Plasma Membrane Profiling Defines an Expanded Class of Cell Surface Proteins Selectively Targeted for Degradation by HCMV US2 in Cooperation with UL141

1. Murphy E, Yu D, Grimwood J, Schmutz J, Dickson M, Jarvis MA, et al. Coding potential of laboratory and clinical strains of human cytomegalovirus. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14976–81. 14657367

2. Yu D, Silva MC, Shenk T. Functional map of human cytomegalovirus AD169 defined by global mutational analysis. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12396–401. 14519856

3. Mocarski ES Jr. Immunomodulation by cytomegaloviruses: manipulative strategies beyond evasion. Trends Microbiol. 2002 Jul;10(7):332–9. 12110212

4. Wilkinson GW, Tomasec P, Stanton RJ, Armstrong M, Prod'homme V, Aicheler R, et al. Modulation of natural killer cells by human cytomegalovirus. J Clin Virol. 2008 Mar;41(3):206–12. 18069056

5. Dunn W, Chou C, Li H, Hai R, Patterson D, Stolc V, et al. Functional profiling of a human cytomegalovirus genome. Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14223–8. 14623981

6. Hansen TH, Bouvier M. MHC class I antigen presentation: learning from viral evasion strategies. Nat Rev Immunol. 2009 Jul;9(7):503–13. doi: 10.1038/nri2575 19498380

7. Jones TR, Wiertz EJ, Sun L, Fish KN, Nelson JA, Ploegh HL. Human cytomegalovirus US3 impairs transport and maturation of major histocompatibility complex class I heavy chains. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11327–33. 8876135

8. Park B, Kim Y, Shin J, Lee S, Cho K, Fruh K, et al. Human cytomegalovirus inhibits tapasin-dependent peptide loading and optimization of the MHC class I peptide cargo for immune evasion. Immunity. 2004 Jan;20(1):71–85. 14738766

9. Lehner PJ, Karttunen JT, Wilkinson GW, Cresswell P. The human cytomegalovirus US6 glycoprotein inhibits transporter associated with antigen processing-dependent peptide translocation. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6904–9. 9192664

10. Ahn K, Gruhler A, Galocha B, Jones TR, Wiertz EJ, Ploegh HL, et al. The ER-luminal domain of the HCMV glycoprotein US6 inhibits peptide translocation by TAP. Immunity. 1997 May;6(5):613–21. 9175839

11. Wiertz EJ, Jones TR, Sun L, Bogyo M, Geuze HJ, Ploegh HL. The human cytomegalovirus US11 gene product dislocates MHC class I heavy chains from the endoplasmic reticulum to the cytosol. Cell. 1996 Mar 8;84(5):769–79. 8625414

12. Wiertz EJ, Tortorella D, Bogyo M, Yu J, Mothes W, Jones TR, et al. Sec61-mediated transfer of a membrane protein from the endoplasmic reticulum to the proteasome for destruction. Nature. 1996 Dec 5;384(6608):432–8. 8945469

13. Stagg HR, Thomas M, van den Boomen D, Wiertz EJ, Drabkin HA, Gemmill RM, et al. The TRC8 E3 ligase ubiquitinates MHC class I molecules before dislocation from the ER. J Cell Biol. 2009 Sep 7;186(5):685–92. doi: 10.1083/jcb.200906110 19720873

14. Lilley BN, Ploegh HL. A membrane protein required for dislocation of misfolded proteins from the ER. Nature. 2004 Jun 24;429(6994):834–40. 15215855

15. van den Boomen DJ, Timms RT, Grice GL, Stagg HR, Skodt K, Dougan G, et al. TMEM129 is a Derlin-1 associated ERAD E3 ligase essential for virus-induced degradation of MHC-I. Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11425–30. doi: 10.1073/pnas.1409099111 25030448

16. van de Weijer ML, Bassik MC, Luteijn RD, Voorburg CM, Lohuis MA, Kremmer E, et al. A high-coverage shRNA screen identifies TMEM129 as an E3 ligase involved in ER-associated protein degradation. Nat Commun. 2014;5 : 3832. doi: 10.1038/ncomms4832 24807418

17. Noriega VM, Hesse J, Gardner TJ, Besold K, Plachter B, Tortorella D. Human cytomegalovirus US3 modulates destruction of MHC class I molecules. Mol Immunol. 2012 Jun;51(2):245–53. doi: 10.1016/j.molimm.2012.03.024 22497807

