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General Information
Manuscript title Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8
PubMed ID 24909362
Journal Metabolic Engineering
Year 2014
Authors Aditi Swarup, Jimg Lu, Kathleen C. DeWoody, Maciek R. Antoniewicz
Affiliations Department of Chemical & Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark DE 19716, USA
Keywords Extremophile, Thermophilic bacterium, Optimal growth, Metabolic network model, Isotopic labeling
Full text article Swarup_2014.pdf
Project name not specified

Experiment Description
Organism Thermus thermophilus
Strain HB8 (ATCC 27634)
Data type flux measurements
Data units % substrate uptake
Execution date not specified

Experimental Details
Temperature (°C) 70
pH 7.9
Carbon source glucose
Culture mode batch
Process condition aerobic
Dilution rate (h⁻¹)
Working volume (L) 0.01
Biomass concentration (g/L) 0.39 (g/L)/OD600 cell dry weight and 25.3 g/C-mol for the molecular weight of dry biomass
Medium composition

Glucose stock solutions were prepared at 20 wt% in distilled water. The optimized minimum medium contained (per liter of medium): 0.50 g K2HPO4, 0.30 g KH2PO4, 0.50 g NH4Cl, 0.50 g NaCl, 0.20 g MgCl2.6H2O, 0.04 g CaSO4.2H2O, 40 mL of 1 M Tris, 5 mL of Wolfe׳s minerals, and 5 mL of Wolfe׳s vitamins.

General protocol information Flux analysis method: 13C constrained MFA

Platform: GC-MS

Methods description - Notes

13C-Metabolic flux analysis - 13C –MFA was performed using the Metran software [1,2], which is based on the elementary metabolite units (EMU) framework [3,4]. Fluxes were estimated by minimizing the variance-weighted sum of squared residuals (SSR) between the experimentally ...

[1] S.B. Crown, M.R. Antoniewicz,Metab. Eng., 20 (2013), pp. 42–48.
[2] H. Yoo, M.R. Antoniewicz, G. Stephanopoulos, J.K. Kelleher, J. Biol. Chem., 283 (2008), pp. 20621–20627.
[3] M.R. Antoniewicz, J.K. Kelleher, G. Stephanopoulos, Metab. Eng., 9 (2007), pp. 68–86.
[4] J.D. Young, J.L. Walther, M.R. Antoniewicz, H. Yoo, G. Stephanopoulos, Biotechnol. Bioeng., 99 (2008), pp. 686–699.
[5] M.R. Antoniewicz, J.K. Kelleher, G. Stephanopoulos, Metab. Eng., 8 (2006), pp. 324–337.
[6] R. Caspi, T. Altman, K. Dreher, C.A. Fulcher, P. Subhraveti, I.M. Keseler, A. Kothari, M. Krummenacker, M. Latendresse, L.A. Mueller, Q. Ong, S. Paley, A. Pujar, A.G. Shearer, M. Travers, D. Weerasinghe, P. Zhang, P.D. Karp, Nucleic Acids Res., 40 (2012), pp.–D753
[7] M. Kanehisa, S. Goto, Nucleic Acids Res., 28 (2000), pp. 27–30.
[8] M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, M. Tanabe, Nucleic Acids Res., 40 (2012), pp. D109–D114.

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Entered by: Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Interests: mathematical modeling, accessible data, use of data

Created: 2015-09-22 12:48:07 UTC

Updated: 2020-04-24 16:10:35 UTC

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Status: (reviewed) 2015-09-22 13:06:46 UTC

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