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Exploring of the feature space of de novo developed post-transcriptional riboregulators

Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered r...

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Autores principales: Peters, Gert, Maertens, Jo, Lammertyn, Jeroen, De Mey, Marjan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114898/
https://www.ncbi.nlm.nih.gov/pubmed/30118473
http://dx.doi.org/10.1371/journal.pcbi.1006170
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author Peters, Gert
Maertens, Jo
Lammertyn, Jeroen
De Mey, Marjan
author_facet Peters, Gert
Maertens, Jo
Lammertyn, Jeroen
De Mey, Marjan
author_sort Peters, Gert
collection PubMed
description Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation.
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spelling pubmed-61148982018-09-15 Exploring of the feature space of de novo developed post-transcriptional riboregulators Peters, Gert Maertens, Jo Lammertyn, Jeroen De Mey, Marjan PLoS Comput Biol Research Article Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation. Public Library of Science 2018-08-17 /pmc/articles/PMC6114898/ /pubmed/30118473 http://dx.doi.org/10.1371/journal.pcbi.1006170 Text en © 2018 Peters et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Peters, Gert
Maertens, Jo
Lammertyn, Jeroen
De Mey, Marjan
Exploring of the feature space of de novo developed post-transcriptional riboregulators
title Exploring of the feature space of de novo developed post-transcriptional riboregulators
title_full Exploring of the feature space of de novo developed post-transcriptional riboregulators
title_fullStr Exploring of the feature space of de novo developed post-transcriptional riboregulators
title_full_unstemmed Exploring of the feature space of de novo developed post-transcriptional riboregulators
title_short Exploring of the feature space of de novo developed post-transcriptional riboregulators
title_sort exploring of the feature space of de novo developed post-transcriptional riboregulators
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114898/
https://www.ncbi.nlm.nih.gov/pubmed/30118473
http://dx.doi.org/10.1371/journal.pcbi.1006170
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