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Aliakbari S, Hasanzadeh L, Sayyah M, Amini N, Pourbadie HG. Induced expression of rabies glycoprotein in the dorsal hippocampus enhances hippocampal dependent memory in a rat model of Alzheimer's disease. J Neurovirol 2024:10.1007/s13365-024-01221-y. [PMID: 38943023 DOI: 10.1007/s13365-024-01221-y] [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: 03/24/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/30/2024]
Abstract
The Rabies virus is a neurotropic virus that manipulates the natural cell death processes of its host to ensure its own survival and replication. Studies have shown that the anti-apoptotic effect of the virus is mediated by one of its protein named, rabies glycoprotein (RVG). Alzheimer's disease (AD) is characterized by the loss of neural cells and memory impairment. We aim to examine whether expression of RVG in the hippocampal cells can shield the detrimental effects induced by Aβ. Oligomeric form of Aβ (oAβ) or vehicle was bilaterally microinjected into the dorsal hippocampus of male Wistar rats. One week later, two μl (108 T.U. /ml) of the lentiviral vector carrying RVG gene was injected into their dorsal hippocampus (post-treatment). In another experiment, the lentiviral vector was microinjected one week before Aβ injection (pre-treatment). One week later, the rat's brain was sliced into cross-sections, and the presence of RVG-expressing neuronal cells was confirmed using fluorescent microscopy. Rats were subjected to assessments of spatial learning and memory as well as passive avoidance using the Morris water maze (MWM) and the Shuttle box apparatuses, respectively. Protein expression of AMPA receptor subunit (GluA1) was determined using western blotting technique. In MWM, Aβ treated rats showed decelerated acquisition of the task and impairment of reference memory. RVG expression in the hippocampus prevented and restored the deficits in both pre- and post- treatment conditions, respectively. It also improved inhibitory memory in the oAβ treated rats. RVG increased the expression level of GluA1 level in the hippocampus. Based on our findings, the expression of RVG in the hippocampus has the potential to enhance both inhibitory and spatial learning abilities, ultimately improving memory performance in an AD rat model. This beneficial effect is likely attributed, at least in part, to the increased expression of GluA1-containing AMPA receptors.
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Affiliation(s)
- Shayan Aliakbari
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Hasanzadeh
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sayyah
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Niloufar Amini
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
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2
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: A new OSPREY-based algorithm for designing de novo D-peptide inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579944. [PMID: 38405797 PMCID: PMC10888900 DOI: 10.1101/2024.02.12.579944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan, which enable exponential reductions in the size of the peptide sequence search space. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a new framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead therapeutic candidates. We provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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3
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors. Protein Eng Des Sel 2024; 37:gzae007. [PMID: 38757573 PMCID: PMC11099876 DOI: 10.1093/protein/gzae007] [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: 09/03/2023] [Revised: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead inhibitors. We also provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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Affiliation(s)
- Nathan Guerin
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
| | - Henry Childs
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
| | - Bruce R Donald
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
- Department of Mathematics, Duke University, 120 Science Drive, Durham, NC 27708, United States
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4
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Javorsky A, Humbert PO, Kvansakul M. Viral manipulation of cell polarity signalling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119536. [PMID: 37437846 DOI: 10.1016/j.bbamcr.2023.119536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Cell polarity refers to the asymmetric distribution of biomacromolecules that enable the correct orientation of a cell in a particular direction. It is thus an essential component for appropriate tissue development and function. Viral infections can lead to dysregulation of polarity. This is associated with a poor prognosis due to viral interference with core cell polarity regulatory scaffolding proteins that often feature PDZ (PSD-95, DLG, and ZO-1) domains including Scrib, Dlg, Pals1, PatJ, Par3 and Par6. PDZ domains are also promiscuous, binding to several different partners through their C-terminal region which contain PDZ-binding motifs (PBM). Numerous viruses encode viral effector proteins that target cell polarity regulators for their benefit and include papillomaviruses, flaviviruses and coronaviruses. A better understanding of the mechanisms of action utilised by viral effector proteins to subvert host cell polarity sigalling will provide avenues for future therapeutic intervention, while at the same time enhance our understanding of cell polarity regulation and its role tissue homeostasis.
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Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Patrick O Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia; Department of Biochemistry & Pharmacology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia.
