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Volumn 20, Issue 5, 2014, Pages 587-593

Highly conserved RNA pseudoknots at the gag-pol junction of HIV-1 suggest a novel mechanism of -1 ribosomal frameshifting

Author keywords

1 ribosomal frameshifting; HIV 1; Recoding; RNA pseudoknot

Indexed keywords

-1 RIBOSOMAL FRAMESHIFTING; HIV-1; RECODING; RNA PSEUDOKNOT;

EID: 84898983118     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.042457.113     Document Type: Article
Times cited : (24)

References (45)
  • 1
    • 21744452846 scopus 로고    scopus 로고
    • The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation
    • DOI 10.1021/bi0502588
    • Abbink TE, Ooms M, Haasnoot PC, Berkhout B. 2005. The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation. Biochemistry 44: 9058-9066. (Pubitemid 40943220)
    • (2005) Biochemistry , vol.44 , Issue.25 , pp. 9058-9066
    • Abbink, T.E.M.1    Ooms, M.2    Haasnoot, P.C.J.3    Berkhout, B.4
  • 2
    • 0025036111 scopus 로고
    • Ribosome gymnastics-degree of difficulty 9.5, style 10.0
    • Atkins JF, Weiss RB, Gesteland RF. 1990. Ribosome gymnastics-degree of difficulty 9.5, style 10.0. Cell 62: 413-423.
    • (1990) Cell , vol.62 , pp. 413-423
    • Atkins, J.F.1    Weiss, R.B.2    Gesteland, R.F.3
  • 3
    • 0037139583 scopus 로고    scopus 로고
    • Recoding: Translational bifurcations in gene expression
    • DOI 10.1016/S0378-1119(02)00423-7, PII S0378111902004237
    • Baranov PV, Gesteland RF, Atkins JF. 2002. Recoding: translational bifurcations in gene expression. Gene 286: 187-201. (Pubitemid 34273875)
    • (2002) Gene , vol.286 , Issue.2 , pp. 187-201
    • Baranov, P.V.1    Gesteland, R.F.2    Atkins, J.F.3
  • 4
    • 0042164371 scopus 로고    scopus 로고
    • The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot
    • DOI 10.1016/S0022-2836(03)00784-8
    • Baril M, Dulude D, Steinberg SV, Brakier-Gingras L. 2003. The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot. J Mol Biol 331: 571-583. (Pubitemid 36937146)
    • (2003) Journal of Molecular Biology , vol.331 , Issue.3 , pp. 571-583
    • Baril, M.1    Dulude, D.2    Steinberg, S.V.3    Brakier-Gingras, L.4
  • 5
    • 0037143642 scopus 로고    scopus 로고
    • A - 1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA
    • DOI 10.1073/pnas.162223099
    • Barry JK, Miller WA. 2002. A -1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA. Proc Natl Acad Sci 99: 11133-11138. (Pubitemid 34920891)
    • (2002) Proceedings of the National Academy of Sciences of the United States of America , vol.99 , Issue.17 , pp. 11133-11138
    • Barry, J.K.1    Miller, W.A.2
  • 7
    • 0842304470 scopus 로고    scopus 로고
    • The Human Immunodeficiency Virus Type 1 Ribosomal Frameshifting Site Is an Invariant Sequence Determinant and an Important Target for Antiviral Therapy
    • DOI 10.1128/JVI.78.4.2082-2087.2004
    • Biswas P, Jiang X, Pacchia AL, Dougherty JP, Peltz SW. 2004. The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy. J Virol 78: 2082-2087. (Pubitemid 38176740)
    • (2004) Journal of Virology , vol.78 , Issue.4 , pp. 2082-2087
    • Biswas, P.1    Jiang, X.2    Pacchia, A.L.3    Dougherty, J.P.4    Peltz, S.W.5
  • 8
    • 0029091681 scopus 로고
    • Ribosomal frameshifting viral RNAs
    • Brierley I. 1995. Ribosomal frameshifting viral RNAs. J Gen Virol 76: 1885-1892.
