KiMoSys: a web-based repository of experimental data for Kinetic Models of biological Systems

Metadata
Data EntryID	63
Entered by	Administrator KiMoSys
Date Added	2013-06-12
Version	0
General Information
Manuscript title	Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli
Pubmed ID	19690571
Journal	Molecular Systems Biology
Year	2009
Authors	Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz
Affiliations	Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA
Keywords	E. coli, ammonia assimilation, nitrogen upshift
Project name	not specified
Experiment Description
Organism	Escherichia coli
Strain	NCM 3722 and mutants
Data type	time-series data of metabolites
Data units	mM
Execution date	not specified
Experimental Details
Temperature (0C)	37
pH	≈ 7.0
Carbon source	glucose
Culture mode	batch
Process condition	anaerobic
Dilution rate (h-1)	—
Working volume (L)	not specified
Biomass concentration (g/L)	not specified
Medium composition	Minimal salts media with 10mM NH4Cl and 0.4% glucose.
General protocol information	Sampling method: filter cultures were prepared by passing 5 ml of exponentially growing liquid batch culture hrough membrane filters.
	Quenching procedure: filters were submerged directly into -75ºC methanol or -20ºC 40:40:20 acetonitrile:methanol:water with 0.1% formic acid.
	Extraction technique: methanol
	Sample analyzing method: LC-ESI-MS
Methods description - Notes	Detailed protocols for preparing filter cultures and extracting metabolites have been published [1,2]. Metabolite measurement - Cell extracts were analyzed by LC-electrospray ionization (ESI)-MS/MS on a Thermo Quantum triple quadrupole mass spectrometer operating in selected reaction monitoring (SRM) mode. All samples were analyzed within 24 h of their preparation. Separate LC runs were conducted for positive and negative ionization modes, using hydrophilic interaction chromatography and ion-pairing reversed phase chromatography, respectively [3]. Amino acids were derivatized before their quantitation by LC-ESIMS/MS. Cell extract (200 µl) was mixed with triethylamine (5 µl) and benzyl chloral formate (1 µl) to convert amines to N-benzylcarbamate (Cbz) derivatives [4]. As internal standard signals did not vary substantially or systematically between samples within a given time course, the reported metabolite concentration changes are between-sample ratios of the peak heights of the SRM chromatograms without correction for the internal standard response, except for glutamate and glutamine, in which correction for internal standards was performed to maximize quantitative accuracy. -----------References------------- [1] Bennett B, Yuan J, Kimball E, Rabinowitz J (2008) Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat Protoc 3: 1299–1311. [2] Yuan J, Bennett B, Rabinowitz J (2008) Kinetic flux profiling for quantitation of cellular metabolic fluxes. Nature Protoc 3: 1328–1340. [3] Lu W, Bennett BD, Rabinowitz JD (2008). Analytical strategies for LCMS-based targeted metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 871: 236–242. [4] Kraml CM, Zhou D, Byrne N, McConnell O (2005) Enhanced chromatographic resolution of amine enantiomers as carbobenzyloxy derivatives in high-performance liquid chromatography and supercritical fluid chromatography. J Chromatogr A 1100: 108–115.
Data URL	http://kdbio.inesc-id.pt/kimosys/repository/63

time [min]	Glutamate [mM]	Std	Glutamine [mM]	Std	α-ketoglutarate [mM]	Std	Malate [mM]	Std	Aspartate [mM]	Std
	ChEBI:16015		ChEBI:18050		ChEBI:16810		ChEBI:30797		ChEBI:22660
-15	76.56	11.59	1.95	0.3	11.65	2.73	3.57	0.54	1.83	0.41
-8	76.56	11.59	1.95	0.3	11.65	2.73	3.57	0.54	1.83	0.41
-4	76.56	11.59	1.95	0.3	11.65	2.73	3.57	0.54	1.83	0.41
0	76.56	11.59	1.95	0.3	11.65	2.73	3.57	0.54	1.83	0.41
0.084	57.53	8.71	14.57	2.26	6.13	1.44	3.86	0.58	1.69	0.41
0.167	51.67	7.82	26.23	4.07	4.89	1.4	2.94	0.44	1.22	0.71
0.334	46.57	10.41	35.05	5.44	4.07	1.08	1.02	0.15	1.43	0.32
0.5	48.32	7.31	39.05	6.06	3.49	1.15	0.75	0.18	2.13	0.65
1	87.39	13.22	45.17	7.01	1.7	0.53	0.55	0.1	1.51	0.6
2	146.66	22.19	28.23	4.4	1.24	0.41	1.21	0.18	5.4	1.22
4	163.31	24.71	15.77	2.45	0.59	0.14	1.28	0.21	5.76	2.09
8	141.87	21.47	12.17	2.15	0.65	0.16	2.32	0.35	8.92	2.02
15	159.88	24.19	9.24	1.43	0.59	0.14	2.45	0.37	5.23	1.28
30	169.46	25.64	10.54	1.72	0.74	0.17	3.03	0.46	5.92	1.94

