title: The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift.
abstract: The -1 programmed ribosomal frameshifts (PRF), which are used by many viruses, occur at a heptanucleotide slippery sequence and are currently thought to involve the tRNAs interacting with the ribosomal P- and A-site codons. We investigated here whether the tRNA occupying the ribosomal E site that precedes a slippery site influences -1 PRF. Using the human immunodeficiency virus type 1 (HIV-1) frameshift region, we found that mutating the E-site codon altered the -1 PRF efficiency. When the HIV-1 slippery sequence was replaced with other viral slippery sequences, mutating the E-site codon also altered the -1 PRF efficiency. Because HIV-1 -1 PRF can be recapitulated in bacteria, we used a bacterial ribosome system to select, by random mutagenesis, 16S ribosomal RNA (rRNA) mutations that modify the expression of a reporter requiring HIV-1 -1 PRF. Three mutants were isolated, which are located in helices 21 and 22 of 16S rRNA, a region involved in translocation and E-site tRNA binding. We propose a novel model where -1 PRF is triggered by an incomplete translocation and depends not only on the tRNAs interacting with the P- and A-site codons, but also on the tRNA occupying the E site.
authors: Département de Biochimie, Université de Montréal, Montréal, Québec, Canada, H3T 1J4.
authors: Mélissa
authors: M
authors: Léger
authors: Dominic
authors: D
authors: Dulude
authors: Sergey V
authors: SV
authors: Steinberg
authors: Léa
authors: L
authors: Brakier-Gingras
mesh_terms: D002460:Cell Line; D003062:Codon / Q000737:chemistry; D018965:Frameshifting, Ribosomal; D017930:Genes, Reporter; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D009154:Mutation; D009711:Nucleotides / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000737:chemistry; D012343:RNA, Transfer / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism
chemical_list: D003062:Codon; D009711:Nucleotides; D012333:RNA, Messenger; D012336:RNA, Ribosomal, 16S; D012367:RNA, Viral; D012343:RNA, Transfer
references: Nucleic Acids Res. 2001 Mar 1;29(5):1125-31
references: 11222762
references: Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15854-9
references: 16249344
references: Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13670-5
references: 16940356
references: Mol Cell Biol. 2000 Feb;20(4):1095-103
references: 10648594
references: J Gen Virol. 1995 Aug;76 ( Pt 8):1885-92
references: 7636469
references: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D139-40
references: 15608164
references: Mol Biol Biochem Biophys. 1979;30:i-x, 1-312
references: 370549
references: Cell. 1988 Nov 4;55(3):447-58
references: 2846182
references: Nucleic Acids Res. 2005 Sep 15;33(16):5291-6
references: 16166657
references: Cell. 2003 Jul 11;114(1):123-34
references: 12859903
references: Annu Rev Biochem. 2001;70:415-35
references: 11395413
references: Mol Cell. 2004 Jan 30;13(2):191-200
references: 14759365
references: J Virol. 2004 Feb;78(4):2082-7
references: 14747573
references: Mol Cell. 2004 Jan 30;13(2):157-68
references: 14759362
references: RNA. 2003 Feb;9(2):168-74
references: 12554858
references: New Biol. 1989 Nov;1(2):159-69
references: 2562219
references: EMBO J. 2004 Mar 10;23(5):1008-19
references: 14976550
references: J Mol Biol. 2005 Jun 24;349(5):1024-35
references: 15907937
references: FEBS Lett. 2002 Mar 6;514(1):11-6
references: 11904173
references: Trends Genet. 2006 Mar;22(3):174-81
references: 16460832
references: Virology. 2006 Feb 5;345(1):127-36
references: 16256163
references: Science. 2006 Sep 29;313(5795):1935-42
references: 16959973
references: J Mol Biol. 2002 Jul 26;320(5):979-89
references: 12126619
references: Nucleic Acids Res. 2003 Jan 1;31(1):87-9
references: 12519954
references: RNA. 2004 Jan;10(1):102-13
references: 14681589
references: Cell. 2006 Sep 22;126(6):1065-77
references: 16962654
references: J Mol Biol. 2004 Mar 12;337(1):15-30
references: 15001349
references: J Virol. 2001 Feb;75(4):1834-41
references: 11160682
references: Science. 2005 Nov 4;310(5749):827-34
references: 16272117
references: Nature. 1988 Jan 21;331(6153):280-3
references: 2447506
references: Trends Biochem Sci. 2002 Sep;27(9):448-54
references: 12217519
references: J Mol Biol. 1999 Mar 12;286(5):1365-78
references: 10064703
references: J Biol Chem. 2003 Nov 7;278(45):44913-20
references: 12937172
references: Mol Cell. 2007 Feb 23;25(4):519-29
references: 17317625
references: Gene. 1989 Apr 15;77(1):51-9
references: 2744487
references: AIDS Res Hum Retroviruses. 2000 Sep 1;16(13):1209-13
references: 10957718
references: Virus Res. 2006 Jul;119(1):29-42
references: 16310880
references: FEBS Lett. 2005 Feb 7;579(4):959-62
references: 15680982
references: Nucleic Acids Res. 2005 Oct 20;33(18):6048-56
references: 16243787
references: J Virol. 1991 Sep;65(9):5111-7
references: 1870215
references: Mol Cell Biol. 2001 Dec;21(24):8657-70
references: 11713298
references: J Mol Biol. 2005 Jun 24;349(5):1011-23
references: 15927637
references: Cold Spring Harb Symp Quant Biol. 2001;66:233-48
references: 12762025
references: Biochimie. 2006 Aug;88(8):1013-9
references: 16644089
references: RNA. 2005 Jun;11(6):906-13
references: 15872184
references: Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8636-40
references: 1528874
references: Cell Mol Life Sci. 2006 Dec;63(23):2725-37
references: 17013564
references: Nucleic Acids Res. 2002 Dec 1;30(23):5094-102
references: 12466532
references: Virology. 1993 Apr;193(2):661-71
references: 7681610
references: Nature. 2006 May 11;441(7090):244-7
references: 16688178
references: RNA. 2004 Feb;10(2):221-30
references: 14730021
references: Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16620-5
references: 16269538
references: RNA. 2004 Aug;10(8):1225-35
references: 15247429
references: Anal Biochem. 2000 Jun 15;282(1):158-61
references: 10860516
references: EMBO J. 1998 Dec 15;17(24):7490-7
references: 9857203
references: Nat Biotechnol. 2002 Jan;20(1):83-7
references: 11753367
references: BMC Bioinformatics. 2002;3:2
references: 11869452
references: J Mol Biol. 2004 Nov 5;343(5):1183-94
references: 15491605
references: Nature. 2000 Jul 20;406(6793):318-22
references: 10917535
references: RNA. 1997 Aug;3(8):870-81
references: 9257646
references: Mol Cell. 2005 Jan 7;17(1):61-8
references: 15629717
references: Science. 2001 May 4;292(5518):883-96
references: 11283358
references: Mol Cell Biol. 1993 Nov;13(11):6931-40
references: 8413285
references: Cold Spring Harb Symp Quant Biol. 2001;66:217-32
references: 12762024