Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection
Tài liệu tham khảo
Ashburner, 2000, Gene ontology: tool for the unification of biology, Nat. Genet., 25, 25, 10.1038/75556
Ayyavoo, 1997, HIV-1 Vpr suppresses immune activation and apoptosis through regulation of nuclear factor kappa B, Nat. Med., 3, 1117, 10.1038/nm1097-1117
Belzile, 2010, HIV-1 Vpr induces the K48-linked polyubiquitination and proteasomal degradation of target cellular proteins to activate ATR and promote G2 arrest, J. Virol., 84, 3320, 10.1128/JVI.02590-09
Berger, 2015, G2/M cell cycle arrest correlates with primate lentiviral Vpr interaction with the SLX4 complex, J. Virol., 89, 230, 10.1128/JVI.02307-14
Boisvert, 2012, A quantitative spatial proteomics analysis of proteome turnover in human cells, Mol. Cell Proteomics, 11, 10.1074/mcp.M111.011429
Bolton, 2007, Vpr cytopathicity independent of G2/M cell cycle arrest in human immunodeficiency virus type 1-infected CD4+ T cells, J. Virol., 81, 8878, 10.1128/JVI.00122-07
Cano, 2015, A non-proteolytic role for ubiquitin in deadenylation of MHC-I mRNA by the RNA-binding E3-ligase MEX-3C, Nat. Commun., 6, 8670, 10.1038/ncomms9670
Chougui, 2018, HIV-2/SIV viral protein X counteracts HUSH repressor complex, Nat. Microbiol., 3, 891, 10.1038/s41564-018-0179-6
Connor, 1995, Vpr is required for efficient replication of human immunodeficiency virus type-1 in mononuclear phagocytes, Virology, 206, 935, 10.1006/viro.1995.1016
Cox, 2008, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat. Biotechnol., 26, 1367, 10.1038/nbt.1511
Coyaud, 2018, Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus, Mol. Cell. Proteomics, 17, 2242, 10.1074/mcp.TIR118.000800
Dai, 2006, Regulation of mitotic chromosome cohesion by Haspin and Aurora B, Dev. Cell, 11, 741, 10.1016/j.devcel.2006.09.018
Dehart, 2008, Human immunodeficiency virus type 1 Vpr links proteasomal degradation and checkpoint activation, J. Virol., 82, 1066, 10.1128/JVI.01628-07
Diamond, 2010, Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics, PLoS Pathog., 6, e1000719, 10.1371/journal.ppat.1000719
Ersing, 2017, A Temporal Proteomic Map of Epstein-Barr Virus Lytic Replication in B Cells, Cell Rep., 19, 1479, 10.1016/j.celrep.2017.04.062
Felzien, 1998, HIV transcriptional activation by the accessory protein, VPR, is mediated by the p300 co-activator, Proc. Natl. Acad. Sci. USA, 95, 5281, 10.1073/pnas.95.9.5281
Fischer, 2016, Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks, Nucleic Acids Res., 44, 6070, 10.1093/nar/gkw523
Fletcher, 1996, Nuclear import and cell cycle arrest functions of the HIV-1 Vpr protein are encoded by two separate genes in HIV-2/SIV(SM), EMBO J., 15, 6155, 10.1002/j.1460-2075.1996.tb01003.x
Foley, 1965, Continuous Culture of Human Lymphoblasts from Peripheral Blood of a Child with Acute Leukemia, Cancer, 18, 522, 10.1002/1097-0142(196504)18:4<522::AID-CNCR2820180418>3.0.CO;2-J
Forget, 1998, Human immunodeficiency virus type 1 vpr protein transactivation function: mechanism and identification of domains involved, J. Mol. Biol., 284, 915, 10.1006/jmbi.1998.2206
Fregoso, 2016, Activation of the DNA Damage Response Is a Conserved Function of HIV-1 and HIV-2 Vpr That Is Independent of SLX4 Recruitment, MBio, 7, 10.1128/mBio.01433-16
Goh, 1998, HIV-1 Vpr increases viral expression by manipulation of the cell cycle: a mechanism for selection of Vpr in vivo, Nat. Med., 4, 65, 10.1038/nm0198-065
Greenwood, 2016, Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants, eLife, 5, e18296, 10.7554/eLife.18296
Guenzel, 2014, HIV-1 Vpr-a still “enigmatic multitasker”, Front. Microbiol., 5, 127, 10.3389/fmicb.2014.00127