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time [min]	Glutamate [mM]	Std	Glutamine [mM]	Std	α-ketoglutarate [mM]	Std	Malate [mM]	Std	Aspartate [mM]	Std
	ChEBI:16015		ChEBI:18050		ChEBI:16810		ChEBI:30797		ChEBI:22660
-15	78.89	16.19	2.07	0.44	9.59	2.55	3.66	0.81	2.03	0.5
-8	78.89	16.19	2.07	0.44	9.59	2.55	3.66	0.81	2.03	0.5
-4	78.89	16.19	2.07	0.44	9.59	2.55	3.66	0.81	2.03	0.5
0	78.89	16.19	2.07	0.44	9.59	2.55	3.66	0.81	2.03	0.5
0.084	81.55	16.73	24.62	11.17	4.37	1.16	3.57	1.48	2.53	0.88
0.167	61.31	12.58	19.37	5.57	4.67	1.24	3.19	0.95	2.67	1.11
0.334	47.16	9.68	29.06	6.16	3.54	0.94	2.01	0.54	1.84	0.5
0.5	69.99	14.36	39.37	10.68	1.87	0.5	1.07	0.37	1.88	0.5
1	74.75	15.34	43.95	9.32	2.02	0.54	0.73	0.22	2.14	0.97
2	131.34	52.74	39.15	8.3	1.25	0.38	1.4	0.46	4.28	2.47
4	158.95	32.61	19.59	4.16	0.8	0.21	1.71	0.75	8.35	3
8	162.74	33.39	18.96	4.02	0.73	0.24	2.6	1.19	6.66	1.95
15	177.8	39.34	12.23	2.59	0.88	0.23	3.38	1.47	4.57	1.12
30	130.34	52.81	10.66	2.49	0.7	0.2	3.16	1.55	3.13	0.8

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time [min]	Glutamate [mM]	Std	Glutamine [mM]	Std	α-ketoglutarate [mM]	Std	Malate [mM]	Std	Aspartate [mM]	Std
	ChEBI:16015		ChEBI:18050		ChEBI:16810		ChEBI:30797		ChEBI:22660
-15	43448	7192	12972	2662	15468	3992	3860	1036	0.421	0.109
-8	43448	7192	12972	2662	15468	3992	3860	1036	0.421	0.109
-4	43448	7192	12972	2662	15468	3992	3860	1036	0.421	0.109
0	43448	7192	12972	2662	15468	3992	3860	1036	0.421	0.109
0.084	60175	9961	15941	6030	11038	2849	3880	2207	0.886	0.377
0.167	60571	12355	14517	6224	6543	1689	2040	0.905	1207	0.649
0.334	89402	14799	14171	6834	4587	1306	1144	0.881	1858	1100
0.5	93704	18335	12076	4282	3858	0.996	0.878	0.579	2502	1400
1	113643	19059	6224	2413	1934	0.59	1362	0.928	5047	2610
2	127745	25786	6282	1289	1274	0.329	1477	1056	6089	3124
4	120461	35213	7640	1567	0.903	0.295	1236	0.979	4971	2169
8	113167	25757	6840	1972	0.781	0.215	1305	1072	4666	2503
15	125657	20800	9075	3748	0.755	0.195	1478	1017	4097	2036
30	118551	19914	7615	2355	0.887	0.229	2515	2024	4141	1837

