Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II

English version

Autoři: Ming Li ^aff001; Christopher B. Ball ^aff002; Geoffrey Collins ^aff002; Qiaolin Hu ^aff001; Donal S. Luse ^aff003; David H. Price ^aff002; Jeffery L. Meier ^aff001
Působiště autorů: Departments of Internal Medicine and Epidemiology, University of Iowa and Iowa City Veterans Affairs Health Care System, Iowa City, IA, United States of America ^aff001; Department of Biochemistry, University of Iowa, Iowa City, IA, United States of America ^aff002; Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America ^aff003
Vyšlo v časopise: Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II. PLoS Pathog 16(4): e1008402. doi:10.1371/journal.ppat.1008402
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.ppat.1008402

Souhrn

Herpesvirus late promoters activate gene expression after viral DNA synthesis has begun. Alphaherpesviruses utilize a viral immediate-early protein to do this, whereas beta- and gammaherpesviruses primarily use a 6-member set of viral late-acting transcription factors (LTF) that are drawn to a TATT sequence in the late promoter. The betaherpesvirus, human cytomegalovirus (HCMV), produces three immediate-early 2 protein isoforms, IE2-86, IE2-60, IE2-40, late in infection, but whether they activate late viral promoters is unknown. Here, we quickly degrade the IE2 proteins in late infection using dTag methodology and analyze effects on transcription using customized PRO-Seq and computational methods combined with multiple validation methods. We discover that the IE2 proteins selectively drive RNA Pol II transcription initiation at a subset of viral early-late and late promoters common to different HCMV strains, but do not substantially affect Pol II transcription of the 9,942 expressed host genes. Most of the IE2-activated viral late infection promoters lack the TATT sequence bound by the HCMV UL87-encoded LTF. The HCMV TATT-binding protein is not mechanistically involved in late RNA expression from the IE2-activated TATT-less UL83 (pp65) promoter, as it is for the TATT-containing UL82 (pp71) promoter. While antecedent viral DNA synthesis is necessary for transcription from the late infection viral promoters, continued viral DNA synthesis is unnecessary. We conclude that in late infection the IE2 proteins target a distinct subset of HCMV early-late and late promoters for transcription initiation by RNA Pol II. Commencement of viral DNA replication renders the HCMV genome late promoters susceptible to late-acting viral transcription factors.

Klíčová slova:

Cytomegalovirus infection – DNA replication – DNA transcription – DNA-binding proteins – Human cytomegalovirus – Polymerase chain reaction – Transcription factors – Viral genomics

Zdroje

1. Stinski MF, Thomsen DR, Stenberg RM, Goldstein LC. Organization and expression of the immediate early genes of human cytomegalovirus. J Virol. 1983;46:1–14. 6298447

2. Stenberg RM, Witte PR, Stinski MF. Multiple spliced and unspliced transcripts from human cytomegalovirus immediate-early region 2 and evidence for a common initiation site within immediate-early region 1. J Virol. 1985;56(3):665–75. 2999423

3. Stenberg RM, Depto AS, Fortney J, Nelson JA. Regulated expression of early and late RNAs and proteins from the human cytomegalovirus immediate-early gene region. J Virol. 1989;63(6):2699–708. 2542583

4. Hermiston TW, Malone CL, Witte PR, Stinski MF. Identification and characterization of the human cytomegalovirus immediate-early region 2 gene that stimulates gene expression from an inducible promoter. J Virol. 1987;61(10):3214–21. 3041043

5. Chang C-P, Malone CL, Stinski MF. A human cytomegalovirus early gene has three inducible promoters that are regulated differentially at various times after infection. J Virol. 1989;63:281–90. 2535734

6. Klucher KM, Spector DH. The human cytomegalovirus 2.7-kilobase RNA promoter contains a functional binding site for the adenovirus major late transcription factor. J Virol. 1990;64:4189–98. 2166813

7. Marchini A, Liu H, Zhu H. Human cytomegalovirus with IE-2 deleted fails to express early lytic genes. J Virol. 2001;75:1870–8. doi: 10.1128/JVI.75.4.1870-1878.2001 11160686

8. Anderson KP, Fox MC, Brown-Driver V, Martin MM, Azad RF. Inhibition of human cytomegalovirus immediate-early gene expression by an antisense oligonucleotide complementary to immediate-early RNA. Antimicrob Agents Chemotherap. 1996;40(9):2004–11.