Gummuluru, 1999, Cell cycle- and Vpr-mediated regulation of human immunodeficiency virus type 1 expression in primary and transformed T-cell lines, J. Virol., 73, 5422, 10.1128/JVI.73.7.5422-5430.1999
Guo, 2016, DCAF1 controls T-cell function via p53-dependent and -independent mechanisms, Nat. Commun., 7, 10307, 10.1038/ncomms10307
Hofmann, 2017, Dual role of the chromatin-binding factor PHF13 in the pre- and post-integration phases of HIV-1 replication, Open Biol., 7, 170115, 10.1098/rsob.170115
Höhne, 2016, Virion encapsidated HIV-1 Vpr induces NFAT to prime non-activated T cells for productive infection, Open Biol., 6, 160046, 10.1098/rsob.160046
Hossain, 2017, Cep78 controls centrosome homeostasis by inhibiting EDD-DYRK2-DDB1VprBP, EMBO Rep., 18, 632, 10.15252/embr.201642377
Hou, 2005, Two human orthologues of Eco1/Ctf7 acetyltransferases are both required for proper sister-chromatid cohesion, Mol. Biol. Cell, 16, 3908, 10.1091/mbc.e04-12-1063
Hrecka, 2011, Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein, Nature, 474, 658, 10.1038/nature10195
Hrecka, 2016, HIV-1 and HIV-2 exhibit divergent interactions with HLTF and UNG2 DNA repair proteins, Proc. Natl. Acad. Sci. USA, 113, E3921, 10.1073/pnas.1605023113
Huber, 2015, Orchestrating high-throughput genomic analysis with Bioconductor, Nat. Methods, 12, 115, 10.1038/nmeth.3252
Hughes, 2014, Ultrasensitive proteome analysis using paramagnetic bead technology, Mol. Syst. Biol., 10, 757, 10.15252/msb.20145625
Jaffar, 2004, The natural history of HIV-1 and HIV-2 infections in adults in Africa: a literature review, Bull. World Health Organ., 82, 462
Jäger, 2011, Global landscape of HIV-human protein complexes, Nature, 481, 365, 10.1038/nature10719
Jordan, 2001, The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation, EMBO J., 20, 1726, 10.1093/emboj/20.7.1726
Jordan, 2003, HIV reproducibly establishes a latent infection after acute infection of T cells in vitro, EMBO J., 22, 1868, 10.1093/emboj/cdg188
Kannan, 2018, Combined deficiency of Senataxin and DNA-PKcs causes DNA damage accumulation and neurodegeneration in spinal muscular atrophy, Nucleic Acids Res., 46, 8326, 10.1093/nar/gky641
Laguette, 2011, SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx, Nature, 474, 654, 10.1038/nature10117
Laguette, 2014, Premature activation of the SLX4 complex by Vpr promotes G2/M arrest and escape from innate immune sensing, Cell, 156, 134, 10.1016/j.cell.2013.12.011
Lahouassa, 2016, HIV-1 Vpr degrades the HLTF DNA translocase in T cells and macrophages, Proc. Natl. Acad. Sci. U.S.A, 113, 5311, 10.1073/pnas.1600485113
Lahti, 2003, Regulation of T cell activation by HIV-1 accessory proteins: Vpr acts via distinct mechanisms to cooperate with Nef in NFAT-directed gene expression and to promote transactivation by CREB, Virology, 310, 190, 10.1016/S0042-6822(03)00164-8
Lapek, 2017, Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Protein Vpr, Mol. Cell. Proteomics, 16, 1447, 10.1074/mcp.M116.066019
Le Rouzic, 2007, HIV1 Vpr arrests the cell cycle by recruiting DCAF1/VprBP, a receptor of the Cul4-DDB1 ubiquitin ligase, Cell Cycle, 6, 182, 10.4161/cc.6.2.3732
León, 2013, Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis, Mol. Cell. Proteomics, 12, 2992, 10.1074/mcp.M112.025585
Liang, 2015, HIV-1 Vpr protein activates the NF-κB pathway to promote G2/M cell cycle arrest, Virol. Sin., 30, 441, 10.1007/s12250-015-3654-8
Lim, 2012, The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx, Cell Host Microbe, 11, 194, 10.1016/j.chom.2012.01.004
Liu, 2014, HIV-1 Vpr stimulates NF-κB and AP-1 signaling by activating TAK1, Retrovirology, 11, 45, 10.1186/1742-4690-11-45
Luo, 2016, HIV-host interactome revealed directly from infected cells, Nat. Microbiol., 1, 16068, 10.1038/nmicrobiol.2016.68