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time [min]	Glutamate [mM]	Std	Glutamine [mM]	Std	α-ketoglutarate [mM]	Std	Malate [mM]	Std	Aspartate [mM]	Std
	ChEBI:16015		ChEBI:18050		ChEBI:16810		ChEBI:30797		ChEBI:22660
-15	76.56	11.59	1.95	0.3	11.65	4.1	3.57	0.54	1.83	0.41
0	76.56	11.59	1.95	0.3	11.65	4.1	3.57	0.54	1.83	0.41
0.084	76.69	11.61	3.85	0.6	6.96	2.68	3.86	0.58	1.88	0.43
0.167	65.27	21.41	7.09	1.1	6.72	3.15	4.1	0.62	1.53	0.56
0.5	67.22	10.17	12.1	1.88	2.82	0.66	2.73	0.41	1.57	0.36
1	69.42	12.78	16.83	2.61	2.04	0.48	2.58	0.39	1.2	0.28
2	103.73	15.7	15.01	2.74	1.44	0.34	2.31	0.37	2	0.48
4	104.35	15.79	7.72	1.2	1.03	0.27	2.77	0.42	3.16	0.9
8	131.05	19.83	7.02	1.59	0.86	0.23	4.53	0.68	3.99	0.92
15	151.85	22.98	7.5	1.16	1.34	0.31	4.32	0.65	3.15	1
30	164.15	24.84	5.87	0.91	1.67	0.78	3.86	1.1	2.01	0.46

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time [min]	Glutamate [mM]	Std	Glutamine [mM]	Std	α-ketoglutarate [mM]	Std	Malate [mM]	Std	Aspartate [mM]	Std
	ChEBI:16015		ChEBI:18050		ChEBI:16810		ChEBI:30797		ChEBI:22660
-15	43.45	7.19	12.97	2.66	15.47	15.47	3.86	1.06	0.42	0.11
0	43.45	7.19	12.97	2.66	15.47	15.47	3.86	1.06	0.42	0.11
0.08	40.69	10.5	14.56	2.99	13.98	13.98	2.73	0.73	0.45	0.11
0.17	53.76	8.9	17.81	3.65	13.32	13.32	3.34	1.34	0.47	0.12
0.5	61.44	10.17	15.43	3.28	9.94	9.94	2.06	1.3	0.86	0.22
1	80.87	13.39	14.01	2.88	5.24	5.24	2.53	0.68	1.48	0.46
2	98.35	16.28	11.76	2.41	3.44	3.44	3.59	1.02	2.36	1.19
4	107.59	17.81	12.7	2.61	2.59	2.59	3.57	1.12	1.65	0.42
8	88.96	17.98	12.57	2.58	2.59	2.59	2.88	1.18	1.16	0.59
15	101.75	16.84	12.36	2.54	3.03	3.03	3.66	2.05	0.77	0.29
30	92.24	15.27	16.82	3.45	7.97	7.97	5.65	2.46	0.58	0.18

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time [min]	Glutamate [mM]	Std	Glutamine [mM]	Std	α-ketoglutarate [mM]	Std	Malate [mM]	Std	Aspartate [mM]	Std
	ChEBI:16015		ChEBI:18050		ChEBI:16810		ChEBI:30797		ChEBI:22660
-15	76.56	11.59	1.95	0.61	11.65	5.9	3.57	0.55	1.83	0.41
0	76.56	11.59	1.95	0.61	11.65	5.9	3.57	0.55	1.83	0.41
0.084	81.45	17.74	1.81	1.34	13.37	12.94	3.87	0.63	1.76	0.4
0.167	76.37	11.56	1.79	1.51	8.82	8.5	2.47	0.3	1.36	0.31
0.5	95.75	24.22	1.07	0.99	12.57	12	3.63	0.55	1.45	0.33
1	80.77	20.08	0.47	0.39	12.94	11.19	3.2	0.44	0.91	0.21
2	66.43	16.58	0.09	0.07	18.54	7.27	5.37	1.33	0.86	0.19
4	48.89	8.22	0.06	0.02	21.99	5.71	4.23	0.64	0.43	0.1
8	43.24	6.54	0.04	0.01	26.25	6.15	3.57	0.69	0.2	0.04
15	35.22	5.33	0.06	0.01	29.76	6.97	3.21	0.68	0.18	0.04
30	34.64	5.24	0.03	0.02	32.68	7.66	3.59	0.71	0.18	0.04