9. Meier JL, Stinski MF. Major immediate-early enhancer and its gene products. In: Reddehase MJ, editor. Cytomegaloviruses: Molecular Biology and Immunology. Norfolk, U. K.: Caister Academic Press; 2006. p. 151–66.

10. Lukac DM, Harel NY, Tanese N, Alwine JC. TAF-like functions of human cytomegalovirus immediate-early proteins. J Virol. 1997;71:7227–39. 9311796

11. Kim ET, Kim YE, Huh YH, Ahn JH. Role of noncovalent SUMO binding by the human cytomegalovirus IE2 transactivator in lytic growth. J Virol. 2010;84(16):8111–23. doi: 10.1128/JVI.00459-10 20519406

12. Huang L, Stinski MF. Binding of cellular repressor protein or the IE2 protein to a cis-acting negative regulatory element upstream of a human cytomegalovirus early promoter. J Virol. 1995;69(12):7612–21. 7494269

13. Arlt H, Lang D, Gebert S, Stamminger T. Identification of binding sites for the 86-kilodalton IE2 protein of human cytomegalovirus within an IE2-responsive viral early promoter. J Virol. 1994;68(7):41117–4125.

14. Klucher KM, Sommer M, Kadonaga JT, Spector DH. In vivo and in vitro analysis of transcriptional activation mediated by the human cytomegalovirus major immediate-early proteins. Mol Cell Biol. 1993;13:1238–50. doi: 10.1128/mcb.13.2.1238 8423789

15. Lee SB, Lee CF, Ou DS, Dulal K, Chang LH, Ma CH, et al. Host-viral effects of chromatin assembly factor 1 interaction with HCMV IE2. Cell Res. 2011;21(8):1230–47. doi: 10.1038/cr.2011.53 21445097

16. Kim JE, Kim YE, Stinski MF, Ahn JH, Song YJ. Human Cytomegalovirus IE2 86 kDa Protein Induces STING Degradation and Inhibits cGAMP-Mediated IFN-β Induction. Front Microbiol. 2018;26(9).

17. Macias MP, Stinski MF. An in vitro system for human cytomegalovirus immediate early 2 protein (IE2)-mediated site-dependent repression of transcription and direct binding of IE2 to the major immediate early promoter. Proc Natl Acad Sci USA. 1993;90:707–11. doi: 10.1073/pnas.90.2.707 8380646

18. Chiou CJ, Zong J, Waheed I, Hayward GS. Identification and mapping of dimerization and DNA-binding domains in the C terminus of the IE2 regulatory protein of human cytomegalovirus. J Virol. 1993;67(10):6201–14. 8396676

19. Pizzorno MC, Hayward GS. The IE2 gene products of human cytomegalovirus specifically down-regulate expression from the major immediate-early promoter through a target sequence located near the cap site. J Virol. 1990;64:6154–65. 2173785

20. Cherrington JM, Khoury EL, Mocarski ES. Human cytomegalovirus ie2 negatively regulates alpha gene expression via a short target sequence near the transcription start site. J Virol. 1991;65(2):887–96. 1846203

21. Liu B, Hermiston TW, Stinski MF. A cis-acting element in the major immediate-early (IE) promoter of human cytomegalovirus is required for negative regulation by IE2. J Virol. 1991;65(2):897–903. 1846204

22. Dremel SE, DeLuca NA. Genome replication affects transcription factor binding mediating the cascade of herpes simplex virus transcription. Proc Natl Acad Sci U S A. 2019;116(9):3734–9. doi: 10.1073/pnas.1818463116 30808759

23. Kim D-B, Zabierowski S, Deluca N. The initiator element in a herpes simplex virus type 1 late-gene promoter enhances activation of ICP4, resulting in abundant late-gene expression. J Virol. 2002;76:1548–58. doi: 10.1128/JVI.76.4.1548-1558.2002 11799149

