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Structural and Functional Analyses of the Interaction of Tetherin with the Dendritic Cell Receptor ILT7 Nicolas Aschman

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Structural and functional analyses of the interaction of tetherin with the dendritic cell receptor ILT7 Nicolas Aschman To cite this version: Nicolas Aschman. Structural and functional analyses of the interaction of tetherin with the dendritic cell receptor ILT7. Biomolecules [q-bio.BM]. Université Grenoble Alpes, 2015. English. NNT : 2015GREAV064. tel-01682995 HAL Id: tel-01682995 https://tel.archives-ouvertes.fr/tel-01682995 Submitted on 12 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés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tructural and functional analysis of the interaction of tetherin with the dendritic cell receptor ILT7 Nicolas Aschman June 28, 2015 ii Abstract Human immunodeficiency virus 1 (HIV-1) specifically infects CD4+ T cells, thereby preventing an appropriate activation of cytotoxic T cells and B cells in response to opportunistic pathogens. In addition, HIV-1 antagonises host restriction factors, in- cluding tetherin. In the absence of the viral protein Vpu, tetherin potently inhibits virus particle release from infected cells. Tetherin also triggers proinflammatory sig- naling upon sensing virus assembly, and activates the dendritic cell receptor ILT7. The principal objective of this thesis was to elucidate the structural details underlying the interaction of tetherin with ILT7. Despite difficulties in the production of recombinant ILT7, the crystal structure of the N-terminal ILT7 domain could be determined. Fur- thermore, binding of tetherin to full-length ILT7, but not to the N-terminal domain, could be confirmed by SPR. These results provide a solid basis for the more detailed characterisation of the interaction. Résumé Le virus d’immunodéficience humaine 1 (VIH-1) cible spécifiquement les cellules CD4+ et empêche ainsi l’activation de cellules T cytotoxiques et B lors d’une infection sec- ondaire. Le VIH-1 antagonise également la plupart des facteurs de restriction de l’hôte, y compris la tétherine. En l’absence de la protéine virale Vpu, la tétherine inhibe le re- larguage de particules virales et provoque leur dégradation. La tétherine est également capable d’induire une signalisation pro-inflammatoire en réponse au bourgeonnement viral ainsi que d’activer le récepteur de cellules dendritiques ILT7. L’objectif princi- pal de cette étude consistait à élucider les bases structurales de l’interaction entre la tétherine et ILT7. Malgré de nombreuses difficultés rencontrées dans la production re- combinante de ILT7, on a pu déterminer la structure cristallographique du domaine N-terminale du récepteur. La ligation de la tétherine à l’ectodomaine entier de ILT7, mais pas au domaine N-terminal, a également été montré. Ces résultats constituent une base solide pour la caractérisation plus détaillée de l’interaction. iii iv Acknowledgements First and foremost, I would like to express my gratitude to my supervisor Winfried Weissenhorn for giving me the chance of joining his team at a time when my back- ground in structural biology was limited to a few rusty memories from early morning lectures. When my project turned out to be more challenging than expected and ini- tially had me seriously struggling, Winfried has always remained supportive and con- fident. Among many other things, I greatly appreciate that the door of Winfried’s office was always open, that he always took time for discussion and was always available for advice. I would like to thank the members of my jury, namely Andrea Cimarelli and Yves Gaudin, who act as rapporteurs, as well as Marc Jamin, Andrew McCarthy and Laurent Terradot. I am very grateful also to Carlo Petosa and Ramesh Pillai for their construc- tive feedback as members of my thesis advisory committee. During the last year of my thesis I have been involved in a fruitful collaboration with the laboratory of Prof Eric Cohen (Institut de Recherches Cliniques de Montréal, Canada). In this regard, I would especially like to thank Mariana Bego for sharing her insights and providing protein samples, as well as Edouard Côté for analysing my samples by flow cytometry. I am indebted to all of my team members for teaching me virtually everything about protein expression, purification and crystallography. I am especially thankful to Patricia Renesto for introducing me to the art of cloning, for sharing her experience of mammalian cell culture, for co-writing my first review article and generally for her helpfulness. I will miss her anecdotes and always remember the good moments shared in the lab. Special thanks also go to Miriam Hock for teaching me many techniques and helping me troubleshoot my experiments countless times ; to Jens Radzimanowski for introducing me to protein crystallisation, X-ray diffraction and data processing ; to Christophe Caillat for his help with model building and refinement, and generally use- ful advice ; and to Aurélien Dordor for untold scientific and