Characterization of chemostats from S. pyogenes wild type vs. arcA- and glnA-deletion mutants

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Metadata Organism_sample Data_ExtracellularMetabolites Results_CalculatedFluxes Instrument_chemostat Instrument_measurements Medium_Composition

Metadata	Values
Asset Title	Characterization of flux distribution of S. pyogenes M9 wildtype and the arcA- and glnA-knockout mutant in continuous cultures
Uploader	Antje Sieg, Silvio Hering
Uploader SEEK ID
Project	SysmoLab

ASSAY
Assay SEEK ID
Assay Title	Characterization of chemostats from S. pyogenes wildetype vs. arcA- and glnA-deletion mutants
Assay_type	catabolic flux distribution
Technology_type	HPLC
Description	S. pyogenes was grown in C-limited cultures at pH 6.5 and 7.5 and at a growth rate of 0.05
Experimentalist	Antje Sieg, Silvio Hering, Martijn Bekker
Date	2011-11-12T0:0:0+0000
SOP	2.1


Experimental_conditions
Item	temperature	Growth_Medium	dilution_rate
Compound (if concentration)		Glucose
Unit	ºC	mM	1/h
Start_value (optional)		53
End_value (optional)	37	0	0.05
Comments		CDM-LAB
Culture Growth	Chemostat
FACTORS_STUDIED
Item	pH
Compound (if concentration)
Unit
Start_value (optional)	6.5
End_value (optional)	7.5
SD (optional)
Comments

Sample							Treatment(s)		Culture_start_date	Date_at_sampling	Age_at_sampling_[hours]
	Organism	NCBI_ID	Strain	Genotype	Phenotype	organism/cell part	pH	Dilution_rate	date	date	age
1	Streptococcus_pyogenes	1314	M49	wild-type		whole cell	6.5	0.05	2012-01-10T0:0:0+0000	2012-01-18T0:0:0+0000	90.5
2	Streptococcus_pyogenes	1314	M49	wild-type		whole cell	7.5	0.05	2012-01-04T0:0:0+0000	2012-01-09T0:0:0+0000	140
3	Streptococcus_pyogenes	1314	M49	glnA deletion		whole cell	6.5	0.05	2011-11-12T0:0:0+0000	2011-11-18T0:0:0+0000	75.5
4	Streptococcus_pyogenes	1314	M49	glnA deletion		whole cell	7.5	0.05	2011-11-08T0:0:0+0000	2011-11-11T0:0:0+0000	166.5
5	Streptococcus_pyogenes	1314	M49	arcA deletion		whole cell	7.5	0.05	2012-01-10T0:0:0+0000	2012-01-13T0:0:0+0000	103
6	Streptococcus_pyogenes	1314	M49	arcA deletion		whole cell	6.5	0.05	2012-01-14T0:0:0+0000	2012-01-18T0:0:0+0000	190

Metabolite	Sample	Glucose	Ethanol	Acetate	Lactate	Formate	Succinate	Pyruvate	Acetoin	2,3 Butanediol	CO2	O2	Aspartic acid	Serine	Glutamate	Glycine	Histidine	NH3	Arginine	Threonine	Alanine	Proline	Cysteine	Tyrosine	Valine	Methionine	Ornithine	Lysine	Isoluecine	Leucine	Phenylalanine
Metabolite ID		CHEBI:17234	CHEBI:16236	CHEBI:30089	CHEBI:24996	CHEBI:15740	CHEBI:30779	CHEBI:15361	CHEBI:15688	CHEBI:62064	CHEBI:16526	CHEBI:15379	CHEBI:22660	CHEBI:17822		CHEBI:15428	CHEBI:27570	CHEBI:16134	CHEBI:29016	CHEBI:26986	CHEBI:16449	CHEBI:26271	CHEBI:15356	CHEBI:18186	CHEBI:27266	CHEBI:16811	CHEBI:18257	CHEBI:25094	CHEBI:24898	CHEBI:25017	CHEBI:28044
Unit		mM	mM	mM	mM	mM	mM	mM	mM	mM	%	%	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	μM	mM	mM	mM	mM
	1	0.281285	6.51461	16.683844999999998	106.58747	8.99381	0	0.31977500000000003	0	0	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	2	0	15.42216	26.74467	62.69813	30.89714	0	1.08538	0	0	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	3	0	1.09063	13.433990000000001	77.398695	8.91426	0	0.42788000000000004	0	0	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	4	0.33895	0	14.38746	105.83433	3.764825	0	1.3148650000000002	0	0	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	5	0.392855	1.409605	1.69	67.13	8.56	0	2.25	0	0	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	6	0.32088	0	2.27	94.9	4.09	0	0.96	0	0	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