24. Mavomara-Nazos P, Roizman B. Dilenation of regulatory domains of early (beta) and late (gamma 2) genes by construction of chimeric genes expressed in herpes simplex virus 1 genomes. Proc Natl Acad Sci U S A. 1989;86:4071–5. doi: 10.1073/pnas.86.11.4071 2542962

25. Isomura H, Stinski MF, Murata T, Yamashita Y, Kanda T, Toyokuni S, et al. The human cytomegalovirus gene products essential for late viral gene expression assemble into prereplication complexes before viral DNA replication. J Virol. 2011;85(13):6629–44. doi: 10.1128/JVI.00384-11 21507978

26. Davis ZH, Verschueren E, Jang GM, Kleffman K, Johnson JR, Park J, et al. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell. 2015;57(2):349–60. doi: 10.1016/j.molcel.2014.11.026 25544563

27. Aubry V, Mure F, Mariamé B, Deschamps T, Wyrwicz LS, Manet E, et al. Epstein-Barr virus late gene transcription depends on the assembly of a virus-specific preinitiation complex. J Virol. 2014;88(21):12825–38. doi: 10.1128/JVI.02139-14 25165108

28. Perng YC, Qian Z, Fehr AR, Xuan B, Yu D. The human cytomegalovirus gene UL79 is required for the accumulation of late viral transcripts. J Virol. 2011;885(10):4841–52.

29. Omoto S, Mocarski ES. Transcription of true late (γ2) cytomegalovirus genes requires UL92 function that is conserved among beta- and gammaherpesviruses. J Virol. 2014;88(1):120–30. doi: 10.1128/JVI.02983-13 24131715

30. Omoto S, Mocarski ES. Cytomegalovirus UL91 is essential for transcription of viral true late (γ2) genes. J Virol. 2013;87(15):8651–64. doi: 10.1128/JVI.01052-13 23720731

31. Puchtler E, Stamminger T. An inducible promoter mediates abudant expression from the immediate-early 2 gene region of the human cytomegalovirus at late times after infection. J Virol. 1991;65(11):6301–6. 1656096

32. White EA, Del Rosario CJ, Sanders RL, Spector DH. The IE2 60-kilodalton and 40-kilodalton proteins are dispensable for human cytomegalovirus replication but are required for efficient delayed early and late gene expression and production of infectious virus. J Virol. 2006;81(6):2573–83.

33. Parida M, Nilson KA, Li M, Ball CBHA, Fuchs HA, Lawson CK, et al. Nucleotide resolution comparison of transcription of human cytomegalovirus and host genomes reveals universal use of RNA polymerase II elongation control driven by dissimilar core promoter elements. MBio. 2019;10:1–20. 30755505

34. Plachter B, Britt W, Vornhagen R, Stamminger T, Jahn G. Analysis of proteins encoded by IE regions 1 and 2 of human cytomegalovirus using monoclonal antibodies generated against recombinant antigens. Virology. 1993;193:642–52. doi: 10.1006/viro.1993.1172 7681609

35. Jenkins DE, Martens CL, Mocarski ES. Human cytomegalovirus late protein encoded by ie2: a trans-activator as well as a repressor of gene expression. J Gen Virol 1994;75:2337–48. doi: 10.1099/0022-1317-75-9-2337 8077932

36. Reuter N, Reichel A, Stilp A-C, Scherer M, Stamminger T. SUMOylation of IE2p86 is required for efficient autorepression of the human cytomegalovirus major immediate-early promoter. J Gen Virol. 2018;99:369–78. doi: 10.1099/jgv.0.001021 29458530

37. Sanders RL, Clark CL, Morello C, Spector DH. Development of cell lines that provide tightly controlled temporal translation of the human cytomegalovirus IE2 proteins for complementation and functional analyses of growth-impaired and nonviable IE2 mutant viruses. J Virol. 2008;82:7059–77. doi: 10.1128/JVI.00675-08 18463148

38. White EA, Clark CL, Sanchez V, Spector DH. Small internal deletions in the human cytomegalovirus IE2 gene result in nonviable recombinant viruses with differential defects in viral gene expression. J Virol. 2004;78:1817–30. doi: 10.1128/JVI.78.4.1817-1830.2004 14747546

