Table 2.
The biomass composition of the average wild type E. coli cell
| Typical ‘wild-type' composition | ||||||
|---|---|---|---|---|---|---|
| Protein (55.0%) | Lipid (9.1%) | |||||
| L-alanine | L-arginine | L-asparagine | structure | |||
| L-aspartate | L-cysteine | L-glutamine | phosphatidylethanolamine | phosphatidylglycerola | cardiolipin | |
| L-glutamate | glycine | L-histidine | acyl chain length: number of unsaturated bonds | |||
| L-isoleucine | L-leucine | L-lysine | 16:0 | 16:1 | 18:1 | |
| L-methionine | L-phenylalanine | L-proline | ||||
| L-serine | L-threonine | L-tryptophan | LPS (3.4%) | |||
| L-tyrosine | L-valine | inner/outer core KDO2 lipid A | ||||
| RNA (20.5%) | Cofactors, Prosthetic Groups and Other (<2.9%) | |||||
| ATP UTP | CTP | GTP | S-adenosylmethionine thiamine diphosphate pyridoxal 5′-phosphateb | FAD riboflavin folates | coenzyme A undecaprenyl pyrophosphate quinones | NAD(P) hemes |
| DNA (3.1%) | chorismate | enterobactin | glutathione | putrescine | ||
| dATP | dCTP | dGTP | spermidine | vitamin B12 | ||
| dTTP | ||||||
| Murein (2.5%) | ||||||
| Inorganic ions (1.0%) | structure | |||||
| ammonium | calcium | chlorine | murein disaccharide | |||
| cobalt | copper | iron | peptide chain length | |||
| magnesium | manganese | molybdate | pentapeptide | |||
| phosphorous | potassium | sulfate | tetrapeptide | tripeptide | ||
| zinc | Glycogen (2.5%) | |||||
| glycogen | ||||||
|
‘Core' biomass composition substitutes | ||||||
| inner/outer core KDO2 lipid A: substituted with KDO2 lipid (IV) A | ||||||
| quinones: substituted with 2-octaprenyl-6-hydroxyphenol | ||||||
| hemes: protoheme; siroheme included | ||||||
| folates: tetrahydrofolate; 10-formyltetrahydrofolate; 5,10-methylenetetrahydrofolate included | ||||||
The average E. coli wild-type macromolecules (and the weight percentage for each) are listed along with their corresponding network metabolites or metabolic precursors. The non-essential wild-type metabolites were determined using gene essentiality data (Baba et al, 2006; Joyce et al, 2006) and are shown in red. Metabolites listed in blue were determined to have a reduced ‘core' structure different from the wild-type metabolite(s) and these are listed in the ‘core' biomass composition substitutes.
Was determined to be non-essential from (Kikuchi et al, 2000).
Determined to be essential under minimal media conditions and was not essential under the rich media condition examined.