eyal E, Jaber L, Magal N, Shohat M. Mutations in ERGIC1 cause Arthrogryposis multiplex congenita, neuropathic type. Clin Genet 2017; 93:160-163. [PMID: 28317099 DOI: 10.1111/cge.13018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 11/29/2022]
Abstract
Arthrogryposis multiplex congenita (AMC) is heterogeneous group of disorders characterized by non-progressive joint contractures from birth that involve more than 1 part of the body. There are various etiologies for AMC including genetic and environmental depends on the specific type, however, for most types, the cause is not fully understood. We previously reported large Israeli Arab kindred consisting of 16 patients affected with AMC neuropathic type, and mapped the locus to a 5.5 cM interval on chromosome 5qter. Using whole exome sequencing, we have now identified homozygous pathogenic variant in the ERGIC1 gene within the previously defined linked region. ERGIC1 encodes a cycling membrane protein which has a possible role in transport between endoplasmic reticulum and Golgi. We further show that this mutation was absent in more than 200 samples of healthy unrelated individuals of the Israeli Arab population. Thus, our findings expand the spectrum of hereditary AMC and suggest that abnormalities in protein trafficking may underlie AMC-related disorders.
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Affiliation(s)
- E Reinstein
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - V Drasinover
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - R Lotan
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - M Gal-Tanamy
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - I Bolocan Nachman
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - E Eyal
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - L Jaber
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - N Magal
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - M Shohat
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel.,Medical Genetics institute, Maccabi HMO, Rechovot, Israel
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31
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Yuen CYL, Wang P, Kang BH, Matsumoto K, Christopher DA. A Non-Classical Member of the Protein Disulfide Isomerase Family, PDI7 of Arabidopsis thaliana, Localizes to the cis-Golgi and Endoplasmic Reticulum Membranes. PLANT & CELL PHYSIOLOGY 2017; 58:1103-1117. [PMID: 28444333 DOI: 10.1093/pcp/pcx057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/13/2017] [Indexed: 06/07/2023]
Abstract
Members of the protein disulfide isomerase (PDI)-C subfamily are chimeric proteins containing the thioredoxin (Trx) domain of PDIs, and the conserved N- and C-terminal Pfam domains of Erv41p/Erv46p-type cargo receptors. They are unique to plants and chromalveolates. The Arabidopsis genome encodes three PDI-C isoforms: PDI7, PDI12 and PDI13. Here we demonstrate that PDI7 is a 65 kDa integral membrane glycoprotein expressed throughout many Arabidopsis tissues. Using a PDI7-specific antibody, we show through immunoelectron microscopy that PDI7 localizes to the endoplasmic reticulum (ER) and Golgi membranes in wild-type root tip cells, and was also detected in vesicles. Tomographic modeling of the Golgi revealed that PDI7 was confined to the cis-Golgi, and accumulated primarily at the cis-most cisterna. Shoot apical meristem cells from transgenic plants overexpressing PDI7 exhibited a dramatic increase in anti-PDI7 labeling at the cis-Golgi. When N- or C-terminal fusions between PDI7 and the green fluorescent protein variant, GFP(S65T), were expressed in mesophyll protoplasts, the fusions co-localized with the ER marker, ER-mCherry. However, when GFP(S65T) was positioned internally within PDI7 (PDI7-GFPint), the fusion strongly co-localized with the cis-Golgi marker, mCherry-SYP31, and faintly labeled the ER. In contrast to the Golgi-resident fusion protein (Man49-mCherry), PDI7-GFPint did not redistribute to the ER after brefeldin A treatment. Protease protection experiments indicated that the Trx domain of PDI7 is located within the ER/Golgi lumen. We propose a model where PDI-C isoforms function as cargo receptors for proteins containing exposed cysteine residues, cycling them from the Golgi back to the ER.
