The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions
Viruses are fully dependent on the cellular translation machinery, and develop diverse mechanisms to co-opt it for their own benefit. However, fundamental questions such as: what is the effect that infection has on the spectrum of host mRNAs that are being translated, and whether, and to what extent, a virus possesses mechanisms to commandeer the translation machinery are still hard to address. Here we show that by simultaneously examining the changes in transcription and translation along Human cytomegalovirus (HCMV) infection, we can uncover extensive transcriptional regulation, but also diverse and dynamic translational control. We were also able to show that, at late time points in infection, translation of viral mRNAs is higher than that of cellular mRNAs. Lastly, we take advantage of our measurements of translation (protein synthesis rate) and integrate these with mass spectrometry measurements (protein abundance). This integration allowed us to unbiasedly reveal dozens of cellular proteins that are being degraded during HCMV infection. Since targeted degradation indicates a strong biological importance, this approach should be applicable for discovering central host functions during viral infection. Our work provides a framework for studying the contribution of transcription, translation and degradation during infection with any virus.
Vyšlo v časopise:
The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions. PLoS Pathog 11(11): e32767. doi:10.1371/journal.ppat.1005288
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1005288
Souhrn
Viruses are fully dependent on the cellular translation machinery, and develop diverse mechanisms to co-opt it for their own benefit. However, fundamental questions such as: what is the effect that infection has on the spectrum of host mRNAs that are being translated, and whether, and to what extent, a virus possesses mechanisms to commandeer the translation machinery are still hard to address. Here we show that by simultaneously examining the changes in transcription and translation along Human cytomegalovirus (HCMV) infection, we can uncover extensive transcriptional regulation, but also diverse and dynamic translational control. We were also able to show that, at late time points in infection, translation of viral mRNAs is higher than that of cellular mRNAs. Lastly, we take advantage of our measurements of translation (protein synthesis rate) and integrate these with mass spectrometry measurements (protein abundance). This integration allowed us to unbiasedly reveal dozens of cellular proteins that are being degraded during HCMV infection. Since targeted degradation indicates a strong biological importance, this approach should be applicable for discovering central host functions during viral infection. Our work provides a framework for studying the contribution of transcription, translation and degradation during infection with any virus.
Zdroje
1. Davison AJ, Dolan A, Akter P, Addison C, Dargan DJ, Alcendor DJ, et al. The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome. J Gen Virol. 2003/01/21 ed. 2003;84: 17–28. 12533697
2. Murphy E, Rigoutsos I, Shibuya T, Shenk TE. Reevaluation of human cytomegalovirus coding potential. Proc Natl Acad Sci U S A. 2003/11/01 ed. 2003;100: 13585–13590. doi: 10.1073/pnas.1735466100 1735466100 [pii] 14593199
3. Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, et al. Decoding human cytomegalovirus. Science (80-). 2012/11/28 ed. 2012;338: 1088–1093. doi: 10.1126/science.1227919
4. Zhu H, Cong JP, Shenk T. Use of differential display analysis to assess the effect of human cytomegalovirus infection on the accumulation of cellular RNAs: induction of interferon-responsive RNAs. Proc Natl Acad Sci U S A. 1998/02/12 ed. 1997;94: 13985–13990. 9391139
5. Zhu H, Cong JP, Mamtora G, Gingeras T, Shenk T. Cellular gene expression altered by human cytomegalovirus: global monitoring with oligonucleotide arrays. Proc Natl Acad Sci U S A. 1998/11/25 ed. 1998;95: 14470–14475. 9826724
6. Kenzelmann M, Muhlemann K. Transcriptome analysis of fibroblast cells immediate-early after human cytomegalovirus infection. J Mol Biol. 2000/12/22 ed. 2000;304: 741–751. doi: 10.1006/jmbi.2000.4271 11124023
7. Browne EP, Wing B, Coleman D, Shenk T. Altered cellular mRNA levels in human cytomegalovirus-infected fibroblasts: viral block to the accumulation of antiviral mRNAs. J Virol. 2001/11/17 ed. 2001;75: 12319–12330. 11711622
8. Simmen KA, Singh J, Luukkonen BG, Lopper M, Bittner A, Miller NE, et al. Global modulation of cellular transcription by human cytomegalovirus is initiated by viral glycoprotein B. Proc Natl Acad Sci U S A. 2001/06/08 ed. 2001;98: 7140–7145. doi: 10.1073/pnas.121177598 11390970
9. Hertel L, Mocarski ES. Global analysis of host cell gene expression late during cytomegalovirus infection reveals extensive dysregulation of cell cycle gene expression and induction of Pseudomitosis independent of US28 function. J Virol. 2004/10/14 ed. 2004;78: 11988–12011. 15479839
10. Challacombe JF, Rechtsteiner A, Gottardo R, Rocha LM, Browne EP, Shenk T, et al. Evaluation of the host transcriptional response to human cytomegalovirus infection. Physiol Genomics. 2004;18: 51–62. doi: 10.1152/physiolgenomics.00155.2003 15069167
11. Song YJ, Stinski MF. Effect of the human cytomegalovirus IE86 protein on expression of E2F-responsive genes: a DNA microarray analysis. Proc Natl Acad Sci U S A. 2002/02/28 ed. 2002;99: 2836–2841. doi: 10.1073/pnas.052010099 11867723
12. 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. 2014/06/07 ed. 2014;157: 1460–1472. doi: 10.1016/j.cell.2014.04.028 24906157
13. Tanaka S, Furukawa T, Plotkin SA. Human cytomegalovirus stimulates host cell RNA synthesis. J Virol. 1975;15: 297–304. 163357
14. Stinski MF. Synthesis of proteins and glycoproteins in cells infected with human cytomegalovirus. J Virol. 1977/09/01 ed. 1977;23: 751–767. 197270
15. Walsh D, Perez C, Notary J, Mohr I. Regulation of the translation initiation factor eIF4F by multiple mechanisms in human cytomegalovirus-infected cells. J Virol. 2005/06/16 ed. 2005;79: 8057–8064. 15956551
16. Ziehr B, Lenarcic E, Vincent HA, Cecil C, Garcia B, Shenk T, et al. Human cytomegalovirus TRS1 protein associates with the 7-methylguanosine mRNA cap and facilitates translation. Proteomics. 2015; doi: 10.1002/pmic.201400616
17. McKinney C, Zavadil J, Bianco C, Shiflett L, Brown S, Mohr I. Global reprogramming of the cellular translational landscape facilitates cytomegalovirus replication. Cell Rep. 2014/01/01 ed. 2014;6: 9–17. doi: 10.1016/j.celrep.2013.11.045 24373965
18. Sullivan R, Fassolitis AC, Larkin EP, Read RB, Peeler JT. Inactivation of thirty viruses by gamma radiation. Appl Microbiol. 1971;22: 61–5. 4999976
19. Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJS, Jackson SE, et al. Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes. Cell Reports. 2014.
20. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4: 44–57. doi: 10.1038/nprot.2008.211 19131956
21. Xiaofei E, Kowalik TF. The DNA damage response induced by infection with human cytomegalovirus and other viruses. Viruses. 2014;6: 2155–85. doi: 10.3390/v6052155 24859341
22. Sanchez V, Spector DH. Subversion of cell cycle regulatory pathways. Curr Top Microbiol Immunol. 2008;325: 243–62. 18637510
23. Gudleski-O’Regan N, Greco TM, Cristea IM, Shenk T. Increased expression of LDL receptor-related protein 1 during human cytomegalovirus infection reduces virion cholesterol and infectivity. Cell Host Microbe. 2012/07/24 ed. 2012;12: 86–96. doi: 10.1016/j.chom.2012.05.012 22817990
24. Jarskaja OO, Medzhidova AA, Fedorova NE, Kusch AA, Zatsepina O V. Immunocytochemical reorganization of the nucleolus in human embryo fibroblasts infected with cytomegalovirus in vitro. Dokl Biol Sci. 387: 589–92. 12577646
25. Tran K, Mahr JA, Spector DH. Proteasome subunits relocalize during human cytomegalovirus infection, and proteasome activity is necessary for efficient viral gene transcription. J Virol. 2010;84: 3079–93. doi: 10.1128/JVI.02236-09 20042513
26. Karttunen H, Savas JN, McKinney C, Chen Y-H, Yates JR, Hukkanen V, et al. Co-opting the Fanconi anemia genomic stability pathway enables herpesvirus DNA synthesis and productive growth. Mol Cell. 2014;55: 111–22. doi: 10.1016/j.molcel.2014.05.020 24954902
27. Mohni KN, Mastrocola AS, Bai P, Weller SK, Heinen CD. DNA mismatch repair proteins are required for efficient herpes simplex virus 1 replication. J Virol. 2011;85: 12241–53. doi: 10.1128/JVI.05487-11 21957315
28. E X, Pickering MT, Debatis M, Castillo J, Lagadinos A, Wang S, et al. An E2F1-mediated DNA damage response contributes to the replication of human cytomegalovirus. PLoS Pathog. 2011;7: e1001342. doi: 10.1371/journal.ppat.1001342 21589897
29. Love KR, Catic A, Schlieker C, Ploegh HL. Mechanisms, biology and inhibitors of deubiquitinating enzymes. Nat Chem Biol. Nature Publishing Group; 2007;3: 697–705.
30. Kim ET, Oh SE, Lee Y-O, Gibson W, Ahn J-H. Cleavage specificity of the UL48 deubiquitinating protease activity of human cytomegalovirus and the growth of an active-site mutant virus in cultured cells. J Virol. 2009;83: 12046–56. doi: 10.1128/JVI.00411-09 19759126
31. Lee J, Koh K, Kim Y-E, Ahn J-H, Kim S. Upregulation of Nrf2 expression by human cytomegalovirus infection protects host cells from oxidative stress. J Gen Virol. 2013;94: 1658–68. doi: 10.1099/vir.0.052142-0 23580430
32. Kolodkin-Gal D, Zamir G, Edden Y, Pikarsky E, Pikarsky A, Haim H, et al. Herpes simplex virus type 1 preferentially targets human colon carcinoma: role of extracellular matrix. J Virol. 2008;82: 999–1010. doi: 10.1128/JVI.01769-07 17977977
33. Esteso G, Luzón E, Sarmiento E, Gómez-Caro R, Steinle A, Murphy G, et al. Altered microRNA expression after infection with human cytomegalovirus leads to TIMP3 downregulation and increased shedding of metalloprotease substrates, including MICA. J Immunol. 2014;193: 1344–52. doi: 10.4049/jimmunol.1303441 24973455
34. Angelova M, Zwezdaryk K, Ferris M, Shan B, Morris CA, Sullivan DE. Human cytomegalovirus infection dysregulates the canonical Wnt/beta-catenin signaling pathway. PLoS Pathog. 2012/10/17 ed. 2012;8: e1002959. doi: 10.1371/journal.ppat.1002959 23071438
35. Lee M, Kim B, Kim VN. Emerging Roles of RNA Modification: m6A and U-Tail. Cell. 2014;158: 980–987. doi: 10.1016/j.cell.2014.08.005 25171402
36. Iadevaia V, Caldarola S, Tino E, Amaldi F, Loreni F. All translation elongation factors and the e, f, and h subunits of translation initiation factor 3 are encoded by 5’-terminal oligopyrimidine (TOP) mRNAs. RNA. 2008;14: 1730–6. doi: 10.1261/rna.1037108 18658124