less-scientific discussions. I will also fondly remember my colleagues Pauline Macheboeuf, Géraldine Mayeux and Nolwenn Miguet, as well as previous team members David Lutje Hulsik, Nicolas Martinelli and Emilie Poudevigne. Many other people have been helpful by teaching me new techniques or providing useful advice, among them Pascal Fender whom I would like to thank for his help with cell culture and SPR, as well as for his eternal good mood and humour ; Vladimir Rybin and Piotr Gerlach for introducing me to ITC and MST analysis, respectively ; Sergiy Avilov for his help with confocal microscopy and Natasha Alexandrovna for her advice on protein expression in mammalian cell lines. Filip Yabukarski has helped me, through countless discussions, make light of some of the more obscure aspects of protein crystallography. I am also thankful to Nicolas Tarbouriech, Max Nanao and v Chloe Zubieta for their spontaneous advice on crystallographic data processing and model refinement. In the context of the Partnership for Structural Biology (PSB, Grenoble), I have made use of several platforms and facilities, most notably the Eukaryotic Expression Facility (EEF) operated by the Berger group where all insect cell expression was carried out. I am grateful to the Berger team for providing this service, with special thanks to Alice Aubert for always providing me with healthy cells at a moment’s notice. I would also like to thank Philippe Mas (thermal shift assays), Daphna Fenel and Guy Schoehn (electron microscopy) and Luca Signor (mass spectrometry). The administrative and technical staff of my host laboratory have been extremely helpful and kind, and I would like to thank Sandrine Vignon in particular for her assis- tance with awkward paperwork of all kind. I would like to acknowledge the financial support of the Agence Nationale de la Recherche sur le SIDA et les hépatites virales (ANRS) and the Fonds National de la Recherche of Luxembourg (FNR). Last but not least I would like to thank my parents for their unconditional support in all my endeavours, and my wife Corinne for her undying optimism, patience and love. Nick Aschman Grenoble, March 2015 vi Contents Abstract......................................... iii Acknowledgements.................................. v Abbreviations ..................................... xi Introduction (français) 15 1 Introduction 17 1.1 Molecular and structural biology of HIV . ..... 19 1.1.1 Assemblyandbudding . 20 1.1.2 Infectionandreplication. 22 1.2 InnateimmuneresponsetoHIV . 26 1.2.1 Interferonresponse.. .. .. .. .. .. .. .. 27 1.2.2 Restrictionfactors. 29 1.3 Tetherinstructureandfunction . .... 31 1.3.1 Expressionandtrafficking. 32 1.3.2 Topologyandstructure . 33 1.3.3 Inhibitionofvirusrelease . 35 1.3.4 Organisation of subcellular structure . ..... 41 1.3.5 Immunesensingandsignalingactivities . ... 42 1.3.6 Modulationoftheinnateimmuneresponse . .. 42 1.4 ILT7 and the leukocyte Ig-like receptor family . ........ 43 1.4.1 Topology, structure and signal transduction . ...... 44 1.4.2 Functional activity and role in HIV-1 infection . ...... 45 Objectives 51 2 Methods 53 2.1 Bioinformatics.................................. 53 2.1.1 Multiple sequence alignment and phylogenetics . ..... 53 2.1.2 Domain, structure and disorder prediction . .... 54 2.1.3 Post-translational modifications and processing . ....... 54 2.1.4 Ab initio protein–protein docking and interface characterisation . 54
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    viruses Article Canine Influenza Virus is Mildly Restricted by Canine Tetherin Protein Yun Zheng 1,2,3,†, Xiangqi Hao 1,2,3,†, Qingxu Zheng 1,2,3, Xi Lin 1,2,3, Xin Zhang 1,2,3, Weijie Zeng 1,2,3, Shiyue Ding 1, Pei Zhou 1,2,3,* and Shoujun Li 1,2,3,* 1 College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; [email protected] (Y.Z.); [email protected] (X.H.); [email protected] (Q.Z.); [email protected] (X.L.); [email protected] (X.Z.); [email protected] (W.Z.); [email protected] (S.D.) 2 Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou 510642, China 3 Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou 510642, China * Correspondence: [email protected] (P.Z.); [email protected] (S.L.) † These authors contributed equally to this work. Received: 10 July 2018; Accepted: 10 October 2018; Published: 16 October 2018 Abstract: Tetherin (BST2/CD317/HM1.24) has emerged as a key host-cell ·defence molecule that acts by inhibiting the release and spread of diverse enveloped virions from infected cells. We analysed the biological features of canine tetherin and found it to be an unstable hydrophilic type I transmembrane protein with one transmembrane domain, no signal peptide, and multiple glycosylation and phosphorylation sites. Furthermore, the tissue expression profile of canine tetherin revealed that it was particularly abundant in immune organs. The canine tetherin gene contains an interferon response element sequence that can be regulated and expressed by canine IFN-α.
  • Tetherin/BST-2 Promotes Dendritic Cell Activation and Function During Acute Retrovirus Infection Received: 21 October 2015 Sam X

