Concerted structural rearrangements enable RNA channeling into the cytoplasmic Ski238-Ski7-exosome assembly.
RNA degradation
Ski238
Ski7
conformational regulation
cryo-EM
cytoplasmic RNA degradation
exosome
helicase
nuclease
Journal
Molecular cell
ISSN: 1097-4164
Titre abrégé: Mol Cell
Pays: United States
ID NLM: 9802571
Informations de publication
Date de publication:
16 Nov 2023
16 Nov 2023
Historique:
received:
06
06
2023
revised:
25
08
2023
accepted:
29
09
2023
medline:
20
11
2023
pubmed:
26
10
2023
entrez:
25
10
2023
Statut:
ppublish
Résumé
The Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the adaptor protein Ski7. We determined different cryo-EM structures of the Ski238 complex depicting the transition from a rigid autoinhibited closed conformation to a flexible active open conformation in which the Ski2 helicase module has detached from the rest of Ski238. The open conformation favors the interaction of the Ski3 subunit with exosome-bound Ski7, leading to the recruitment of the exosome. In the Ski238-Ski7-exosome holocomplex, the Ski2 helicase module binds the exosome cap, enabling the RNA to traverse from the helicase through the internal exosome channel to the Rrp44 exoribonuclease. Our study pinpoints how conformational changes within the Ski238 complex regulate exosome recruitment for RNA degradation. We also reveal the remarkable conservation of helicase-exosome RNA channeling mechanisms throughout eukaryotic nuclear and cytoplasmic exosome complexes.
Identifiants
pubmed: 37879335
pii: S1097-2765(23)00803-1
doi: 10.1016/j.molcel.2023.09.037
pmc: PMC10659929
pii:
doi:
Substances chimiques
RNA
63231-63-0
Saccharomyces cerevisiae Proteins
0
Exosome Multienzyme Ribonuclease Complex
EC 3.1.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
4093-4105.e7Informations de copyright
Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests E.C. is a member of the Molecular Cell advisory board.
Références
Nature. 2021 Aug;596(7873):590-596
pubmed: 34293799
Nat Methods. 2017 Mar;14(3):290-296
pubmed: 28165473
Nature. 2013 Mar 7;495(7439):70-5
pubmed: 23376952
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Mol Cell. 2020 Mar 19;77(6):1222-1236.e13
pubmed: 32048998
J Bacteriol. 1978 Dec;136(3):1002-7
pubmed: 363683
Methods Mol Biol. 2020;2062:491-513
pubmed: 31768992
Nat Protoc. 2007;2(1):31-4
pubmed: 17401334
Curr Biol. 2021 Jul 26;31(14):2984-2994.e7
pubmed: 33989522
Genes Dev. 2017 Jan 15;31(2):88-100
pubmed: 28202538
EMBO J. 2019 Jul 15;38(14):e100640
pubmed: 31304628
Nat Methods. 2019 Nov;16(11):1153-1160
pubmed: 31591578
EMBO Rep. 2010 Dec;11(12):936-42
pubmed: 21072061
Science. 2002 Mar 22;295(5563):2262-4
pubmed: 11910110
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Cell Rep. 2017 Sep 5;20(10):2279-2286
pubmed: 28877463
Cell. 2009 Oct 30;139(3):547-59
pubmed: 19879841
Trends Biochem Sci. 2003 Mar;28(3):159-65
pubmed: 12633996
Nat Rev Mol Cell Biol. 2013 Oct;14(10):654-60
pubmed: 23989960
Nat Struct Mol Biol. 2007 Jan;14(1):15-22
pubmed: 17173052
Cell. 2018 Jun 14;173(7):1663-1677.e21
pubmed: 29906447
Yeast. 2004 Aug;21(11):947-62
pubmed: 15334558
Nat Methods. 2019 Jun;16(6):471-477
pubmed: 31086343
J Bacteriol. 1974 Feb;117(2):681-6
pubmed: 4590482
Science. 2016 Dec 16;354(6318):1431-1433
pubmed: 27980209
Cell. 1997 Nov 14;91(4):457-66
pubmed: 9390555
Curr Opin Struct Biol. 2021 Apr;67:86-94
pubmed: 33147539
RNA. 2012 Jan;18(1):124-34
pubmed: 22114319
EMBO J. 2014 Dec 1;33(23):2829-46
pubmed: 25319414
Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544
pubmed: 29872004
Structure. 2015 Jul 7;23(7):1336-43
pubmed: 26051716
Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):E690-7
pubmed: 22366317
J Struct Biol. 2017 May;198(2):124-133
pubmed: 28344036
Methods Mol Biol. 2020;2062:3-33
pubmed: 31768969
Commun Biol. 2021 Jul 15;4(1):874
pubmed: 34267316
PLoS Genet. 2013;9(3):e1003376
pubmed: 23516382
Mol Cell. 2022 Feb 17;82(4):756-769.e8
pubmed: 35120588
EMBO J. 2001 Sep 3;20(17):4684-93
pubmed: 11532933
Trends Biochem Sci. 2012 Feb;37(2):49-57
pubmed: 22154230
Mol Cell. 2003 May;11(5):1405-13
pubmed: 12769863
Biol Chem. 2021 Jan 06;402(5):605-616
pubmed: 33857361
Adv Exp Med Biol. 2019;1203:113-132
pubmed: 31811632
Cold Spring Harb Symp Quant Biol. 2019;84:155-163
pubmed: 32493762
Mol Cell. 2016 Jul 7;63(1):125-34
pubmed: 27345150
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
Mol Cell. 2020 Mar 19;77(6):1340-1349.e6
pubmed: 32006463
Elife. 2018 Jul 26;7:
pubmed: 30047866
Science. 2018 Apr 13;360(6385):219-222
pubmed: 29519915
Nucleic Acids Res. 2017 Feb 28;45(4):2068-2080
pubmed: 28204585
Elife. 2017 Jul 25;6:
pubmed: 28742025
Nat Struct Mol Biol. 2007 Jul;14(7):647-52
pubmed: 17558417
Biochim Biophys Acta. 2013 Jun-Jul;1829(6-7):552-60
pubmed: 23352926
Cell. 2013 Aug 15;154(4):814-26
pubmed: 23953113
EMBO J. 1998 Mar 2;17(5):1497-506
pubmed: 9482746
Nat Methods. 2017 Apr;14(4):331-332
pubmed: 28250466
Gene. 1990 Oct 30;95(1):85-90
pubmed: 1979303
PLoS Genet. 2021 Feb 18;17(2):e1009390
pubmed: 33600438
Mol Cell Biol. 1995 May;15(5):2719-27
pubmed: 7739552
Protein Sci. 2018 Jan;27(1):14-25
pubmed: 28710774