37. Meyuhas O. Synthesis of the translational apparatus is regulated at the translational level. Eur J Biochem. 2000;267: 6321–30. 11029573
38. Thoreen CC, Chantranupong L, Keys HR, Wang T, Gray NS, Sabatini DM. A unifying model for mTORC1-mediated regulation of mRNA translation. Nature. 2012;485: 109–13. doi: 10.1038/nature11083 22552098
39. Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature. 2012;485: 55–61. doi: 10.1038/nature10912 22367541
40. Stumpf CR, Moreno M V, Olshen AB, Taylor BS, Ruggero D. The translational landscape of the mammalian cell cycle. Mol Cell. 2013;52: 574–82. doi: 10.1016/j.molcel.2013.09.018 24120665
41. Han K, Jaimovich A, Dey G, Ruggero D, Meyuhas O, Sonenberg N, et al. Parallel measurement of dynamic changes in translation rates in single cells. Nat Methods. 2014;11: 86–93. doi: 10.1038/nmeth.2729 24213167
42. Tanenbaum ME, Stern-Ginossar N, Weissman JS, Vale RD. Regulation of mRNA translation during mitosis. Elife. 2015;4. doi: 10.7554/eLife.07957
43. Powers C, DeFilippis V, Malouli D, Früh K. Cytomegalovirus immune evasion. Curr Top Microbiol Immunol. 2008;325: 333–59. 18637515
44. 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;384: 432–8. 8945469
45. 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;84: 769–79. 8625414
46. Tomasec P, Wang ECY, Davison AJ, Vojtesek B, Armstrong M, Griffin C, et al. Downregulation of natural killer cell-activating ligand CD155 by human cytomegalovirus UL141. Nat Immunol. 2005;6: 181–8. 15640804
47. Hsu J-L, van den Boomen DJH, Tomasec P, Weekes MP, Antrobus R, Stanton RJ, et al. Plasma Membrane Profiling Defines an Expanded Class of Cell Surface Proteins Selectively Targeted for Degradation by HCMV US2 in Cooperation with UL141. PLoS Pathog. 2015;11: e1004811. doi: 10.1371/journal.ppat.1004811 25875600
48. Le VT, Trilling M, Hengel H. The cytomegaloviral protein pUL138 acts as potentiator of tumor necrosis factor (TNF) receptor 1 surface density to enhance ULb’-encoded modulation of TNF-alpha signaling. J Virol. 2011/10/07 ed. 2011;85: 13260–13270. doi: 10.1128/JVI.06005-11 21976655
49. Seidel E, Le VTK, Bar-On Y, Tsukerman P, Enk J, Yamin R, et al. Dynamic Co-evolution of Host and Pathogen: HCMV Downregulates the Prevalent Allele MICA*008 to Escape Elimination by NK Cells. Cell Rep. 2015; doi: 10.1016/j.celrep.2015.01.029
50. 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;287: 1031. 10669413
51. Schofield A V., Bernard O. Rho-associated coiled-coil kinase (ROCK) signaling and disease. Crit Rev Biochem Mol Biol. 2013;48: 301–316. doi: 10.3109/10409238.2013.786671 23601011
52. Ducut Sigala JL, Bottero V, Young DB, Shevchenko A, Mercurio F, Verma IM. Activation of transcription factor NF-kappaB requires ELKS, an IkappaB kinase regulatory subunit. Science. 2004;304: 1963–7. 15218148
53. Calderwood SK. Cdc37 as a Co-chaperone to Hsp90. Subcell Biochem. 2015;78: 103–12. doi: 10.1007/978-3-319-11731-7_5 25487018
54. Jaehning JA. The Paf1 complex: platform or player in RNA polymerase II transcription? Biochim Biophys Acta. 2010;1799: 379–88. doi: 10.1016/j.bbagrm.2010.01.001 20060942
55. 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;16: 201–14. doi: 10.1016/j.chom.2014.07.005 25121749
56. Challacombe JF, Rechtsteiner A, Gottardo R, Rocha LM, Browne EP, Shenk T, et al. Evaluation of the host transcriptional response to human cytomegalovirus infection. Physiol Genomics. 2004/04/08 ed. 2004;18: 51–62. doi: 10.1152/physiolgenomics.00155.2003 15069167
