Data for Intramolecular Carbon Isotope Fractionations Associated with Glucose Metabolism in Escherichia coli

Youki Sato; Juliana Kristine Drozd; Elliott Mueller; Allison Ann Baczynski; Alexis Gilbert; Kate Freeman

Data for Intramolecular Carbon Isotope Fractionations Associated with Glucose Metabolism in Escherichia coli

To better understand metabolic controls on carbon isotope patterns within acetogenic lipids and their building blocks, we determined intramolecular δ13C values of acetate excreted from E. coli grown on glucose at different growth stages. These analyses revealed a stepwise reversal in the isotopic difference between the carboxyl and methyl carbons of acetate sampled in exponential versus stationary growth. Optimization of a method using GC-Orbitrap mass spectrometry enabled sufficiently accurate and precise measurements of low mM concentrations for natural abundance isotope ratios. To aid in interpretation, an isotope model for E. coli central metabolism using glucose was run with varying relative carbon fluxes through pyruvate dehydrogenase (ƒPDH). The model was also modified to account for acetate re-uptake through the phosphate transacetylase/acetate kinase (pta-ackA) pathway. Models employed carbon flux and enzymatic fractionation data from published studies and the QIRN model framework.

During exponential growth, extracellular acetate’s carboxyl carbon was depleted in 13C by -11.3 ± 1.9‰ relative to its methyl carbon. This difference is consistent with a high relative carbon flux commitment from pyruvate to acetate, as modeled with ƒPDH = 0.89. However, as glucose was further consumed and acetate accumulated, intramolecular patterns reversed to +7.8± 1.9‰, representing 13C enrichment in the carboxyl carbon relative to the methyl carbon. This intramolecular isotope reversal cannot be accounted for by changes in ƒPDH. Instead, our data and modeling illustrate that it resulted from a reversible “acetate switch” metabolism, which has implications for understanding isotope patterns within larger microbial biomolecules synthesized from acetyl-CoA.

Citation

Sato, Youki; Drozd, Juliana; Mueller, Elliott; Baczynski, Allison; Gilbert, Alexis; Freeman, Kate (2026). Data for Intramolecular Carbon Isotope Fractionations Associated with Glucose Metabolism in Escherichia coli [Data set]. Scholarsphere. https://doi.org/10.26207/shys-g826

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Metadata

Work Title	Data for Intramolecular Carbon Isotope Fractionations Associated with Glucose Metabolism in Escherichia coli
Access	Open Access
Creators	Youki Sato Juliana Kristine Drozd Elliott Mueller Allison Ann Baczynski Alexis Gilbert Kate Freeman
Keyword	E. coli Acetate Acetyl-CoA Orbitrap MS Intramolecular Isotope Analysis Stable Isotopes
License	CC BY-NC 4.0 (Attribution-NonCommercial)
Work Type	Dataset
Acknowledgments	NASA Astrobiology Institute Grant 80NSSC18M009
Publication Date	2026
DOI	doi:10.26207/shys-g826
Related URLs	https://doi.org/10.1016/j.orggeochem.2026.105245
Deposited	February 06, 2026

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Version 1
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Created

February 06, 2026 07:53 by yws5168
Updated

February 06, 2026 07:53 by [unknown user]
Updated Keyword, Publisher, Description, and 1 more Show Changes

