HIV Rev response element
The HIV-1 Rev response element (RRE) is a highly structured, ~350 nucleotide RNA segment present in the Env coding region of unspliced and partially spliced viral mRNAs. In the presence of the HIV-1 accessory protein Rev, HIV-1 mRNAs that contain the RRE can be exported from the nucleus to the cytoplasm for downstream events such as translation and virion packaging.[1][2]
RRE and HIV-1 biology
Early phase
The HIV-1 genome contains a single promoter and uses multiple reading frames and alternative splicing to encode 15 proteins from a single pre-mRNA species.[3] Transcription from an integrated HIV-1 provirus generates a single 9 kilobase (kb) pre-mRNA containing multiple splice sites and nuclear retention signals. In the early phase of the viral life cycle, this pre-RNA is completely spliced to RRE-free, 2 kb messages. These smaller messages are then transported from the nucleus to the cytoplasm via standard mRNA nuclear export pathways [4] (see Figure). One of these small, 2kb messages encodes the HIV-1 Rev protein which is imported into the nucleus via its nuclear localization sequence. This phase of the virus life cycle is both Rev and RRE independent.[2]
Late phase
The late phase of the viral life cycle is characterized by the expression of viral proteins that are encoded on the long, unspliced (9kb) or partially spliced (4 kb) messages containing the RRE. Because of their retention and splicing signals, these intron-containing RNAs are initially retained in the nucleus for splicing/degradation. However, after a sufficient level of Rev has been produced by the 2 kb messages, these longer messages can be exported to the cytoplasm via a Rev dependent export pathway. Nuclear export of these RNAs is achieved by a specific, co-operative assembly of multiple Rev molecules on the RRE. Assembly of this Rev-RRE complex is followed by the recruitment of a human protein complex containing the proteins exportin-1 (XPO1/CRM1) and Ran-GTP. Rev recruits this export machinery via a nuclear export sequence (NES) present in Rev. This Rev-RRE-Xpo1/RanGTP complex is then transported to the cytoplasm. In the cytoplasm, these messages are translated to produce all the remaining viral proteins or packaged as genomes for newly budding virions (see Figure).[2]
Secondary Structure and Rev Recognition
The RRE is a highly structured RNA element. Computational predictions, later verified by chemical and enzymatic probing, indicate that RRE contains multiple stem loops and bulges (see Figure). Rev binds to RRE in a sequence specific manner with Rev-RNA recognition mediated by a 17-residue a-helical stretch on Rev, the Arginine-Rich-Motif (ARM).
Stem IIB: a high-affinity binding site
Stem IIB is a site on the RRE which Rev binds with high affinity and specificity. The structure of an isolated stem IIB bound to a peptide corresponding to a Rev-ARM has been solved by NMR.[5] This structure reveals an RNA A-form major groove widened by purine-purine base pairs at the purine-rich bulge to accommodate the a-helical Rev-ARM. Binding is achieved through a combination of base-specific contacts and electrostatic contacts with the phosphate backbone (see figure). More recent studies have identified another region on the RRE, stem IA, that binds Rev in a specific manner, but with a 5-fold weaker affinity than stem IIB.[6]
Co-operative Rev assembly required for RRE function
Although Stems IIB and IA can bind Rev in isolation, a full-length RRE (at least ~250 nt) is required for viral function. Multiple molecules of Rev bind to the full RRE in a specific and co-operative manner through a combination of Rev-RNA and Rev-Rev interactions.[6][7][8] It is believed that IIB acts as an "anchor point", with the Rev molecules bound at secondary sites (such as IA) stabilized by protein-protein interactions with other Rev molecules (in addition to the RNA-protein interactions). Biochemical studies on a 242-nucleotide RRE have established a ratio of 6 Rev monomers to each RRE.[9]
In a sense, the RRE acts as a scaffolding platform onto which a specific and co-operative complex of Revs (and eventually cellular export machinery) assembles. This cooperativity that is dictated by RRE structure and sequence is required for the formation of a high affinity, export-competent complex.[10] Current models of Rev assembly on the RRE suggest an initial Rev nucleation event at stem IIB followed by progressive addition of Rev molecules to form the full complex.[7][8][11][12]
Rev-RRE Complexes recruit additional partners
After assembly of a Rev-RRE complex, cellular export machinery must be added to guide the RNA through the nuclear pore. Nuclear export of Rev-RRE containing mRNAs is achieved using the human Crm1-RanGTP nuclear export pathway. Rev contains a nuclear export sequence (NES) that binds Crm1,[13][14] and Crm1 guides the entire complex out of the nucleus.
