期刊论文详细信息
Cell & Bioscience
Replication competent HIV-1 viruses that express intragenomic microRNA reveal discrete RNA-interference mechanisms that affect viral replication
Kuan-Teh Jeang1  Laurent Houzet1  Zachary Klase1 
[1] Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda MD, 20892, USA
关键词: miR211;    miR326;    viral replication;    RNA interference;    HIV-1;    miRNA;   
Others  :  793751
DOI  :  10.1186/2045-3701-1-38
 received in 2011-11-09, accepted in 2011-11-23,  发布年份 2011
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【 摘 要 】

Background

It remains unclear whether retroviruses can encode and express an intragenomic microRNA (miRNA). Some have suggested that processing by the Drosha and Dicer enzymes might preclude the viability of a replicating retroviral RNA genome that contains a cis-embedded miRNA. To date, while many studies have shown that lentiviral vectors containing miRNAs can transduce mammalian cells and express the inserted miRNA efficiently, no study has examined the impact on the replication of a lentivirus such as HIV-1 after the deliberate intragenomic insertion of a bona fide miRNA.

Results

We have constructed several HIV-1 molecular clones, each containing a discrete cellular miRNA positioned in Nef. These retroviral genomes express the inserted miRNA and are generally replication competent in T-cells. The inserted intragenomic miRNA was observed to elicit two different consequences for HIV-1 replication. First, the expression of miRNAs with predicted target sequences in the HIV-1 genome was found to reduce viral replication. Second, in one case, where an inserted miRNA was unusually well-processed by Drosha, this processing event inhibited viral replication.

Conclusion

This is the first study to examine in detail the replication competence of HIV-1 genomes that express cis-embedded miRNAs. The results indicate that a replication competent retroviral genome is not precluded from encoding and expressing a viral miRNA.