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Honrubia JM, Gutierrez-Álvarez J, Sanz-Bravo A, González-Miranda E, Muñoz-Santos D, Castaño-Rodriguez C, Wang L, Villarejo-Torres M, Ripoll-Gómez J, Esteban A, Fernandez-Delgado R, Sánchez-Cordón PJ, Oliveros JC, Perlman S, McCray PB, Sola I, Enjuanes L. SARS-CoV-2-Mediated Lung Edema and Replication Are Diminished by Cystic Fibrosis Transmembrane Conductance Regulator Modulators. mBio 2023; 14:e0313622. [PMID: 36625656 PMCID: PMC9973274 DOI: 10.1128/mbio.03136-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 01/11/2023] Open
Abstract
Coronaviruses (CoVs) of genera α, β, γ, and δ encode proteins that have a PDZ-binding motif (PBM) consisting of the last four residues of the envelope (E) protein (PBM core). PBMs may bind over 400 cellular proteins containing PDZ domains (an acronym formed by the combination of the first letter of the names of the three first proteins where this domain was identified), making them relevant for the control of cell function. Three highly pathogenic human CoVs have been identified to date: severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. The PBMs of the three CoVs were virulence factors. SARS-CoV mutants in which the E protein PBM core was replaced by the E protein PBM core from virulent or attenuated CoVs were constructed. These mutants showed a gradient of virulence, depending on whether the alternative PBM core introduced was derived from a virulent or an attenuated CoV. Gene expression patterns in the lungs of mice infected with SARS-CoVs encoding each of the different PBMs were analyzed by RNA sequencing of infected lung tissues. E protein PBM of SARS-CoV and SARS-CoV-2 dysregulated gene expression related to ion transport and cell homeostasis. Decreased expression of cystic fibrosis transmembrane conductance regulator (CFTR) mRNA, essential for alveolar edema resolution, was shown. Reduced CFTR mRNA levels were associated with edema accumulation in the alveoli of mice infected with SARS-CoV and SARS-CoV-2. Compounds that increased CFTR expression and activity, significantly reduced SARS-CoV-2 growth in cultured cells and protected against mouse infection, suggesting that E protein virulence is mediated by a decreased CFTR expression. IMPORTANCE Three highly pathogenic human CoVs have been identified: SARS-CoV, MERS-CoV, and SARS-CoV-2. The E protein PBMs of these three CoVs were virulence factors. Gene expression patterns associated with the different PBM motifs in the lungs of infected mice were analyzed by deep sequencing. E protein PBM motif of SARS-CoV and SARS-CoV-2 dysregulated the expression of genes related to ion transport and cell homeostasis. A decrease in the mRNA expression of the cystic fibrosis transmembrane conductance regulator (CFTR), which is essential for edema resolution, was observed. The reduction of CFTR mRNA levels was associated with edema accumulation in the lungs of mice infected with SARS-CoV-2. Compounds that increased the expression and activity of CFTR drastically reduced the production of SARS-CoV-2 and protected against its infection in a mice model. These results allowed the identification of cellular targets for the selection of antivirals.
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Affiliation(s)
- Jose M. Honrubia
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Javier Gutierrez-Álvarez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Alejandro Sanz-Bravo
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ezequiel González-Miranda
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Carlos Castaño-Rodriguez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Li Wang
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Marta Villarejo-Torres
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Jorge Ripoll-Gómez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ana Esteban
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Raul Fernandez-Delgado
- Department of Infectious Diseases and Global Health, Animal Health Research Center (CISA), National Institute of Research, Agricultural and Food Technology (INIA-CSIC), Valdeolmos, Madrid, Spain
| | - Pedro José Sánchez-Cordón
- Veterinary Pathology Department, Animal Health Research Center (CISA), National Institute of Research, Agricultural and Food Technology (INIA-CSIC), Valdeolmos, Madrid, Spain
| | - Juan Carlos Oliveros
- Bioinformatics for Genomics and Proteomics Unit, CNB-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, USA
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, Iowa, USA
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, USA
| | - Paul B. McCray
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, Iowa, USA
- Pappajohn Biomedical Institute, The University of Iowa, Iowa City, Iowa, USA
- Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
| | - Isabel Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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Genera M, Colcombet-Cazenave B, Croitoru A, Raynal B, Mechaly A, Caillet J, Haouz A, Wolff N, Caillet-Saguy C. Interactions of the protein tyrosine phosphatase PTPN3 with viral and cellular partners through its PDZ domain: insights into structural determinants and phosphatase activity. Front Mol Biosci 2023; 10:1192621. [PMID: 37200868 PMCID: PMC10185773 DOI: 10.3389/fmolb.2023.1192621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023] Open
Abstract
The human protein tyrosine phosphatase non-receptor type 3 (PTPN3) is a phosphatase containing a PDZ (PSD-95/Dlg/ZO-1) domain that has been found to play both tumor-suppressive and tumor-promoting roles in various cancers, despite limited knowledge of its cellular partners and signaling functions. Notably, the high-risk genital human papillomavirus (HPV) types 16 and 18 and the hepatitis B virus (HBV) target the PDZ domain of PTPN3 through PDZ-binding motifs (PBMs) in their E6 and HBc proteins respectively. This study focuses on the interactions between the PTPN3 PDZ domain (PTPN3-PDZ) and PBMs of viral and cellular protein partners. We solved the X-ray structures of complexes between PTPN3-PDZ and PBMs of E6 of HPV18 and the tumor necrosis factor-alpha converting enzyme (TACE). We provide new insights into key structural determinants of PBM recognition by PTPN3 by screening the selectivity of PTPN3-PDZ recognition of PBMs, and by comparing the PDZome binding profiles of PTPN3-recognized PBMs and the interactome of PTPN3-PDZ. The PDZ domain of PTPN3 was known to auto-inhibit the protein's phosphatase activity. We discovered that the linker connecting the PDZ and phosphatase domains is involved in this inhibition, and that the binding of PBMs does not impact this catalytic regulation. Overall, the study sheds light on the interactions and structural determinants of PTPN3 with its cellular and viral partners, as well as on the inhibitory role of its PDZ domain on its phosphatase activity.