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Affiliation(s)
- Christen Y L Yuen
- University of Hawaii, Molecular Biosciences & Bioengineering, Honolulu, HI, USA
| | - Pengfei Wang
- Chinese University of Hong Kong, Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong, China
| | - Byung-Ho Kang
- Chinese University of Hong Kong, Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong, China
| | - Kristie Matsumoto
- University of Hawaii, Molecular Biosciences & Bioengineering, Honolulu, HI, USA
| | - David A Christopher
- University of Hawaii, Molecular Biosciences & Bioengineering, Honolulu, HI, USA
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32
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Klink VP, Sharma K, Pant SR, McNeece B, Niraula P, Lawrence GW. Components of the SNARE-containing regulon are co-regulated in root cells undergoing defense. PLANT SIGNALING & BEHAVIOR 2017; 12:e1274481. [PMID: 28010187 PMCID: PMC5351740 DOI: 10.1080/15592324.2016.1274481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 05/23/2023]
Abstract
The term regulon has been coined in the genetic model plant Arabidopsis thaliana, denoting a structural and physiological defense apparatus defined genetically through the identification of the penetration (pen) mutants. The regulon is composed partially by the soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) syntaxin PEN1. PEN1 has homology to a Saccharomyces cerevisae gene that regulates a Secretion (Sec) protein, Suppressor of Sec 1 (Sso1p). The regulon is also composed of the β-glucosidase (PEN2) and an ATP binding cassette (ABC) transporter (PEN3). While important in inhibiting pathogen infection, limited observations have been made regarding the transcriptional regulation of regulon genes until now. Experiments made using the model agricultural Glycine max (soybean) have identified co-regulated gene expression of regulon components. The results explain the observation of hundreds of genes expressed specifically in the root cells undergoing the natural process of defense. Data regarding additional G. max genes functioning within the context of the regulon are presented here, including Sec 14, Sec 4 and Sec 23. Other examined G. max homologs of membrane fusion genes include an endosomal bromo domain-containing protein1 (Bro1), syntaxin6 (SYP6), SYP131, SYP71, SYP8, Bet1, coatomer epsilon (ϵ-COP), a coatomer zeta (ζ-COP) paralog and an ER to Golgi component (ERGIC) protein. Furthermore, the effectiveness of biochemical pathways that would function within the context of the regulon ave been examined, including xyloglucan xylosyltransferase (XXT), reticuline oxidase (RO) and galactinol synthase (GS). The experiments have unveiled the importance of the regulon during defense in the root and show how the deposition of callose relates to the process.
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Affiliation(s)
- Vincent P. Klink
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Keshav Sharma
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Shankar R. Pant
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Brant McNeece
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Prakash Niraula
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Gary W. Lawrence
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
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33
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Thornbrough JM, Gopinath A, Hundley T, Worley MJ. Human Genome-Wide RNAi Screen for Host Factors That Facilitate Salmonella Invasion Reveals a Role for Potassium Secretion in Promoting Internalization. PLoS One 2016; 11:e0166916. [PMID: 27880807 PMCID: PMC5120809 DOI: 10.1371/journal.pone.0166916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/07/2016] [Indexed: 02/06/2023] Open
Abstract
Salmonella enterica can actively invade the gastro-intestinal epithelium. This frequently leads to diarrheal disease, and also gives the pathogen access to phagocytes that can serve as vehicles for dissemination into deeper tissue. The ability to invade host cells is also important in maintaining the carrier state. While much is known about the bacterial factors that promote invasion, relatively little is known about the host factors involved. To gain insight into how Salmonella enterica serovar Typhimurium is able to invade normally non-phagocytic cells, we undertook a global RNAi screen with S. Typhimurium-infected human epithelial cells. In all, we identified 633 genes as contributing to bacterial internalization. These genes fall into a diverse group of functional categories revealing that cytoskeletal regulators are not the only factors that modulate invasion. In fact, potassium ion transport was the most enriched molecular function category in our screen, reinforcing a link between potassium and internalization. In addition to providing new insights into the molecular mechanisms underlying the ability of pathogens to invade host cells, all 633 host factors identified are candidates for new anti-microbial targets for treating Salmonella infections, and may be useful in curtailing infections with other pathogens as well.
