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Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli

The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing exp...

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Autores principales: Park, Joon Young, Lee, Sang-Mok, Ebrahim, Ali, Scott-Nevros, Zoe K, Kim, Jaehyung, Yang, Laurence, Sastry, Anand, Seo, Sang Woo, Palsson, Bernhard O, Kim, Donghyuk
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9853098/
https://www.ncbi.nlm.nih.gov/pubmed/36685725
http://dx.doi.org/10.1093/nargab/lqad006
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author Park, Joon Young
Lee, Sang-Mok
Ebrahim, Ali
Scott-Nevros, Zoe K
Kim, Jaehyung
Yang, Laurence
Sastry, Anand
Seo, Sang Woo
Palsson, Bernhard O
Kim, Donghyuk
author_facet Park, Joon Young
Lee, Sang-Mok
Ebrahim, Ali
Scott-Nevros, Zoe K
Kim, Jaehyung
Yang, Laurence
Sastry, Anand
Seo, Sang Woo
Palsson, Bernhard O
Kim, Donghyuk
author_sort Park, Joon Young
collection PubMed
description The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in Escherichia coli. We comprehensively predict alternative nitrogen sources, including cytosine and cytidine, which trigger differential activation of Nac using a model-driven workflow. In accordance with the prediction, genome-wide measurements with ChIP-exo and RNA-seq were performed. Integrative data analysis reveals that the Nac and NtrC regulons consist of 97 and 43 genes under alternative nitrogen conditions, respectively. Functional analysis of Nac at the transcriptional level showed that Nac directly down-regulates amino acid biosynthesis and restores expression of tricarboxylic acid (TCA) cycle genes to alleviate nitrogen-limiting stress. We also demonstrate that both TFs coherently modulate α-ketoglutarate accumulation stress due to nitrogen limitation by co-activating amino acid and diamine degradation pathways. A systems-biology approach provided a detailed and quantitative understanding of both TF’s roles and how nitrogen and carbon metabolic networks respond complementarily to nitrogen-limiting stress.
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spelling pubmed-98530982023-01-20 Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli Park, Joon Young Lee, Sang-Mok Ebrahim, Ali Scott-Nevros, Zoe K Kim, Jaehyung Yang, Laurence Sastry, Anand Seo, Sang Woo Palsson, Bernhard O Kim, Donghyuk NAR Genom Bioinform Standard Article The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in Escherichia coli. We comprehensively predict alternative nitrogen sources, including cytosine and cytidine, which trigger differential activation of Nac using a model-driven workflow. In accordance with the prediction, genome-wide measurements with ChIP-exo and RNA-seq were performed. Integrative data analysis reveals that the Nac and NtrC regulons consist of 97 and 43 genes under alternative nitrogen conditions, respectively. Functional analysis of Nac at the transcriptional level showed that Nac directly down-regulates amino acid biosynthesis and restores expression of tricarboxylic acid (TCA) cycle genes to alleviate nitrogen-limiting stress. We also demonstrate that both TFs coherently modulate α-ketoglutarate accumulation stress due to nitrogen limitation by co-activating amino acid and diamine degradation pathways. A systems-biology approach provided a detailed and quantitative understanding of both TF’s roles and how nitrogen and carbon metabolic networks respond complementarily to nitrogen-limiting stress. Oxford University Press 2023-01-20 /pmc/articles/PMC9853098/ /pubmed/36685725 http://dx.doi.org/10.1093/nargab/lqad006 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Standard Article
Park, Joon Young
Lee, Sang-Mok
Ebrahim, Ali
Scott-Nevros, Zoe K
Kim, Jaehyung
Yang, Laurence
Sastry, Anand
Seo, Sang Woo
Palsson, Bernhard O
Kim, Donghyuk
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli
title Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli
title_full Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli
title_fullStr Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli
title_full_unstemmed Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli
title_short Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli
title_sort model-driven experimental design workflow expands understanding of regulatory role of nac in escherichia coli
topic Standard Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9853098/
https://www.ncbi.nlm.nih.gov/pubmed/36685725
http://dx.doi.org/10.1093/nargab/lqad006
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