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Affiliation(s)
- Mariano Genera
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
- Sorbonne Université, Complexité du Vivant, F-75005, Paris, France
| | - Baptiste Colcombet-Cazenave
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
- Sorbonne Université, Complexité du Vivant, F-75005, Paris, France
| | - Anastasia Croitoru
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform-C2RT, CNRS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Ariel Mechaly
- Crystallography Platform-C2RT, Institut Pasteur, Université Paris Cité, Paris, France
| | - Joël Caillet
- CNRS, Institut de Biologie Physico-Chimique, Université Paris Cité, Paris, France
| | - Ahmed Haouz
- Crystallography Platform-C2RT, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nicolas Wolff
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
| | - Célia Caillet-Saguy
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
- *Correspondence: Célia Caillet-Saguy,
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7
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Fidler G, Szilágyi-Rácz AA, Dávid P, Tolnai E, Rejtő L, Szász R, Póliska S, Biró S, Paholcsek M. Circulating microRNA sequencing revealed miRNome patterns in hematology and oncology patients aiding the prognosis of invasive aspergillosis. Sci Rep 2022; 12:7144. [PMID: 35504997 PMCID: PMC9065123 DOI: 10.1038/s41598-022-11239-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 04/18/2022] [Indexed: 11/20/2022] Open
Abstract
Invasive aspergillosis (IA) may occur as a serious complication of hematological malignancy. Delays in antifungal therapy can lead to an invasive disease resulting in high mortality. Currently, there are no well-established blood circulating microRNA biomarkers or laboratory tests which can be used to diagnose IA. Therefore, we aimed to define dysregulated miRNAs in hematology and oncology (HO) patients to identify biomarkers predisposing disease. We performed an in-depth analysis of high-throughput small transcriptome sequencing data obtained from the whole blood samples of our study cohort of 50 participants including 26 high-risk HO patients and 24 controls. By integrating in silico bioinformatic analyses of small noncoding RNA data, 57 miRNAs exhibiting significant expression differences (P < 0.05) were identified between IA-infected patients and non-IA HO patients. Among these, we found 36 differentially expressed miRNAs (DEMs) irrespective of HO malignancy. Of the top ranked DEMs, we found 14 significantly deregulated miRNAs, whose expression levels were successfully quantified by qRT-PCR. MiRNA target prediction revealed the involvement of IA related miRNAs in the biological pathways of tumorigenesis, the cell cycle, the immune response, cell differentiation and apoptosis.
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Affiliation(s)
- Gábor Fidler
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - Anna Anita Szilágyi-Rácz
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - Péter Dávid
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - Emese Tolnai
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - László Rejtő
- Department of Hematology, Jósa András Teaching Hospital, Nyíregyháza, Hungary
| | - Róbert Szász
- Division of Hematology, Institute of Internal Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilárd Póliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Sándor Biró
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - Melinda Paholcsek
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary.
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8
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Kim S, Larrous F, Varet H, Legendre R, Feige L, Dumas G, Matsas R, Kouroupi G, Grailhe R, Bourhy H. Early Transcriptional Changes in Rabies Virus-Infected Neurons and Their Impact on Neuronal Functions. Front Microbiol 2021; 12:730892. [PMID: 34970230 PMCID: PMC8713068 DOI: 10.3389/fmicb.2021.730892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022] Open
Abstract
Rabies is a zoonotic disease caused by rabies virus (RABV). As rabies advances, patients develop a variety of severe neurological symptoms that inevitably lead to coma and death. Unlike other neurotropic viruses that can induce symptoms of a similar range, RABV-infected post-mortem brains do not show significant signs of inflammation nor the structural damages on neurons. This suggests that the observed neurological symptoms possibly originate from dysfunctions of neurons. However, many aspects of neuronal dysfunctions in the context of RABV infection are only partially understood, and therefore require further investigation. In this study, we used differentiated neurons to characterize the RABV-induced transcriptomic changes at the early time-points of infection. We found that the genes modulated in response to the infection are particularly involved in cell cycle, gene expression, immune response, and neuronal function-associated processes. Comparing a wild-type RABV to a mutant virus harboring altered matrix proteins, we found that the RABV matrix protein plays an important role in the early down-regulation of host genes, of which a significant number is involved in neuronal functions. The kinetics of differentially expressed genes (DEGs) are also different between the wild type and mutant virus datasets. The number of modulated genes remained constant upon wild-type RABV infection up to 24 h post-infection, but dramatically increased in the mutant condition. This result suggests that the intact viral matrix protein is important to control the size of host gene modulation. We then examined the signaling pathways previously studied in relation to the innate immune responses against RABV, and found that these pathways contribute to the changes in neuronal function-associated processes. We further examined a set of regulated genes that could impact neuronal functions collectively, and demonstrated in calcium imaging that indeed the spontaneous activity of neurons is influenced by RABV infection. Overall, our findings suggest that neuronal function-associated genes are modulated by RABV early on, potentially through the viral matrix protein-interacting signaling molecules and their downstream pathways.
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Affiliation(s)
- Seonhee Kim
- Technology Development Platform, Institut Pasteur Korea, Seongnam, South Korea
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
- Université de Paris, Doctoral School Bio Sorbonne Paris Cité, Paris, France
| | - Florence Larrous
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | - Hugo Varet
- Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Paris, France
- Institut Pasteur, Université de Paris, Plate-Forme Technologique Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Paris, France
- Institut Pasteur, Université de Paris, Plate-Forme Technologique Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Lena Feige
- Technology Development Platform, Institut Pasteur Korea, Seongnam, South Korea
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
- Université de Paris, Doctoral School Bio Sorbonne Paris Cité, Paris, France
| | - Guillaume Dumas
- Department of Psychiatry, CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, Canada
- Mila, Quebec Artificial Intelligence Institute, University of Montreal, Montreal, QC, Canada
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Georgia Kouroupi
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Regis Grailhe
- Technology Development Platform, Institut Pasteur Korea, Seongnam, South Korea
| | - Hervé Bourhy
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
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9
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Abstract
Viruses are obligatory intracellular parasites that use cell proteins to take the control of the cell functions in order to accomplish their life cycle. Studying the viral-host interactions would increase our knowledge of the viral biology and mechanisms of pathogenesis. Studies on pathogenesis mechanisms of lyssaviruses, which are the causative agents of rabies, have revealed some important host protein partners for viral proteins, especially for most studied species, i.e. RABV. In this review article, the key physical lyssavirus-host protein interactions, their contributions to rabies infection, and their exploitation are discussed to improve the knowledge about rabies pathogenesis.
