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Investigation of useful carbon tracers for (13)C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions
The (13)C-MFA experiments require an optimal design since the precision or confidence intervals of the estimated flux levels depends on factors such as the composition of (13)C-labeled carbon sources, as well as the metabolic flux distribution of interest. In this study, useful compositions of (13)C...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678827/ https://www.ncbi.nlm.nih.gov/pubmed/29142823 http://dx.doi.org/10.1016/j.meteno.2016.06.001 |
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author | Maeda, Kousuke Okahashi, Nobuyuki Toya, Yoshihiro Matsuda, Fumio Shimizu, Hiroshi |
author_facet | Maeda, Kousuke Okahashi, Nobuyuki Toya, Yoshihiro Matsuda, Fumio Shimizu, Hiroshi |
author_sort | Maeda, Kousuke |
collection | PubMed |
description | The (13)C-MFA experiments require an optimal design since the precision or confidence intervals of the estimated flux levels depends on factors such as the composition of (13)C-labeled carbon sources, as well as the metabolic flux distribution of interest. In this study, useful compositions of (13)C-labeled glucose for (13)C-metabolic flux analysis ((13)C-MFA) of Escherichia coli are investigated using a computer simulation of the stable isotope labeling experiment. Following the generation of artificial mass spectra datasets of amino acid fragments using five literature-reported flux distributions of E. coli, the best fitted flux distribution and the 95% confidence interval were estimated by the (13)C-MFA procedure. A comparison of the precision scores showed that [1, 2-(13)C]glucose and a mixture of [1-(13)C] and [U-(13)C]glucose at 8:2 are one of the best carbon sources for a precise estimation of flux levels of the pentose phosphate pathway, glycolysis and the TCA cycle. Although the precision scores of the anaplerotic and glyoxylate pathway reactions were affected by both the carbon source and flux distribution, it was also shown that the mixture of non-labeled, [1-(13)C], and [U-(13)C]glucose at 4:1:5 was specifically effective for the flux estimation of the glyoxylate pathway reaction. These findings were confirmed by wet (13)C-MFA experiments. |
format | Online Article Text |
id | pubmed-5678827 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-56788272017-11-15 Investigation of useful carbon tracers for (13)C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions Maeda, Kousuke Okahashi, Nobuyuki Toya, Yoshihiro Matsuda, Fumio Shimizu, Hiroshi Metab Eng Commun Article The (13)C-MFA experiments require an optimal design since the precision or confidence intervals of the estimated flux levels depends on factors such as the composition of (13)C-labeled carbon sources, as well as the metabolic flux distribution of interest. In this study, useful compositions of (13)C-labeled glucose for (13)C-metabolic flux analysis ((13)C-MFA) of Escherichia coli are investigated using a computer simulation of the stable isotope labeling experiment. Following the generation of artificial mass spectra datasets of amino acid fragments using five literature-reported flux distributions of E. coli, the best fitted flux distribution and the 95% confidence interval were estimated by the (13)C-MFA procedure. A comparison of the precision scores showed that [1, 2-(13)C]glucose and a mixture of [1-(13)C] and [U-(13)C]glucose at 8:2 are one of the best carbon sources for a precise estimation of flux levels of the pentose phosphate pathway, glycolysis and the TCA cycle. Although the precision scores of the anaplerotic and glyoxylate pathway reactions were affected by both the carbon source and flux distribution, it was also shown that the mixture of non-labeled, [1-(13)C], and [U-(13)C]glucose at 4:1:5 was specifically effective for the flux estimation of the glyoxylate pathway reaction. These findings were confirmed by wet (13)C-MFA experiments. Elsevier 2016-06-07 /pmc/articles/PMC5678827/ /pubmed/29142823 http://dx.doi.org/10.1016/j.meteno.2016.06.001 Text en © 2016 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Maeda, Kousuke Okahashi, Nobuyuki Toya, Yoshihiro Matsuda, Fumio Shimizu, Hiroshi Investigation of useful carbon tracers for (13)C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions |
title | Investigation of useful carbon tracers for (13)C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions |
title_full | Investigation of useful carbon tracers for (13)C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions |
title_fullStr | Investigation of useful carbon tracers for (13)C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions |
title_full_unstemmed | Investigation of useful carbon tracers for (13)C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions |
title_short | Investigation of useful carbon tracers for (13)C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions |
title_sort | investigation of useful carbon tracers for (13)c-metabolic flux analysis of escherichia coli by considering five experimentally determined flux distributions |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678827/ https://www.ncbi.nlm.nih.gov/pubmed/29142823 http://dx.doi.org/10.1016/j.meteno.2016.06.001 |
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