Recent crystal structures of Rev,[15][16] the Rev-ARM/Stem IIB structure and the information on Rev-RRE stoichiometry have led to the proposal of a jelly-fish model for a functionally active complex. In this model, The RRE provides a structural scaffold to assemble a Rev hexamer, and this assembly forms the head of the jelly-fish. The NESs from the 6 Rev monomers form the jelly-fish "tentacles" that could interact with the host Crm1-RanGTP proteins.[15] This entire "jellyfish" would then be exported to the cytoplasm (see Figure).
Tertiary structure
Images of the tertiary structure of RRE (and the Rev-RRE complex) have been captured using atomic force microscopy.[17] These images show a globular "head" with a long stalk extending from it and are in accordance with 3D predictions from computer models, as well as electron microscope (EM) images of assembled Rev-RRE complexes.[15]
Rev-RRE as a Drug Target
As the export of RRE-containing RNAs is essential for HIV replication, the association of RRE and Rev is an attractive therapeutic target.[18] Various RNA cleavage methods and small molecule screens[19] have been implemented in an effort to design antiviral drugs to treat HIV infection.[18][20] Rev and RRE are particularly attractive drug targets as both elements exist in reading frames that code other proteins (Tat and Env for Rev, Env for RRE), theoretically restricting potential escape mutations. However, to date there are no clinically approved therapies that target Rev-RRE.
Relationship to Other Viruses
All complex retroviruses face the problem of exporting unspliced and partially spliced mRNAs. Some use systems similar to Rev/RRE; these include HIV-2 and SIV (Simian Immunodeficiency Virus) which use their own Rev-RRE systems, some betaretroviruses, which use a Rem/RmRE system, and all deltaretroviruses which use a Rex/RxRRE systems.[21][22]
Many simple retroviruses, most notably Mason–Pfizer monkey virus (MPMV), do not encode a Rev-like protein, but instead have evolved a cis-acting RNA element, the constitutive transport element (CTE), that directly binds to components of the host mRNA export machinery. The MPMV CTE is ~220 nucleotides and consists of two identical binding sites for the cellular export protein Tap. Tap directly binds the viral RNA and exports it to the cytoplasm.[23][24]
See also
References
- ↑ Cullen, Bryan R (2003). "Nuclear mRNA export: Insights from virology". Trends in Biochemical Sciences 28 (8): 419–24. doi:10.1016/S0968-0004(03)00142-7. PMID 12932730.
- 1 2 3 Pollard, Victoria W.; Malim, Michael H. (1998). "The Hiv-1 Rev Protein". Annual Review of Microbiology 52: 491–532. doi:10.1146/annurev.micro.52.1.491. PMID 9891806.
- ↑ Frankel, Alan D.; Young, John A. T. (1998). "HIV-1: Fifteen Proteins and an RNA". Annual Review of Biochemistry 67: 1–25. doi:10.1146/annurev.biochem.67.1.1. PMID 9759480.
- ↑ Cullen, Bryan R. (2005). "Human immunodeficiency virus: Nuclear RNA export unwound". Nature 433 (7021): 26–7. doi:10.1038/433026a. PMID 15635396.
- ↑ Battiste, J. L.; Mao, H.; Rao, N. S.; Tan, R.; Muhandiram, D. R.; Kay, L. E.; Frankel, A. D.; Williamson, J. R. (1996). "Alpha Helix-RNA Major Groove Recognition in an HIV-1 Rev Peptide-RRE RNA Complex". Science 273 (5281): 1547–51. doi:10.1126/science.273.5281.1547. PMID 8703216.
