title: Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators.
abstract: Escherichia coli and yeast DNA-dependent RNA polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent RNA-DNA hybrid realignment. The realignment was discovered on the heteropolymeric sequence T5C5 and yields transcripts lacking a C residue within a corresponding U5C4. The sequence studied is derived from a Roseiflexus insertion sequence (IS) element where the resulting transcriptional slippage is required for transposase synthesis. The stability of the RNA structure, the proximity of the stem loop to the slippage site, the length and composition of the slippage site motif, and the identity of its 3' adjacent nucleotides (nt) are crucial for transcripts lacking a single C. In many respects, the RNA structure requirements for this slippage resemble those for hairpin-dependent transcription termination. In a purified in vitro system, the slippage efficiency ranges from 5% to 75% depending on the concentration ratios of the nucleotides specified by the slippage sequence and the 3' nt context. The only previous proposal of stem loop mediated slippage, which was in Ebola virus expression, was based on incorrect data interpretation. We propose a mechanical slippage model involving the RNAP translocation state as the main motor in slippage directionality and efficiency. It is distinct from previously described models, including the one proposed for paramyxovirus, where following random movement efficiency is mainly dependent on the stability of the new realigned hybrid. In broadening the scope for utilization of transcription slippage for gene expression, the stimulatory structure provides parallels with programmed ribosomal frameshifting at the translation level.
authors.affiliation: Schools of Biochemistry & Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland;
authors.forename: Christophe
authors.initials: C
authors.lastname: Penno
authors.affiliation: Schools of Biochemistry & Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland;
authors.forename: Virag
authors.initials: V
authors.lastname: Sharma
authors.affiliation: Schools of Biochemistry & Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland;
authors.forename: Arthur
authors.initials: A
authors.lastname: Coakley
authors.affiliation: Schools of Biochemistry & Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland;
authors.forename: Mary
authors.initials: M
authors.lastname: O'Connell Motherway
authors.affiliation: Schools of Biochemistry & Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland;
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
authors.affiliation: Center for Cancer Research, National Cancer Institute, Frederick, MD 21702; and.
authors.forename: Lucyna
authors.initials: L
authors.lastname: Lubkowska
authors.affiliation: Center for Cancer Research, National Cancer Institute, Frederick, MD 21702; and.
authors.forename: Maria L
authors.initials: ML
authors.lastname: Kireeva
authors.affiliation: Center for Cancer Research, National Cancer Institute, Frederick, MD 21702; and.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Kashlev
authors.affiliation: Schools of Biochemistry & Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland;
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
authors.affiliation: Schools of Biochemistry & Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 j.atkins@ucc.ie.
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D041862:Chloroflexi / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D057345:Sequence Inversion; D013728:Terminator Regions, Genetic; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D012321:DNA-Directed RNA Polymerases
keywords: frameshifting; heteropolymeric slippage-prone motifs; stem loop stimulator; transcriptional realignment
references.citation: J Mol Biol. 1999 Mar 12;286(5):1365-78
references.pmid: 10064703
references.citation: Mol Cell. 1999 Apr;3(4):495-504
references.pmid: 10230402
references.citation: J Virol. 1999 Jul;73(7):5568-76
references.pmid: 10364305