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Affiliation(s)
- Joshua M. Thornbrough
- Department of Biology, University of Louisville, Louisville, KY, 40292, United States of America
| | - Adarsh Gopinath
- Department of Biology, University of Louisville, Louisville, KY, 40292, United States of America
| | - Tom Hundley
- Department of Biology, University of Louisville, Louisville, KY, 40292, United States of America
| | - Micah J. Worley
- Department of Biology, University of Louisville, Louisville, KY, 40292, United States of America
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, United States of America
- * E-mail:
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34
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Budayeva HG, Cristea IM. Human Sirtuin 2 Localization, Transient Interactions, and Impact on the Proteome Point to Its Role in Intracellular Trafficking. Mol Cell Proteomics 2016; 15:3107-3125. [PMID: 27503897 DOI: 10.1074/mcp.m116.061333] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 11/06/2022] Open
Abstract
Human sirtuin 2 (SIRT2) is an NAD+-dependent deacetylase that primarily functions in the cytoplasm, where it can regulate α-tubulin acetylation levels. SIRT2 is linked to cancer progression, neurodegeneration, and infection with bacteria or viruses. However, the current knowledge about its interactions and the means through which it exerts its functions has remained limited. Here, we aimed to gain a better understanding of its cellular functions by characterizing SIRT2 subcellular localization, the identity and relative stability of its protein interactions, and its impact on the proteome of primary human fibroblasts. To assess the relative stability of SIRT2 interactions, we used immunoaffinity purification in conjunction with both label-free and metabolic labeling quantitative mass spectrometry. In addition to the expected associations with cytoskeleton proteins, including its known substrate TUBA1A, our results reveal that SIRT2 specifically interacts with proteins functioning in membrane trafficking, secretory processes, and transcriptional regulation. By quantifying their relative stability, we found most interactions to be transient, indicating a dynamic SIRT2 environment. We discover that SIRT2 localizes to the ER-Golgi intermediate compartment (ERGIC), and that this recruitment requires an intact ER-Golgi trafficking pathway. Further expanding these findings, we used microscopy and interaction assays to establish the interaction and coregulation of SIRT2 with liprin-β1 scaffolding protein (PPFiBP1), a protein with roles in focal adhesions disassembly. As SIRT2 functions may be accomplished via interactions, enzymatic activity, and transcriptional regulation, we next assessed the impact of SIRT2 levels on the cellular proteome. SIRT2 knockdown led to changes in the levels of proteins functioning in membrane trafficking, including some of its interaction partners. Altogether, our study expands the knowledge of SIRT2 cytoplasmic functions to define a previously unrecognized involvement in intracellular trafficking pathways, which may contribute to its roles in cellular homeostasis and human diseases.
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Affiliation(s)
- Hanna G Budayeva
- From the ‡Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544
| | - Ileana M Cristea
- From the ‡Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544
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35
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Margulis NG, Wilson JD, Bentivoglio CM, Dhungel N, Gitler AD, Barlowe C. Analysis of COPII Vesicles Indicates a Role for the Emp47-Ssp120 Complex in Transport of Cell Surface Glycoproteins. Traffic 2016; 17:191-210. [PMID: 26650540 DOI: 10.1111/tra.12356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 11/30/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
Coat protein complex II (COPII) vesicle formation at the endoplasmic reticulum (ER) transports nascent secretory proteins forward to the Golgi complex. To further define the machinery that packages secretory cargo and targets vesicles to Golgi membranes, we performed a comprehensive proteomic analysis of purified COPII vesicles. In addition to previously known proteins, we identified new vesicle proteins including Coy1, Sly41 and Ssp120, which were efficiently packaged into COPII vesicles for trafficking between the ER and Golgi compartments. Further characterization of the putative calcium-binding Ssp120 protein revealed a tight association with Emp47 and in emp47Δ cells Ssp120 was mislocalized and secreted. Genetic analyses demonstrated that EMP47 and SSP120 display identical synthetic positive interactions with IRE1 and synthetic negative interactions with genes involved in cell wall assembly. Our findings support a model in which the Emp47-Ssp120 complex functions in transport of plasma membrane glycoproteins through the early secretory pathway.
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Affiliation(s)
- Neil G Margulis
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Joshua D Wilson
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | | | - Nripesh Dhungel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Present address: Singer Instruments, Roadwater, Watchet, Somerset, TA23 0RE, UK
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Charles Barlowe
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
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36
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Saraste J, Marie M. Intermediate Compartment: A Sorting Station between the Endoplasmic Reticulum and the Golgi Apparatus. ENCYCLOPEDIA OF CELL BIOLOGY 2016. [PMCID: PMC7150006 DOI: 10.1016/b978-0-12-394447-4.20013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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37
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Lin QH, Zhang KD, Duan HX, Liu MX, Wei WL, Cao Y. ERGIC3, which is regulated by miR-203a, is a potential biomarker for non-small cell lung cancer. Cancer Sci 2015; 106:1463-73. [PMID: 26177443 PMCID: PMC4638005 DOI: 10.1111/cas.12741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/29/2015] [Accepted: 07/09/2015] [Indexed: 01/10/2023] Open
Abstract
In a previous study, we found that ERGIC3 was a novel lung cancer-related gene by screening libraries of differentially expressed genes. In this study, we developed a new murine monoclonal antibody (mAb) against ERGIC3. This avid antibody (6-C4) is well suited for immunohistochemistry, immunoblotting and solid-phase immunoassays. Furthermore, we systematically investigated expressions of ERGIC3 in a broad variety of normal human tissues and various types of tumors by immunohistochemistry. In normal human tissues, 6-C4 reacted only in some epithelial cells, such as hepatocytes, gastrointestinal epithelium, ducts and acini of the pancreas, proximal and distal tubules of the kidney, and mammary epithelial cells; however, most normal human tissues were not stained. Moreover, almost all carcinomas that originated from the epithelial cells were positive for 6-C4, whereas all sarcomas were negative. Notably, 6-C4 strongly stained non-small cell lung cancer (NSCLC) cells but did not react with normal lung tissues. Hence, ERGIC3 mAb could be used in histopathological diagnosis and cytopathological testing to detect early-stage NSCLC. We also studied the mechanisms of ERGIC3 regulation in vitro and in vivo by means of bioinformatics analysis, luciferase reporter assay, miRNA expression profiling and miRNA transfection. Results showed that miR-203a downregulation induced ERGIC3 overexpression in NSCLC cells.