Lv, 2018, Vpr Targets TET2 for Degradation by CRL4(VprBP) E3 Ligase to Sustain IL-6 Expression and Enhance HIV-1 Replication, Mol. Cell, 70, 961, 10.1016/j.molcel.2018.05.007
Ly, 2015, Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells, eLife, 4, 10.7554/eLife.04534
Mashiba, 2015, Vpr Overcomes Macrophage-Specific Restriction of HIV-1 Env Expression and Virion Production, Cell Host Microbe, 17, 414, 10.1016/j.chom.2015.02.016
Matheson, 2014, Antibody-free magnetic cell sorting of genetically modified primary human CD4+ T cells by one-step streptavidin affinity purification, PLoS ONE, 9, e111437, 10.1371/journal.pone.0111437
Matheson, 2015, Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef, Cell Host Microbe, 18, 409, 10.1016/j.chom.2015.09.003
Matheson, 2016, Manipulation of immunometabolism by HIV-accessories to the crime?, Curr. Opin. Virol., 19, 65, 10.1016/j.coviro.2016.06.014
Maudet, 2013, HIV-1 Vpr induces the degradation of ZIP and sZIP, adaptors of the NuRD chromatin remodeling complex, by hijacking DCAF1/VprBP, PLoS ONE, 8, e77320, 10.1371/journal.pone.0077320
Mellacheruvu, 2013, The CRAPome: a contaminant repository for affinity purification-mass spectrometry data, Nat. Methods, 10, 730, 10.1038/nmeth.2557
Mi, 2017, PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements, Nucleic Acids Res., 45, D183, 10.1093/nar/gkw1138
Miller, 2017, Virion-Associated Vpr Alleviates a Postintegration Block to HIV-1 Infection of Dendritic Cells, J. Virol., 91, 10.1128/JVI.00051-17
Murray, 2011, Timing of the components of the HIV life cycle in productively infected CD4+ T cells in a population of HIV-infected individuals, J. Virol., 85, 10798, 10.1128/JVI.05095-11
Muthumani, 2006, The HIV-1 Vpr and glucocorticoid receptor complex is a gain-of-function interaction that prevents the nuclear localization of PARP-1, Nat. Cell Biol., 8, 170, 10.1038/ncb1352
Naamati, 2019, Functional proteomic atlas of HIV infection in primary human CD4+ T cells, eLife, 8, e41431, 10.7554/eLife.41431
Peng, 2010, Repo-man controls a protein phosphatase 1-dependent threshold for DNA damage checkpoint activation, Curr. Biol., 20, 387, 10.1016/j.cub.2010.01.020
Perelson, 1996, HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time, Science, 271, 1582, 10.1126/science.271.5255.1582
Poon, 1998, Cell cycle arrest by Vpr in HIV-1 virions and insensitivity to antiretroviral agents, Science, 281, 266, 10.1126/science.281.5374.266
2013
Rankin, 2005, Sororin, a substrate of the anaphase-promoting complex, is required for sister chromatid cohesion in vertebrates, Mol. Cell, 18, 185, 10.1016/j.molcel.2005.03.017
Re, 1995, Human immunodeficiency virus type 1 Vpr arrests the cell cycle in G2 by inhibiting the activation of p34cdc2-cyclin B, J. Virol., 69, 6859, 10.1128/JVI.69.11.6859-6864.1995
Richard, 2010, HIV-1 Vpr up-regulates expression of ligands for the activating NKG2D receptor and promotes NK cell-mediated killing, Blood, 115, 1354, 10.1182/blood-2009-08-237370
Rogel, 1995, The human immunodeficiency virus type 1 vpr gene prevents cell proliferation during chronic infection, J. Virol., 69, 882, 10.1128/JVI.69.2.882-888.1995
Romani, 2015, HIV-1 Vpr Protein Enhances Proteasomal Degradation of MCM10 DNA Replication Factor through the Cul4-DDB1[VprBP] E3 Ubiquitin Ligase to Induce G2/M Cell Cycle Arrest, J. Biol. Chem., 290, 17380, 10.1074/jbc.M115.641522
Roshal, 2003, Activation of the ATR-mediated DNA damage response by the HIV-1 viral protein R, J. Biol. Chem., 278, 25879, 10.1074/jbc.M303948200
Roux, 2000, Activation of transcription factors NF-kappaB and NF-IL-6 by human immunodeficiency virus type 1 protein R (Vpr) induces interleukin-8 expression, J. Virol., 74, 4658, 10.1128/JVI.74.10.4658-4665.2000
