Cyclin T1-dependent genes in activated CD4+ T and macrophage cell lines appear enriched in HIV-1 co-factors

PLoS ONE

Volumn 3, Issue 9, 2008, Pages

  Yu, Wendong ^a   Ramakrishnan, Rajesh ^a   Wang, Yan ^a   Chiang, Karen ^a   Sung, Tzu Ling ^a   Rice, Andrew P ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CASEIN KINASE I; CASEIN KINASE I GAMMA 1; CYCLIN DEPENDENT KINASE; CYCLIN DEPENDENT KINASE 11; CYCLIN DEPENDENT KINASE 9; CYCLIN T1; SHORT HAIRPIN RNA; STEROL REGULATORY ELEMENT BINDING PROTEIN 1; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR PITX2; UNCLASSIFIED DRUG; CCNT1 PROTEIN, HUMAN; CDC2L2 PROTEIN, HUMAN; CYCLINE;

ARTICLE; BINDING SITE; CD4+ T LYMPHOCYTE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; GENE FUNCTION; GENE IDENTIFICATION; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; LEUKEMIA CELL LINE; MACROPHAGE; NONHUMAN; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN RNA BINDING; RNA ANALYSIS; RNA TRANSCRIPTION; T LYMPHOCYTE ACTIVATION; VIRUS REPLICATION; CYTOLOGY; DOMINANT GENE; GENE EXPRESSION REGULATION; LYMPHOCYTE ACTIVATION; METABOLISM; MONOCYTE; T LYMPHOCYTE; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

BINDING SITES; CASEIN KINASE I; CD4-POSITIVE T-LYMPHOCYTES; CYCLIN-DEPENDENT KINASES; CYCLINS; GENE EXPRESSION REGULATION, VIRAL; GENES, DOMINANT; HIV-1; HUMANS; JURKAT CELLS; LYMPHOCYTE ACTIVATION; MACROPHAGES; MONOCYTES; T-LYMPHOCYTES; TAT GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS;

EID: 52149093714     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003146     Document Type: Article

References (73)

