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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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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. |
format | Online Article Text |
id | pubmed-9853098 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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