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Cited by 2RNA and protein synthesis mechanismsAdvanced biosensing and bioanalysis techniquesDNA and Nucleic Acid Chemistry

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DNA aptamer AptERA 2 targets ERA from Staphylococcus aureus and limits GTP hydrolysis

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Peñaranda, Katherin, Pereira, Nicolle, Savva, Orestis, Petrelli, Dezemona, Spurio, Roberto, Corrigan, Rebecca M., Milon, Pohl·2025·Scientific Reports
DOI 10.1038/s41598-025-15180-9PMC PMC12373895

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Abstract

Abstract Ribosome assembly is a multistep process that ensures a functional ribosome structure. The molecular mechanism that ribosome­associated GTPases (RA­GTPases) use to enhance ribosome assembly accuracy, remains largely to be elucidated. Here, we use systematic evolution of ligands by exponential enrichment (SELEX), followed by sequencing, comprehensive bioinformatics analysis, and biochemical characterization to identify aptamers that target the RA-GTPase ERA of Staphylococcus aureus. ELONA and thermophoresis assays show that the AptERA 2 interaction with ERA is in the 200 nM range of affinity, displays a high level of specificity, and depends on the target structure. Docking to ERA suggests that AptERA 2 interacts with the protein's KH domain, consistent with the aptamer's similarities with helix 45 of the 16S rRNA. AptERA 2 did not interact with a similar RA-GTPase RbgA, conserved at the GTPase core but lacking the KH domain, confirming that the aptamer recognizes and binds the KH domain of ERA. This interaction leads to a significant reduction of 30S-dependent GTP hydrolysis, indicative of allosteric modulation of the enzyme activity or limiting the KH domain interaction with the 3’ end of the 16S rRNA rather than directly blocking GTP binding. Altogether, this work highlights the versatility of aptamers as tools to understand the complex processes of ribosome biogenesis further, offering new insights into bacterial protein synthesis mechanisms.

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Metadata

Authors
Peñaranda, K., Pereira, N., Savva, O., Petrelli, D., Spurio, R., Corrigan, R. M., & Milon, P.
Affiliations
  • Università di Camerino (IT)
  • Peruvian University of Applied Sciences (PE)
  • University of Sheffield (GB)
  • University College Dublin (IE)
Corresponding author
Peñaranda, Katherin
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2025-08-22
Volume
15
Issue
1
Pages
30879-30879
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-025-15180-9
PMC
PMC12373895
OpenAlex
W4413430676
Cited by
2
References
4
Citations by year
2026: 2
FWCI
0.60
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by-nc-nd)
  • Research Square (acceptedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Unicam Scientific Publications (University of Camerino) (submittedVersion, cc-by-nc-nd)
  • Repositorio Académico UPC (Universidad Peruana de Ciencias Aplicadas) (submittedVersion)
Funders
  • Horizon 2020 (Marie Sklodowska-Curie Grant Agreement No. 872869)
  • Universidad Peruana de Ciencias Aplicadas
  • BBSRC DTP studentship (grant BB/T007222/1)
  • Wellcome Trust (104110/Z/14/A)
  • Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica (PE501079419-2022)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords
DNA aptamers, Staphylococcus aureus, ribosome-associated GTPase, ribosome assembly, KH domain, GTP hydrolysis, allosteric modulation, ribosome biogenesis, SELEX, aptamer-protein binding
MeSH terms
Bacterial Proteins, Guanosine Triphosphate, Hydrolysis, Protein Binding, Ribosomes, RNA, Ribosomal, 16S, Staphylococcus aureus, GTP Phosphohydrolases, SELEX Aptamer Technique, Aptamers, Nucleotide, Molecular Docking Simulation

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