1. Zack JA, Arrigo SJ, Weitsman SR, Go AS, Haislip A, Chen IS (1990) HIV-1 entry into quiescent primary lymphocytes: molecular analysis reveals a labile, latent viral structure. Cell 61: 213-222.
2. Spina CA, Guatelli JC, Richman DD (1995) Establishment of a stable, inducible form of human immunodeficiency virus type 1 DNA in quiescent CD4 lymphocytes in vitro. J Virol 69: 2977-2988.
3. Rich EA, Chen IS, Zack JA, Leonard ML, O'Brien WA (1992) Increased susceptibility of differentiated mononuclear phagocytes to productive infection with human immunodeficiency virus-1 (HIV-1). J Clin Invest JID -7802877 89: 176-183
4. Bukrinsky MI, Stanwick TL, Dempsey MP, Stevenson M (1991) Quiescent T lymphocytes as an inducible virus reservoir in HIV-1 infection. Science 254: 423-427.
5. Stevenson M, Stanwick TL, Dempsey MP, Lamonica CA (1990) HIV-1 replication is controlled at the level of T cell activation and proviral integration. EMBO J 9: 1551-1560.
6. Bukrinsky MI, Haggerty S, Dempsey MP, Sharova N, Adzhubel A, et al. (1993) A nuclear localization signal within HIV-1 matrix protein that governs infection of non-dividing cells. Nature 365: 666-669.
7. Heinzinger NK, Bukinsky MI, Haggerty SA, Ragland AM, Kewalramani V, et al. (1994) The Vpr protein of human immunodeficiency virus type 1 influences nuclear localization of viral nucleic acids in nondividing host cells. Proc Natl Acad Sci U S A 91: 7311-7315.
8. Lassen KG, Ramyar KX, Bailey JR, Zhou Y, Siliciano RF (2006) Nuclear retention of multiply spliced HIV-1 RNA in resting CD4+ T cells. PLoS Pathog 2: e68.
9. Pierson T, McArthur J, Siliciano RF (2000) Reservoirs for HIV-1: mechanisms for viral persistence in the presence of antiviral immune responses and antiretroviral therapy. Annu Rev Immunol 18: 665-708.:665-708.
10. Rice AP, Herrmann CH (2003) Regulation of TAK/P-TEFb in CD4+ T lymphocytes and macrophages. Curr HIV Res 1: 395-404.
11. Barboric M, Peterlin BM (2005) A new paradigm in eukaryotic biology: HIV Tat and the control of transcriptional elongation. PLoS Biol 3: e76.
12. Karn J (1999) Tackling Tat. J Mol Biol 293: 235-254.
13. Garber ME, Jones KA (1999) HIV-1 Tat: coping with negative elongation factors. Curr Opin Immunol 11: 460-465.
14. Peterlin BM, Price DH (2006) Controlling the elongation phase of transcription with P-TEFb. Mol Cell 23: 297-305.
15. Zhou Q, Yik JH (2006) The Yin and Yang of P-TEFb regulation: implications for human immunodeficiency virus gene expression and global control of cell growth and differentiation. Microbiol Mol Biol Rev 70: 646-659.
16. Chao SH, Price DH (2001) Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J Biol Chem 276: 31793-31799.
17. Lam LT, Pickeral OK, Peng AC, Rosenwald A, Hurt EM, Giltnane JM, et al. (2001) Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol. Genome Biol 2: RESEARCH0041.
18. Shore SM, Byers SA, Maury W, Price DH (2003) Identification of a novel isoform of Cdk9. Gene 307: 175-82.:175-182.
19. Yang Z, Zhu Q, Luo K, Zhou Q (2001) The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 414: 317-322.
20. Nguyen VT, Kiss T, Michels AA, Bensaude O (2001) 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 414: 322-325.
21. Yik JH, Chen R, Nishimura R, Jennings JL, Link AJ, Zhou Q (2003) Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Mol Cell 12: 971-982.
22. Michels AA, Nguyen VT, Fraldi A, Labas V, Edwards M, Bonnet F, Lania L, Bensaude O (2003) MAQ1 and 7SK RNA interact with CDK9/cyclin T complexes in a transcription-dependent manner. Mol Cell Biol 23: 4859-4869.
23. Wei P, Garber ME, Fang SM, Fischer WH, Jones KA (1998) A Novel CDK9-Associated C-type Cyclin Interacts Directly with HIV-1 Tat and Mediates Its High-Affinity, Loop-Specific Binding to TAR RNA. Cell 92: 451-462.
24. Sung TL, Rice AP (2006) Effects of prostratin on Cyclin T1/P-TEFb function and the gene expression profile in primary resting CD4+ T cells. Retrovirology 3: 66.
25. Herrmann CH, Carroll RG, Wei P, Jones KA, Rice AP (1998) Tat-associated kinase, TAK, activity is regulated by distinct mechanisms in peripheral blood lymphocytes and promonocytic cell lines. J Virol 72: 9881-9888.
26. Liou LY, Herrmann CH, Rice AP (2002) Transient induction of cyclin T1 during human macrophage differentiation regulates human immunodeficiency virus type 1 Tat transactivation function. J Virol 76: 10579-10587.