18. Hegde NR, Tomazin RA, Wisner TW, Dunn C, Boname JM, Lewinsohn DM, et al. Inhibition of HLA-DR assembly, transport, and loading by human cytomegalovirus glycoprotein US3: a novel mechanism for evading major histocompatibility complex class II antigen presentation. J Virol. 2002 Nov;76(21):10929–41. 12368336

19. Tomazin R, Boname J, Hegde NR, Lewinsohn DM, Altschuler Y, Jones TR, et al. Cytomegalovirus US2 destroys two components of the MHC class II pathway, preventing recognition by CD4+ T cells. Nat Med. 1999 Sep;5(9):1039–43. 10470081

20. Tomasec P, Braud VM, Rickards C, Powell MB, McSharry BP, Gadola S, et al. Surface expression of HLA-E, an inhibitor of natural killer cells, enhanced by human cytomegalovirus gpUL40. Science. 2000 Feb 11;287(5455):1031–3. 10669413

21. Wang EC, McSharry B, Retiere C, Tomasec P, Williams S, Borysiewicz LK, et al. UL40-mediated NK evasion during productive infection with human cytomegalovirus. Proc Natl Acad Sci U S A. 2002 May 28;99(11):7570–5. 12032324

22. Prod'homme V, Tomasec P, Cunningham C, Lemberg MK, Stanton RJ, McSharry BP, et al. Human cytomegalovirus UL40 signal peptide regulates cell surface expression of the NK cell ligands HLA-E and gpUL18. J Immunol. 2012 Mar 15;188(6):2794–804. doi: 10.4049/jimmunol.1102068 22345649

23. Browne H, Smith G, Beck S, Minson T. A complex between the MHC class I homologue encoded by human cytomegalovirus and beta 2 microglobulin. Nature. 1990 Oct 25;347(6295):770–2. 2172831

24. Fahnestock ML, Johnson JL, Feldman RM, Neveu JM, Lane WS, Bjorkman PJ. The MHC class I homolog encoded by human cytomegalovirus binds endogenous peptides. Immunity. 1995 Nov;3(5):583–90. 7584148

25. Prod'homme V, Sugrue DM, Stanton RJ, Nomoto A, Davies J, Rickards CR, et al. Human cytomegalovirus UL141 promotes efficient downregulation of the natural killer cell activating ligand CD112. J Gen Virol. 2010 Aug;91(Pt 8):2034–9. doi: 10.1099/vir.0.021931-0 20410314

26. Tomasec P, Wang EC, Davison AJ, Vojtesek B, Armstrong M, Griffin C, et al. Downregulation of natural killer cell-activating ligand CD155 by human cytomegalovirus UL141. Nature immunology. 2005 Feb;6(2):181–8. 15640804

27. de Andrade LF, Smyth MJ, Martinet L. DNAM-1 control of natural killer cells functions through nectin and nectin-like proteins. Immunology and cell biology. 2014 Mar;92(3):237–44. doi: 10.1038/icb.2013.95 24343663

28. Weekes MP, Antrobus R, Talbot S, Hor S, Simecek N, Smith DL, et al. Proteomic plasma membrane profiling reveals an essential role for gp96 in the cell surface expression of LDLR family members, including the LDL receptor and LRP6. J Proteome Res. 2012 Mar 2;11(3):1475–84. doi: 10.1021/pr201135e 22292497

29. Weekes MP, Tan SY, Poole E, Talbot S, Antrobus R, Smith DL, et al. Latency-associated degradation of the MRP1 drug transporter during latent human cytomegalovirus infection. Science. 2013 Apr 12;340(6129):199–202. doi: 10.1126/science.1235047 23580527

30. Weekes MP, Tomasec P, Huttlin EL, Fielding CA, Nusinow D, Stanton RJ, et al. Quantitative temporal viromics: an approach to investigate host-pathogen interaction. Cell. 2014 Jun 5;157(6):1460–72. doi: 10.1016/j.cell.2014.04.028 24906157

31. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002 May;1(5):376–86. 12118079

32. Furman MH, Ploegh HL, Tortorella D. Membrane-specific, host-derived factors are required for US2 -⁠ and US11-mediated degradation of major histocompatibility complex class I molecules. J Biol Chem. 2002 Feb 1;277(5):3258–67. 11717308

33. Abshire MY, Thomas KS, Owen KA, Bouton AH. Macrophage motility requires distinct alpha5beta1/FAK and alpha4beta1/paxillin signaling events. J Leukoc Biol. 2011 Feb;89(2):251–7. doi: 10.1189/jlb.0710395 21084629

