Methods to assess helicase and translocation activities of human nuclear RNA exosome and RNA adaptor complexes.
DExH-box
Helicase
RNA exosome
RNA–protein complex
SF2
Translocase
Journal
Methods in enzymology
ISSN: 1557-7988
Titre abrégé: Methods Enzymol
Pays: United States
ID NLM: 0212271
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
14
8
2022
pubmed:
15
8
2022
medline:
17
8
2022
Statut:
ppublish
Résumé
The nuclear RNA exosome collaborates with the MTR4 helicase and RNA adaptor complexes to process, surveil, and degrade RNA. Here we outline methods to characterize RNA translocation and strand displacement by exosome-associated helicases and adaptor complexes using fluorescence-based strand displacement assays. The design and preparation of substrates suitable for analysis of helicase and decay activities of reconstituted MTR4-exosome complexes are described. To aid structural and biophysical studies, we present strategies for engineering substrates that can stall helicases during translocation, providing a means to capture snapshots of interactions and molecular steps involved in substrate translocation and delivery to the exosome.
Identifiants
pubmed: 35965016
pii: S0076-6879(22)00151-3
doi: 10.1016/bs.mie.2022.03.060
pmc: PMC9382703
mid: NIHMS1802014
pii:
doi:
Substances chimiques
Oligonucleotides
0
RNA, Nuclear
0
Saccharomyces cerevisiae Proteins
0
RNA
63231-63-0
Exosome Multienzyme Ribonuclease Complex
EC 3.1.-
DNA Helicases
EC 3.6.4.-
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
453-473Subventions
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM118080
Pays : United States
Informations de copyright
Copyright © 2022 Elsevier Inc. All rights reserved.
Références
Mol Cell. 2016 Nov 17;64(4):734-745
pubmed: 27818140
Nat Rev Mol Cell Biol. 2013 Oct;14(10):654-60
pubmed: 23989960
Cell. 2018 Jun 14;173(7):1663-1677.e21
pubmed: 29906447
Curr Opin Struct Biol. 2021 Apr;67:86-94
pubmed: 33147539
Biotechniques. 2008 Oct;45(4):433-40, 442
pubmed: 18855770
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20209-14
pubmed: 19088201
Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5506-E5515
pubmed: 29844170
Methods Enzymol. 2012;511:29-63
pubmed: 22713314
EMBO J. 2010 Jul 7;29(13):2205-16
pubmed: 20512111
Nucleic Acids Res. 2014 Dec 16;42(22):13861-72
pubmed: 25414331
Cell. 2006 Dec 15;127(6):1223-37
pubmed: 17174896
Genes Dev. 2017 Jan 15;31(2):88-100
pubmed: 28202538
Cell. 2019 Sep 19;179(1):282-282.e1
pubmed: 31539497
Nat Rev Mol Cell Biol. 2006 Jul;7(7):529-39
pubmed: 16829983
Biochemistry. 1994 Jul 12;33(27):8262-71
pubmed: 8031761
Cell. 2011 Jun 10;145(6):890-901
pubmed: 21663793
Genes Dev. 2017 Jun 15;31(12):1257-1271
pubmed: 28733371
EMBO J. 2002 Mar 1;21(5):1168-76
pubmed: 11867545
Proc Natl Acad Sci U S A. 2012 May 8;109(19):7292-7
pubmed: 22532666
Elife. 2018 Jul 26;7:
pubmed: 30047866
Elife. 2017 Jul 25;6:
pubmed: 28742025
Mol Cell. 2011 Aug 19;43(4):624-37
pubmed: 21855801
Mol Cell. 2016 Nov 3;64(3):520-533
pubmed: 27871484
Nat Protoc. 2014 Jul;9(7):1645-61
pubmed: 24945382
Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12139-44
pubmed: 20566885
Nature. 2014 Jul 24;511(7510):435-9
pubmed: 25043052
Cell. 2015 Aug 27;162(5):1029-38
pubmed: 26317469
Methods Enzymol. 2013;533:325-34
pubmed: 24182937