Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution Fluxomics
We have developed a robust workflow to measure high-resolution fluxotypes (metabolic flux phenotypes) for large strain libraries under fully controlled growth conditions. This was achieved by optimizing and automating the whole high-throughput fluxomics process and integrating all relevant software...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-04-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/11/5/271 |
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| author | Cécilia Bergès Edern Cahoreau Pierre Millard Brice Enjalbert Mickael Dinclaux Maud Heuillet Hanna Kulyk Lara Gales Noémie Butin Maxime Chazalviel Tony Palama Matthieu Guionnet Sergueï Sokol Lindsay Peyriga Floriant Bellvert Stéphanie Heux Jean-Charles Portais |
| author_facet | Cécilia Bergès Edern Cahoreau Pierre Millard Brice Enjalbert Mickael Dinclaux Maud Heuillet Hanna Kulyk Lara Gales Noémie Butin Maxime Chazalviel Tony Palama Matthieu Guionnet Sergueï Sokol Lindsay Peyriga Floriant Bellvert Stéphanie Heux Jean-Charles Portais |
| author_sort | Cécilia Bergès |
| collection | DOAJ |
| description | We have developed a robust workflow to measure high-resolution fluxotypes (metabolic flux phenotypes) for large strain libraries under fully controlled growth conditions. This was achieved by optimizing and automating the whole high-throughput fluxomics process and integrating all relevant software tools. This workflow allowed us to obtain highly detailed maps of carbon fluxes in the central carbon metabolism in a fully automated manner. It was applied to investigate the glucose fluxotypes of 180 <i>Escherichia coli</i> strains deleted for y-genes. Since the products of these y-genes potentially play a role in a variety of metabolic processes, the experiments were designed to be agnostic as to their potential metabolic impact. The obtained data highlight the robustness of <i>E. coli</i>’s central metabolism to y-gene deletion. For two y-genes, deletion resulted in significant changes in carbon and energy fluxes, demonstrating the involvement of the corresponding y-gene products in metabolic function or regulation. This work also introduces novel metrics to measure the actual scope and quality of high-throughput fluxomics investigations. |
| first_indexed | 2024-03-10T11:56:20Z |
| format | Article |
| id | doaj.art-c761429155da4cd3aca1f0b21e6492dc |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-10T11:56:20Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-c761429155da4cd3aca1f0b21e6492dc2023-11-21T17:16:21ZengMDPI AGMetabolites2218-19892021-04-0111527110.3390/metabo11050271Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution FluxomicsCécilia Bergès0Edern Cahoreau1Pierre Millard2Brice Enjalbert3Mickael Dinclaux4Maud Heuillet5Hanna Kulyk6Lara Gales7Noémie Butin8Maxime Chazalviel9Tony Palama10Matthieu Guionnet11Sergueï Sokol12Lindsay Peyriga13Floriant Bellvert14Stéphanie Heux15Jean-Charles Portais16Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToxalim (Research Centre in Food Toxicology), UMR1331, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceToulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, FranceWe have developed a robust workflow to measure high-resolution fluxotypes (metabolic flux phenotypes) for large strain libraries under fully controlled growth conditions. This was achieved by optimizing and automating the whole high-throughput fluxomics process and integrating all relevant software tools. This workflow allowed us to obtain highly detailed maps of carbon fluxes in the central carbon metabolism in a fully automated manner. It was applied to investigate the glucose fluxotypes of 180 <i>Escherichia coli</i> strains deleted for y-genes. Since the products of these y-genes potentially play a role in a variety of metabolic processes, the experiments were designed to be agnostic as to their potential metabolic impact. The obtained data highlight the robustness of <i>E. coli</i>’s central metabolism to y-gene deletion. For two y-genes, deletion resulted in significant changes in carbon and energy fluxes, demonstrating the involvement of the corresponding y-gene products in metabolic function or regulation. This work also introduces novel metrics to measure the actual scope and quality of high-throughput fluxomics investigations.https://www.mdpi.com/2218-1989/11/5/271high-resolution fluxotypingfluxomicshigh throughputy-ome phenotyping<i>E. coli</i> |
| spellingShingle | Cécilia Bergès Edern Cahoreau Pierre Millard Brice Enjalbert Mickael Dinclaux Maud Heuillet Hanna Kulyk Lara Gales Noémie Butin Maxime Chazalviel Tony Palama Matthieu Guionnet Sergueï Sokol Lindsay Peyriga Floriant Bellvert Stéphanie Heux Jean-Charles Portais Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution Fluxomics Metabolites high-resolution fluxotyping fluxomics high throughput y-ome phenotyping <i>E. coli</i> |
| title | Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution Fluxomics |
| title_full | Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution Fluxomics |
| title_fullStr | Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution Fluxomics |
| title_full_unstemmed | Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution Fluxomics |
| title_short | Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution Fluxomics |
| title_sort | exploring the glucose fluxotype of the i e coli i y ome using high resolution fluxomics |
| topic | high-resolution fluxotyping fluxomics high throughput y-ome phenotyping <i>E. coli</i> |
| url | https://www.mdpi.com/2218-1989/11/5/271 |
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