references.citation: Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1683-8
references.pmid: 10677518
references.citation: Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7090-5
references.pmid: 10860976
references.citation: Science. 2001 Apr 27;292(5517):730-3
references.pmid: 11326100
references.citation: Nature. 2002 Jun 13;417(6890):712-9
references.pmid: 12000971
references.citation: RNA. 2002 Aug;8(8):1056-67
references.pmid: 12212849
references.citation: Mol Cell. 2002 Nov;10(5):1151-62
references.pmid: 12453422
references.citation: Nucleic Acids Res. 1992 Sep 11;20(17):4397-400
references.pmid: 1329024
references.citation: Proc Natl Acad Sci U S A. 1962 Jan 15;48:81-94
references.pmid: 13877961
references.citation: EMBO J. 2003 Nov 3;22(21):5941-50
references.pmid: 14592990
references.citation: Methods Enzymol. 2003;371:233-51
references.pmid: 14712704
references.citation: J Bacteriol. 2004 May;186(10):3274-7
references.pmid: 15126494
references.citation: Phys Rev Lett. 2004 Nov 5;93(19):198102
references.pmid: 15600885
references.citation: Cell. 2005 Jan 28;120(2):183-93
references.pmid: 15680325
references.citation: Mol Microbiol. 2005 Apr;56(1):204-14
references.pmid: 15773990
references.citation: Genome Biol. 2005;6(3):R25
references.pmid: 15774026
references.citation: J Gen Virol. 2005 Jul;86(Pt 7):1869-77
references.pmid: 15958664
references.citation: Trends Genet. 2006 Mar;22(3):174-81
references.pmid: 16460832
references.citation: Mol Microbiol. 2006 Dec;62(5):1460-8
references.pmid: 17059566
references.citation: J Biol Chem. 2007 Jul 27;282(30):21578-82
references.pmid: 17526498
references.citation: Nature. 2007 Jul 12;448(7150):157-62
references.pmid: 17581590
references.citation: Mol Cell. 2008 Jun 6;30(5):557-66
references.pmid: 18538654
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14934-9
references.pmid: 18815381
references.citation: J Virol. 2009 Apr;83(8):3982-7
references.pmid: 19211754
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8900-5
references.pmid: 19416863
references.citation: Mol Biol Evol. 2010 Apr;27(4):833-9
references.pmid: 19955479
references.citation: Genes Dev. 1991 May;5(5):707-13
references.pmid: 2026325
references.citation: Mol Biol Evol. 2011 Nov;28(11):3195-211
references.pmid: 21673094
references.citation: J Bacteriol. 2011 Aug;193(16):4113-22
references.pmid: 21685293
references.citation: J Biol Chem. 2011 Sep 2;286(35):30898-910
references.pmid: 21730074
references.citation: Nucleic Acids Res. 1990 Jun 25;18(12):3529-35
references.pmid: 2194164
references.citation: EMBO J. 2012 Feb 1;31(3):630-9
references.pmid: 22124324
references.citation: Transcription. 2012 Sep-Oct;3(5):260-9
references.pmid: 23132506
references.citation: J Biol Chem. 2013 Jan 25;288(4):2689-99
references.pmid: 23223234
references.citation: J Biol Chem. 2013 Jan 25;288(4):2700-10
references.pmid: 23223236
references.citation: Nucleic Acids Res. 2013 Jul;41(13):6514-30
references.pmid: 23649834
references.citation: J Am Chem Soc. 2013 Jun 5;135(22):8274-82
references.pmid: 23692220
references.citation: Nucleic Acids Res. 2013 Oct;41(19):9090-104
references.pmid: 23925128
references.citation: PLoS Pathog. 2013;9(10):e1003677
references.pmid: 24146620
references.citation: Nucleic Acids Res. 2014 May;42(9):5823-9
references.pmid: 24711367
references.citation: J Mol Biol. 2014 Sep 9;426(18):3095-3107
references.pmid: 24976131
references.citation: Nat Struct Mol Biol. 2014 Sep;21(9):794-802
references.pmid: 25108353
references.citation: PLoS Genet. 2014 Dec 04;10(12):e1004869
references.pmid: 25474156
references.citation: Transcription. 2014;5(1):e28285
references.pmid: 25764114
references.citation: Cell. 1988 Sep 9;54(6):891-902
references.pmid: 3044614
references.citation: Cold Spring Harb Symp Quant Biol. 1987;52:687-93
references.pmid: 3135981
references.citation: EMBO J. 1994 Nov 15;13(22):5496-503
references.pmid: 7957115
references.citation: Annu Rev Biochem. 1997;66:117-72
references.pmid: 9242904
references.citation: RNA. 1998 Apr;4(4):479-86
references.pmid: 9630253