An automated DIY framework for experimental evolution of Pseudomonas putida

Summary Adaptive laboratory evolution (ALE) is a general and effective strategy for optimizing the design of engineered genetic circuits and upgrading metabolic phenotypes. However, the specific characteristics of each microorganism typically ask for exclusive conditions that need to be adjusted to...

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Autores principales:	David R. Espeso, Pavel Dvořák, Tomás Aparicio, Víctor deLorenzo
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	Biotechnology TP248.13-248.65
Acceso en línea:	https://doaj.org/article/0bbcc3bfade140428628e1b41f252434
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spelling	oai:doaj.org-article:0bbcc3bfade140428628e1b41f2524342021-11-18T15:39:53ZAn automated DIY framework for experimental evolution of Pseudomonas putida1751-791510.1111/1751-7915.13678https://doaj.org/article/0bbcc3bfade140428628e1b41f2524342021-11-01T00:00:00Zhttps://doi.org/10.1111/1751-7915.13678https://doaj.org/toc/1751-7915Summary Adaptive laboratory evolution (ALE) is a general and effective strategy for optimizing the design of engineered genetic circuits and upgrading metabolic phenotypes. However, the specific characteristics of each microorganism typically ask for exclusive conditions that need to be adjusted to the biological chassis at stake. In this work, we have adopted a do‐it‐yourself (DIY) approach to implement a flexible and automated framework for performing ALE experiments with the environmental bacterium and metabolic engineering platform Pseudomonas putida. The setup includes a dual‐chamber semi‐continuous log‐phase bioreactor design combined with an anti‐biofilm layout to manage specific traits of this bacterium in long‐term cultivation experiments. As a way of validation, the prototype was instrumental for selecting fast‐growing variants of a P. putida strain engineered to metabolize D‐xylose as sole carbon and energy source after running an automated 42 days protocol of iterative regrowth. Several genomic changes were identified in the evolved population that pinpointed the role of RNA polymerase in controlling overall physiological conditions during metabolism of the new carbon source.David R. EspesoPavel DvořákTomás AparicioVíctor deLorenzoWileyarticleBiotechnologyTP248.13-248.65ENMicrobial Biotechnology, Vol 14, Iss 6, Pp 2679-2685 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biotechnology TP248.13-248.65
spellingShingle	Biotechnology TP248.13-248.65 David R. Espeso Pavel Dvořák Tomás Aparicio Víctor deLorenzo An automated DIY framework for experimental evolution of Pseudomonas putida
description	Summary Adaptive laboratory evolution (ALE) is a general and effective strategy for optimizing the design of engineered genetic circuits and upgrading metabolic phenotypes. However, the specific characteristics of each microorganism typically ask for exclusive conditions that need to be adjusted to the biological chassis at stake. In this work, we have adopted a do‐it‐yourself (DIY) approach to implement a flexible and automated framework for performing ALE experiments with the environmental bacterium and metabolic engineering platform Pseudomonas putida. The setup includes a dual‐chamber semi‐continuous log‐phase bioreactor design combined with an anti‐biofilm layout to manage specific traits of this bacterium in long‐term cultivation experiments. As a way of validation, the prototype was instrumental for selecting fast‐growing variants of a P. putida strain engineered to metabolize D‐xylose as sole carbon and energy source after running an automated 42 days protocol of iterative regrowth. Several genomic changes were identified in the evolved population that pinpointed the role of RNA polymerase in controlling overall physiological conditions during metabolism of the new carbon source.
format	article
author	David R. Espeso Pavel Dvořák Tomás Aparicio Víctor deLorenzo
author_facet	David R. Espeso Pavel Dvořák Tomás Aparicio Víctor deLorenzo
author_sort	David R. Espeso
title	An automated DIY framework for experimental evolution of Pseudomonas putida
title_short	An automated DIY framework for experimental evolution of Pseudomonas putida
title_full	An automated DIY framework for experimental evolution of Pseudomonas putida
title_fullStr	An automated DIY framework for experimental evolution of Pseudomonas putida
title_full_unstemmed	An automated DIY framework for experimental evolution of Pseudomonas putida
title_sort	automated diy framework for experimental evolution of pseudomonas putida
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/0bbcc3bfade140428628e1b41f252434
work_keys_str_mv	AT davidrespeso anautomateddiyframeworkforexperimentalevolutionofpseudomonasputida AT paveldvorak anautomateddiyframeworkforexperimentalevolutionofpseudomonasputida AT tomasaparicio anautomateddiyframeworkforexperimentalevolutionofpseudomonasputida AT victordelorenzo anautomateddiyframeworkforexperimentalevolutionofpseudomonasputida AT davidrespeso automateddiyframeworkforexperimentalevolutionofpseudomonasputida AT paveldvorak automateddiyframeworkforexperimentalevolutionofpseudomonasputida AT tomasaparicio automateddiyframeworkforexperimentalevolutionofpseudomonasputida AT victordelorenzo automateddiyframeworkforexperimentalevolutionofpseudomonasputida
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An automated DIY framework for experimental evolution of Pseudomonas putida

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