Different views of the dynamic landscape covered by the 5'-hairpin of the 7SK small nuclear RNA.
Binding Sites
/ genetics
HIV-1
/ genetics
Magnetic Resonance Spectroscopy
/ methods
Nucleic Acid Conformation
Positive Transcriptional Elongation Factor B
/ genetics
Protein Binding
/ genetics
RNA Polymerase II
/ genetics
RNA, Small Interfering
/ genetics
RNA, Small Nuclear
/ genetics
RNA, Viral
/ genetics
RNA-Binding Proteins
/ genetics
Structure-Activity Relationship
7SK
HEXIM
RNA
Tat
structure
Journal
RNA (New York, N.Y.)
ISSN: 1469-9001
Titre abrégé: RNA
Pays: United States
ID NLM: 9509184
Informations de publication
Date de publication:
09 2020
09 2020
Historique:
received:
28
01
2020
accepted:
13
05
2020
pubmed:
21
5
2020
medline:
6
10
2020
entrez:
21
5
2020
Statut:
ppublish
Résumé
The 7SK small nuclear RNA (7SKsnRNA) plays a key role in the regulation of RNA polymerase II by sequestrating and inhibiting the positive transcription elongation factor b (P-TEFb) in the 7SK ribonucleoprotein complex (7SKsnRNP), a process mediated by interaction with the protein HEXIM. P-TEFb is also an essential cellular factor recruited by the viral protein Tat to ensure the replication of the viral RNA in the infection cycle of the human immunodeficiency virus (HIV-1). Tat promotes the release of P-TEFb from the 7SKsnRNP and subsequent activation of transcription, by displacing HEXIM from the 5'-hairpin of the 7SKsnRNA. This hairpin (HP1), comprising the signature sequence of the 7SKsnRNA, has been the subject of three independent structural studies aimed at identifying the structural features that could drive the recognition by the two proteins, both depending on arginine-rich motifs (ARM). Interestingly, four distinct structures were determined. In an attempt to provide a comprehensive view of the structure-function relationship of this versatile RNA, we present here a structural analysis of the models, highlighting how HP1 is able to adopt distinct conformations with significant impact on the compactness of the molecule. Since these models are solved under different conditions by nuclear magnetic resonance (NMR) and crystallography, the impact of the buffer composition on the conformational variation was investigated by complementary biophysical approaches. Finally, using isothermal titration calorimetry, we determined the thermodynamic signatures of the Tat-ARM and HEXIM-ARM peptide interactions with the RNA, showing that they are associated with distinct binding mechanisms.
Identifiants
pubmed: 32430362
pii: rna.074955.120
doi: 10.1261/rna.074955.120
pmc: PMC7430674
doi:
Substances chimiques
RNA, Small Interfering
0
RNA, Small Nuclear
0
RNA, Viral
0
RNA-Binding Proteins
0
Positive Transcriptional Elongation Factor B
EC 2.7.11.-
RNA Polymerase II
EC 2.7.7.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1184-1197Informations de copyright
© 2020 Brillet et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Références
Nat Struct Biol. 2000 Oct;7(10):834-7
pubmed: 11017187
Proc Natl Acad Sci U S A. 2007 Sep 4;104(36):14312-7
pubmed: 17724342
RNA. 2010 Feb;16(2):417-29
pubmed: 20047989
Genes Dev. 1997 Oct 15;11(20):2633-44
pubmed: 9334326
J Mol Biol. 2010 Dec 10;404(4):555-67
pubmed: 20816986
Curr Pharm Des. 2017;23(28):4098-4102