【 授权许可】

   
2011 Klase et al; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Agrawal N, Dasaradhi PV, Mohmmed A, Malhotra P, Bhatnagar RK, Mukherjee SK: RNA interference: biology, mechanism, and applications. Microbiol Mol Biol Rev 2003, 67:657-685.
  • [2]Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
  • [3]Hannon GJ: RNA interference. Nature 2002, 418:244-251.
  • [4]Cenik ES, Zamore PD: Argonaute proteins. Curr Biol 21:R446-449.
  • [5]Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R: TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 2005, 436:740-744.
  • [6]Chi YH, Semmes OJ, Jeang KT: A proteomic study of TAR-RNA binding protein (TRBP)-associated factors. Cell Biosci 1:9.
  • [7]Ghildiyal M, Zamore PD: Small silencing RNAs: an expanding universe. Nat Rev Genet 2009, 10:94-108.
  • [8]Haase AD, Jaskiewicz L, Zhang H, Laine S, Sack R, Gatignol A, Filipowicz W: TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep 2005, 6:961-967.
  • [9]miRBase: the microRNA database [http://www.mirbase.org/index.shtml] webcite
  • [10]Bernstein E, Caudy AA, Hammond SM, Hannon GJ: Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001, 409:363-366.
  • [11]Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R: The Microprocessor complex mediates the genesis of microRNAs. Nature 2004, 432:235-240.
  • [12]Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN: The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425:415-419.
  • [13]Sigova A, Rhind N, Zamore PD: A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in Schizosaccharomyces pombe. Genes Dev 2004, 18:2359-2367.
  • [14]Sontheimer EJ: Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol 2005, 6:127-138.
  • [15]Easow G, Teleman AA, Cohen SM: Isolation of microRNA targets by miRNP immunopurification. Rna 2007, 13:1198-1204.
  • [16]Lytle JR, Yario TA, Steitz JA: Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR. Proc Natl Acad Sci USA 2007, 104:9667-9672.
  • [17]Orom UA, Nielsen FC, Lund AH: MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 2008, 30:460-471.
  • [18]Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, et al.: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129-141.
  • [19]Rigoutsos I: New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites. Cancer Res 2009, 69:3245-3248.
  • [20]Olsen PH, Ambros V: The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol 1999, 216:671-680.
  • [21]Doench JG, Sharp PA: Specificity of microRNA target selection in translational repression. Genes Dev 2004, 18:504-511.
  • [22]Nicolas FE, Lopez-Martinez AF: MicroRNAs in human diseases. Recent Pat DNA Gene Seq 4:142-154.
  • [23]Sayed D, Abdellatif M: MicroRNAs in development and disease. Physiol Rev 91:827-887.
  • [24]Yeung ML, Jeang KT: MicroRNAs and Cancer Therapeutics. Pharm Res 3000.
  • [25]Llave C: Virus-derived small interfering RNAs at the core of plant-virus interactions. Trends Plant Sci 15:701-707.
  • [26]Pantaleo V: Plant RNA silencing in viral defence. Adv Exp Med Biol 722:39-58.
  • [27]Qu F: Antiviral role of plant-encoded RNA-dependent RNA polymerases revisited with deep sequencing of small interfering RNAs of virus origin. Mol Plant Microbe Interact 23:1248-1252.
  • [28]Grundhoff A, Sullivan CS: Virus-encoded microRNAs. Virology 411:325-343.
  • [29]Lei X, Bai Z, Ye F, Huang Y, Gao SJ: Regulation of herpesvirus lifecycle by viral microRNAs. Virulence 1:433-435.
  • [30]Dhuruvasan K, Sivasubramanian G, Pellett PE: Roles of host and viral microRNAs in human cytomegalovirus biology. Virus Res 157:180-192.
  • [31]Plaisance-Bonstaff K, Renne R: Viral miRNAs. Methods Mol Biol 721:43-66.
  • [32]Boss IW, Renne R: Viral miRNAs: tools for immune evasion. Curr Opin Microbiol 13:540-545.
  • [33]Bivalkar-Mehla S, Vakharia J, Mehla R, Abreha M, Kanwar JR, Tikoo A, Chauhan A: Viral RNA silencing suppressors (RSS): novel strategy of viruses to ablate the host RNA interference (RNAi) defense system. Virus Res 155:1-9.
  • [34]de Vries W, Berkhout B: RNAi suppressors encoded by pathogenic human viruses. Int J Biochem Cell Biol 2008, 40:2007-2012.
  • [35]Ding SW: RNA-based antiviral immunity. Nat Rev Immunol 10:632-644.
  • [36]Grassmann R, Jeang KT: The roles of microRNAs in mammalian virus infection. Biochim Biophys Acta 2008, 1779:706-711.
  • [37]Haasnoot J, Berkhout B: RNAi and cellular miRNAs in infections by mammalian viruses. Methods Mol Biol 721:23-41.
  • [38]Haasnoot J, Westerhout EM, Berkhout B: RNA interference against viruses: strike and counterstrike. Nat Biotechnol 2007, 25:1435-1443.
  • [39]Houzet L, Jeang KT: MicroRNAs and human retroviruses. Biochim Biophys Acta 3000.
  • [40]Song L, Gao S, Jiang W, Chen S, Liu Y, Zhou L, Huang W: Silencing suppressors: viral weapons for countering host cell defenses. Protein Cell 2:273-281.
  • [41]Yang N, Kazazian HH J: L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol 2006, 13:763-771.
  • [42]Hakim ST, Alsayari M, McLean DC, Saleem S, Addanki KC, Aggarwal M, Mahalingam K, Bagasra O: A large number of the human microRNAs target lentiviruses, retroviruses, and endogenous retroviruses. Biochem Biophys Res Commun 2008, 369:357-362.
  • [43]Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H: Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 2006, 20:1732-1743.
  • [44]Carmell MA, Girard A, van de Kant HJ, Bourc'his D, Bestor TH, de Rooij DG, Hannon GJ: MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell 2007, 12:503-514.
  • [45]Calabrese JM, Seila AC, Yeo GW, Sharp PA: RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci USA 2007, 104:18097-18102.
