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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Growth Medium: MOPS medium with 0.4% glucose

Summary:
The goals for this medium were to find a convenient and well defined composition that allowed varying all of the elements independently to facilitate isotopic labelling. This required using much less phosphate than in older media, which served roles of pH buffering and chelation of metals like Fe2+. For buffering, MOPS was used instead, with some Tricine added to help chelate Fe2+.

E. coli can use MOPS as a sulfur source if no other sulfur source is added. However, sulfate easily outcompetes MOPS if both are present.

To increase ionic strength and thus optimize the growth rate, NaCl was added. However, it is probably the case that KCl would work just as well, which would allow completely eliminating Na+ from this medium.

Citations: [Neidhardt74]

Recipe Substances: ?
Substances Concentration Role Comment
β-D-glucose 4 g/l Source of C  
3-(N-morpholino)propanesulfonate 40 mM pH Buffer  
ammonium chloride 9.5 mM Source of N  
ammonium heptamolybdate 3 nM    
borate 400 nM    
calcium chloride 0.5 µM    
cobalt chloride 30.0 nM    
copper sulfate 10 nM    
dipotassium phosphate 1.32 mM Source of P  
iron sulfate 10 µM    
manganese chloride 80 nM   Mn source
MgCl2 528 µM    
potassium sulfate 276 µM Source of S  
sodium chloride 50 mM    
tricine 4 mM pH Buffer  
zinc sulfate 10 nM    
Composition: ?
Constituents Concentration
chloride 60.557 mM
Na+ 50 mM
3-(N-morpholino)propanesulfonate 40 mM
borate 24.732 mM
β-D-glucose 22.203 mM
ammonium 9.5 mM
tricine 4 mM
K+ 3.192 mM
phosphate 1.32 mM
Mg2+ 528 µM
sulfate 286.02 µM
Fe2+ 10 µM
Ca2+ 500 nM
Mn2+ 80 nM
Co2+ 30.0 nM
Cu2+ 10 nM
Zn2+ 10 nM
heptamolybdate 3 nM

pH: 7.2

Osmolarity (approximate, computed from constituents): 0.22 Osm/L

Wildtype growth observations:

T (°C) O2 Growth?
37 Aerobic Yes

30 single gene knockouts exhibit no growth (aerobic):
argH , aroA , carA , carB , guaA , ppc , proB , proC , purA , purC , purE , purH , serC , thrC , thyA (T=37°C) [Feist07, Baba06, Comment 1]

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4732 single gene knockouts exhibit growth (aerobic):


aaeA , aaeB , aaeR , aaeX , aat , abgA , abgB , abgR , abgT , abrB , aceK , acrA , acrB , acrD , acrR , acrZ , ada , adeP , adeQ , adiY , adrA , aegA , aer , aes , afuB , afuC , agaA , agaB , agaC , agaD , agaI , agaR , agaS , agaV , agaW , ahpC , ahpF , ahr , aidB , ais (T=37°C) [Baba06, Comment 2] + 3696 more... [Show All]

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Genes with inconsistent growth observations:

Knockout Growth? T (°C) O2 Growth Observations
aceF Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
argA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
argB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
argC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
argE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
argG Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
aroB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
aroC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
aroE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
atpB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
atpC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
atpE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
bioA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
bioB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
bioD Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
bioF Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
cysC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
cysE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
cysG Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
cysH Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
cysI Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
cysJ Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
cysN Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
glnA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
gltA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
glyA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
guaB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
hisA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
hisB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
hisC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
hisD Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
hisF Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
hisG Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
hisH Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
hisI Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
icd Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
ilvA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
ilvC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
ilvD Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
ilvE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
iscS Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
leuA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
leuB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
leuC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
leuD Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
lpd Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
lysA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
metA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
metB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
metC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
metE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
metF Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
metL Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
nadA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
nadB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
nadC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pabA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pabB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
panB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
panC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
panD Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pdxA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pdxB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pdxH Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pdxJ Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pfkA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pheA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
proA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
ptsH Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
ptsI Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
purD Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
purF Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
purK Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
purL Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
purM Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pyrB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pyrC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pyrD Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pyrE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
pyrF Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
serA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
serB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
thrA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
thrB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
tnaB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
trpA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
trpB Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
trpC Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
trpD Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
trpE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
tyrA Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]
ubiE Indeterminate 37 Aerobic
Yes [Baba06, Comment 2]
No [Feist07, Comment 4]

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References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Neidhardt74: Neidhardt FC, Bloch PL, Smith DF (1974). "Culture medium for enterobacteria." J Bacteriol 119(3);736-47. PMID: 4604283


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Dec 18, 2014, biocyc13.