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Engineering gene overlaps to sustain genetic constructs in vivo

Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability o...

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Autores principales: Decrulle, Antoine L., Frénoy, Antoine, Meiller-Legrand, Thomas A., Bernheim, Aude, Lotton, Chantal, Gutierrez, Arnaud, Lindner, Ariel B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8528312/
https://www.ncbi.nlm.nih.gov/pubmed/34624014
http://dx.doi.org/10.1371/journal.pcbi.1009475
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author Decrulle, Antoine L.
Frénoy, Antoine
Meiller-Legrand, Thomas A.
Bernheim, Aude
Lotton, Chantal
Gutierrez, Arnaud
Lindner, Ariel B.
author_facet Decrulle, Antoine L.
Frénoy, Antoine
Meiller-Legrand, Thomas A.
Bernheim, Aude
Lotton, Chantal
Gutierrez, Arnaud
Lindner, Ariel B.
author_sort Decrulle, Antoine L.
collection PubMed
description Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of costly genes by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% of E. coli genes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, reducing the evolutionary potential of the system and thus increasing its stability over time.
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spelling pubmed-85283122021-10-21 Engineering gene overlaps to sustain genetic constructs in vivo Decrulle, Antoine L. Frénoy, Antoine Meiller-Legrand, Thomas A. Bernheim, Aude Lotton, Chantal Gutierrez, Arnaud Lindner, Ariel B. PLoS Comput Biol Research Article Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of costly genes by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% of E. coli genes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, reducing the evolutionary potential of the system and thus increasing its stability over time. Public Library of Science 2021-10-08 /pmc/articles/PMC8528312/ /pubmed/34624014 http://dx.doi.org/10.1371/journal.pcbi.1009475 Text en © 2021 Decrulle et al 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 use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Decrulle, Antoine L.
Frénoy, Antoine
Meiller-Legrand, Thomas A.
Bernheim, Aude
Lotton, Chantal
Gutierrez, Arnaud
Lindner, Ariel B.
Engineering gene overlaps to sustain genetic constructs in vivo
title Engineering gene overlaps to sustain genetic constructs in vivo
title_full Engineering gene overlaps to sustain genetic constructs in vivo
title_fullStr Engineering gene overlaps to sustain genetic constructs in vivo
title_full_unstemmed Engineering gene overlaps to sustain genetic constructs in vivo
title_short Engineering gene overlaps to sustain genetic constructs in vivo
title_sort engineering gene overlaps to sustain genetic constructs in vivo
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8528312/
https://www.ncbi.nlm.nih.gov/pubmed/34624014
http://dx.doi.org/10.1371/journal.pcbi.1009475
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