Schröfelbauer, 2005, Human immunodeficiency virus type 1 Vpr induces the degradation of the UNG and SMUG uracil-DNA glycosylases, J. Virol., 79, 10978, 10.1128/JVI.79.17.10978-10987.2005
Schwämmle, 2013, Assessment and improvement of statistical tools for comparative proteomics analysis of sparse data sets with few experimental replicates, J. Proteome Res., 12, 3874, 10.1021/pr400045u
Selig, 1997, Uracil DNA glycosylase specifically interacts with Vpr of both human immunodeficiency virus type 1 and simian immunodeficiency virus of sooty mangabeys, but binding does not correlate with cell cycle arrest, J. Virol., 71, 4842, 10.1128/JVI.71.6.4842-4846.1997
Shimura, 2011, Epigenetic displacement of HP1 from heterochromatin by HIV-1 Vpr causes premature sister chromatid separation, J. Cell Biol., 194, 721, 10.1083/jcb.201010118
Simon, 2015, Intrinsic host restrictions to HIV-1 and mechanisms of viral escape, Nat. Immunol., 16, 546, 10.1038/ni.3156
Sugden, 2016, Remodeling of the Host Cell Plasma Membrane by HIV-1 Nef and Vpu: A Strategy to Ensure Viral Fitness and Persistence, Viruses, 8, 67, 10.3390/v8030067
Sumner, 2017, Are Evolution and the Intracellular Innate Immune System Key Determinants in HIV Transmission?, Front. Immunol., 8, 1246, 10.3389/fimmu.2017.01246
Tchasovnikarova, 2015, GENE SILENCING. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells, Science, 348, 1481, 10.1126/science.aaa7227
Terada, 2006, Human immunodeficiency virus type 1 Vpr induces G2 checkpoint activation by interacting with the splicing factor SAP145, Mol. Cell. Biol., 26, 8149, 10.1128/MCB.01170-06
2019, The Gene Ontology Resource: 20 years and still GOing strong, Nucleic Acids Res., 47, D330, 10.1093/nar/gky1055
Tyanova, 2016, The Perseus computational platform for comprehensive analysis of (prote)omics data, Nat. Methods, 13, 731, 10.1038/nmeth.3901
2019, UniProt: a worldwide hub of protein knowledge, Nucleic Acids Res., 47, D506, 10.1093/nar/gky1049
van den Boomen, 2014, TMEM129 is a Derlin-1 associated ERAD E3 ligase essential for virus-induced degradation of MHC-I, Proc. Natl. Acad. Sci. USA, 111, 11425, 10.1073/pnas.1409099111
Vassena, 2013, The human immunodeficiency virus type 1 Vpr protein upregulates PVR via activation of the ATR-mediated DNA damage response pathway, J. Gen. Virol., 94, 2664, 10.1099/vir.0.055541-0
Vizcaíno, 2016, 2016 update of the PRIDE database and its related tools, Nucleic Acids Res., 44, 11033, 10.1093/nar/gkw880
Waterhouse, 2009, Jalview Version 2—a multiple sequence alignment editor and analysis workbench, Bioinformatics, 25, 1189, 10.1093/bioinformatics/btp033
Weekes, 2014, Quantitative temporal viromics: an approach to investigate host-pathogen interaction, Cell, 157, 1460, 10.1016/j.cell.2014.04.028
Wu, 2016, The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction, Nat. Struct. Mol. Biol., 23, 933, 10.1038/nsmb.3284
Yurkovetskiy, 2018, Primate immunodeficiency virus proteins Vpx and Vpr counteract transcriptional repression of proviruses by the HUSH complex, Nat. Microbiol., 3, 1354, 10.1038/s41564-018-0256-x
Zhang, 2004, Novel single-cell-level phenotypic assay for residual drug susceptibility and reduced replication capacity of drug-resistant human immunodeficiency virus type 1, J. Virol., 78, 1718, 10.1128/JVI.78.4.1718-1729.2004
Zhou, 2000, Phosphorylation of human immunodeficiency virus type 1 Vpr regulates cell cycle arrest, J. Virol., 74, 6520, 10.1128/JVI.74.14.6520-6527.2000
Zhou, 2016, SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr), J. Biol. Chem., 291, 16936, 10.1074/jbc.M116.721183
Zufferey, 1997, Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo, Nat. Biotechnol., 15, 871, 10.1038/nbt0997-871