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10
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Spill YG, Karami Y, Maisonneuve P, Wolff N, Nilges M. Automatic Bayesian Weighting for SAXS Data. Front Mol Biosci 2021; 8:671011. [PMID: 34150847 PMCID: PMC8212126 DOI: 10.3389/fmolb.2021.671011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/14/2021] [Indexed: 11/24/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) experiments are important in structural biology because they are solution methods, and do not require crystallization of protein complexes. Structure determination from SAXS data, however, poses some difficulties. Computation of a SAXS profile from a protein model is expensive in CPU time. Hence, rather than directly refining against the data, most computational methods generate a large number of conformers and then filter the structures based on how well they satisfy the SAXS data. To address this issue in an efficient manner, we propose here a Bayesian model for SAXS data and use it to directly drive a Monte Carlo simulation. We show that the automatic weighting of SAXS data is the key to finding optimal structures efficiently. Another key problem with obtaining structures from SAXS data is that proteins are often flexible and the data represents an average over a structural ensemble. To address this issue, we first characterize the stability of the best model with extensive molecular dynamics simulations. We analyse the resulting trajectories further to characterize a dynamic structural ensemble satisfying the SAXS data. The combination of methods is applied to a tandem of domains from the protein PTPN4, which are connected by an unstructured linker. We show that the SAXS data contain information that supports and extends other experimental findings. We also show that the conformation obtained by the Bayesian analysis is stable, but that a minor conformation is present. We propose a mechanism in which the linker may maintain PTPN4 in an inhibited enzymatic state.
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Affiliation(s)
- Yannick G Spill
- Department of Structural Biology and Chemistry, Structural Bioinformatics Unit, CNRS UMR 3528, Institute Pasteur, Paris, France
| | - Yasaman Karami
- Department of Structural Biology and Chemistry, Structural Bioinformatics Unit, CNRS UMR 3528, Institute Pasteur, Paris, France
| | - Pierre Maisonneuve
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France.,Department of Structural Biology and Chemistry, NMR of Biomolecules Unit, CNRS UMR 3528, Institute Pasteur, Paris, France.,Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Nicolas Wolff
- Department of Structural Biology and Chemistry, NMR of Biomolecules Unit, CNRS UMR 3528, Institute Pasteur, Paris, France.,Department of Neuroscience, Current Address, Channel-Receptors Unit, CNRS UMR 3571, Institut Pasteur, Paris, France
| | - Michael Nilges
- Department of Structural Biology and Chemistry, Structural Bioinformatics Unit, CNRS UMR 3528, Institute Pasteur, Paris, France
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Caillet-Saguy C, Durbesson F, Rezelj VV, Gogl G, Tran QD, Twizere JC, Vignuzzi M, Vincentelli R, Wolff N. Host PDZ-containing proteins targeted by SARS-CoV-2. FEBS J 2021; 288:5148-5162. [PMID: 33864728 PMCID: PMC8250131 DOI: 10.1111/febs.15881] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022]
Abstract
Small linear motifs targeting protein interacting domains called PSD‐95/Dlg/ZO‐1 (PDZ) have been identified at the C terminus of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) proteins E, 3a, and N. Using a high‐throughput approach of affinity‐profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS‐CoV‐2 proteins E, 3A, and N showing significant interactions with dissociation constants values ranging from 3 to 82 μm. Six of them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also recognized by SARS‐CoV while three (NHERF1, MAST2, RADIL) are specific to SARS‐CoV‐2 E protein. Most of these SARS‐CoV‐2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection. Among the binders of the SARS‐CoV‐2 proteins E, 3a, or N, seven significantly affect viral replication under knock down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS‐CoV‐2 can help to understand the multifactorial severity of COVID19 and to conceive effective anti‐coronaviral agents for therapeutic purposes.