pubmed: 28677507
Mol Biol Evol. 2009 Dec;26(12):2821-30
pubmed: 19734296
Microbiol Mol Biol Rev. 2006 Sep;70(3):646-59
pubmed: 16959964
Mol Cell. 2008 Mar 14;29(5):588-99
pubmed: 18249148
J Mol Biol. 2009 Mar 6;386(4):1094-107
pubmed: 19244621
Protein Sci. 2018 Jan;27(1):293-315
pubmed: 29067766
Chem Biol. 1995 Dec;2(12):827-40
pubmed: 8807816
Nat Struct Biol. 1998 Dec;5(12):1065-74
pubmed: 9846877
Nucleic Acids Res. 2008 Apr;36(7):2219-29
pubmed: 18281698
Transcription. 2018;9(4):262-271
pubmed: 29345523
Science. 1996 Sep 13;273(5281):1547-51
pubmed: 8703216
Nature. 1988 Sep 22;335(6188):375-8
pubmed: 2458530
Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11555-60
pubmed: 9751704
Nucleic Acids Res. 2007;35(6):2003-12
pubmed: 17341462
RNA. 2016 Dec;22(12):1844-1858
pubmed: 27852926
Nucleic Acids Res. 2010 Nov;38(21):7749-63
pubmed: 20675720
Cell. 1990 Nov 16;63(4):791-802
pubmed: 2225077
J Mol Biol. 2011 Dec 16;414(5):639-53
pubmed: 22033481
Mol Cell Biol. 2004 Jun;24(12):5094-105
pubmed: 15169877
Biophys J. 2004 Jun;86(6):3444-60
pubmed: 15189846
Science. 1992 Jul 3;257(5066):76-80
pubmed: 1621097
Mol Cell Biol. 2006 Jan;26(2):630-42
pubmed: 16382153
J Mol Biol. 1995 Oct 20;253(2):313-32
pubmed: 7563092
Nat Commun. 2018 Oct 15;9(1):4266
pubmed: 30323330
Annu Rev Virol. 2017 Sep 29;4(1):261-285
pubmed: 28715973
Biopolymers. 2007 Aug 5-15;86(5-6):384-402
pubmed: 17594140
Biochimie. 2015 Oct;117:63-71
pubmed: 25863285
Nucleic Acids Res. 2020 Jan 10;48(1):373-389
pubmed: 31732748
Nucleic Acids Res. 2010 Jan;38(2):360-9
pubmed: 19906723
PLoS One. 2010 Aug 23;5(8):e12335
pubmed: 20808803
J Biomol NMR. 1995 Jan;5(1):87-92
pubmed: 7533570
RNA. 2000 Feb;6(2):282-95
pubmed: 10688366
Mol Cell. 2006 Aug 4;23(3):297-305
pubmed: 16885020
Methods Enzymol. 2000;318:423-38
pubmed: 10890003
Methods Enzymol. 1989;180:51-62
pubmed: 2482430
PLoS Pathog. 2010 Oct 14;6(10):e1001152
pubmed: 20976203
Cell. 1987 Feb 27;48(4):691-701
pubmed: 3643816
Nucleic Acids Res. 2002 Aug 15;30(16):3497-531
pubmed: 12177293
J Biol Chem. 2005 Jul 1;280(26):24968-77
pubmed: 15855166
J Mol Biol. 1999 Oct 22;293(2):235-54
pubmed: 10550206
Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):12721-12726
pubmed: 27791144
Nucleic Acids Res. 2003 Aug 1;31(15):e82
pubmed: 12888534
Nature. 2001 Nov 15;414(6861):322-5
pubmed: 11713533
J Mol Biol. 1999 Jul 30;290(5):929-41
pubmed: 10438593
Nucleic Acids Res. 2017 Apr 7;45(6):3568-3579
pubmed: 28082395
J Biomol NMR. 1992 Nov;2(6):661-5
pubmed: 1490109
Mol Cell. 2007 Jul 20;27(2):262-74
pubmed: 17643375
Nucleic Acids Res. 2018 Aug 21;46(14):7354-7365
pubmed: 29762712
EMBO Rep. 2008 Jun;9(6):569-75
pubmed: 18483487
Nature. 2001 Nov 15;414(6861):317-22
pubmed: 11713532
EMBO J. 2004 Jul 7;23(13):2608-19
pubmed: 15201869
Nucleic Acids Res. 2012 Feb;40(4):1407-23
pubmed: 22053086
J Biol Chem. 2005 Apr 22;280(16):16368-76
pubmed: 15713661
Biochemistry. 2015 Oct 27;54(42):6545-54
pubmed: 26422686
J Am Chem Soc. 2005 Mar 30;127(12):4223-31
pubmed: 15783204
Biotechniques. 1991 Dec;11(6):764-9
pubmed: 1809333
Nucleic Acids Res. 2017 Jun 20;45(11):6864-6880
pubmed: 28431135
J Vis Exp. 2013 Apr 26;(74):e4401
pubmed: 23644419
RNA Biol. 2009 Apr-Jun;6(2):122-8
pubmed: 19246988
Biochemistry. 2010 Apr 13;49(14):3083-91
pubmed: 20210365