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Affiliation(s)
- Qing-Hai Lin
- Laboratory of Molecular and Experimental Pathology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Kui-Dong Zhang
- Laboratory of Molecular and Experimental Pathology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - He-Xian Duan
- Laboratory of Molecular and Experimental Pathology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Min-Xia Liu
- Laboratory of Molecular and Experimental Pathology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wan-Li Wei
- Department of Pathology, Yunnan Tumor Hospital, Kunming, China
| | - Yi Cao
- Laboratory of Molecular and Experimental Pathology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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38
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Alterio J, Masson J, Diaz J, Chachlaki K, Salman H, Areias J, Al Awabdh S, Emerit MB, Darmon M. Yif1B Is Involved in the Anterograde Traffic Pathway and the Golgi Architecture. Traffic 2015; 16:978-93. [DOI: 10.1111/tra.12306] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/03/2015] [Accepted: 06/08/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Jeanine Alterio
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Justine Masson
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Jorge Diaz
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Konstantina Chachlaki
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Haysam Salman
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Julie Areias
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Sana Al Awabdh
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Michel Boris Emerit
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Michèle Darmon
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
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39
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Johnson A, Bhattacharya N, Hanna M, Pennington JG, Schuh AL, Wang L, Otegui MS, Stagg SM, Audhya A. TFG clusters COPII-coated transport carriers and promotes early secretory pathway organization. EMBO J 2015; 34:811-27. [PMID: 25586378 DOI: 10.15252/embj.201489032] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In mammalian cells, cargo-laden secretory vesicles leave the endoplasmic reticulum (ER) en route to ER-Golgi intermediate compartments (ERGIC) in a manner dependent on the COPII coat complex. We report here that COPII-coated transport carriers traverse a submicron, TFG (Trk-fused gene)-enriched zone at the ER/ERGIC interface. The architecture of TFG complexes as determined by three-dimensional electron microscopy reveals the formation of flexible, octameric cup-like structures, which are able to self-associate to generate larger polymers in vitro. In cells, loss of TFG function dramatically slows protein export from the ER and results in the accumulation of COPII-coated carriers throughout the cytoplasm. Additionally, the tight association between ER and ERGIC membranes is lost in the absence of TFG. We propose that TFG functions at the ER/ERGIC interface to locally concentrate COPII-coated transport carriers and link exit sites on the ER to ERGIC membranes. Our findings provide a new mechanism by which COPII-coated carriers are retained near their site of formation to facilitate rapid fusion with neighboring ERGIC membranes upon uncoating, thereby promoting interorganellar cargo transport.
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Affiliation(s)
- Adam Johnson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | | | - Michael Hanna
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Janice G Pennington
- Departments of Botany and Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Amber L Schuh
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Lei Wang
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Marisa S Otegui
- Departments of Botany and Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
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40
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Shibuya A, Margulis N, Christiano R, Walther TC, Barlowe C. The Erv41-Erv46 complex serves as a retrograde receptor to retrieve escaped ER proteins. ACTA ACUST UNITED AC 2015; 208:197-209. [PMID: 25583996 PMCID: PMC4298680 DOI: 10.1083/jcb.201408024] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Signal-dependent sorting of proteins in the early secretory pathway is required for dynamic retention of endoplasmic reticulum (ER) and Golgi components. In this study, we identify the Erv41-Erv46 complex as a new retrograde receptor for retrieval of non-HDEL-bearing ER resident proteins. In cells lacking Erv41-Erv46 function, the ER enzyme glucosidase I (Gls1) was mislocalized and degraded in the vacuole. Biochemical experiments demonstrated that the luminal domain of Gls1 bound to the Erv41-Erv46 complex in a pH-dependent manner. Moreover, in vivo disturbance of the pH gradient across membranes by bafilomycin A1 treatment caused Gls1 mislocalization. Whole cell proteomic analyses of deletion strains using stable isotope labeling by amino acids in culture identified other ER resident proteins that depended on the Erv41-Erv46 complex for efficient localization. Our results support a model in which pH-dependent receptor binding of specific cargo by the Erv41-Erv46 complex in Golgi compartments identifies escaped ER resident proteins for retrieval to the ER in coat protein complex I-formed transport carriers.