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Affiliation(s)
| | | | - Veronica V Rezelj
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France
| | - Gergö Gogl
- IGBMC, INSERM U1258/UMR CNRS 7104, Illkirch, France
| | - Quang Dinh Tran
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France.,École doctorale BioSPC, Université Paris Diderot, Sorbonne Paris Cité, France
| | - Jean-Claude Twizere
- GIGA Institute, Molecular Biology of Diseases, Viral Interactomes laboratory, University of Liege, Belgium
| | - Marco Vignuzzi
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France
| | | | - Nicolas Wolff
- Institut Pasteur, Unité Récepteurs-Canaux, UMR CNRS 3571, Paris, France
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12
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Vincenzi M, Mercurio FA, Leone M. Protein Interaction Domains: Structural Features and Drug Discovery Applications (Part 2). Curr Med Chem 2021; 28:854-892. [PMID: 31942846 DOI: 10.2174/0929867327666200114114142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Proteins present a modular organization made up of several domains. Apart from the domains playing catalytic functions, many others are crucial to recruit interactors. The latter domains can be defined as "PIDs" (Protein Interaction Domains) and are responsible for pivotal outcomes in signal transduction and a certain array of normal physiological and disease-related pathways. Targeting such PIDs with small molecules and peptides able to modulate their interaction networks, may represent a valuable route to discover novel therapeutics. OBJECTIVE This work represents a continuation of a very recent review describing PIDs able to recognize post-translationally modified peptide segments. On the contrary, the second part concerns with PIDs that interact with simple peptide sequences provided with standard amino acids. METHODS Crucial structural information on different domain subfamilies and their interactomes was gained by a wide search in different online available databases (including the PDB (Protein Data Bank), the Pfam (Protein family), and the SMART (Simple Modular Architecture Research Tool)). Pubmed was also searched to explore the most recent literature related to the topic. RESULTS AND CONCLUSION PIDs are multifaceted: they have all diverse structural features and can recognize several consensus sequences. PIDs can be linked to different diseases onset and progression, like cancer or viral infections and find applications in the personalized medicine field. Many efforts have been centered on peptide/peptidomimetic inhibitors of PIDs mediated interactions but much more work needs to be conducted to improve drug-likeness and interaction affinities of identified compounds.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
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13
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Rabies virus glycoprotein enhances spatial memory via the PDZ binding motif. J Neurovirol 2021; 27:434-443. [PMID: 33788140 DOI: 10.1007/s13365-021-00972-2] [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: 07/06/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
Rabies is a life-threatening viral infection of the brain. Rabies virus (RABV) merely infects excitable cells including neurons provoking drastic behaviors including negative emotional memories. RABV glycoprotein (RVG) plays a critical role in RABV pathogenesis. RVG interacts with various cytoplasmic PDZ (PSD-95/Dlg/ZO-1) containing proteins through its PDZ binding motif (PBM). PTZ domains have crucial role in formation and function of signal transduction. Hippocampus is one of the cerebral regions that contain high load of viral antigens. We examined impact of RVG expression in the dorsal hippocampus on aversive as well as spatial learning and memory performance in rats. Two microliter of the lentiviral vector (~108 T.U./ml) encoding RVG or ∆RVG (deleted PBM) genomes was microinjected into the hippocampal CA1. After 1 week, rat's brain was cross-sectioned and RVG/∆RVG-expressing neuronal cells were confirmed by fluorescent microscopy. Passive avoidance and spatial learning and memory were assessed in rats by Shuttle box and Morris water maze (MWM). In the shuttle box, both RVG and ∆RVG decreased the time spent in the dark compartment compared to control (p < 0.05). In MWM, RVG and ∆RVG did not affect the acquisition of spatial task. In the probe test, RVG-expressing rats spent more time in the target quadrant, and also reached the platform position sooner than control group (p < 0.05). Rats expressing ∆RVG significantly swam farther from the hidden platform than RVG group (p < 0.05). Our data indicate RVG expression in the hippocampus strengthens aversive and spatial learning and memory performance. The boosting effect on spatial but not avoidance memory is mediated through PBM.
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14
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Ghassemi S, Asgari T, Mirzapour-Delavar H, Aliakbari S, Pourbadie HG, Prehaud C, Lafon M, Gholami A, Azadmanesh K, Naderi N, Sayyah M. Lentiviral Expression of Rabies Virus Glycoprotein in the Rat Hippocampus Strengthens Synaptic Plasticity. Cell Mol Neurobiol 2021; 42:1429-1440. [PMID: 33462779 DOI: 10.1007/s10571-020-01032-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/16/2020] [Indexed: 11/30/2022]
Abstract
Rabies virus (RABV) is a neurotropic virus exclusively infecting neurons in the central nervous system. RABV encodes five proteins. Among them, the viral glycoprotein (RVG) plays a key role in viral entry into neurons and rabies pathogenesis. It was shown that the nature of the C-terminus of the RABV G protein, which possesses a PDZ-binding motif (PBM), modulates the virulence of the RABV strain. The neuronal protein partners recruited by this PBM may alter host cell function. This study was conducted to investigate the effect of RVG on synaptic function in the hippocampal dentate gyrus (DG) of rat. Two μl (108 T.U./ml) of the lentiviral vector containing RVG gene was injected into the DG of rat hippocampus. After 2 weeks, the rat's brain was cross-sectioned and RVG-expressing cells were detected by fluorescent microscopy. Hippocampal synaptic activity of the infected rats was then examined by recording the local field potentials from DG after stimulation of the perforant pathway. Short-term synaptic plasticity was also assessed by double pulse stimulation. Expression of RVG in DG increased long-term potentiation population spikes (LTP-PS), whereas no facilitation of LTP-PS was found in neurons expressing δRVG (deleted PBM). Furthermore, RVG and δRVG strengthened paired-pulse facilitation. Heterosynaptic long-term depression (LTD) in the DG was significantly blocked in RVG-expressing group compared to the control group. This blockade was dependent to PBM motif as rats expressing δRVG in the DG-expressed LTD comparable to the RVG group. Our data demonstrate that RVG expression facilitates both short- and long-term synaptic plasticity in the DG indicating that it may involve both pre- and postsynaptic mechanisms to alter synaptic function. Further studies are needed to elucidate the underlying mechanisms.
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Affiliation(s)
- Soheil Ghassemi
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Tara Asgari
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Shayan Aliakbari
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Christophe Prehaud
- Institut Pasteur, Unité de Neuroimmunologie Virale, UMR 3569, CNRS, Paris, France
| | - Monique Lafon
- Institut Pasteur, Unité de Neuroimmunologie Virale, UMR 3569, CNRS, Paris, France
| | - Alireza Gholami
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | | | - Nima Naderi
- Department of Pharmacology and Toxicology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Sayyah
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran.