39. Sanders RL, Spector DA. Human cytomegalovirus IE2 86 and IE2 40 proteins differentially regulate UL84 protein expression posttranscriptionally in the absence of other viral gene products. J Virol. 2010;84:5158–70. doi: 10.1128/JVI.00090-10 20200242

40. Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science. 2013;339(6122):950–3. doi: 10.1126/science.1229386 23430654

41. Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008;322(5909):1845–8. doi: 10.1126/science.1162228 19056941

42. Winter GE, Buckley DL, Paulk J, Roberts JM, Souza A, Dhe-Paganon S, et al. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science. 2015;348:1376–8. doi: 10.1126/science.aab1433 25999370

43. Nabet B, Roberts JM, Buckley DL, Paulk J, Dastjerdi S, Yang A, et al. The dTAG system for immediate and target-specific protein degradation. Nat Chem Biol. 2018;14(5):431–41. doi: 10.1038/s41589-018-0021-8 29581585

44. Nilson KA, Lawson CK, Mullen NJ, Ball CB, Spector BM, Meier JL, et al. Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome. Nucleic Acids Res. 2017;45(19):11088–105. doi: 10.1093/nar/gkx724 28977633

45. Depto AS, Stenberg RM. Regulated expression of the human cytomegalovirus pp65 gene: octomer sequence in the promoter is requierd for activation by viral gene products. J Virol. 1989;63:1232–8. 2536831

46. Ruger B, Klages S, Birgitt W, Albrecht J, Fleckenstein B, Tomlinson P, et al. Primary structure and transcription of the genes coding for the two virion phosphoproteins pp65 and pp7l of human cytomegalovirus. J Virol. 1987;61:446–53. 3027374

47. Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, et al. Decoding human cytomegalovirus. Science. 2012;338:1088–93. doi: 10.1126/science.1227919 23180859

48. 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;157(6):1460–72. doi: 10.1016/j.cell.2014.04.028 24906157

49. He SY, Xu L, Huang ES. Characterization of human cytomegalovirus UL84 early geme and identification of its putative protein product. J Virol. 1992;66:1098–108. 1309892

50. Adam BL, Jervey TY, Kohler CP, Wright GL, Nelson JA, Stenberg RM. The human cytomegalovirus UL98 gene transcription unit overlaps with the pp28 true late gene (UL99) and encode a 58-kilodalton early protein. J Virol. 1995;69:5304–10. 7636973

51. Stinski MF, Petrik DT. Functional roles of the human cytomegalovirus essential IE86 protein. In: Shenk T, Stinski MF, editors. Human Cytomegalovirus Current Topics in Microbiology and Immunology 325. Berlin Heidelberg: Springer-Verlag; 2008. p. 133–52.

52. McKenzie J, Lopez-Giraldez F, Delecluse H-J, Walsh A, El-Guindy A. The Epstein-Barr virus immunoevasins BCRF1 and BPLF1 are expressed by a mechanism independent of the canonical late preinitiation complex. PLoS Pathog. 2016;12(11):e1006008. doi: 10.1371/journal.ppat.1006008 27855219

53. Djavadian R, Hayes M, Johannsen E. CAGE-seq analysis of Epstein-Barr virus lytic gene transcription: 3 kinetic classes from 2 mechanisms. PLoS Pathog. 2018;14(6).

54. Lurain NS, Fox AM, Lichy HM, Bhorade SM, Ware CF, Huang DD, et al. Analysis of the human cytomegalovirus genomic region from UL146 through UL147A reveals sequence hypervariability, genotypic stability, and overlapping transcripts. Virology Journal. 2006;3:4. doi: 10.1186/1743-422X-3-4 16409621

55. Huang L, Stinski MF. Binding of cellular repressor protein or the IE2 protein to a cis-acting negative regulatory element upstream of a human cytomegalovirus early promoter. J Virol. 1995;69(12):7612–21. 7494269

56. Rodems SM, Clark CL, Spector DH. Separate DNA elements containing ATF/CREB and IE86 binding sites differentially regulate the human cytomegalovirus UL112-113 promoter at early and late times in the infection. J Virol. 1998;72:2697–707. 9525587