    Tetherin/BST-2 Promotes Dendritic Cell Activation and Function During Acute Retrovirus Infection Received: 21 October 2015 Sam X

    www.nature.com/scientificreports OPEN Tetherin/BST-2 promotes dendritic cell activation and function during acute retrovirus infection Received: 21 October 2015 Sam X. Li1,2, Bradley S. Barrett1, Kejun Guo1, George Kassiotis3, Kim J. Hasenkrug4, Accepted: 06 January 2016 Ulf Dittmer5, Kathrin Gibbert5 & Mario L. Santiago1,2 Published: 05 February 2016 Tetherin/BST-2 is a host restriction factor that inhibits retrovirus release from infected cells in vitro by tethering nascent virions to the plasma membrane. However, contradictory data exists on whether Tetherin inhibits acute retrovirus infection in vivo. Previously, we reported that Tetherin-mediated inhibition of Friend retrovirus (FV) replication at 2 weeks post-infection correlated with stronger natural killer, CD4+ T and CD8+ T cell responses. Here, we further investigated the role of Tetherin in counteracting retrovirus replication in vivo. FV infection levels were similar between wild-type (WT) and Tetherin KO mice at 3 to 7 days post-infection despite removal of a potent restriction factor, Apobec3/Rfv3. However, during this phase of acute infection, Tetherin enhanced myeloid dendritic cell (DC) function. DCs from infected, but not uninfected, WT mice expressed significantly higher MHC class II and the co-stimulatory molecule CD80 compared to Tetherin KO DCs. Tetherin-associated DC activation during acute FV infection correlated with stronger NK cell responses. Furthermore, Tetherin+ DCs from FV-infected mice more strongly stimulated FV-specific CD4+ T cells ex vivo compared to Tetherin KO DCs. The results link the antiretroviral and immunomodulatory activity of Tetherin in vivo to improved DC activation and MHC class II antigen presentation. Restriction factors are host-encoded type I interferon-stimulated genes (ISG) that directly inhibit virus replication1.
  • 9-Azido Analogs of Three Sialic Acid Forms for Metabolic Remodeling Of

    9-Azido Analogs of Three Sialic Acid Forms for Metabolic Remodeling Of

    Supporting Information 9-Azido Analogs of Three Sialic Acid Forms for Metabolic Remodeling of Cell-Surface Sialoglycans Bo Cheng,†,‡ Lu Dong,†,§ Yuntao Zhu,†,‡ Rongbing Huang,†,‡ Yuting Sun,†,‖ Qiancheng You,†,‡ Qitao Song,†,§ James C. Paton, ∇ Adrienne W. Paton,∇ and Xing Chen*,†,‡,§,⊥,# †College of Chemistry and Molecular Engineering, ‡Beijing National Laboratory for Molecular Sciences, §Peking−Tsinghua Center for Life Sciences,‖Academy for Advanced Interdisciplinary Studies, ⊥Synthetic and Functional Biomolecules Center, and #Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China ∇Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide SA 5005, Australia Page S1 Table of Contents: Scheme S1.……………………………………………………….........……………. S3 Figure S1……………………………………………………..………..……………. S3 Figure S2……………………………………………………..………..…………… S4 Figure S3……………………………………………………..………..…………… S4 Figure S4……………………………………………………..………..…………… S5 Figure S5……………………………………………………..………..…………… S6 Figure S6……………………………………………………..………..…………….S7 Figure S7……………………………………………………..………..…………….S8 Figure S8……………………………………………………..………..…………….S9 Experimental Procedures……………………………….…........…………....S10-S27 Table S1………………………………………………..………..…………….S28-S48 Supporting Reference……………………………………………….......………...S49 Page S2 Scheme S1. Synthesis of 9AzNeu5Gc Figure S1: a, b, c, d) Representative scatter plots (FSC vs. SSC) and histograms of flow cytometry analysis