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15
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Caillet-Saguy C, Brûlé S, Wolff N, Raynal B. PDZ Sample Quality Assessment by Biochemical and Biophysical Characterizations. Methods Mol Biol 2021; 2256:89-124. [PMID: 34014518 DOI: 10.1007/978-1-0716-1166-1_6] [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] [Indexed: 06/12/2023]
Abstract
PDZ domains are small globular domains involved in protein-protein interactions. They participate in a wide range of critical cellular processes. These domains, very abundant in the human proteome, are widely studied by high-throughput interactomics approaches and by biophysical and structural methods. However, the quality of the results is strongly related to the optimal folding and solubility of the domains. We provide here a detailed description of protocols for a strict quality assessment of the PDZ constructs. We describe appropriate experimental approaches that have been selected to overcome the small size of such domains to check the purity, identity, homogeneity, stability, and folding of samples.
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Affiliation(s)
| | - Sébastien Brûlé
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
| | - Nicolas Wolff
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS UMR 3571, Paris, France.
| | - Bertrand Raynal
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
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16
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Viruses in connectomics: Viral transneuronal tracers and genetically modified recombinants as neuroscience research tools. J Neurosci Methods 2020; 346:108917. [PMID: 32835704 DOI: 10.1016/j.jneumeth.2020.108917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/25/2022]
Abstract
Connectomic studies have become 'viral', as viral pathogens have been turned into irreplaceable neuroscience research tools. Highly sensitive viral transneuronal tracing technologies are available, based on the use of alpha-herpesviruses and a rhabdovirus (rabies virus), which function as self-amplifying markers by replicating in recipient neurons. These viruses highly differ with regard to host range, cellular receptors, peripheral uptake, replication, transport direction and specificity. Their characteristics, that make them useful for different purposes, will be highlighted and contrasted. Only transneuronal tracing with rabies virus is entirely specific. The neuroscientist toolbox currently include wild-type alpha-herpesviruses and rabies virus strains enabling polysynaptic tracing of neuronal networks across multiple synapses, as well as genetically modified viral tracers for dual transneuronal tracing, and complementary viral tools including defective and chimeric recombinants that function as single step or monosynaptically restricted tracers, or serve for monitoring and manipulating neuronal activity and gene expression. Methodological issues that are crucial for appropriate use of these technologies will be summarized. Among wild-type and genetically engineered viral tools, rabies virus and chimeric recombinants based on rabies virus as virus backbone are the most powerful, because of the ability of rabies virus to propagate exclusively among connected neurons unidirectionally (retrogradely), without affecting neuronal function. Understanding in depth viral properties is essential for neuroscientists who intend to exploit alpha-herpesviruses, rhabdoviruses or derived recombinants as research tools. Key knowledge will be summarized regarding their cellular receptors, intracellular trafficking and strategies to contrast host defense that explain their different pathophysiology and properties as research tools.
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17
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Thomas M, Banks L. Upsetting the Balance: When Viruses Manipulate Cell Polarity Control. J Mol Biol 2018; 430:3481-3503. [PMID: 29680664 PMCID: PMC7094317 DOI: 10.1016/j.jmb.2018.04.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 12/20/2022]
Abstract
The central importance of cell polarity control is emphasized by the frequency with which it is targeted by many diverse viruses. It is clear that in targeting key polarity control proteins, viruses affect not only host cell polarity, but also influence many cellular processes, including transcription, replication, and innate and acquired immunity. Examination of the interactions of different virus proteins with the cell and its polarity controls during the virus life cycles, and in virally-induced cell transformation shows ever more clearly how intimately all cellular processes are linked to the control of cell polarity.
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18
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Saccon E, Vitiello A, Trevisan M, Salata C, Palù G. Sixth European Seminar in Virology on Virus⁻Host Interaction at Single Cell and Organism Level. Viruses 2018; 10:v10080400. [PMID: 30060596 PMCID: PMC6116093 DOI: 10.3390/v10080400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 11/30/2022] Open
Abstract
The 6th European Seminar in Virology (EuSeV) was held in Bertinoro, Italy, 22–24 June 2018, and brought together international scientists and young researchers working in the field of Virology. Sessions of the meeting included: virus–host-interactions at organism and cell level; virus evolution and dynamics; regulation; immunity/immune response; and disease and therapy. This report summarizes lectures by the invited speakers and highlights advances in the field.
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Affiliation(s)
- Elisa Saccon
- Department of Molecular Medicine, University of Padova, 35121 Padova PD, Italy.
| | - Adriana Vitiello
- Department of Molecular Medicine, University of Padova, 35121 Padova PD, Italy.
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, 35121 Padova PD, Italy.
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padova, 35121 Padova PD, Italy.
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, 35121 Padova PD, Italy.