57. Nandakumar D, Glaunsinger BA. An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kapos’s sarcoma-associated herpesvirus. PLoS Pathog. 2019;15(5):e1007774. doi: 10.1371/journal.ppat.1007774 31095645

58. Du G, Stinski MF. Interaction network of proteins associated with human cytomegalovirus IE2-p86 protein during infection: a proteomic analysis. PLoS One. 2013;8:e81583. doi: 10.1371/journal.pone.0081583 24358118

59. Gibeault RL, Conn KL, Bildersheim MD, Schang LM. An essential viral transcription activator modulates chromatin dynamics. PLoS Pathog. 2016;12:e1005842. doi: 10.1371/journal.ppat.1005842 27575707

60. O” Conner CM, Murphy EA. A myeloid progenitor cell line capable of supporting human cytomegalovirus latency and reactivation, resulting in infectious progeny. J Virol. 2012;86(18):9854–65. doi: 10.1128/JVI.01278-12 22761372

61. Warming S, Costantino N, Court DL, Jenkins NA, Copeland NG. Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Research 2005;30:e36.

62. Meier JL. Reactivation of the human cytomegalovirus major immediate-early regulatory region and viral replication in embryonal NTera2 cells: Role of trichostatin A, retinoic acid, and deletion of the 21-base-pair repeats and modulator. J Virol. 2001;75:1581–93. doi: 10.1128/JVI.75.4.1581-1593.2001 11160656

63. Yuan J, M. L, Torres YR, Galle CS, Meier JL. Differentiation-coupled induction of human cytomegalovirus replication by union of the major enhancer retinoic Acid, cyclic AMP, and NF-κB response elements. J Virol. 2015;89:12284–98. doi: 10.1128/JVI.00965-15 26423948

64. Meier JL, Stinski MF. Effect of a modulator deletion on transcription of the human cytomegalovirus major immediate-early genes in infected undifferentiated and differentiated cells. J Virol. 1997;71:1246–55. 8995648

65. Yuan J, Liu X, Wu AW, McGonagill PW, Keller MJ, Galle CS, et al. Breaking human cytomegalovirus major immediate-early gene silence by vasoactive intestinal peptide stimulation of the protein kinase A-CREB-TORC2 signaling cascade in human pluripotent embryonal NTera2 cells. J Virol. 2009;83:6391–401. doi: 10.1128/JVI.00061-09 19369332

66. Bradley AJ, Lurain NS, Ghazal P, Trivedi U, Cunningham C, Baluchova K, et al. High-throughput sequence analysis of variants of human cytomegalovirus strains Towne and AD169. J Gen Virol. 2009;90:2375–80. doi: 10.1099/vir.0.013250-0 19553388

67. 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. Nat Immunol. 2005;6:181–8. doi: 10.1038/ni1156 15640804

68. Quinalan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2. doi: 10.1093/bioinformatics/btq033 20110278

69. Ball CB, Nilson KA, Price DH. Use of the nuclear walk-on methodology to determine sites of RNA polymerase II initiation and pausing and quantify of nascent RNAs in cells. Methods 2019;S1046–2023(18).

70. Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, et al. The UCSC Genome Browser database: 2019 update Nucleic Acids Res. 2019;47:D853–8. doi: 10.1093/nar/gky1095 30407534

71. Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2014;30(7):1003–5. doi: 10.1093/bioinformatics/btt637 24227676

Článek CD300lf is the primary physiologic receptor of murine norovirus but not human norovirus

Článek Drosophila as a model for the gut microbiome

Článek Genetic interaction analysis comes to the diploid human pathogen Candida albicans

Článek Battling brain-eating amoeba: Enigmas surrounding immunity to Naegleria fowleri

Článek The B-cell inhibitory receptor CD22 is a major factor in host resistance to Streptococcus pneumoniae infection

Článek Non-pathogenic Escherichia coli acquires virulence by mutating a growth-essential LPS transporter

Článek Role for the shelterin protein TRF2 in human herpesvirus 6A/B chromosomal integration

Článek Natural killer cells expanded in vivo or ex vivo with IL-15 overcomes the inherent susceptibility of CAST mice to lethal infection with orthopoxviruses

Článek Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response

Článek vyšel v časopise