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Affiliation(s)
- Aya Shibuya
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Neil Margulis
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Romain Christiano
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520
| | - Tobias C Walther
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520
| | - Charles Barlowe
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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41
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Sugawara T, Kano F, Murata M. Rab2A is a pivotal switch protein that promotes either secretion or ER-associated degradation of (pro)insulin in insulin-secreting cells. Sci Rep 2014; 4:6952. [PMID: 25377857 PMCID: PMC5381769 DOI: 10.1038/srep06952] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/14/2014] [Indexed: 12/15/2022] Open
Abstract
Rab2A, a small GTPase localizing to the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC), regulates COPI-dependent vesicular transport from the ERGIC. Rab2A knockdown inhibited glucose-stimulated insulin secretion and concomitantly enlarged the ERGIC in insulin-secreting cells. Large aggregates of polyubiquitinated proinsulin accumulated in the cytoplasmic vicinity of a unique large spheroidal ERGIC, designated the LUb-ERGIC. Well-known components of ER-associated degradation (ERAD) also accumulated at the LUb-ERGIC, creating a suitable site for ERAD-mediated protein quality control. Moreover, chronically high glucose levels, which induced the enlargement of the LUb-ERGIC and ubiquitinated protein aggregates, impaired Rab2A activity by promoting dissociation from its effector, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), in response to poly (ADP-ribosyl)ation of GAPDH. The inactivation of Rab2A relieved glucose-induced ER stress and inhibited ER stress-induced apoptosis. Collectively, these results suggest that Rab2A is a pivotal switch that controls whether insulin should be secreted or degraded at the LUb-ERGIC and Rab2A inactivation ensures alleviation of ER stress and cell survival under chronic glucotoxicity.
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Affiliation(s)
- Taichi Sugawara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Fumi Kano
- 1] Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan [2] PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Masayuki Murata
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
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42
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Yu X, Woolery AR, Luong P, Hao YH, Grammel M, Westcott N, Park J, Wang J, Bian X, Demirkan G, Hang HC, Orth K, LaBaer J. Copper-catalyzed azide-alkyne cycloaddition (click chemistry)-based detection of global pathogen-host AMPylation on self-assembled human protein microarrays. Mol Cell Proteomics 2014; 13:3164-76. [PMID: 25073739 PMCID: PMC4223499 DOI: 10.1074/mcp.m114.041103] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
AMPylation (adenylylation) is a recently discovered mechanism employed by infectious bacteria to regulate host cell signaling. However, despite significant effort, only a few host targets have been identified, limiting our understanding of how these pathogens exploit this mechanism to control host cells. Accordingly, we developed a novel nonradioactive AMPylation screening platform using high-density cell-free protein microarrays displaying human proteins produced by human translational machinery. We screened 10,000 unique human proteins with Vibrio parahaemolyticus VopS and Histophilus somni IbpAFic2, and identified many new AMPylation substrates. Two of these, Rac2, and Rac3, were confirmed in vivo as bona fide substrates during infection with Vibrio parahaemolyticus. We also mapped the site of AMPylation of a non-GTPase substrate, LyGDI, to threonine 51, in a region regulated by Src kinase, and demonstrated that AMPylation prevented its phosphorylation by Src. Our results greatly expanded the repertoire of potential host substrates for bacterial AMPylators, determined their recognition motif, and revealed the first pathogen-host interaction AMPylation network. This approach can be extended to identify novel substrates of AMPylators with different domains or in different species and readily adapted for other post-translational modifications.