57. Cooper GM. Peroxisomes. Sinauer Associates; 2000.
58. Moorman NJ, Cristea IM, Terhune SS, Rout MP, Chait BT, Shenk T. Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex. Cell Host Microbe. 2008/04/15 ed. 2008;3: 253–262. S1931-3128(08)00087-5 [pii] doi: 10.1016/j.chom.2008.03.002 18407068
59. Malcherek G, Mayr L, Roda-Navarro P, Rhodes D, Miller N, Trowsdale J. The B7 Homolog Butyrophilin BTN2A1 Is a Novel Ligand for DC-SIGN. J Immunol. American Association of Immunologists; 2007;179: 3804–3811. doi: 10.4049/jimmunol.179.6.3804
60. Stipp CS, Kolesnikova T V, Hemler ME. EWI-2 is a major CD9 and CD81 partner and member of a novel Ig protein subfamily. J Biol Chem. 2001;276: 40545–54. doi: 10.1074/jbc.M107338200 11504738
61. Gordón-Alonso M, Sala-Valdés M, Rocha-Perugini V, Pérez-Hernández D, López-Martín S, Ursa A, et al. EWI-2 association with α-actinin regulates T cell immune synapses and HIV viral infection. J Immunol. American Association of Immunologists; 2012;189: 689–700. doi: 10.4049/jimmunol.1103708
62. Riento K, Ridley AJ. Rocks: multifunctional kinases in cell behaviour. Nat Rev Mol Cell Biol. 2003;4: 446–56. 12778124
63. Jones NL, Lewis JC, Kilpatrick BA. Cytoskeletal disruption during human cytomegalovirus infection of human lung fibroblasts. Eur J Cell Biol. 1986;41: 304–12. 3019700
64. Stanton RJ, McSharry BP, Rickards CR, Wang EC, Tomasec P, Wilkinson GW. Cytomegalovirus destruction of focal adhesions revealed in a high-throughput Western blot analysis of cellular protein expression. J Virol. 2007/05/25 ed. 2007;81: 7860–7872. doi: 10.1128/JVI.02247-06 17522202
65. Wu Z-H, Wong ET, Shi Y, Niu J, Chen Z, Miyamoto S, et al. ATM- and NEMO-dependent ELKS ubiquitination coordinates TAK1-mediated IKK activation in response to genotoxic stress. Mol Cell. 2010;40: 75–86. doi: 10.1016/j.molcel.2010.09.010 20932476
66. E X, Pickering MT, Debatis M, Castillo J, Lagadinos A, Wang S, et al. An E2F1-mediated DNA damage response contributes to the replication of human cytomegalovirus. PLoS Pathog. 2011/05/19 ed. 2011;7: e1001342. doi: 10.1371/journal.ppat.1001342 21589897
67. Le VTK, Trilling M, Hengel H. The Cytomegaloviral Protein pUL138 Acts as Potentiator of Tumor Necrosis Factor (TNF) Receptor 1 Surface Density To Enhance ULb’-Encoded Modulation of TNF- Signaling. J Virol. 2011;85: 13260–13270. doi: 10.1128/JVI.06005-11 21976655
68. Rölle A, Pollmann J, Ewen E-M, Le VTK, Halenius A, Hengel H, et al. IL-12-producing monocytes and HLA-E control HCMV-driven NKG2C+ NK cell expansion. J Clin Invest. 2014;124: 5305–16. doi: 10.1172/JCI77440 25384219
69. Darling AJ, Boose JA, Spaltro J. Virus Assay Methods: Accuracy and Validation. Biologicals. 1998;26: 105–110. doi: 10.1006/biol.1998.0134 9811514
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
2015 Číslo 11
- Očkování proti virové hemoragické horečce Ebola experimentální vakcínou rVSVDG-ZEBOV-GP
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Koronavirus hýbe světem: Víte jak se chránit a jak postupovat v případě podezření?
Najčítanejšie v tomto čísle
- Dengue Virus Non-structural Protein 1 Modulates Infectious Particle Production via Interaction with the Structural Proteins
- On the Discovery of TOR As the Target of Rapamycin
- Parasite Glycobiology: A Bittersweet Symphony
- Lactate Dehydrogenase Is Associated with the Parasitophorous Vacuole Membrane and Is a Potential Target for Developing Therapeutics