Metabolite	Sample	Glucose	Ethanol	Acetate	Lactate	Formate	Succinate	Pyruvate	Acetoin	2,3 Butanediol	CO2	O2	Aspartic acid	Serine	Glutamate	Glycine	Histidine	NH3	Arginine	Threonine	Alanine	Proline	Cysteine	Tyrosine	Valine	Methionine	Ornithine	Lysine	Isoluecine	Leucine	Phenylalanine	Yield glucose	Yield glucose	ATP (calculated)	Lactate (mol/mol glucose)	Formate (mol/mol glucose)	EtOH (mol/mol glucose)	Acetate (mol/mol glucose)	EtOH+ Acetate (mol/mol glucose)
Metabolite ID		CHEBI:17234	CHEBI:16236	CHEBI:30089	CHEBI:24996	CHEBI:15740	CHEBI:30779	CHEBI:15361	CHEBI:15688	CHEBI:62064	CHEBI:16526	CHEBI:15379	CHEBI:22660	CHEBI:17822		CHEBI:15428	CHEBI:27570	CHEBI:16134	CHEBI:29016	CHEBI:26986	CHEBI:16449	CHEBI:26271	CHEBI:15356	CHEBI:18186	CHEBI:27266	CHEBI:16811	CHEBI:18257	CHEBI:25094	CHEBI:24898	CHEBI:25017	CHEBI:28044
Unit		mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	mmol/gram/hour	g/mol	g/g	mmol/gram/hour	mol/mol	mol/mol	mol/mol	mol/mol	mol/mol
	1	-3.122217261904763	0.38777440476190483	0.9930860119047619	6.344492261904763	0.5353458333333333	0	0.019034226190476195	0	-0.18561785714285728	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44.2970094	0.24609449666666666	ND	2.0212081134307907	0.17054876846832914	-0.021328527880259105	0.1171677156155828	0.4399101082431086
	2	-3.681250694444445	1.0709833333333334	1.85726875	4.354036805555555	2.1456347222222223	0	0.07537361111111113	0	-0.6410385416666669	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	38.1672072	0.21204004	ND	1.182760199441577	0.582854823079641	0.23586167970917188	0.3114112787377327	0.7954503309846573
	3	-2.4520355	0.054531500000000004	0.6716995000000001	3.8699347500000005	0.445713	0	0.021394000000000003	0	-0.26568099999999967	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	49.04071	0.2724483888888889	ND	1.5686990461598131	0.1817726537809098	-0.05336933335589962	0.07453440213243247	0.29617474950913236
	4	-1.5219300000000002	0	0.449608125	3.3073228125	0.11765078125000002	0	0.041089531250000005	0	-0.007794687499999898	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	78.465136	0.43591742222222224	ND	2.148536389460919	0.0767693820093551	-0.07560861170239991	0.09397682048241147	0.29337788951261107
	5	-2.93	0.08	0.1	4	0.51	0	0.13	0	0	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44.519999999999996	0.24733333333333332	ND	1.37	0.17	0.03	0.03	0.05848311320754717
	6	-3.62	0	0.17	6.98	0.3	0	0.07	0	0	ND	ND	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	36.04	0.20022222222222222	ND	1.93	0.08	0	0.05	0.04283018867924528

Identifier	Sample	Chemostat	Medium flow	Volume	Temperature	pH Chemostat	Dilution rate	O2 input	Airflow	N2 flow	Total flow	Comments
Unit		name	ml/hour	ml	°C		1/hour	volume%	ml/min	ml/min	ml/min
	1	A7.2	37.5	750	37	6.5	0.05	0	50	50	50
	2	A7.1	37.5	750	37	7.5	0.05	0	50	50	50
	3	A3.2	37.5	750	37	6.5	0.05	0	50	50	50
	4	A3.1	37.5	750	37	7.5	0.05	0	50	50	50
	5	Silvio1	37.5	750	37	7.5	0.05	0	0	500	100	ΔarcA
	6	Silvio1	37.5	750	37	6.5	0.05	0	0	500	100	ΔarcA

Identifier	Sample	N2	CO2	O2	CO2	pH	RPM	OD	standard deviation OD	Dry weight	standard deviation dryweight
Unit		volume%	volume%	volume%	volume%		rpm			gram/liter	gram/liter
Description		Inputgas	Inputgas	Outputgas	Outputgas		stirring rate	Optical density (600nm)	Optical density (600nm)	Calculated
	1	100	0	ND	ND	6.5	150	1.56		0.84
	2	100	0	ND	ND	7.5	150	0.856		0.72
	3	100	0	ND	ND	6.5	150	1.43		1
	4	100	0	ND	ND	7.5	150	1.196		1.6
	5	100	0	ND	ND	7.43	150	1.638		0.84
	6	100	0	ND	ND	6.43	150	1.35		0.68

Metabolite	Sample	Glucose	Ethanol	Acetate	Lactate	Formiate	Succinate	Pyruvate	Acetoin	2,3 Butanediol	O2	CO2	Aspartic acid	Serine	Glutamate	Glycine	Histidine	NH3	Arginine	Threonine	Alanine	Proline	Cysteine	Tyrosine	Valine	Methionine	Ornithine	Lysine	Isoluecine	Leucine	Phenylalanine
Metabolite ID		CHEBI:17234	CHEBI:16236	CHEBI:30089	CHEBI:24996	CHEBI:15740	CHEBI:30779	CHEBI:15361	CHEBI:15688	CHEBI:62064	CHEBI:16526	CHEBI:15379	CHEBI:22660	CHEBI:17822		CHEBI:15428	CHEBI:27570	CHEBI:16134	CHEBI:29016	CHEBI:26986	CHEBI:16449	CHEBI:26271	CHEBI:15356	CHEBI:18186	CHEBI:27266	CHEBI:16811	CHEBI:18257	CHEBI:25094	CHEBI:24898	CHEBI:25017	CHEBI:28044
Unit		mM	mM	mM	mM	mM	mM	mM	mM	mM	%	%	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	mM	μM	mM	mM	mM	mM
	1	52.734535	0	0	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	2	53.01001	0	0	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	3	49.04071	0	0	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	4	49.04071	0	0	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	5	53	0	0	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	6	53	0	0	0	0	0	0	0	0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0