- 1 2 Daugherty, Matthew D.; D'orso, Iván; Frankel, Alan D. (2008). "A Solution to Limited Genomic Capacity: Using Adaptable Binding Surfaces to Assemble the Functional HIV Rev Oligomer on RNA". Molecular Cell 31 (6): 824–34. doi:10.1016/j.molcel.2008.07.016. PMC 2651398. PMID 18922466.
- 1 2 Jain, Chaitanya; Belasco, Joel G (2001). "Structural Model for the Cooperative Assembly of HIV-1 Rev Multimers on the RRE as Deduced from Analysis of Assembly-Defective Mutants". Molecular Cell 7 (3): 603–14. doi:10.1016/S1097-2765(01)00207-6. PMID 11463385.
- 1 2 Mann, D; Mikaélian, I; Zemmel, RW; Green, SM; Lowe, AD; Kimura, T; Singh, M; Butler, PJ; et al. (1994). "A Molecular Rheostat Co-operative Rev Binding to Stem I of the Rev-response Element Modulates Human Immunodeficiency Virus Type-1 Late Gene Expression". Journal of Molecular Biology 241 (2): 193–207. doi:10.1006/jmbi.1994.1488. PMID 8057359.
- ↑ Daugherty, M. D.; Booth, D. S.; Jayaraman, B.; Cheng, Y.; Frankel, A. D. (2010). "HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes". Proceedings of the National Academy of Sciences 107 (28): 12481–6. doi:10.1073/pnas.1007022107. PMC 2906596. PMID 20616058.
- ↑ Daugherty, Matthew D.; D'orso, Iván; Frankel, Alan D. (2008). "A Solution to Limited Genomic Capacity: Using Adaptable Binding Surfaces to Assemble the Functional HIV Rev Oligomer on RNA". Molecular Cell 31 (6): 824–34. doi:10.1016/j.molcel.2008.07.016. PMC 2651398. PMID 18922466.
- ↑ Zemmel, R; Kelley, AC; Karn, J; Butler, PJ (1996). "Flexible Regions of RNA Structure Facilitate Co-operative Rev Assembly on the Rev-response Element". Journal of Molecular Biology 258 (5): 763–77. doi:10.1006/jmbi.1996.0285. PMID 8637008.
- ↑ Pond, S. J. K.; Ridgeway, W. K.; Robertson, R.; Wang, J.; Millar, D. P. (2009). "HIV-1 Rev protein assembles on viral RNA one molecule at a time". Proceedings of the National Academy of Sciences 106 (5): 1404–8. doi:10.1073/pnas.0807388106. PMC 2635779. PMID 19164515.
- ↑ Fischer, U; Huber, J; Boelens, WC; Mattaj, IW; Lührmann, R (1995). "The HIV-1 Rev Activation Domain is a nuclear export signal that accesses an export pathway used by specific cellular RNAs". Cell 82 (3): 475–83. doi:10.1016/0092-8674(95)90436-0. PMID 7543368.
- ↑ Fornerod, Maarten; Ohno, Mutsuhito; Yoshida, Minoru; Mattaj, Iain W. (1997). "CRM1 Is an Export Receptor for Leucine-Rich Nuclear Export Signals". Cell 90 (6): 1051–60. doi:10.1016/S0092-8674(00)80371-2. PMID 9323133.
- 1 2 3 Daugherty, Matthew D; Liu, Bella; Frankel, Alan D (2010). "Structural basis for cooperative RNA binding and export complex assembly by HIV Rev". Nature Structural & Molecular Biology 17 (11): 1337–42. doi:10.1038/nsmb.1902. PMC 2988976. PMID 20953181.
- ↑ Dimattia, M. A.; Watts, N. R.; Stahl, S. J.; Rader, C.; Wingfield, P. T.; Stuart, D. I.; Steven, A. C.; Grimes, J. M. (2010). "Implications of the HIV-1 Rev dimer structure at 3.2 A resolution for multimeric binding to the Rev response element". Proceedings of the National Academy of Sciences 107 (13): 5810–4. doi:10.1073/pnas.0914946107. PMC 2851902. PMID 20231488.