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19
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Castaño-Rodriguez C, Honrubia JM, Gutiérrez-Álvarez J, DeDiego ML, Nieto-Torres JL, Jimenez-Guardeño JM, Regla-Nava JA, Fernandez-Delgado R, Verdia-Báguena C, Queralt-Martín M, Kochan G, Perlman S, Aguilella VM, Sola I, Enjuanes L. Role of Severe Acute Respiratory Syndrome Coronavirus Viroporins E, 3a, and 8a in Replication and Pathogenesis. mBio 2018; 9:e02325-17. [PMID: 29789363 PMCID: PMC5964350 DOI: 10.1128/mbio.02325-17] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 12/24/2022] Open
Abstract
Viroporins are viral proteins with ion channel (IC) activity that play an important role in several processes, including virus replication and pathogenesis. While many coronaviruses (CoVs) encode two viroporins, severe acute respiratory syndrome CoV (SARS-CoV) encodes three: proteins 3a, E, and 8a. Additionally, proteins 3a and E have a PDZ-binding motif (PBM), which can potentially bind over 400 cellular proteins which contain a PDZ domain, making them potentially important for the control of cell function. In the present work, a comparative study of the functional motifs included within the SARS-CoV viroporins was performed, mostly focusing on the roles of the IC and PBM of E and 3a proteins. Our results showed that the full-length E and 3a proteins were required for maximal SARS-CoV replication and virulence, whereas viroporin 8a had only a minor impact on these activities. A virus missing both the E and 3a proteins was not viable, whereas the presence of either protein with a functional PBM restored virus viability. E protein IC activity and the presence of its PBM were necessary for virulence in mice. In contrast, the presence or absence of the homologous motifs in protein 3a did not influence virus pathogenicity. Therefore, dominance of the IC and PBM of protein E over those of protein 3a was demonstrated in the induction of pathogenesis in mice.IMPORTANCE Collectively, these results demonstrate key roles for the ion channel and PBM domains in optimal virus replication and pathogenesis and suggest that the viral viroporins and PBMs are suitable targets for antiviral therapy and for mutation in attenuated SARS-CoV vaccines.
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Affiliation(s)
- Carlos Castaño-Rodriguez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose M Honrubia
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Javier Gutiérrez-Álvarez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta L DeDiego
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose L Nieto-Torres
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose M Jimenez-Guardeño
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose A Regla-Nava
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Raul Fernandez-Delgado
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Carmina Verdia-Báguena
- Department of Physics, Laboratory of Molecular Biophysics, Universitat Jaume I, Castelló, Spain
| | - Maria Queralt-Martín
- Eunice Kennedy Shriver NICHD, NIH, Bethesda, Maryland, USA
- Department of Physics, Laboratory of Molecular Biophysics, Universitat Jaume I, Castelló, Spain
| | - Grazyna Kochan
- Immunomodulation Group, Navarrabiomed-Biomedical Research Centre, IdISNA, Pamplona, Navarra, Spain
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
| | - Vicente M Aguilella
- Department of Physics, Laboratory of Molecular Biophysics, Universitat Jaume I, Castelló, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
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21
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Fooks AR, Cliquet F, Finke S, Freuling C, Hemachudha T, Mani RS, Müller T, Nadin-Davis S, Picard-Meyer E, Wilde H, Banyard AC. Rabies. Nat Rev Dis Primers 2017; 3:17091. [PMID: 29188797 DOI: 10.1038/nrdp.2017.91] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Rabies is a life-threatening neglected tropical disease: tens of thousands of cases are reported annually in endemic countries (mainly in Africa and Asia), although the actual numbers are most likely underestimated. Rabies is a zoonotic disease that is caused by infection with viruses of the Lyssavirus genus, which are transmitted via the saliva of an infected animal. Dogs are the most important reservoir for rabies viruses, and dog bites account for >99% of human cases. The virus first infects peripheral motor neurons, and symptoms occur after the virus reaches the central nervous system. Once clinical disease develops, it is almost certainly fatal. Primary prevention involves dog vaccination campaigns to reduce the virus reservoir. If exposure occurs, timely post-exposure prophylaxis can prevent the progression to clinical disease and involves appropriate wound care, the administration of rabies immunoglobulin and vaccination. A multifaceted approach for human rabies eradication that involves government support, disease awareness, vaccination of at-risk human populations and, most importantly, dog rabies control is necessary to achieve the WHO goal of reducing the number of cases of dog-mediated human rabies to zero by 2030.
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Affiliation(s)
- Anthony R Fooks
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector Borne Diseases Research Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, World Organisation for Animal Health (OIE) Reference Laboratory for Rabies), Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK.,Institute of Infection &Global Health, University of Liverpool, Liverpool, UK.,Institute for Infection and Immunity, St. George's Hospital Medical School, University of London, London, UK
| | - Florence Cliquet
- French Agency for Food, Environmental and Occupational Health &Safety (ANSES)-Nancy Laboratory for Rabies and Wildlife (European Union Reference Laboratory for Rabies, WHO Collaborating Centre for Research and Management in Zoonoses Control, OIE Reference Laboratory for Rabies, European Union Reference Institute for Rabies Serology), Technopôle Agricole et Vétérinaire de Pixérécourt, Malzéville, France
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology (WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Conrad Freuling
- Institute of Molecular Virology and Cell Biology (WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Thiravat Hemachudha
- Department of Medicine (Neurology) and (WHO Collaborating Centre for Research and Training on Viral Zoonoses), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Thai Red Cross Emerging Infectious Disease-Health Science Centre, Thai Red Cross Society, Bangkok, Thailand
| | - Reeta S Mani
- Department of Neurovirology (WHO Collaborating Centre for Reference and Research in Rabies), National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology (WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Susan Nadin-Davis
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency (WHO Collaborating Centre for Control, Pathogenesis and Epidemiology of Rabies in Carnivores), Ottawa, Ontario, Canada
| | - Evelyne Picard-Meyer
- French Agency for Food, Environmental and Occupational Health &Safety (ANSES)-Nancy Laboratory for Rabies and Wildlife (European Union Reference Laboratory for Rabies, WHO Collaborating Centre for Research and Management in Zoonoses Control, OIE Reference Laboratory for Rabies, European Union Reference Institute for Rabies Serology), Technopôle Agricole et Vétérinaire de Pixérécourt, Malzéville, France
| | - Henry Wilde
- Department of Medicine (Neurology) and (WHO Collaborating Centre for Research and Training on Viral Zoonoses), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ashley C Banyard
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector Borne Diseases Research Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, World Organisation for Animal Health (OIE) Reference Laboratory for Rabies), Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
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Gessner BD, Knobel DL, Conan A, Finn A. Could the RTS,S/AS01 meningitis safety signal really be a protective effect of rabies vaccine? Vaccine 2017; 35:716-721. [PMID: 28065475 DOI: 10.1016/j.vaccine.2016.12.067] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/18/2016] [Accepted: 12/29/2016] [Indexed: 10/20/2022]
Abstract
The RTS,S/AS01 malaria vaccine has been associated with meningitis and cerebral malaria safety signals. Key characteristics of the meningitis signal include presence, in the 5-17month but not the 6-12week age group, of delayed and variable meningitis onset after vaccination, and multiple etiologies. For both meningitis and cerebral malaria, the 5-17month old age group control arm had abnormally low incidences while other arms in both age groups had meningitis and cerebral malaria incidences similar to background rates. No single hypothesis postulating an adverse effect from RTS,S/AS01 unites these observations. Unlike the 6-12week group, the control population in the 5-17month old age group received rabies vaccine. This raises the possibility that non-specific rabies vaccine effects had a protective effect against central nervous system infection, a hypothesis consistent with the epidemiologic data. The lack of a confirmed biologic mechanism for such an effect emphasizes the need for additional studies.