    • (1995) J Gen Virol , vol.76 , pp. 1885-1892
    • Brierley, I.1
  • 9
    • 34447538279 scopus 로고    scopus 로고
    • Viral RNA pseudoknots: Versatile motifs in gene expression and replication
    • DOI 10.1038/nrmicro1704, PII NRMICRO1704
    • Brierley I, Pennell S, Gilbert RJ. 2007. Viral RNA pseudoknots: versatile motifs in gene expression and replication. Nat Rev Microbiol 5: 598-610. (Pubitemid 47074115)
    • (2007) Nature Reviews Microbiology , vol.5 , Issue.8 , pp. 598-610
    • Brierley, I.1    Pennell, S.2    Gilbert, R.J.C.3
  • 10
    • 84876949005 scopus 로고    scopus 로고
    • Regulation of programmed ribosomal frameshifting by co-translational refolding RNA hairpins
    • Cho CP, Lin SC, Chou MY, Hsu HT, Chang KY. 2013. Regulation of programmed ribosomal frameshifting by co-translational refolding RNA hairpins. PLoS One 8: e62283.
    • (2013) PLoS One , vol.8
    • Cho, C.P.1    Lin, S.C.2    Chou, M.Y.3    Hsu, H.T.4    Chang, K.Y.5
  • 11
    • 0026483177 scopus 로고
    • Structural and functional aspects of RNA pseudoknots
    • Dam E, Pleij K, Draper D. 1992. Structural and functional aspects of RNA pseudoknots. Biochemistry 31: 11665-11676.
    • (1992) Biochemistry , vol.31 , pp. 11665-11676
    • Dam, E.1    Pleij, K.2    Draper, D.3
  • 13
    • 0030819836 scopus 로고    scopus 로고
    • An NMR and mutational study of the pseudoknot within the gene 32 mRNA of bacteriophage T2: Insights into a family of structurally related RNA pseudoknots
    • DOI 10.1093/nar/25.6.1130
    • Du Z, Hoffman D. 1997. An NMR and mutational study of the pseudoknot within the gene 32 mRNA of bacteriophage T2: insights into a family of structurally related RNA pseudoknots. Nucleic Acids Res 25: 1130-1135. (Pubitemid 27303202)
    • (1997) Nucleic Acids Research , vol.25 , Issue.6 , pp. 1130-1135
    • Du, Z.1    Hoffman, D.W.2
  • 14
    • 0029882170 scopus 로고    scopus 로고
    • Structure of the autoregulatory pseudoknot within the gene 32 messenger RNA of bacteriophages T2 and T6: A model for a possible family of structurally related RNA pseudoknots
    • DOI 10.1021/bi9527350
    • Du Z, Giedroc DP, Hoffman DW. 1996. Structure of the autoregulatory pseudoknot within the gene 32 messenger RNA of bacteriophages T2 and T6: a model for a possible family of structurally related RNA pseudoknots. Biochemistry 35: 4187-4198. (Pubitemid 26113477)
    • (1996) Biochemistry , vol.35 , Issue.13 , pp. 4187-4198
    • Du, Z.1    Giedroc, D.P.2    Hoffman, D.W.3
  • 15
    • 0031577308 scopus 로고    scopus 로고
    • Base-pairings within the RNA pseudoknot associated with the simian retrovirus-1 gag-pro frameshift site
    • DOI 10.1006/jmbi.1997.1127
    • Du Z, Holland JA, Hansen MR, Giedroc DP, Hoffman DW. 1997. Basepairings within the RNA pseudoknot associated with the simian retrovirus- 1 gag-pro frameshift site. J Mol Biol 270: 464-470. (Pubitemid 27326684)
    • (1997) Journal of Molecular Biology , vol.270 , Issue.3 , pp. 464-470
    • Du, Z.1    Holland, J.A.2    Hansen, M.R.3    Giedroc, D.P.4    Hoffman, D.W.5
  • 16
    • 0036924931 scopus 로고    scopus 로고
    • Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1
    • DOI 10.1093/nar/gkf657
    • Dulude D, Baril M, Brakier-Gingras L. 2002. Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1. Nucleic Acids Res 30: 5094-5102. (Pubitemid 36033026)
    • (2002) Nucleic Acids Research , vol.30 , Issue.23 , pp. 5094-5102
    • Dulude, D.1    Baril, M.2    Brakier-Gingras, L.3
  • 17
    • 0029870925 scopus 로고    scopus 로고
    • Programmed translational frameshifting
    • Farabaugh PJ. 1996. Programmed translational frameshifting. Microbiol Rev 60: 103-134. (Pubitemid 26087764)
    • (1996) Microbiological Reviews , vol.60 , Issue.1 , pp. 103-134
    • Farabaugh, P.J.1
  • 18
    • 62249145571 scopus 로고    scopus 로고
    • Ribosomal frameshifting: An emerging drug target for HIV
    • Gareiss PC, Miller BL. 2009. Ribosomal frameshifting: an emerging drug target for HIV. Curr Opin Investig Drugs 10: 121-128.