34. Liu S, Thomas SM, Woodside DG, Rose DM, Kiosses WB, Pfaff M, et al. Binding of paxillin to alpha4 integrins modifies integrin-dependent biological responses. Nature. 1999 Dec 9;402(6762):676–81. 10604475

35. Schaller MD. Paxillin: a focal adhesion-associated adaptor protein. Oncogene. 2001 Oct 1;20(44):6459–72. 11607845

36. Wade R, Bohl J, Vande Pol S. Paxillin null embryonic stem cells are impaired in cell spreading and tyrosine phosphorylation of focal adhesion kinase. Oncogene. 2002 Jan 3;21(1):96–107. 11791180

37. Sampaio KL, Cavignac Y, Stierhof YD, Sinzger C. Human cytomegalovirus labeled with green fluorescent protein for live analysis of intracellular particle movements. J Virol. 2005 Mar;79(5):2754–67. 15708994

38. Smith W, Tomasec P, Aicheler R, Loewendorf A, Nemcovicova I, Wang EC, et al. Human cytomegalovirus glycoprotein UL141 targets the TRAIL death receptors to thwart host innate antiviral defenses. Cell Host Microbe. 2013 Mar 13;13(3):324–35. doi: 10.1016/j.chom.2013.02.003 23498957

39. Eberle F, Dubreuil P, Mattei MG, Devilard E, Lopez M. The human PRR2 gene, related to the human poliovirus receptor gene (PVR), is the true homolog of the murine MPH gene. Gene. 1995 Jul 4;159(2):267–72. 7622062

40. Tenney DJ, Colberg-Poley AM. Human cytomegalovirus UL36-38 and US3 immediate-early genes: temporally regulated expression of nuclear, cytoplasmic, and polysome-associated transcripts during infection. J Virol. 1991 Dec;65(12):6724–34. 1658371

41. Nemcovicova I, Zajonc DM. The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding. Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):851–62. doi: 10.1107/S1399004713033750 24598754

42. Nemcovicova I, Benedict CA, Zajonc DM. Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions. PLoS Pathog. 2013 Mar;9(3):e1003224. doi: 10.1371/journal.ppat.1003224 23555243

43. Warren AP, Owens CN, Borysiewicz LK, Patel K. Down-regulation of integrin alpha 1/beta 1 expression and association with cell rounding in human cytomegalovirus-infected fibroblasts. The Journal of general virology. 1994 Dec;75 (Pt 12):3319–25. 7996126

44. Ho MK, Springer TA. Biosynthesis and assembly of the alpha and beta subunits of Mac-1, a macrophage glycoprotein associated with complement receptor function. J Biol Chem. 1983 Mar 10;258(5):2766–9. 6338004

45. Tiwari S, Askari JA, Humphries MJ, Bulleid NJ. Divalent cations regulate the folding and activation status of integrins during their intracellular trafficking. J Cell Sci. 2011 May 15;124(Pt 10):1672–80. doi: 10.1242/jcs.084483 21511727

46. Kishimoto TK, Hollander N, Roberts TM, Anderson DC, Springer TA. Heterogeneous mutations in the beta subunit common to the LFA-1, Mac-1, and p150,95 glycoproteins cause leukocyte adhesion deficiency. Cell. 1987 Jul 17;50(2):193–202. 3594570

47. Barczyk M, Carracedo S, Gullberg D. Integrins. Cell Tissue Res. 2010 Jan;339(1):269–80. doi: 10.1007/s00441-009-0834-6 19693543

48. Price AA, Cumberbatch M, Kimber I, Ager A. Alpha 6 integrins are required for Langerhans cell migration from the epidermis. J Exp Med. 1997 Nov 17;186(10):1725–35. 9362532

49. Staquet MJ, Levarlet B, Dezutter-Dambuyant C, Schmitt D. Human epidermal Langerhans cells express beta 1 integrins that mediate their adhesion to laminin and fibronectin. J Invest Dermatol. 1992 Nov;99(5):12S–4S. 1431200

50. D'Amico G, Bianchi G, Bernasconi S, Bersani L, Piemonti L, Sozzani S, et al. Adhesion, transendothelial migration, and reverse transmigration of in vitro cultured dendritic cells. Blood. 1998 Jul 1;92(1):207–14. 9639518

51. Stuve O, Gold R, Chan A, Mix E, Zettl U, Kieseier BC. alpha4-Integrin antagonism with natalizumab: effects and adverse effects. J Neurol. 2008 Dec;255 Suppl 6 : 58–65. doi: 10.1007/s00415-008-6011-0 19300961