- ↑ Pallesen, Jesper; Dong, Mingdong; Besenbacher, Flemming; Kjems, JøRgen (2009). "Structure of the HIV-1 Rev response element alone and in complex with regulator of virion (rev) studied by atomic force microscopy". FEBS Journal 276 (15): 4223–32. doi:10.1111/j.1742-4658.2009.07130.x. PMID 19583776.
- 1 2 Sullenger, Bruce A.; Gilboa, Eli (2002). "Emerging clinical applications of RNA". Nature 418 (6894): 252–8. doi:10.1038/418252a. PMID 12110902.
- ↑ Shuck-Lee, D.; Chen, F. F.; Willard, R.; Raman, S.; Ptak, R.; Hammarskjold, M.-L.; Rekosh, D. (2008). "Heterocyclic Compounds That Inhibit Rev-RRE Function and Human Immunodeficiency Virus Type 1 Replication". Antimicrobial Agents and Chemotherapy 52 (9): 3169–79. doi:10.1128/AAC.00274-08. PMC 2533482. PMID 18625767.
- ↑ Jin, Yan; Cowan, J. A. (2006). "Targeted Cleavage of HIV Rev Response Element RNA by Metallopeptide Complexes". Journal of the American Chemical Society 128 (2): 410–1. doi:10.1021/ja055272m. PMID 16402818.
- ↑ Bodem, J.; Schied, T.; Gabriel, R.; Rammling, M.; Rethwilm, A. (2010). "Foamy Virus Nuclear RNA Export Is Distinct from That of Other Retroviruses". Journal of Virology 85 (5): 2333–41. doi:10.1128/JVI.01518-10. PMC 3067772. PMID 21159877.
- ↑ Ahmed, Y F; Hanly, S M; Malim, M H; Cullen, B R; Greene, W C (1990). "Structure-function analyses of the HTLV-I Rex and HIV-1 Rev RNA response elements: insights into the mechanism of Rex and Rev action". Genes & Development 4 (6): 1014–22. doi:10.1101/gad.4.6.1014.
- ↑ Bray, M.; Prasad, S.; Dubay, J. W.; Hunter, E.; Jeang, K. T.; Rekosh, D.; Hammarskjold, M. L. (1994). "A Small Element from the Mason-Pfizer Monkey Virus Genome Makes Human Immunodeficiency Virus Type 1 Expression and Replication Rev-Independent". Proceedings of the National Academy of Sciences 91 (4): 1256–60. doi:10.1073/pnas.91.4.1256.
- ↑ Braun, I. C.; Rohrbach, E; Schmitt, C; Izaurralde, E (1999). "TAP binds to the constitutive transport element (CTE) through a novel RNA-binding motif that is sufficient to promote CTE-dependent RNA export from the nucleus". The EMBO Journal 18 (7): 1953–65. doi:10.1093/emboj/18.7.1953. PMC 1171280. PMID 10202158.
Further reading
- ↑ Daugherty, Matthew D; Liu, Bella; Frankel, Alan D (2010). "Structural basis for cooperative RNA binding and export complex assembly by HIV Rev". Nature Structural & Molecular Biology 17 (11): 1337–42. doi:10.1038/nsmb.1902. PMC 2988976. PMID 20953181.
- ↑ Daugherty, M. D.; Booth, D. S.; Jayaraman, B.; Cheng, Y.; Frankel, A. D. (2010). "HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes". Proceedings of the National Academy of Sciences 107 (28): 12481–6. doi:10.1073/pnas.1007022107. PMC 2906596. PMID 20616058.
- ↑ Dimattia, M. A.; Watts, N. R.; Stahl, S. J.; Rader, C.; Wingfield, P. T.; Stuart, D. I.; Steven, A. C.; Grimes, J. M. (2010). "Implications of the HIV-1 Rev dimer structure at 3.2 a resolution for multimeric binding to the Rev response element". Proceedings of the National Academy of Sciences 107 (13): 5810–4. doi:10.1073/pnas.0914946107. PMC 2851902. PMID 20231488.