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Affiliation(s)
- Xiaobo Yu
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Andrew R Woolery
- §Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9148, USA
| | - Phi Luong
- §Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9148, USA
| | - Yi Heng Hao
- §Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9148, USA
| | - Markus Grammel
- ¶The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York 10065, USA
| | - Nathan Westcott
- ¶The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York 10065, USA
| | - Jin Park
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Jie Wang
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Xiaofang Bian
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Gokhan Demirkan
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Howard C Hang
- ¶The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York 10065, USA
| | - Kim Orth
- §Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9148, USA
| | - Joshua LaBaer
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA;
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Saatchi M, Schnabel RD, Taylor JF, Garrick DJ. Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds. BMC Genomics 2014; 15:442. [PMID: 24906442 PMCID: PMC4102727 DOI: 10.1186/1471-2164-15-442] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/30/2014] [Indexed: 11/10/2022] Open
Abstract
Background The availability of high-density SNP assays including the BovineSNP50 (50 K) enables the identification of novel quantitative trait loci (QTL) and improvement of the resolution of the locations of previously mapped QTL. We performed a series of genome-wide association studies (GWAS) using 50 K genotypes scored in 18,274 animals from 10 US beef cattle breeds with observations for twelve body weights, calving ease and carcass traits. Results A total of 159 large-effects QTL (defined as 1-Mb genome windows explaining more than 1% of additive genetic variance) were identified. In general, more QTL were identified in analyses with bigger sample sizes. Four large-effect pleiotropic or closely linked QTLs located on BTA6 at 37–42 Mb (primarily at 38 Mb), on BTA7 at 93 Mb, on BTA14 at 23–26 Mb (primarily at 25 Mb) and on BTA20 at 4 Mb were identified in more than one breed. Several breed-specific large-effect pleiotropic or closely linked QTL were also identified. Some identified QTL regions harbor genes known to have large effects on a variety of traits in cattle such as PLAG1 and MSTN and others harbor promising candidate genes including NCAPG, ARRDC3, ERGIC1, SH3PXD2B, HMGA2, MSRB3, LEMD3, TIGAR, SEPT7, and KIRREL3. Gene ontology analysis revealed that genes involved in ossification and in adipose tissue development were over-represented in the identified pleiotropic QTL. Also, the MAPK signaling pathway was identified as a common pathway affected by the genes located near the pleiotropic QTL. Conclusions This largest GWAS ever performed in beef cattle, led us to discover several novel across-breed and breed-specific large-effect pleiotropic QTL that cumulatively account for a significant percentage of additive genetic variance (e.g. more than a third of additive genetic variance of birth and mature weights; and calving ease direct in Hereford). These results will improve our understanding of the biology of growth and body composition in cattle. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-442) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Dorian J Garrick
- Department of Animal Science, Iowa State University, Ames 50011, USA.
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Molecular characterization and expression profiling of the protein disulfide isomerase gene family in Brachypodium distachyon L. PLoS One 2014; 9:e94704. [PMID: 24747843 PMCID: PMC3991636 DOI: 10.1371/journal.pone.0094704] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/17/2014] [Indexed: 01/09/2023] Open
Abstract
Protein disulfide isomerases (PDI) are involved in catalyzing protein disulfide bonding and isomerization in the endoplasmic reticulum and functions as a chaperone to inhibit the aggregation of misfolded proteins. Brachypodium distachyon is a widely used model plant for temperate grass species such as wheat and barley. In this work, we report the first molecular characterization, phylogenies, and expression profiles of PDI and PDI-like (PDIL) genes in B. distachyon in different tissues under various abiotic stresses. Eleven PDI and PDIL genes in the B. distachyon genome by in silico identification were evenly distributed across all five chromosomes. The plant PDI family has three conserved motifs that are involved in catalyzing protein disulfide bonding and isomerization, but a different exon/intron structural organization showed a high degree of structural differentiation. Two pairs of genes (BdPDIL4-1 and BdPDIL4-2; BdPDIL7-1 and BdPDIL7-2) contained segmental duplications, indicating each pair originated from one progenitor. Promoter analysis showed that Brachypodium PDI family members contained important cis-acting regulatory elements involved in seed storage protein synthesis and diverse stress response. All Brachypodium PDI genes investigated were ubiquitously expressed in different organs, but differentiation in expression levels among different genes and organs was clear. BdPDIL1-1 and BdPDIL5-1 were expressed abundantly in developing grains, suggesting that they have important roles in synthesis and accumulation of seed storage proteins. Diverse treatments (drought, salt, ABA, and H2O2) induced up- and down-regulated expression of Brachypodium PDI genes in seedling leaves. Interestingly, BdPDIL1-1 displayed significantly up-regulated expression following all abiotic stress treatments, indicating that it could be involved in multiple stress responses. Our results provide new insights into the structural and functional characteristics of the plant PDI gene family.
