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Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts

The process of translation initiation in prokaryotes is mediated by the hybridization of the 16S rRNA of the small ribosomal subunit with the mRNA in a short region called the ribosomal binding site. However, translation initiation in chloroplasts, which have evolved from an ancestral bacterium, is...

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Autores principales: Carmel Ezra, Stav, Tuller, Tamir
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9157439/
https://www.ncbi.nlm.nih.gov/pubmed/35685358
http://dx.doi.org/10.1016/j.csbj.2022.05.030
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author Carmel Ezra, Stav
Tuller, Tamir
author_facet Carmel Ezra, Stav
Tuller, Tamir
author_sort Carmel Ezra, Stav
collection PubMed
description The process of translation initiation in prokaryotes is mediated by the hybridization of the 16S rRNA of the small ribosomal subunit with the mRNA in a short region called the ribosomal binding site. However, translation initiation in chloroplasts, which have evolved from an ancestral bacterium, is not well understood. Some studies suggest that in many cases it differs from translation initiation in bacteria and involves various novel interactions of the mRNA structures with intracellular factors; however currently, there is no generic quantitative model related to these aspects in chloroplasts. We developed a novel computational pipeline and models that can be used for understanding and modeling translation regulation in chloroplasts. We demonstrate that local folding and co-folding energy of the rRNA and the mRNA correlates with codon usage estimators of expression levels (r = −0.63) and infer predictive models that connect these energies and codon usage to protein levels (with correlation up to 0.71). In addition, we demonstrate that the ends of the transcripts in chloroplasts are populated with various structural elements that may be functional. Furthermore, we report a database of 166 novel structures in the chloroplast transcripts that are predicted to be functional. We believe that the models reported here improve existing understandings of genomic evolution and the biophysics of translation in chloroplasts; as such, they can aid gene expression engineering in chloroplasts for various biotechnological objectives.
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spelling pubmed-91574392022-06-08 Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts Carmel Ezra, Stav Tuller, Tamir Comput Struct Biotechnol J Research Article The process of translation initiation in prokaryotes is mediated by the hybridization of the 16S rRNA of the small ribosomal subunit with the mRNA in a short region called the ribosomal binding site. However, translation initiation in chloroplasts, which have evolved from an ancestral bacterium, is not well understood. Some studies suggest that in many cases it differs from translation initiation in bacteria and involves various novel interactions of the mRNA structures with intracellular factors; however currently, there is no generic quantitative model related to these aspects in chloroplasts. We developed a novel computational pipeline and models that can be used for understanding and modeling translation regulation in chloroplasts. We demonstrate that local folding and co-folding energy of the rRNA and the mRNA correlates with codon usage estimators of expression levels (r = −0.63) and infer predictive models that connect these energies and codon usage to protein levels (with correlation up to 0.71). In addition, we demonstrate that the ends of the transcripts in chloroplasts are populated with various structural elements that may be functional. Furthermore, we report a database of 166 novel structures in the chloroplast transcripts that are predicted to be functional. We believe that the models reported here improve existing understandings of genomic evolution and the biophysics of translation in chloroplasts; as such, they can aid gene expression engineering in chloroplasts for various biotechnological objectives. Research Network of Computational and Structural Biotechnology 2022-05-18 /pmc/articles/PMC9157439/ /pubmed/35685358 http://dx.doi.org/10.1016/j.csbj.2022.05.030 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Carmel Ezra, Stav
Tuller, Tamir
Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts
title Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts
title_full Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts
title_fullStr Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts
title_full_unstemmed Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts
title_short Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts
title_sort modeling the effect of rrna-mrna interactions and mrna folding on mrna translation in chloroplasts
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9157439/
https://www.ncbi.nlm.nih.gov/pubmed/35685358
http://dx.doi.org/10.1016/j.csbj.2022.05.030
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