- ↑ Legiewicz, M.; Badorrek, C. S.; Turner, K. B.; Fabris, D.; Hamm, T. E.; Rekosh, D.; Hammarskjold, M.-L.; Le Grice, S. F. J. (2008). "Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element". Proceedings of the National Academy of Sciences 105 (38): 14365–70. doi:10.1073/pnas.0804461105. PMC 2567145. PMID 18776047.
- ↑ Srinivasakumar, Narasimhachar (2008). "Substitution of the Rev-response element in an HIV-1-based gene delivery system with that of SIVmac239 allows efficient delivery of Rev M10 into T-lymphocytes". AIDS Research and Therapy 5: 11. doi:10.1186/1742-6405-5-11. PMC 2438438. PMID 18534033.
- ↑ Sugaya, Maki; Nishino, Norikazu; Katoh, Akira; Harada, Kazuo (2008). "Amino acid requirement for the high affinity binding of a selected arginine-rich peptide with the HIV Rev-response element RNA". Journal of Peptide Science 14 (8): 924–35. doi:10.1002/psc.1027. PMID 18351707.
- ↑ Moehle, Kerstin; Athanassiou, Zafiria; Patora, Krystyna; Davidson, Amy; Varani, Gabriele; Robinson, John A. (2007). "Design of β-Hairpin Peptidomimetics That Inhibit Binding of α-Helical HIV-1 Rev Protein to the Rev Response Element RNA". Angewandte Chemie International Edition 46 (47): 9101–4. doi:10.1002/anie.200702801.
- ↑ Prater, Chrissy E.; Saleh, Anthony D.; Wear, Maggie P.; Miller, Paul S. (2007). "Chimeric RNase H-competent oligonucleotides directed to the HIV-1 Rev response element". Bioorganic & Medicinal Chemistry 15 (16): 5386–95. doi:10.1016/j.bmc.2007.05.066. PMC 1987364. PMID 17566743.
- ↑ Phuphuakrat, Angsana; Auewarakul, Prasert (2005). "Functional Variability of Rev Response Element in HIV-1 Primary Isolates". Virus Genes 30 (1): 23–9. doi:10.1007/s11262-004-4578-9. PMID 15744559.
- ↑ Phuphuakrat, Angsana; Paris, Robert M.; Nittayaphan, Sorachai; Louisirirotchanakul, Suda; Auewarakul, Prasert (2005). "Functional variation of HIV-1 Rev response element in a longitudinally studied cohort". Journal of Medical Virology 75 (3): 367–73. doi:10.1002/jmv.20279. PMID 15648073.
- ↑ Luedtke, Nathan W.; Liu, Qi; Tor, Yitzhak (2003). "RNA−Ligand Interactions: Affinity and Specificity of Aminoglycoside Dimers and Acridine Conjugates to the HIV-1 Rev Response Element†". Biochemistry 42 (39): 11391–403. doi:10.1021/bi034766y. PMID 14516190.
- ↑ Phuphuakrat, Angsana; Auewarakul, Prasert (2003). "Heterogeneity of HIV-1 Rev Response Element". AIDS Research and Human Retroviruses 19 (7): 569–74. doi:10.1089/088922203322230932. PMID 12908934.
- ↑ Chapman, Richard L.; Stanley, Thomas B.; Hazen, Richard; Garvey, Edward P. (2002). "Small molecule modulators of HIV Rev/Rev response element interaction identified by random screening". Antiviral Research 54 (3): 149–62. doi:10.1016/S0166-3542(01)00222-4. PMID 12062388.
- ↑ Nishizono, Naozumi; Nair, Vasu (2000). "Synthesis of Biomimetic Analogs of Neomycin B: Potential Inhibitors of the HIV RNA Rev Response Element". Nucleosides, Nucleotides and Nucleic Acids 19: 283–95. doi:10.1080/15257770008033010.
- ↑ Van Ryk, D. I.; Venkatesan, S (1999). "Real-time Kinetics of HIV-1 Rev-Rev Response Element Interactions. DEFINITION OF MINIMAL BINDING SITES ON RNA AND PROTEIN AND STOICHIOMETRIC ANALYSIS". Journal of Biological Chemistry 274 (25): 17452–63. doi:10.1074/jbc.274.25.17452. PMID 10364175.