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Affiliation(s)
| | - Darryn L Knobel
- Ross University School of Veterinary Medicine, Island Main Road, West Farm, Saint Kitts and Nevis
| | - Anne Conan
- Ross University School of Veterinary Medicine, Island Main Road, West Farm, Saint Kitts and Nevis
| | - Adam Finn
- Bristol Children's Vaccine Centre, University of Bristol, United Kingdom
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23
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Maisonneuve P, Caillet-Saguy C, Vaney MC, Bibi-Zainab E, Sawyer K, Raynal B, Haouz A, Delepierre M, Lafon M, Cordier F, Wolff N. Molecular Basis of the Interaction of the Human Protein Tyrosine Phosphatase Non-receptor Type 4 (PTPN4) with the Mitogen-activated Protein Kinase p38γ. J Biol Chem 2016; 291:16699-708. [PMID: 27246854 DOI: 10.1074/jbc.m115.707208] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 11/06/2022] Open
Abstract
The human protein tyrosine phosphatase non-receptor type 4 (PTPN4) prevents cell death induction in neuroblastoma and glioblastoma cell lines in a PDZ·PDZ binding motifs-dependent manner, but the cellular partners of PTPN4 involved in cell protection are unknown. Here, we described the mitogen-activated protein kinase p38γ as a cellular partner of PTPN4. The main contribution to the p38γ·PTPN4 complex formation is the tight interaction between the C terminus of p38γ and the PDZ domain of PTPN4. We solved the crystal structure of the PDZ domain of PTPN4 bound to the p38γ C terminus. We identified the molecular basis of recognition of the C-terminal sequence of p38γ that displays the highest affinity among all endogenous partners of PTPN4. We showed that the p38γ C terminus is also an efficient inducer of cell death after its intracellular delivery. In addition to recruiting the kinase, the binding of the C-terminal sequence of p38γ to PTPN4 abolishes the catalytic autoinhibition of PTPN4 and thus activates the phosphatase, which can efficiently dephosphorylate the activation loop of p38γ. We presume that the p38γ·PTPN4 interaction promotes cellular signaling, preventing cell death induction.
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Affiliation(s)
- Pierre Maisonneuve
- From the Département de Biologie Structurale et Chimie, Unité de Résonance Magnétique Nucléaire des Biomolécules, UMR 3528 and Université Pierre et Marie Curie, Cellule Pasteur UPMC, 75005 Paris, France
| | - Célia Caillet-Saguy
- From the Département de Biologie Structurale et Chimie, Unité de Résonance Magnétique Nucléaire des Biomolécules, UMR 3528 and
| | - Marie-Christine Vaney
- Unité de Virologie Structurale, Département de Virologie, UMR 3569, CNRS, F-75724 Paris, France, and
| | - Edoo Bibi-Zainab
- From the Département de Biologie Structurale et Chimie, Unité de Résonance Magnétique Nucléaire des Biomolécules, UMR 3528 and
| | - Kristi Sawyer
- From the Département de Biologie Structurale et Chimie, Unité de Résonance Magnétique Nucléaire des Biomolécules, UMR 3528 and
| | - Bertrand Raynal
- UMR 3528 and Plate-Forme de Biophysique des Macromolécules, and
| | - Ahmed Haouz
- UMR 3528 and Plate-Forme de Cristallographie, Institut Pasteur, F-75724 Paris, France
| | - Muriel Delepierre
- From the Département de Biologie Structurale et Chimie, Unité de Résonance Magnétique Nucléaire des Biomolécules, UMR 3528 and
| | - Monique Lafon
- UMR 3569, CNRS, F-75724 Paris, France, and Unité de Neuro-Immunologie Virale, Département de Virologie
| | - Florence Cordier
- From the Département de Biologie Structurale et Chimie, Unité de Résonance Magnétique Nucléaire des Biomolécules, UMR 3528 and
| | - Nicolas Wolff
- From the Département de Biologie Structurale et Chimie, Unité de Résonance Magnétique Nucléaire des Biomolécules, UMR 3528 and
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