February 06, 2026 07:55 by yws5168
Keyword
- E.coli, Acetate, Acetyl-CoA, Orbitrap MS, Intramolecular Isotope Analysis, Stable Isotopes
Publisher
- Organic Geochemistry
Description
- To better understand metabolic controls on carbon isotope patterns within acetogenic lipids and their building blocks, we determined intramolecular δ13C values of acetate excreted from E. coli grown on glucose at different growth stages. These analyses revealed a stepwise reversal in the isotopic difference between the carboxyl and methyl carbons of acetate sampled in exponential versus stationary growth. Optimization of a method using GC-Orbitrap mass spectrometry enabled sufficiently accurate and precise measurements of low mM concentrations for natural abundance isotope ratios. To aid in interpretation, an isotope model for E. coli central metabolism using glucose was run with varying relative carbon fluxes through pyruvate dehydrogenase (ƒPDH). The model was also modified to account for acetate re-uptake through the phosphate transacetylase/acetate kinase (pta-ackA) pathway. Models employed carbon flux and enzymatic fractionation data from published studies and the QIRN model framework.
- During exponential growth, extracellular acetate’s carboxyl carbon was depleted in 13C by -11.3 ± 1.9‰ relative to its methyl carbon. This difference is consistent with a high relative carbon flux commitment from pyruvate to acetate, as modeled with ƒPDH = 0.89. However, as glucose was further consumed and acetate accumulated, intramolecular patterns reversed to +7.8± 1.9‰, representing 13C enrichment in the carboxyl carbon relative to the methyl carbon. This intramolecular isotope reversal cannot be accounted for by changes in ƒPDH. Instead, our data and modeling illustrate that it resulted from a reversible “acetate switch” metabolism, which has implications for understanding isotope patterns within larger microbial biomolecules synthesized from acetyl-CoA.
Publication Date
- 2026
Updated Acknowledgments Show Changes

February 06, 2026 07:59 by yws5168
Acknowledgments
- NASA Astrobiology Institute Grant 80NSSC18M009
Added Creator Youki Sato

February 06, 2026 07:59 by yws5168
Added Creator Juliana Kristine Drozd

February 06, 2026 07:59 by yws5168
Added Creator Elliott Mueller

February 06, 2026 07:59 by yws5168
Added Creator Allison Ann Baczynski

February 06, 2026 07:59 by yws5168
Added Creator Alexis Gilbert

February 06, 2026 07:59 by yws5168
Added Creator Kate Freeman

February 06, 2026 07:59 by yws5168
Added E.coli Master Data For Upload.xlsx

February 06, 2026 08:22 by yws5168
Added QIRN f-PDH Track_ACC - For Upload.xlsx

February 06, 2026 08:22 by yws5168
Added 082225 HAc Cal Curve - For Upload.xlsx

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Added README.txt

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Updated License Show Changes

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- https://creativecommons.org/licenses/by-nc/4.0/
Published

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Updated

February 06, 2026 21:13 by [unknown user]
Updated Keyword, Publisher Show Changes

February 10, 2026 13:06 by avs5190
Keyword
- ~~E.coli, Acetate, Acetyl-CoA, Orbitrap MS, Intramolecular Isotope Analysis, Stable Isotopes~~
- E. coli, Acetate, Acetyl-CoA, Orbitrap MS, Intramolecular Isotope Analysis, Stable Isotopes
Publisher
- ~~Organic Geochemistry~~

Version 2
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Created

May 04, 2026 03:34 by yws5168
Deleted 082225 HAc Cal Curve - For Upload.xlsx

May 04, 2026 03:35 by yws5168
Deleted E.coli Master Data For Upload.xlsx

May 04, 2026 03:35 by yws5168
Deleted QIRN f-PDH Track_ACC - For Upload.xlsx

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May 04, 2026 03:35 by yws5168
Added 20250201_Ecoli_growth_curve.xlsx

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Added 20250822_HAc_Cal_Curve_For_Upload.xlsx

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Added E.coli_Master_Data_ForUpload_1.xlsx

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May 04, 2026 03:36 by yws5168
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May 04, 2026 03:36 by yws5168
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Published

May 04, 2026 03:36 by yws5168
Updated

May 04, 2026 22:10 by [unknown user]

Version 3
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Created

June 25, 2026 03:18 by yws5168
Updated Publisher, Related URLs Show Changes

June 25, 2026 03:19 by yws5168
Publisher
- Organic Geochemistry
Related URLs
- https://doi.org/10.1016/j.orggeochem.2026.105245
Deleted README.txt

June 25, 2026 03:19 by yws5168
Added README.txt

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Published

June 25, 2026 03:20 by yws5168
Updated

June 25, 2026 22:04 by [unknown user]
Updated Publisher Show Changes

July 09, 2026 13:12 by avs5190
Publisher
- ~~Organic Geochemistry~~

Data for Intramolecular Carbon Isotope Fractionations Associated with Glucose Metabolism in Escherichia coli

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