  • [46]De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O'Carroll D: The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature
  • [47]Huang J, Wang F, Argyris E, Chen K, Liang Z, Tian H, Huang W, Squires K, Verlinghieri G, Zhang H: Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med 2007, 13:1241-1247.
  • [48]Wang X, Ye L, Hou W, Zhou Y, Wang YJ, Metzger DS, Ho WZ: Cellular microRNA expression correlates with susceptibility of monocytes/macrophages to HIV-1 infection. Blood 2009, 113:671-674.
  • [49]Ahluwalia JK, Khan SZ, Soni K, Rawat P, Gupta A, Hariharan M, Scaria V, Lalwani M, Pillai B, Mitra D, Brahmachari SK: Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication. Retrovirology 2008, 5:117. BioMed Central Full Text
  • [50]Hariharan M, Scaria V, Pillai B, Brahmachari SK: Targets for human encoded microRNAs in HIV genes. Biochem Biophys Res Commun 2005, 337:1214-1218.
  • [51]Nathans R, Chu CY, Serquina AK, Lu CC, Cao H, Rana TM: Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol Cell 2009, 34:696-709.
  • [52]Triboulet R, Mari B, Lin YL, Chable-Bessia C, Bennasser Y, Lebrigand K, Cardinaud B, Maurin T, Barbry P, Baillat V, et al.: Suppression of microRNA-silencing pathway by HIV-1 during virus replication. Science 2007, 315:1579-1582.
  • [53]Sung TL, Rice AP: miR-198 inhibits HIV-1 gene expression and replication in monocytes and its mechanism of action appears to involve repression of cyclin T1. PLoS Pathog 2009, 5:e1000263.
  • [54]Chable-Bessia C, Meziane O, Latreille D, Triboulet R, Zamborlini A, Wagschal A, Jacquet JM, Reynes J, Levy Y, Saib A, et al.: Suppression of HIV-1 replication by microRNA effectors. Retrovirology 2009, 6:26. BioMed Central Full Text
  • [55]Matskevich AA, Moelling K: Dicer is involved in protection against influenza A virus infection. J Gen Virol 2007, 88:2627-2635.
  • [56]Otsuka M, Jing Q, Georgel P, New L, Chen J, Mols J, Kang YJ, Jiang Z, Du X, Cook R, et al.: Hypersusceptibility to vesicular stomatitis virus infection in Dicer1-deficient mice is due to impaired miR24 and miR93 expression. Immunity 2007, 27:123-134.
  • [57]Liu YP, Vink MA, Westerink JT, Ramirez de Arellano E, Konstantinova P, Ter Brake O, Berkhout B: Titers of lentiviral vectors encoding shRNAs and miRNAs are reduced by different mechanisms that require distinct repair strategies. Rna 2010, 16:1328-1339.
  • [58]Poluri A, Sutton RE: Titers of HIV-based vectors encoding shRNAs are reduced by a dicer-dependent mechanism. Mol Ther 2008, 16:378-386.
  • [59]ter Brake O, Berkhout B: Lentiviral vectors that carry anti-HIV shRNAs: problems and solutions. J Gene Med 2007, 9:743-750.
  • [60]Westerhout EM, ter Brake O, Berkhout B: The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference. Retrovirology 2006, 3:57. BioMed Central Full Text
  • [61]Klase Z, Kale P, Winograd R, Gupta MV, Heydarian M, Berro R, McCaffrey T, Kashanchi F: HIV-1 TAR element is processed by Dicer to yield a viral micro-RNA involved in chromatin remodeling of the viral LTR. BMC Mol Biol 2007, 8:63. BioMed Central Full Text
  • [62]Klase Z, Winograd R, Davis J, Carpio L, Hildreth R, Heydarian M, Fu S, McCaffrey T, Meiri E, Ayash-Rashkovsky M, et al.: HIV-1 TAR miRNA protects against apoptosis by altering cellular gene expression. Retrovirology 2009, 6:18. BioMed Central Full Text
  • [63]Ouellet DL, Plante I, Landry P, Barat C, Janelle ME, Flamand L, Tremblay MJ, Provost P: Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res 2008, 36:2353-2365.
  • [64]Yeung ML, Bennasser Y, Watashi K, Le SY, Houzet L, Jeang KT: Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid. Nucleic Acids Res 2009, 37:6575-6586.
  • [65]Purzycka KJ, Adamiak RW: The HIV-2 TAR RNA domain as a potential source of viral-encoded miRNA. A reconnaissance study. Nucleic Acids Symp Ser (Oxf) 2008, 511-512.
  • [66]Smith SM, Markham RB, Jeang KT: Conditional reduction of human immunodeficiency virus type 1 replication by a gain-of-herpes simplex virus 1 thymidine kinase function. Proc Natl Acad Sci USA 1996, 93:7955-7960.
  • [67]Kim S, Ikeuchi K, Byrn R, Groopman J, Baltimore D: Lack of a negative influence on viral growth by the nef gene of human immunodeficiency virus type 1. Proc Natl Acad Sci USA 1989, 86:9544-9548.
  • [68]Bartel DP: MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
  • [69]Miura S, Nozawa M, Nei M: Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species. Genome Biol Evol 3:129-139.
  • [70]Vella MC, Choi EY, Lin SY, Reinert K, Slack FJ: The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. Genes Dev 2004, 18:132-137.
  • [71]Wei X, Decker JM, Liu H, Zhang Z, Arani RB, Kilby JM, Saag MS, Wu X, Shaw GM, Kappes JC: Emergence of resistant human immunodeficiency virus type 1 in patients receiving fusion inhibitor (T-20) monotherapy. Antimicrob Agents Chemother 2002, 46:1896-1905.
  • [72]Martin F, Bangham CR, Ciminale V, Lairmore MD, Murphy EL, Switzer WM, Mahieux R: Conference Highlights of the 15th International Conference on Human Retrovirology: HTLV and Related Retroviruses,4-8 June 2011, Leuven, Gembloux, Belgium. Retrovirology 8:86.
  • [73]Hussain M, Torres S, Schnettler E, Funk A, Grundhoff A, Pijlman GP, Khromykh AA, Asgari S: West Nile virus encodes a microRNA-like small RNA in the 3' untranslated region which up-regulates GATA4 mRNA and facilitates virus replication in mosquito cells. Nucleic Acids Res, in press. PMID: 22080551
  • [74]Griffiths-Jones S: The microRNA Registry. Nucleic Acids Res 2004, 32:D109-111.
  • [75]Kozomara A, Griffiths-Jones S: miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152-157.
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