27. Wang Y, Rice AP (2006) Interleukin-10 inhibits HIV-1 LTR-directed gene expression in human macrophages through the induction of cyclin T1 proteolysis. Virology 352: 485-492.
28. Liou LY, Herrmann CH, Rice AP (2004) Human immunodeficiency virus type 1 infection induces cyclin T1 expression in macrophages. J Virol 78: 8114-8119.
29. Liou LY, Haaland RE, Herrmann CH, Rice AP (2006) Cyclin T1 but not cyclin T2a is induced by a post-transcriptional mechanism in PAMP-activated monocyte-derived macrophages. J Leukoc Biol 79: 388-396.
30. Yu W, Wang Y, Shaw CA, Qin XF, Rice AP (2006) Induction of the HIV-1 Tat co-factor cyclin T1 during monocyte differentiation is required for the regulated expression of a large portion of cellular mRNAs. Retrovirology 3: 32.
31. Moriuchi M, Moriuchi H, Turner W, Fauci AS (1998) Exposure to bacterial products renders macrophages highly susceptible to T-tropic HIV-1. J Clin Invest 102: 1540-1550.
32. Gillis S, Watson J (1980) Biochemical and biological characterization of lymphocyte regulatory molecules. V. Identification of an interleukin 2-producing human leukemia T cell line. J Exp Med JID -2985109R 152: 1709-1719.
33. Abraham RT, Weiss A (2004) Jurkat T cells and development of the T-cell receptor signalling paradigm. Nat Rev Immunol 4: 301-308.
34. Ziegler-Heitbrock HW, Thiel E, Futterer A, Herzog V, Wirtz A, et al. (1988) Establishment of a human cell line (Mono Mac 6) with characteristics of mature monocytes. Int J Cancer 41: 456-461.
35. Qin XF, An DS, Chen IS, Baltimore D (2003) Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5. Proc Natl Acad Sci U S A 100: 183-188.
36. Morita E, Sundquist WI (2004) Retrovirus budding. Annu Rev Cell Dev Biol 20: 395-425.
37. Freed EO (2004) HIV-1 and the host cell: an intimate association. Trends Microbiol 12: 170-177.
38. Aerts S, Van Loo P, Thijs G, Mayer H, de Martin R, et al. (2005) TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res 33: W393-W396.
39. Ma XT, Qian MP, Tang HX (2004) Predicting polymerase II core promoters by cooperating transcription factor binding sites in eukaryotic genes. Acta Biochim Biophys Sin.(Shanghai.) 36: 250-258.
40. Bengoechea-Alonso MT, Ericsson J (2007) SREBP in signal transduction: cholesterol metabolism and beyond. Curr Opin Cell Biol 19: 215-222.
41. De Martino MU, Bhattachryya N, Alesci S, Ichijo T, Chrousos GP, et al. (2004) The glucocorticoid receptor and the orphan nuclear receptor chicken ovalbumin upstream promoter-transcription factor II interact with and mutually affect each other's transcriptional activities: implications for intermediary metabolism. Mol Endocrinol 18: 820-833.
42. Barboric M, Zhang F, Besenicar M, Plemenitas A, Peterlin BM (2005) Ubiquitylation of Cdk9 by Skp2 facilitates optimal Tat transactivation. J Virol 79: 11135-11141.
43. Le Gall S, Erdtmann L, Benichou S, Berlioz-Torrent C, Liu L, et al. (1998) Nef interacts with the mu subunit of clathrin adaptor complexes and reveals a cryptic sorting signal in MHC I molecules. Immunity 8: 483-495.
44. Piguet V, Chen YL, Mangasarian A, Foti M, Carpentier JL, et al. (1998) Mechanism of Nef-induced CD4 endocytosis: Nef connects CD4 with the mu chain of adaptor complexes. EMBO J 17: 2472-2481.
45. Bevec D, Jaksche H, Oft M, Wohl T, Himmelspach M, et al. (1996) Inhibition of HIV-1 replication in lymphocytes by mutants of the Rev cofactor eIF-5A. Science 271: 1858-1860.
46. Hauber I, Bevec D, Heukeshoven J, Kratzer F, Horn F, Choidas A, Harrer T, Hauber J (2005) Identification of cellular deoxyhypusine synthase as a novel target for antiretroviral therapy. J Clin Invest 115: 76-85.
47. Komano J, Miyauchi K, Matsuda Z, Yamamoto N (2004) Inhibiting the Arp2/3 complex limits infection of both intracellular mature vaccinia virus and primate lentiviruses. Mol Biol Cell 15: 5197-5207.
48. Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science 319: 921-926.
49. Dufner A, Pownall S, Mak TW (2006) Caspase recruitment domain protein 6 is a microtubule-interacting protein that positively modulates NF-kappaB activation. Proc Natl Acad Sci U S A 103: 988-993.
50. Raposo G, Moore M, Innes D, Leijendekker R, Leigh-Brown A, Benaroch P, Geuze H (2002) Human macrophages accumulate HIV-1 particles in MHC II compartments. Traffic 3: 718-729.
