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PreprintCited by 12RNA and protein synthesis mechanismsNuclear Structure and FunctionRNA modifications and cancer

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The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis

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Cruz, Victor E., Weirich, Christine S., Peddada, Nagesh, Erzberger, Jan P.·2023·Nature Communications
DOI 10.1101/2023.11.01.565222PMC PMC11024185

Preprint — published as 10.1038/s41467-024-47616-7

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Abstract

DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this study, we present cryo-EM reconstructions of nucleolar pre-60S intermediates that reveal an unexpected, alternate secondary structure within the nascent peptidyl-transferase-center (PTC). Our analysis of three sequential nucleolar pre-60S intermediates reveals that the DEAD-box ATPase Dbp10/DDX54 remodels this alternate base pairing and enables the formation of the rRNA junction that anchors the mature form of the universally conserved PTC A-loop. Post-catalysis, Dbp10 captures rRNA helix H61, initiating the concerted exchange of biogenesis factors during late nucleolar 60S maturation. Our findings show that Dbp10 activity is essential for the formation of the ribosome active site and reveal how this function is integrated with subsequent assembly steps to drive the biogenesis of the large ribosomal subunit.

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Metadata

Authors
Cruz, V. E., Weirich, C. S., Peddada, N., & Erzberger, J. P.
Affiliations
The University of Texas Southwestern Medical Center (US)
Corresponding author
Erzberger, Jan P.
ORCID
Venue
Nature Communications
Publisher
openRxiv
Published
2023-11-02
Volume
15
Issue
1
Pages
3296-3296
ISSN
2041-1723 (ISSN-L)
DOI
10.1101/2023.11.01.565222
PMC
PMC11024185
OpenAlex
W4394891042
Cited by
12
References
1
Citations by year
2026: 6 · 2025: 4 · 2024: 2
FWCI
1.63
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, cc-by)
  • PubMed Central (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • U.S. Department of Energy
  • U.S. Department of Health and Human Services (GM135617-01)
  • Welch Foundation (I-1897)
  • Cancer Prevention and Research Institute of Texas (RP170644, 1P30 CA142543, RR150074)
  • Oregon Health and Science University
  • University of Texas Southwestern Medical Center (CA142543)
  • National Institutes of Health (RP170644)
  • Office of Science
  • National Cancer Institute ((CA142543), P30CA142543)
  • National Institute of General Medical Sciences (GM135617-01, U24GM129547, R01GM135617)
  • Biological and Environmental Research
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords
DEAD-box ATPase, peptidyl transferase center, rRNA secondary structure, A-loop, cryo-EM structure

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