    • (2009) Curr Opin Investig Drugs , vol.10 , pp. 121-128
    • Gareiss, P.C.1    Miller, B.L.2
  • 20
    • 0026667889 scopus 로고
    • Recoding: Reprogrammed genetic decoding
    • Gesteland RF, Weiss RB, Atkins JF. 1992. Recoding: reprogrammed genetic decoding. Science 257: 1640-1641.
    • (1992) Science , vol.257 , pp. 1640-1641
    • Gesteland, R.F.1    Weiss, R.B.2    Atkins, J.F.3
  • 21
    • 0034724565 scopus 로고    scopus 로고
    • Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting
    • Giedroc DP, Theimer CA, Nixon PL. 2000. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol 298: 167-185.
    • (2000) J Mol Biol , vol.298 , pp. 167-185
    • Giedroc, D.P.1    Theimer, C.A.2    Nixon, P.L.3
  • 23
    • 84898987414 scopus 로고    scopus 로고
    • PKscan: A program to identify H-type RNA pseudoknots in any RNA sequence with unlimited length
    • Huang X, Du Z, Cheng J, Cheng Q. 2013. PKscan: a program to identify H-type RNA pseudoknots in any RNA sequence with unlimited length. Bioinformation 9: 440-442.
    • (2013) Bioinformation , vol.9 , pp. 440-442
    • Huang, X.1    Du, Z.2    Cheng, J.3    Cheng, Q.4
  • 24
    • 0023870815 scopus 로고
    • Characterization of ribosomal frameshifting in HIV-1 gag-pol expression
    • DOI 10.1038/331280a0
    • Jacks T, Power MD, Masiarz FR, Luciw PA, Barr PJ, Varmus HE. 1988. Characterization of ribosomal frameshifting in HIV-1 gag-pol expression. Nature 331: 280-283. (Pubitemid 18040598)
    • (1988) Nature , vol.331 , Issue.6153 , pp. 280-283
    • Jacks, T.1    Power, M.D.2    Masiarz, F.R.3    Luciw, P.A.4    Barr, P.J.5    Varmus, H.E.6
  • 25
    • 0035282697 scopus 로고    scopus 로고
    • Comparative mutational analysis of cis-acting RNA signals for translational frameshifting in HIV-1 and HTLV-2
    • Kim YG, Maas S, Rich A. 2001. Comparative mutational analysis of cisacting RNA signals for translational frameshifting in HIV-1 and HTLV-2. Nucleic Acids Res 29: 1125-1131. (Pubitemid 32186198)
    • (2001) Nucleic Acids Research , vol.29 , Issue.5 , pp. 1125-1131
    • Kim, Y.-G.1    Maas, S.2    Rich, A.3
  • 26
    • 80052729501 scopus 로고    scopus 로고
    • Understanding the errors of SHAPE-directed RNA structure modeling
    • Kladwang W, VanLang CC, Cordero P, Das R. 2011. Understanding the errors of SHAPE-directed RNA structure modeling. Biochemistry 50: 8049-8056.