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45
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Noda Y, Hara T, Ishii M, Yoda K. Distinct adaptor proteins assist exit of Kre2-family proteins from the yeast ER. Biol Open 2014; 3:209-24. [PMID: 24585773 PMCID: PMC4001239 DOI: 10.1242/bio.20146312] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Svp26 protein of S. cerevisiae is an ER- and Golgi-localized integral membrane protein with 4 potential membrane-spanning domains. It functions as an adaptor protein that facilitates the ER exit of Ktr3, a mannosyltransferase required for biosynthesis of O-linked oligosaccharides, and the ER exit of Mnn2 and Mnn5, mannosyltransferases, which participate in the biosynthesis of N-linked oligosaccharides. Ktr3 belongs to the Kre2 family, which consists of 9 members of type-II membrane proteins sharing sequence similarities. In this report, we examined all Kre2 family members and found that the Golgi localizations of two others, Kre2 and Ktr1, were dependent on Svp26 by immunofluorescence microscopy and cell fractionations in sucrose density gradients. We show that Svp26 functions in facilitating the ER exit of Kre2 and Ktr1 by an in vitro COPII budding assay. Golgi localization of Ktr4 was not dependent on Svp26. Screening null mutants of the genes encoding abundant COPII membrane proteins for those showing mislocalization of Ktr4 in the ER revealed that Erv41 and Erv46 are required for the correct Golgi localization of Ktr4. We provide biochemical evidence that the Erv41-Erv46 complex functions as an adaptor protein for ER exit of Ktr4. This is the first demonstration of the molecular function of this evolutionally conserved protein complex. The domain switching experiments show that the lumenal domain of Ktr4 is responsible for recognition by the Erv41-Erv46 complex. Thus, ER exit of Kre2-family proteins is dependent on distinct adaptor proteins and our results provide new insights into the traffic of Kre2-family mannosyltransferases.
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Affiliation(s)
- Yoichi Noda
- Department of Biotechnology, University of Tokyo, Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan
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Abstract
ERGIC2 (formerly known as PTX1) is a gene identified by subtractive hybridization on the basis that it is expressed in normal human prostate, but not in prostate carcinoma. It is unrelated to the gene encoding pituitary homeobox protein (Ptx1 or Pitx1), which regulates pituitary hormone gene expression. Based on sequence homology with the yeast Erv41 protein, it is suggested that the ERGIC2 protein is an endoplasmic reticulum (ER) resident protein involved in protein trafficking between the ER and Golgi intermediate compartment (ERGIC) and cis-Golgi. However, studies from our laboratory and others have shown that it may have other functions. In this study, we have identified a variant ERGIC2 transcript with a four base deletion at the junction of exons 8-9, resulting in frame shift after codon #189. As a result, a truncated protein of 215 residues (24.5 kDa) is predicted as compared with the 377-residue (42.6 kDa) wild-type (WT) protein. The truncated variant ERGIC2 protein loses 45% of the luminal domain and the transmembrane domain near the C-terminus, and this effectively abrogates its function as the ERGIC-Golgi protein transport shuttle. The variant, like the WT protein, was found to upregulate the heme oxygenase 1 gene, suggesting that it may be involved in the oxidative stress pathway.
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Affiliation(s)
- Simon C M Kwok
- 1 ORTD, Albert Einstein Medical Center , Philadelphia, Pennsylvania
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47
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de Las Heras JI, Meinke P, Batrakou DG, Srsen V, Zuleger N, Kerr AR, Schirmer EC. Tissue specificity in the nuclear envelope supports its functional complexity. Nucleus 2013; 4:460-77. [PMID: 24213376 PMCID: PMC3925691 DOI: 10.4161/nucl.26872] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nuclear envelope links to inherited disease gave the conundrum of how mutations in near-ubiquitous proteins can yield many distinct pathologies, each focused in different tissues. One conundrum-resolving hypothesis is that tissue-specific partner proteins mediate these pathologies. Such partner proteins may have now been identified with recent proteome studies determining nuclear envelope composition in different tissues. These studies revealed that the majority of the total nuclear envelope proteins are tissue restricted in their expression. Moreover, functions have been found for a number these tissue-restricted nuclear envelope proteins that fit with mechanisms proposed to explain how the nuclear envelope could mediate disease, including defects in mechanical stability, cell cycle regulation, signaling, genome organization, gene expression, nucleocytoplasmic transport, and differentiation. The wide range of functions to which these proteins contribute is consistent with not only their involvement in tissue-specific nuclear envelope disease pathologies, but also tissue evolution.