51. Hoque M, Young TM, Lee CG, Serrero G, Mathews MB, Pe'ery T (2003) The growth factor granulin interacts with cyclin T1 and modulates P-TEFb-dependent transcription. Mol Cell Biol 23: 1688-1702.
52. Zamborlini A, Usami Y, Radoshitzky SR, Popova E, Palu G, Gottlinger H (2006) Release of autoinhibition converts ESCRT-III components into potent inhibitors of HIV-1 budding. Proc Natl Acad Sci U S A 103: 19140-19145.
53. Nybakken K, Vokes SA, Lin TY, McMahon AP, Perrimon N (2005) A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nat Genet 37: 1323-1332.
54. Loyer P, Trembley JH, Katona R, Kidd VJ, Lahti JM (2005) Role of CDK/ cyclin complexes in transcription and RNA splicing. Cell Signal 17: 1033-1051.
55. Davidson G, Wu W, Shen J, Bilic J, Fenger U, Stannek P, Glinka A, Niehrs C (2005) Casein kinase 1 gamma couples Wnt receptor activation to cytoplasmic signal transduction. Nature 438: 867-872.
56. Dufner A, Pownall S, Mak TW (2006) Caspase recruitment domain protein 6 is a microtubule-interacting protein that positively modulates NF-kappaB activation. Proc Natl Acad Sci U S A 103: 988-993.
57. Barboric M, Zhang F, Besenicar M, Plemenitas A, Peterlin BM (2005) Ubiquitylation of Cdk9 by Skp2 facilitates optimal Tat transactivation. J Virol 79: 11135-11141.
58. Hoque M, Young TM, Lee CG, Serrero G, Mathews MB, Pe'ery T (2003) The growth factor granulin interacts with cyclin T1 and modulates P-TEFb-dependent transcription. Mol Cell Biol 23: 1688-1702.
59. Hauber I, Bevec D, Heukeshoven J, Kratzer F, Horn F, Choidas A, Harrer T, Hauber J (2005) Identification of cellular deoxyhypusine synthase as a novel target for antiretroviral therapy. J Clin Invest 115: 76-85.
60. Le Gall , Erdtmann L, Benichou S, Berlioz-Torrent C, Liu L, Benarous R, Heard JM, Schwartz O (1998) Nef interacts with the mu subunit of clathrin adaptor complexes and reveals a cryptic sorting signal in MHC I molecules. Immunity 8: 483-495.
61. Piguet V, Chen YL, Mangasarian A, Foti M, Carpentier JL, Trono D (1998) Mechanism of Nef-induced CD4 endocytosis: Nef connects CD4 with the mu chain of adaptor complexes. EMBO J 17: 2472-2481.
62. Zamborlini A, Usami Y, Radoshitzky SR, Popova E, Palu G, Gottlinger H (2006) Release of autoinhibition converts ESCRT-III components into potent inhibitors of HIV-1 budding. Proc Natl Acad Sci U S A 103: 19140-19145.
63. Pereira LA, Bentley K, Peeters A, Churchill MJ, Deacon NJ (2000) A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter. Nucleic Acids Res 28: 663-668.
64. Berkhout B, Jeang KT (1992) Functional roles for the TATA promoter and enhancers in basal and Tat-induced expression of the human immunodeficiency virus type 1 long terminal repeat. J Virol 66: 139-149.
65. Huang LM, Jeang KT (1993) Increased spacing between Sp1 and TATAA renders human immunodeficiency virus type 1 replication defective: implication for Tat function. J Virol 67: 6937-6944.
66. Southgate CD, Green MR (1991) The HIV-1 Tat protein activates transcription from an upstream DNA-binding site: implications for Tat function. Genes Dev 5: 2496-2507.
67. Rittner K, Churcher MJ, Gait MJ, Karn J (1995) The human immunodeficiency virus long terminal repeat includes a specialised initiator element which is required for Tat-responsive transcription. J Mol Biol 248: 562-580.
68. Bengoechea-Alonso MT, Ericsson J (2007) SREBP in signal transduction: cholesterol metabolism and beyond. Curr Opin Cell Biol 19: 215-222.
69. Park JI, Tsai SY, Tsai MJ (2003) Molecular mechanism of chicken ovalbumin upstream promoter-transcription factor (COUP-TF) actions. Keio J Med 52: 174-181.
70. Rice AP, Sutton RS. Targeting protein-protein interactions for HIV therapeutics. Future HIV Therapy 1, 369-385. 9-1-2007.
71. Meanwell NA, Kadow JF (2007) Maraviroc, a chemokine CCR5 receptor antagonist for the treatment of HIV infection and AIDS. Curr Opin Investig. Drugs 8: 669-681.
72. Herrmann CH, Rice AP (1995) Lentivirus Tat proteins specifically associate with a cellular protein kinase, TAK, that hyperphosphorylates the carboxylterminal domain of the large subunit of RNA polymerase II: candidate for a Tat cofactor. J Virol 69: 1612-1620.
73. Yang X, Herrmann CH, Rice AP (1996) The human immunodeficiency virus Tat proteins specifically associate with TAK in vivo and require the carboxyl-terminal domain of RNA polymerase II for function. J Virol 70: 4576-4584.