52. del Pilar Martin M, Cravens PD, Winger R, Frohman EM, Racke MK, Eagar TN, et al. Decrease in the numbers of dendritic cells and CD4+ T cells in cerebral perivascular spaces due to natalizumab. Arch Neurol. 2008 Dec;65(12):1596–603. doi: 10.1001/archneur.65.12.noc80051 18852339

53. Stanton RJ, Prod'homme V, Purbhoo MA, Moore M, Aicheler RJ, Heinzmann M, et al. HCMV pUL135 remodels the actin cytoskeleton to impair immune recognition of infected cells. Cell Host Microbe. 2014 Aug 13;16(2):201–14. doi: 10.1016/j.chom.2014.07.005 25121749

54. Robbiani DF, Finch RA, Jager D, Muller WA, Sartorelli AC, Randolph GJ. The leukotriene C(4) transporter MRP1 regulates CCL19 (MIP-3beta, ELC)-dependent mobilization of dendritic cells to lymph nodes. Cell. 2000 Nov 22;103(5):757–68. 11114332

55. Yang JT, Rayburn H, Hynes RO. Cell adhesion events mediated by alpha 4 integrins are essential in placental and cardiac development. Development. 1995 Feb;121(2):549–60. 7539359

56. Fisher S, Genbacev O, Maidji E, Pereira L. Human cytomegalovirus infection of placental cytotrophoblasts in vitro and in utero: implications for transmission and pathogenesis. J Virol. 2000 Aug;74(15):6808–20. 10888620

57. Esmon NL, Owen WG, Esmon CT. Isolation of a membrane-bound cofactor for thrombin-catalyzed activation of protein C. J Biol Chem. 1982 Jan 25;257(2):859–64. 6895633

58. Bachem A, Guttler S, Hartung E, Ebstein F, Schaefer M, Tannert A, et al. Superior antigen cross-presentation and XCR1 expression define human CD11c+CD141+ cells as homologues of mouse CD8+ dendritic cells. J Exp Med. 2010 Jun 7;207(6):1273–81. doi: 10.1084/jem.20100348 20479115

59. Jongbloed SL, Kassianos AJ, McDonald KJ, Clark GJ, Ju X, Angel CE, et al. Human CD141+ (BDCA-3)+ dendritic cells (DCs) represent a unique myeloid DC subset that cross-presents necrotic cell antigens. J Exp Med. 2010 Jun 7;207(6):1247–60. doi: 10.1084/jem.20092140 20479116

60. Ma CY, Shi GY, Shi CS, Kao YC, Lin SW, Wu HL. Monocytic thrombomodulin triggers LPS -⁠ and gram-negative bacteria-induced inflammatory response. J Immunol. 2012 Jun 15;188(12):6328–37. doi: 10.4049/jimmunol.1102266 22573811

61. Dolan A, Cunningham C, Hector RD, Hassan-Walker AF, Lee L, Addison C, et al. Genetic content of wild-type human cytomegalovirus. The Journal of general virology. 2004 May;85(Pt 5):1301–12. 15105547

62. Stanton RJ, Baluchova K, Dargan DJ, Cunningham C, Sheehy O, Seirafian S, et al. Reconstruction of the complete human cytomegalovirus genome in a BAC reveals RL13 to be a potent inhibitor of replication. J Clin Invest. 2010 Sep;120(9):3191–208. doi: 10.1172/JCI42955 20679731

63. Timms RT, Duncan LM, Tchasovnikarova IA, Antrobus R, Smith DL, Dougan G, et al. Haploid genetic screens identify an essential role for PLP2 in the downregulation of novel plasma membrane targets by viral E3 ubiquitin ligases. PLoS pathogens. 2013 Nov;9(11):e1003772. doi: 10.1371/journal.ppat.1003772 24278019

64. Lesniak D, Xu Y, Deschenes J, Lai R, Thoms J, Murray D, et al. Beta1-integrin circumvents the antiproliferative effects of trastuzumab in human epidermal growth factor receptor-2-positive breast cancer. Cancer research. 2009 Nov 15;69(22):8620–8. doi: 10.1158/0008-5472.CAN-09-1591 19887601

65. Rappsilber J, Mann M, Ishihama Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc. 2007;2(8):1896–906. 17703201

66. Cox J, Matic I, Hilger M, Nagaraj N, Selbach M, Olsen JV, et al. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc. 2009;4(5):698–705. doi: 10.1038/nprot.2009.36 19373234

67. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res. 2011 Apr 1;10(4):1794–805. doi: 10.1021/pr101065j 21254760

68. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008 Dec;26(12):1367–72. doi: 10.1038/nbt.1511 19029910