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Affiliation(s)
- Jose I de Las Heras
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Peter Meinke
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Dzmitry G Batrakou
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Vlastimil Srsen
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Nikolaj Zuleger
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Alastair Rw Kerr
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology; University of Edinburgh; Edinburgh, UK
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48
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Morgan GW, Kail M, Hollinshead M, Vaux DJ. Combined biochemical and cytological analysis of membrane trafficking using lectins. Anal Biochem 2013; 441:21-31. [PMID: 23756734 DOI: 10.1016/j.ab.2013.05.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 05/30/2013] [Accepted: 05/31/2013] [Indexed: 02/03/2023]
Abstract
We have tested the application of high-mannose-binding lectins as analytical reagents to identify N-glycans in the early secretory pathway of HeLa cells during subcellular fractionation and cytochemistry. Post-endoplasmic reticulum (ER) pre-Golgi intermediates were separated from the ER on Nycodenz-sucrose gradients, and the glycan composition of each gradient fraction was profiled using lectin blotting. The fractions containing the post-ER pre-Golgi intermediates are found to contain a subset of N-linked α-mannose glycans that bind the lectins Galanthus nivalis agglutinin (GNA), Pisum sativum agglutinin (PSA), and Lens culinaris agglutinin (LCA) but not lectins binding Golgi-modified glycans. Cytochemical analysis demonstrates that high-mannose-containing glycoproteins are predominantly localized to the ER and the early secretory pathway. Indirect immunofluorescence microscopy revealed that GNA colocalizes with the ER marker protein disulfide isomerase (PDI) and the COPI coat protein β-COP. In situ competition with concanavalin A (ConA), another high-mannose specific lectin, and subsequent GNA lectin histochemistry refined the localization of N-glyans containing nonreducing mannosyl groups, accentuating the GNA vesicular staining. Using GNA and treatments that perturb ER-Golgi transport, we demonstrate that lectins can be used to detect changes in membrane trafficking pathways histochemically. Overall, we find that conjugated plant lectins are effective tools for combinatory biochemical and cytological analysis of membrane trafficking of glycoproteins.
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Affiliation(s)
- Gareth W Morgan
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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49
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Brandizzi F, Barlowe C. Organization of the ER-Golgi interface for membrane traffic control. Nat Rev Mol Cell Biol 2013; 14:382-92. [PMID: 23698585 DOI: 10.1038/nrm3588] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Coat protein complex I (COPI) and COPII are required for bidirectional membrane trafficking between the endoplasmic reticulum (ER) and the Golgi. While these core coat machineries and other transport factors are highly conserved across species, high-resolution imaging studies indicate that the organization of the ER-Golgi interface is varied in eukaryotic cells. Regulation of COPII assembly, in some cases to manage distinct cellular cargo, is emerging as one important component in determining this structure. Comparison of the ER-Golgi interface across different systems, particularly mammalian and plant cells, reveals fundamental elements and distinct organization of this interface. A better understanding of how these interfaces are regulated to meet varying cellular secretory demands should provide key insights into the mechanisms that control efficient trafficking of proteins and lipids through the secretory pathway.
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Affiliation(s)
- Federica Brandizzi
- DOE Plant Research Laboratory and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
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50
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Kuijpers M, Yu KL, Teuling E, Akhmanova A, Jaarsma D, Hoogenraad CC. The ALS8 protein VAPB interacts with the ER-Golgi recycling protein YIF1A and regulates membrane delivery into dendrites. EMBO J 2013; 32:2056-72. [PMID: 23736259 DOI: 10.1038/emboj.2013.131] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/07/2013] [Indexed: 02/06/2023] Open
Abstract
The vesicle-associated membrane protein (VAMP) associated protein B (VAPB) is an integral membrane protein localized to the endoplasmic reticulum (ER). The P56S mutation in VAPB has been linked to motor neuron degeneration in amyotrophic lateral sclerosis type 8 (ALS8) and forms ER-like inclusions in various model systems. However, the role of wild-type and mutant VAPB in neurons is poorly understood. Here, we identified Yip1-interacting factor homologue A (YIF1A) as a new VAPB binding partner and important component in the early secretory pathway. YIF1A interacts with VAPB via its transmembrane regions, recycles between the ER and Golgi and is mainly localized to the ER-Golgi intermediate compartments (ERGICs) in rat hippocampal neurons. VAPB strongly affects the distribution of YIF1A and is required for intracellular membrane trafficking into dendrites and normal dendritic morphology. When VAPB-P56S is present, YIF1A is recruited to the VAPB-P56S clusters and loses its ERGIC localization. These data suggest that both VAPB and YIF1A are important for ER-to-Golgi transport and that missorting of YIF1A may contribute to VAPB-associated motor neuron disease.
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Affiliation(s)
- Marijn Kuijpers
- Division of Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
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