Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering
- Swastik De1,8,
- Michelle Zhou2,8,
- Zuben P. Brown1,7,8,
- Raymond N. Burton-Smith3,
- Yaser Hashem4,
- Tatyana V. Pestova5,
- Christopher U.T. Hellen5 and
- Joachim Frank1,6
- 1Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
- 2Irvington High School, Irvington, New York 10533, USA
- 3Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- 4Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 33607 Pessac, France
- 5Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, New York 11203, USA
- 6Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- Corresponding authors: christopher.hellen{at}downstate.edu, jf2192{at}cumc.columbia.edu
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↵8 These authors contributed equally to this work.
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Handling editor: Marina Rodnina
Abstract
Examination of all publicly available Oryctolagus cuniculus (rabbit) ribosome cryo-EM structures reveals numerous confusing inconsistencies. First, there are a plethora of single-nucleotide differences among the various rabbit 28S and 18S rRNA structures. Second, two nucleotides are absent from the NCBI Reference Sequence for the 18S rRNA gene. Moving forward, we propose using the Broad Institute's rabbit whole-genome shotgun sequence and numbering to reduce modeling ambiguity and improve consistency between ribosome models.
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Footnotes
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.080294.124.
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Freely available online through the RNA Open Access option.
- Received October 22, 2024.
- Accepted February 24, 2025.
This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
