Gene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments

ABSTRACT Central metabolism is a topic that has been studied for decades, and yet, this process is still not fully understood in Escherichia coli, perhaps the most amenable and well-studied model organism in biology. To further our understanding, we used a high-throughput method to measure the growt...

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Autores principales:	Madeline Tong, Shawn French, Sara S. El Zahed, Wai kit Ong, Peter D. Karp, Eric D. Brown
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Escherichia coli carbon metabolism carbon source central metabolism genetics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/e33f055cd08b4832bfa4994e08979872
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spelling	oai:doaj.org-article:e33f055cd08b4832bfa4994e089798722021-11-15T16:19:08ZGene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments10.1128/mBio.02259-202150-7511https://doaj.org/article/e33f055cd08b4832bfa4994e089798722020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02259-20https://doaj.org/toc/2150-7511ABSTRACT Central metabolism is a topic that has been studied for decades, and yet, this process is still not fully understood in Escherichia coli, perhaps the most amenable and well-studied model organism in biology. To further our understanding, we used a high-throughput method to measure the growth kinetics of each of 3,796 E. coli single-gene deletion mutants in 30 different carbon sources. In total, there were 342 genes (9.01%) encompassing a breadth of biological functions that showed a growth phenotype on at least 1 carbon source, demonstrating that carbon metabolism is closely linked to a large number of processes in the cell. We identified 74 genes that showed low growth in 90% of conditions, defining a set of genes which are essential in nutrient-limited media, regardless of the carbon source. The data are compiled into a Web application, Carbon Phenotype Explorer (CarPE), to facilitate easy visualization of growth curves for each mutant strain in each carbon source. Our experimental data matched closely with the predictions from the EcoCyc metabolic model which uses flux balance analysis to predict growth phenotypes. From our comparisons to the model, we found that, unexpectedly, phosphoenolpyruvate carboxylase (ppc) was required for robust growth in most carbon sources other than most trichloroacetic acid (TCA) cycle intermediates. We also identified 51 poorly annotated genes that showed a low growth phenotype in at least 1 carbon source, which allowed us to form hypotheses about the functions of these genes. From this list, we further characterized the ydhC gene and demonstrated its role in adenosine efflux. IMPORTANCE While there has been much study of bacterial gene dispensability, there is a lack of comprehensive genome-scale examinations of the impact of gene deletion on growth in different carbon sources. In this context, a lot can be learned from such experiments in the model microbe Escherichia coli where much is already understood and there are existing tools for the investigation of carbon metabolism and physiology (1). Gene deletion studies have practical potential in the field of antibiotic drug discovery where there is emerging interest in bacterial central metabolism as a target for new antibiotics (2). Furthermore, some carbon utilization pathways have been shown to be critical for initiating and maintaining infection for certain pathogens and sites of infection (3–5). Here, with the use of high-throughput solid medium phenotyping methods, we have generated kinetic growth measurements for 3,796 genes under 30 different carbon source conditions. This data set provides a foundation for research that will improve our understanding of genes with unknown function, aid in predicting potential antibiotic targets, validate and advance metabolic models, and help to develop our understanding of E. coli metabolism.Madeline TongShawn FrenchSara S. El ZahedWai kit OngPeter D. KarpEric D. BrownAmerican Society for MicrobiologyarticleEscherichia colicarbon metabolismcarbon sourcecentral metabolismgeneticsMicrobiologyQR1-502ENmBio, Vol 11, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Escherichia coli carbon metabolism carbon source central metabolism genetics Microbiology QR1-502
spellingShingle	Escherichia coli carbon metabolism carbon source central metabolism genetics Microbiology QR1-502 Madeline Tong Shawn French Sara S. El Zahed Wai kit Ong Peter D. Karp Eric D. Brown Gene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments
description	ABSTRACT Central metabolism is a topic that has been studied for decades, and yet, this process is still not fully understood in Escherichia coli, perhaps the most amenable and well-studied model organism in biology. To further our understanding, we used a high-throughput method to measure the growth kinetics of each of 3,796 E. coli single-gene deletion mutants in 30 different carbon sources. In total, there were 342 genes (9.01%) encompassing a breadth of biological functions that showed a growth phenotype on at least 1 carbon source, demonstrating that carbon metabolism is closely linked to a large number of processes in the cell. We identified 74 genes that showed low growth in 90% of conditions, defining a set of genes which are essential in nutrient-limited media, regardless of the carbon source. The data are compiled into a Web application, Carbon Phenotype Explorer (CarPE), to facilitate easy visualization of growth curves for each mutant strain in each carbon source. Our experimental data matched closely with the predictions from the EcoCyc metabolic model which uses flux balance analysis to predict growth phenotypes. From our comparisons to the model, we found that, unexpectedly, phosphoenolpyruvate carboxylase (ppc) was required for robust growth in most carbon sources other than most trichloroacetic acid (TCA) cycle intermediates. We also identified 51 poorly annotated genes that showed a low growth phenotype in at least 1 carbon source, which allowed us to form hypotheses about the functions of these genes. From this list, we further characterized the ydhC gene and demonstrated its role in adenosine efflux. IMPORTANCE While there has been much study of bacterial gene dispensability, there is a lack of comprehensive genome-scale examinations of the impact of gene deletion on growth in different carbon sources. In this context, a lot can be learned from such experiments in the model microbe Escherichia coli where much is already understood and there are existing tools for the investigation of carbon metabolism and physiology (1). Gene deletion studies have practical potential in the field of antibiotic drug discovery where there is emerging interest in bacterial central metabolism as a target for new antibiotics (2). Furthermore, some carbon utilization pathways have been shown to be critical for initiating and maintaining infection for certain pathogens and sites of infection (3–5). Here, with the use of high-throughput solid medium phenotyping methods, we have generated kinetic growth measurements for 3,796 genes under 30 different carbon source conditions. This data set provides a foundation for research that will improve our understanding of genes with unknown function, aid in predicting potential antibiotic targets, validate and advance metabolic models, and help to develop our understanding of E. coli metabolism.
format	article
author	Madeline Tong Shawn French Sara S. El Zahed Wai kit Ong Peter D. Karp Eric D. Brown
author_facet	Madeline Tong Shawn French Sara S. El Zahed Wai kit Ong Peter D. Karp Eric D. Brown
author_sort	Madeline Tong
title	Gene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments
title_short	Gene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments
title_full	Gene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments
title_fullStr	Gene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments
title_full_unstemmed	Gene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments
title_sort	gene dispensability in <named-content content-type="genus-species">escherichia coli</named-content> grown in thirty different carbon environments
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/e33f055cd08b4832bfa4994e08979872
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Gene Dispensability in <named-content content-type="genus-species">Escherichia coli</named-content> Grown in Thirty Different Carbon Environments

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