iRAPs curb antisense transcription in E. coli.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
18 11 2019
18 11 2019
Historique:
accepted:
09
09
2019
revised:
03
09
2019
received:
09
05
2019
pubmed:
20
9
2019
medline:
13
5
2020
entrez:
20
9
2019
Statut:
ppublish
Résumé
RNA polymerase-binding RNA aptamers (RAPs) are natural RNA elements that control transcription in cis by directly contacting RNA polymerase. Many RAPs inhibit transcription by inducing Rho-dependent termination in Escherichia coli. Here, we studied the role of inhibitory RAPs (iRAPs) in modulation of antisense transcription (AT) using in silico and in vivo approaches. We revisited the antisense transcriptome in cells with impaired AT regulators (Rho, H-NS and RNaseIII) and searched for the presence of RAPs within antisense RNAs. Many of these RAPs were found at key genomic positions where they terminate AT. By exploring the activity of several RAPs both in a reporter system and in their natural genomic context, we confirmed their significant role in AT regulation. RAPs coordinate Rho activity at the antisense strand and terminate antisense transcripts. In some cases, they stimulated sense expression by alleviating ongoing transcriptional interference. Essentially, our data postulate RAPs as key determinants of Rho-mediated AT regulation in E. coli.
Identifiants
pubmed: 31535128
pii: 5571581
doi: 10.1093/nar/gkz791
pmc: PMC6847712
doi:
Substances chimiques
Aptamers, Nucleotide
0
RNA, Antisense
0
DNA-Directed RNA Polymerases
EC 2.7.7.6
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
10894-10905Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM126891
Pays : United States
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Transcription. 2014;5(4):e944039
pubmed: 25483405
Science. 2008 May 16;320(5878):935-8
pubmed: 18487194
Science. 1997 Sep 5;277(5331):1453-62
pubmed: 9278503
Nat Rev Microbiol. 2014 Sep;12(9):647-53
pubmed: 25069631
Biochem Soc Trans. 2016 Dec 15;44(6):1561-1569
pubmed: 27913665
Curr Opin Microbiol. 2013 Apr;16(2):118-24
pubmed: 23347833
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
J Bacteriol. 2007 Jan;189(1):142-50
pubmed: 17085567
Trends Genet. 2005 Jun;21(6):339-45
pubmed: 15922833
J Mol Biol. 2019 Sep 20;431(20):4030-4039
pubmed: 30978344
Science. 2005 May 27;308(5726):1321-3
pubmed: 15919996
Microbiol Mol Biol Rev. 2011 Jun;75(2):286-300
pubmed: 21646430
J Bacteriol. 2015 Jan 1;197(1):18-28
pubmed: 25266388
RNA Biol. 2008 Jan-Mar;5(1):30-40
pubmed: 18388495
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Genome Biol. 2014;15(12):550
pubmed: 25516281
mBio. 2010 May 18;1(1):
pubmed: 20689751
Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):13132-7
pubmed: 23878253
Biochemistry. 1993 Apr 13;32(14):3564-70
pubmed: 8466900
Nature. 1979 Jul 5;280(5717):80-2
pubmed: 15305587
Cell. 2016 Sep 22;167(1):111-121.e13
pubmed: 27662085
PLoS One. 2018 Mar 23;13(3):e0194438
pubmed: 29570714
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73
pubmed: 16845028
Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3134-9
pubmed: 24453212
Mol Cell. 2017 Jul 6;67(1):30-43.e6
pubmed: 28648779
Transcription. 2018;9(3):182-189
pubmed: 28980880
mBio. 2019 Mar 5;10(2):
pubmed: 30837344
Annu Rev Genet. 2010;44:167-88
pubmed: 20707673
Nat Microbiol. 2017 Jan 09;2:16249
pubmed: 28067866
RNA Biol. 2018;15(7):967-975
pubmed: 29683387
Nucleic Acids Res. 2016 Jul 8;44(W1):W46-53
pubmed: 27154273
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
J Cell Sci. 2007 Aug 15;120(Pt 16):2755-61
pubmed: 17690303
Nucleic Acids Res. 2016 Jun 2;44(10):e95
pubmed: 26932362
Genes Dev. 2012 Dec 1;26(23):2621-33
pubmed: 23207917
Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20172-7
pubmed: 22123973
Genes Dev. 2014 Feb 1;28(3):214-9
pubmed: 24449106
Nucleic Acids Res. 2018 Jul 27;46(13):6797-6805
pubmed: 29669055
Nature. 2010 Jan 14;463(7278):245-9
pubmed: 20075920
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
FEMS Microbiol Rev. 2010 Sep;34(5):883-923
pubmed: 20659169
Genes Cells. 2002 Aug;7(8):755-68
pubmed: 12167155
Annu Rev Microbiol. 2017 Sep 8;71:687-709
pubmed: 28731845
Microbiol Spectr. 2018 Jul;6(4):
pubmed: 30003872