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Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria

Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gen...

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Autores principales: Hegelmeyer, Nuri K., Previti, Mary L., Andrade, Joshua, Utama, Raditya, Sejour, Richard J., Gardin, Justin, Muller, Stephanie, Ketchum, Steven, Yurovsky, Alisa, Futcher, Bruce, Goodwin, Sara, Ueberheide, Beatrix, Seeliger, Jessica C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055193/
https://www.ncbi.nlm.nih.gov/pubmed/36993691
http://dx.doi.org/10.1101/2023.03.17.532606
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author Hegelmeyer, Nuri K.
Previti, Mary L.
Andrade, Joshua
Utama, Raditya
Sejour, Richard J.
Gardin, Justin
Muller, Stephanie
Ketchum, Steven
Yurovsky, Alisa
Futcher, Bruce
Goodwin, Sara
Ueberheide, Beatrix
Seeliger, Jessica C.
author_facet Hegelmeyer, Nuri K.
Previti, Mary L.
Andrade, Joshua
Utama, Raditya
Sejour, Richard J.
Gardin, Justin
Muller, Stephanie
Ketchum, Steven
Yurovsky, Alisa
Futcher, Bruce
Goodwin, Sara
Ueberheide, Beatrix
Seeliger, Jessica C.
author_sort Hegelmeyer, Nuri K.
collection PubMed
description Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular codons but by their proper juxtaposition. We therefore hypothesized that non-optimal codon pairing could likewise attenuate Mtb genes. We explored the role of codon pair bias by recoding Mtb genes (rpoB, mmpL3, ndh) and assessing their expression in the closely related and tractable model organism M. smegmatis. To our surprise, recoding caused the expression of multiple smaller protein isoforms from all three genes. We confirmed that these smaller proteins were not due to protein degradation, but instead issued from new transcription initiation sites positioned within the open reading frame. New transcripts gave rise to intragenic translation initiation sites, which in turn led to the expression of smaller proteins. We next identified the nucleotide changes associated with these new sites of transcription and translation. Our results demonstrated that apparently benign, synonymous changes can drastically alter gene expression in mycobacteria. More generally, our work expands our understanding of the codon-level parameters that control translation and transcription initiation.
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spelling pubmed-100551932023-03-30 Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria Hegelmeyer, Nuri K. Previti, Mary L. Andrade, Joshua Utama, Raditya Sejour, Richard J. Gardin, Justin Muller, Stephanie Ketchum, Steven Yurovsky, Alisa Futcher, Bruce Goodwin, Sara Ueberheide, Beatrix Seeliger, Jessica C. bioRxiv Article Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular codons but by their proper juxtaposition. We therefore hypothesized that non-optimal codon pairing could likewise attenuate Mtb genes. We explored the role of codon pair bias by recoding Mtb genes (rpoB, mmpL3, ndh) and assessing their expression in the closely related and tractable model organism M. smegmatis. To our surprise, recoding caused the expression of multiple smaller protein isoforms from all three genes. We confirmed that these smaller proteins were not due to protein degradation, but instead issued from new transcription initiation sites positioned within the open reading frame. New transcripts gave rise to intragenic translation initiation sites, which in turn led to the expression of smaller proteins. We next identified the nucleotide changes associated with these new sites of transcription and translation. Our results demonstrated that apparently benign, synonymous changes can drastically alter gene expression in mycobacteria. More generally, our work expands our understanding of the codon-level parameters that control translation and transcription initiation. Cold Spring Harbor Laboratory 2023-03-17 /pmc/articles/PMC10055193/ /pubmed/36993691 http://dx.doi.org/10.1101/2023.03.17.532606 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Hegelmeyer, Nuri K.
Previti, Mary L.
Andrade, Joshua
Utama, Raditya
Sejour, Richard J.
Gardin, Justin
Muller, Stephanie
Ketchum, Steven
Yurovsky, Alisa
Futcher, Bruce
Goodwin, Sara
Ueberheide, Beatrix
Seeliger, Jessica C.
Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
title Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
title_full Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
title_fullStr Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
title_full_unstemmed Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
title_short Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
title_sort gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055193/
https://www.ncbi.nlm.nih.gov/pubmed/36993691
http://dx.doi.org/10.1101/2023.03.17.532606
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