Assembly landscape for the bacterial large ribosomal subunit.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
26 08 2023
26 08 2023
Historique:
received:
20
12
2022
accepted:
14
08
2023
medline:
28
8
2023
pubmed:
27
8
2023
entrez:
26
8
2023
Statut:
epublish
Résumé
Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic perturbations of the assembly process create bottlenecks where intermediates accumulate, facilitating structural characterization. We use cryo-electron microscopy, with iterative subclassification to identify intermediates in the assembly of the 50S ribosomal subunit from E. coli. The analysis of the ensemble of intermediates that spans the entire biogenesis pathway for the 50 S subunit was facilitated by a dimensionality reduction and cluster picking approach using PCA-UMAP-HDBSCAN. The identity of the cooperative folding units in the RNA with associated proteins is revealed, and the hierarchy of these units reveals a complete assembly map for all RNA and protein components. The assembly generally proceeds co-transcriptionally, with some flexibility in the landscape to ensure efficiency for this central cellular process under a variety of growth conditions.
Identifiants
pubmed: 37633970
doi: 10.1038/s41467-023-40859-w
pii: 10.1038/s41467-023-40859-w
pmc: PMC10460392
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
5220Informations de copyright
© 2023. Springer Nature Limited.
Références
Nat Methods. 2017 Aug;14(8):793-796
pubmed: 28671674
Mol Syst Biol. 2006;2:2006.0008
pubmed: 16738554
Elife. 2017 May 30;6:
pubmed: 28556777
Elife. 2015 Dec 14;4:
pubmed: 26670735
Annu Rev Microbiol. 2009;63:155-76
pubmed: 19575570
J Biol Chem. 1987 Jun 25;262(18):8826-33
pubmed: 3298242
Nucleic Acids Res. 2004 May 17;32(9):2751-9
pubmed: 15148362
Crit Rev Biochem Mol Biol. 2007 May-Jun;42(3):187-219
pubmed: 17562451
J Mol Biol. 2020 Feb 14;432(4):978-990
pubmed: 31877323
Mol Microbiol. 2014 Jun;92(5):945-58
pubmed: 24708042
Nature. 2018 Apr 5;556(7699):126-129
pubmed: 29512650
Nat Commun. 2023 Feb 17;14(1):898
pubmed: 36797249
Mol Cell. 2021 Mar 18;81(6):1200-1215.e9
pubmed: 33639093
J Struct Biol. 2009 Apr;166(1):95-102
pubmed: 19263523
Eur J Biochem. 1980 Jan;103(1):95-8
pubmed: 6153613
Cell. 2016 Dec 1;167(6):1610-1622.e15
pubmed: 27912064
Proc Natl Acad Sci U S A. 1982 Feb;79(3):729-33
pubmed: 7038683
J Struct Biol. 2015 Nov;192(2):216-21
pubmed: 26278980
Nat Methods. 2017 Mar;14(3):290-296
pubmed: 28165473
Biopolymers. 2007 Sep;87(1):1-11
pubmed: 17514744
Structure. 2022 Apr 7;30(4):498-509.e4
pubmed: 34990602
J Bacteriol. 1989 Aug;171(8):4207-16
pubmed: 2666391
Annu Rev Biochem. 2011;80:501-26
pubmed: 21529161
Protein Sci. 2021 Jan;30(1):70-82
pubmed: 32881101
Proc Natl Acad Sci U S A. 1975 Jul;72(7):2743-7
pubmed: 1101264
Nat Struct Mol Biol. 2023 Oct;30(10):1468-1480
pubmed: 37653244
Cell. 2017 Dec 14;171(7):1599-1610.e14
pubmed: 29245012
Nucleic Acids Res. 2013 Aug;41(15):7522-35
pubmed: 23771137
Nucleic Acids Res. 2019 Nov 4;47(19):10414-10425
pubmed: 31665744
Mol Biosyst. 2012 Oct 30;8(12):3325-34
pubmed: 23090316
Nucleic Acids Res. 2023 Apr 11;51(6):2862-2876
pubmed: 36864669
Nucleic Acids Res. 1981 Nov 25;9(22):6167-89
pubmed: 7031608
Nature. 2009 Feb 19;457(7232):977-80
pubmed: 19225518
J Struct Biol. 2000 Oct;132(1):33-45
pubmed: 11121305
RNA. 2020 Sep;26(9):1160-1169
pubmed: 32414857
Nat Methods. 2017 Apr;14(4):331-332
pubmed: 28250466