    • (2011) Biochemistry , vol.50 , pp. 8049-8056
    • Kladwang, W.1    Vanlang, C.C.2    Cordero, P.3    Das, R.4
  • 27
    • 77953806388 scopus 로고    scopus 로고
    • Identification of a cellular factor that modulates HIV-1 programmed ribosomal frameshifting
    • Kobayashi Y, Zhuang J, Peltz S, Dougherty J. 2010. Identification of a cellular factor that modulates HIV-1 programmed ribosomal frameshifting. J Biol Chem 285: 19776-19784.
    • (2010) J Biol Chem , vol.285 , pp. 19776-19784
    • Kobayashi, Y.1    Zhuang, J.2    Peltz, S.3    Dougherty, J.4
  • 28
    • 0035200990 scopus 로고    scopus 로고
    • Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency
    • DOI 10.1128/MCB.21.24.8657-8670.2001
    • Kontos H, Napthine S, Brierley I. 2001. Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency. Mol Cell Biol 21: 8657-8670. (Pubitemid 33108622)
    • (2001) Molecular and Cellular Biology , vol.21 , Issue.24 , pp. 8657-8670
    • Kontos, H.1    Napthine, S.2    Brierley, I.3
  • 29
    • 34548768192 scopus 로고    scopus 로고
    • The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift
    • DOI 10.1093/nar/gkm578
    • Leger M, Dulude D, Steinberg SV, Brakier-Gingras L. 2007. The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift. Nucleic Acids Res 35: 5581-5592. (Pubitemid 47423929)
    • (2007) Nucleic Acids Research , vol.35 , Issue.16 , pp. 5581-5592
    • Leger, M.1    Dulude, D.2    Steinberg, S.V.3    Brakier-Gingras, L.4
  • 30
    • 77957139491 scopus 로고    scopus 로고
    • SHAPE-directed RNA secondary structure prediction
    • Low JT, Weeks KM. 2010. SHAPE-directed RNA secondary structure prediction. Methods 52: 150-158.
    • (2010) Methods , vol.52 , pp. 150-158
    • Low, J.T.1    Weeks, K.M.2
  • 31
    • 70350167221 scopus 로고    scopus 로고
    • Selection and characterization of small molecules that bind the HIV-1 frameshift site RNA
    • Marcheschi RJ, Mouzakis KD, Butcher SE. 2009. Selection and characterization of small molecules that bind the HIV-1 frameshift site RNA. ACS Chem Biol 4: 844-854.
    • (2009) ACS Chem Biol , vol.4 , pp. 844-854
    • Marcheschi, R.J.1    Mouzakis, K.D.2    Butcher, S.E.3
  • 32
    • 80051955672 scopus 로고    scopus 로고
    • Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication
    • Marcheschi RJ, Tonelli M, Kumar A, Butcher SE. 2011. Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication. ACS Chem Biol 6: 857-864.
    • (2011) ACS Chem Biol , vol.6 , pp. 857-864
    • Marcheschi, R.J.1    Tonelli, M.2    Kumar, A.3    Butcher, S.E.4
  • 33
    • 35048828472 scopus 로고    scopus 로고
    • Identification of a selective small-molecule ligand for HIV-1 frameshift-inducing stem-loop RNA from an 11,325 member resin bound dynamic combinatorial library
    • DOI 10.1021/ja072114h
    • McNaughton BR, Gareiss PC, Miller BL. 2007. Identification of a selective small-molecule ligand for HIV-1 frameshift-inducing stem-loop RNA from an 11, 325 member resin bound dynamic combinatorial library. J Am Chem Soc 129: 11306-11307. (Pubitemid 47555529)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.37 , pp. 11306-11307
    • McNaughton, B.R.1    Gareiss, P.C.2    Miller, B.L.3
  • 35
    • 33646557329 scopus 로고    scopus 로고
    • A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting
    • Namy O, Moran SJ, Stuart DI, Gilbert RJC, Brierley I. 2006. A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting. Nature 441: 244-247.