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time [min]	Glutamate [mM]	Std	Glutamine [mM]	Std	α-ketoglutarate [mM]	Std	Malate [mM]	Std	Aspartate [mM]	Std
	ChEBI:16015		ChEBI:18050		ChEBI:16810		ChEBI:30797		ChEBI:22660
-15	43.45	7.19	12.97	2.66	15.47	4.43	3.86	1.04	0.42	0.11
0	43.45	7.19	12.97	2.66	15.47	4.43	3.86	1.04	0.42	0.11
0.08	45.49	9.21	13.04	2.68	12.38	3.19	3.47	1.02	0.3	0.08
0.17	36.32	6.8	15.48	3.3	13.74	3.55	2.99	0.8	0.3	0.09
0.5	36.37	10.87	14.82	3.04	15.85	4.09	3.54	0.95	0.22	0.07
1	22.61	3.74	15.77	3.24	16.24	4.19	3.25	0.87	0.14	0.07
2	14.04	2.53	14.62	3	22.52	5.81	2.34	0.63	0.07	0.03
4	9.29	2.8	11.58	2.38	30.23	9.15	2.05	0.9	0.09	0.03
8	8.47	3.08	7.62	1.56	33.73	11.41	1.08	0.66	0.03	0.01
15	5.19	1.34	4.06	0.83	37.44	15.36	0.86	0.44	0.06	0.01
30	3.37	0.83	2.1	0.43	39.98	12.56	0.88	0.43	0.06	0.02

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time [min]	Glutamate [mM]	Std	Glutamine [mM]	Std	α-ketoglutarate [mM]	Std	Malate [mM]	Std	Aspartate [mM]	Std
	ChEBI:16015		ChEBI:18050		ChEBI:16810		ChEBI:30797		ChEBI:22660
-15	76.44	16.84	2.66	0.64	13.19	4.16	7.59	2.19	1.67	0.43
-8	76.44	16.84	2.66	0.64	13.19	4.16	7.59	2.19	1.67	0.43
-4	76.44	16.84	2.66	0.64	13.19	4.16	7.59	2.19	1.67	0.43
0	76.44	16.84	2.66	0.64	13.19	4.16	7.59	2.19	1.67	0.43
0.084	75.56	16.65	21.82	6.63	7.75	4.18	9.27	2.68	2.1	0.59
0.167	77.22	18.13	24.56	8.98	5.32	4.12	9.81	2.83	2.32	0.87
0.334	50.88	14.09	41.46	17.4	4.12	3.31	2.95	0.85	1.79	0.57
0.5	41.45	9.13	50.15	15.92	2.73	1.83	2.52	0.88	1.46	0.63
1	36.19	7.98	57.02	21.97	2.31	1.5	1.8	0.75	1.18	0.32
2	55.49	19.24	164.66	61.2	1.09	0.71	1.62	0.65	1.39	0.45
4	47.96	10.57	193.81	87.1	0.65	0.49	2.07	0.63	1.92	1.11
8	69.94	20.35	323.78	111.22	0.46	0.29	2.16	0.66	2.59	0.97
15	104.43	34.37	341.93	116.09	0.23	0.15	2.64	0.76	2.59	1.35
30	113.01	58.08	340.5	82.26	0.23	0.18	3.49	1.04	2.78	2.8

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Manuscript title	Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.
PubMed ID	19690571
Journal	Molecular Systems Biology
Year	2009
Authors	Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz
Affiliations	Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA
Keywords	E. coli, ammonia assimilation, nitrogen upshift
Full text article	Yuan_2009.pdf
Project name	not specified

Organism	Escherichia coli
Strain	NCM 3722 and mutants
Data type	time-series data of metabolites
Data units	mM
Execution date	not specified

APA	KiMoSys (https://kimosys.org). (2020, December 30). Data EntryID 63 (Escherichia coli). https://doi.org/10.34619/bspb-ek47
MLA	KiMoSys (https://kimosys.org). "Data EntryID 63 (Escherichia coli)." 2024, https://doi.org/10.34619/bspb-ek47
ISO-690	KiMoSys (https://kimosys.org). Data EntryID 63 (Escherichia coli). [online], [Accessed 30 December 2024]. Available from: https://doi.org/10.34619/bspb-ek47
BibTeX	@misc{ KiMoSysDataEntryID63, author = "{KiMoSys (https://kimosys.org)}", title = "Data EntryID 63 (Escherichia coli)", url = https://doi.org/10.34619/bspb-ek47", doi = "10.34619/bspb-ek47", note = "[Online; accessed 30-December-2024]" }

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