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Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli

During initiation, the ribosome is tasked to efficiently recognize open reading frames (ORFs) for accurate and fast translation of mRNAs. A critical step is start codon recognition, which is modulated by initiation factors, mRNA structure, a Shine Dalgarno (SD) sequence and the start codon itself. W...

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Autores principales: Kohl, Maximilian P, Kompatscher, Maria, Clementi, Nina, Holl, Lena, Erlacher, Matthias D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9841429/
https://www.ncbi.nlm.nih.gov/pubmed/36546769
http://dx.doi.org/10.1093/nar/gkac1175
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author Kohl, Maximilian P
Kompatscher, Maria
Clementi, Nina
Holl, Lena
Erlacher, Matthias D
author_facet Kohl, Maximilian P
Kompatscher, Maria
Clementi, Nina
Holl, Lena
Erlacher, Matthias D
author_sort Kohl, Maximilian P
collection PubMed
description During initiation, the ribosome is tasked to efficiently recognize open reading frames (ORFs) for accurate and fast translation of mRNAs. A critical step is start codon recognition, which is modulated by initiation factors, mRNA structure, a Shine Dalgarno (SD) sequence and the start codon itself. Within the Escherichia coli genome, we identified more than 50 annotated initiation sites harboring AUGUG or GUGUG sequence motifs that provide two canonical start codons, AUG and GUG, in immediate proximity. As these sites may challenge start codon recognition, we studied if and how the ribosome is accurately guided to the designated ORF, with a special focus on the SD sequence as well as adenine at the fourth coding sequence position (A4). By in vitro and in vivo experiments, we characterized key requirements for unambiguous start codon recognition, but also discovered initiation sites that lead to the translation of both overlapping reading frames. Our findings corroborate the existence of an ambiguous translation initiation mechanism, implicating a multitude of so far unrecognized ORFs and translation products in bacteria.
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spelling pubmed-98414292023-01-18 Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli Kohl, Maximilian P Kompatscher, Maria Clementi, Nina Holl, Lena Erlacher, Matthias D Nucleic Acids Res Molecular Biology During initiation, the ribosome is tasked to efficiently recognize open reading frames (ORFs) for accurate and fast translation of mRNAs. A critical step is start codon recognition, which is modulated by initiation factors, mRNA structure, a Shine Dalgarno (SD) sequence and the start codon itself. Within the Escherichia coli genome, we identified more than 50 annotated initiation sites harboring AUGUG or GUGUG sequence motifs that provide two canonical start codons, AUG and GUG, in immediate proximity. As these sites may challenge start codon recognition, we studied if and how the ribosome is accurately guided to the designated ORF, with a special focus on the SD sequence as well as adenine at the fourth coding sequence position (A4). By in vitro and in vivo experiments, we characterized key requirements for unambiguous start codon recognition, but also discovered initiation sites that lead to the translation of both overlapping reading frames. Our findings corroborate the existence of an ambiguous translation initiation mechanism, implicating a multitude of so far unrecognized ORFs and translation products in bacteria. Oxford University Press 2022-12-22 /pmc/articles/PMC9841429/ /pubmed/36546769 http://dx.doi.org/10.1093/nar/gkac1175 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Molecular Biology
Kohl, Maximilian P
Kompatscher, Maria
Clementi, Nina
Holl, Lena
Erlacher, Matthias D
Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli
title Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli
title_full Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli
title_fullStr Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli
title_full_unstemmed Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli
title_short Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli
title_sort initiation at augug and gugug sequences can lead to translation of overlapping reading frames in e. coli
topic Molecular Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9841429/
https://www.ncbi.nlm.nih.gov/pubmed/36546769
http://dx.doi.org/10.1093/nar/gkac1175
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