- ↑ Powell, D. M.; Amaral, M. C.; Wu, J. Y.; Maniatis, T.; Greene, W. C. (1997). "HIV Rev-dependent binding of SF2/ASF to the Rev response element: Possible role in Rev-mediated inhibition of HIV RNA splicing". Proceedings of the National Academy of Sciences 94 (3): 973–8. doi:10.1073/pnas.94.3.973. PMC 19624. PMID 9023367.
- ↑ Yamada, O; Kraus, G; Luznik, L; Yu, M; Wong-Staal, F (1996). "A chimeric human immunodeficiency virus type 1 (HIV-1) minimal Rev response element-ribozyme molecule exhibits dual antiviral function and inhibits cell-cell transmission of HIV-1". Journal of Virology 70 (3): 1596–601. PMC 189982. PMID 8627679.
- ↑ Dandekar, T; Koch, G (1996). "DNA and mRNA sequence of the immune protective DNA ligase I gene match the rev response element of HIV". DNA sequence 6 (2): 119–21. doi:10.3109/10425179609010198. PMID 8907308.
- ↑ Williamson, JR; Battiste, JL; Mao, H; Frankel, AD (1995). "Interaction of HIV Rev peptides with the Rev response element RNA". Nucleic acids symposium series (33): 46–8. PMID 8643394.
- ↑ Bevec, Dorian; Volc-Platzer, Beatrix; Zimmermann, Klaus; Dobrovnik, Marika; Hauber, Joachim; Veres, Gabor; Böhnlein, Ernst (1994). "Constitutive Expression of ChimericNeo-Rev Response Element Transcripts Suppresses HIV-1 Replication in Human CD4+T Lymphocytes". Human Gene Therapy 5 (2): 193–201. doi:10.1089/hum.1994.5.2-193. PMID 8186299.
- ↑ Cohli, H; Fan, B; Joshi, RL; Ramezani, A; Li, X; Joshi, S (1994). "Inhibition of HIV-1 multiplication in a human CD4+ lymphocytic cell line expressing antisense and sense RNA molecules containing HIV-1 packaging signal and Rev response element(s)". Antisense research and development 4 (1): 19–26. PMID 7914762.
- ↑ Kawamura, Meiko; Katahira, Jun; Fukasawa, Masashi; Sakuragi, Jun-Ichi; Ishikawa, Koh-Ichi; Nakai, Masuyo; Mingle, Julius A.A.; Osei-Kwasi, Mubarak; et al. (1992). "Isolation and characterization of a highly divergent HIV-2[GH-2]: Generation of an infectious molecular clone and functional analysis of its rev-responsive element in response to primate retrovirus transactivators (rev and rex)". Virology 188 (2): 850–3. doi:10.1016/0042-6822(92)90540-6. PMID 1585652.
- ↑ Zimmermann, Klaus; Weber, Sabine; Dobrovnik, Marika; Hauber, Joachim; Böhnlein, Ernst (1992). "Expression of Chimeric Neo-Rev Response Element Sequences Interferes with Rev-Dependent HIV-1 Gag Expression". Human Gene Therapy 3 (2): 155–61. doi:10.1089/hum.1992.3.2-155. PMID 1391035.
- ↑ Vaishnav, YN; Vaishnav, M; Wong-Staal, F (1991). "Identification and characterization of a nuclear factor that specifically binds to the Rev response element (RRE) of human immunodeficiency virus type 1 (HIV-1)". The New biologist 3 (2): 142–50. PMID 2065010.
- ↑ Heaphy, Shaun; Dingwall, Colin; Ernberg, Ingemar; Gait, Michaet J.; Green, Sheila M.; Kern, Jonathan; Lowe, Anthony D.; Singh, Mohinder; Skinner, Michael A. (1990). "HIV-1 regulator of virion expression (Rev) protein binds to an RNA stem-loop structure located within the Rev response element region". Cell 60 (4): 685–93. doi:10.1016/0092-8674(90)90671-Z. PMID 1689218.