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

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rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly

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Sekulski, Kamil, Cruz, Victor Emmanuel, Weirich, Christine S., Erzberger, Jan P.·2023·Nature Communications
DOI 10.1038/s41467-023-36867-5PMC PMC9981671

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Abstract

Biogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation. Spb1 methylates the A-loop nucleotide G2922 and a catalytically deficient mutant strain ( spb 1 D52A ) has a severe 60S biogenesis defect. However, the assembly function of this modification is currently unknown. Here, we present cryo-EM reconstructions that reveal that unmethylated G2922 leads to the premature activation of Nog2 GTPase activity and capture a Nog2-GDP-AlF 4 − transition state structure that implicates the direct involvement of unmodified G2922 in Nog2 GTPase activation. Genetic suppressors and in vivo imaging indicate that premature GTP hydrolysis prevents the efficient binding of Nog2 to early nucleoplasmic 60S intermediates. We propose that G2922 methylation levels regulate Nog2 recruitment to the pre-60S near the nucleolar/nucleoplasmic phase boundary, forming a kinetic checkpoint to regulate 60S production. Our approach and findings provide a template to study the GTPase cycles and regulatory factor interactions of the other K-loop GTPases involved in ribosome assembly.

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Metadata

Authors
Sekulski, K., Cruz, V. E., Weirich, C. S., & Erzberger, J. P.
Affiliations
The University of Texas Southwestern Medical Center (US)
Corresponding author
Erzberger, Jan P.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-03-02
Volume
14
Issue
1
Pages
1207-1207
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-36867-5
PMC
PMC9981671
OpenAlex
W4322764097
Cited by
12
References
2
Citations by year
2026: 2 · 2025: 3 · 2024: 3 · 2023: 3
FWCI
0.98
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Welch Foundation (I-1897)
  • Cancer Prevention and Research Institute of Texas (RR150074)
  • U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (GM135617-01)
  • UTSW Endowed Scholars Fund
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
rRNA methylation, 60S ribosomal subunit assembly, ribosome biogenesis, GTPase activation, cryo-EM structure, genetic suppressors
MeSH terms
Kinetics, Methylation, Methyltransferases, RNA Processing, Post-Transcriptional, GTP Phosphohydrolases, Ribosome Subunits, Large, Eukaryotic

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