    • (2006) Nature , vol.441 , pp. 244-247
    • Namy, O.1    Moran, S.J.2    Stuart, D.I.3    Gilbert, R.J.C.4    Brierley, I.5
  • 36
    • 4544337311 scopus 로고    scopus 로고
    • A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions
    • DOI 10.1128/JVI.78.19.10814-10819.2004
    • Ooms M, Huthoff H, Russell R, Liang C, Berkhout B. 2004. A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions. J Virol 78: 10814-10819. (Pubitemid 39258406)
    • (2004) Journal of Virology , vol.78 , Issue.19 , pp. 10814-10819
    • Ooms, M.1    Huthoff, H.2    Russell, R.3    Liang, C.4    Berkhout, B.5
  • 37
    • 79959876045 scopus 로고    scopus 로고
    • Identification of RNA pseudoknotbinding ligand that inhibits the -1 ribosomal frameshifting of SARS-coronavirus by structure-based virtual screening
    • Park SJ, Kim YG, Park HJ. 2011. Identification of RNA pseudoknotbinding ligand that inhibits the -1 ribosomal frameshifting of SARS-coronavirus by structure-based virtual screening. J Am Chem Soc 133: 10094-10100.
    • (2011) J Am Chem Soc , vol.133 , pp. 10094-10100
    • Park, S.J.1    Kim, Y.G.2    Park, H.J.3
  • 38
    • 0026717107 scopus 로고
    • Human immunodeficiency virus type 1 gag-pol frameshifting is dependent on downstream mRNA secondary structure: Demonstration by expression in vivo
    • Parkin NT, Chamorro M, Varmus HE. 1992. Human immunodeficiency virus type 1 gag-pol frameshifting is dependent on downstream mRNA secondary structure: demonstration by expression in vivo. J Virol 66: 5147-5151.
    • (1992) J Virol , vol.66 , pp. 5147-5151
    • Parkin, N.T.1    Chamorro, M.2    Varmus, H.E.3
  • 39
    • 17844384225 scopus 로고    scopus 로고
    • Torsional restraint: A new twist on frameshifting pseudoknots
    • DOI 10.1093/nar/gki329
    • Plant EP, Dinman JD. 2005. Torsional restraint: a new twist on frameshifting pseudoknots. Nucleic Acids Res 33: 1825-1833. (Pubitemid 41748329)
    • (2005) Nucleic Acids Research , vol.33 , Issue.6 , pp. 1825-1833
    • Plant, E.P.1    Dinman, J.D.2
  • 40
    • 0025351085 scopus 로고
    • Pseudoknots: A new motif in the RNA game
    • Pleij CW. 1990. Pseudoknots: a new motif in the RNA game. Trends Biochem Sci 15: 143-147. (Pubitemid 20186842)
    • (1990) Trends in Biochemical Sciences , vol.15 , Issue.4 , pp. 143-147
    • Pleij, C.W.A.1
  • 41
    • 0022423219 scopus 로고
    • A new principle of RNA folding based on pseudoknotting
    • Pleij CW, Rietveld K, Bosch L. 1985. A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res 13: 1717-1731.
    • (1985) Nucleic Acids Res , vol.13 , pp. 1717-1731
    • Pleij, C.W.1    Rietveld, K.2    Bosch, L.3
  • 42
    • 0029100233 scopus 로고
    • Predicting thermodynamic properties of RNA
    • Serra MJ, Turner DH. 1995. Predicting thermodynamic properties of RNA. Methods Enzymol 259: 242-261.
    • (1995) Methods Enzymol , vol.259 , pp. 242-261
    • Serra, M.J.1    Turner, D.H.2
  • 44
    • 0026733573 scopus 로고
    • Ribosomal movement impeded at a pseudoknot required for frameshifting
    • Tu C, Tzeng TH, Bruenn JA. 1992. Ribosomal movement impeded at a pseudoknot required for frameshifting. Proc Natl Acad Sci 89: 8636-8640.
    • (1992) Proc Natl Acad Sci , vol.89 , pp. 8636-8640
    • Tu, C.1    Tzeng, T.H.2    Bruenn, J.A.3


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