Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions

BMC Bioinformatics

Table 1 Optimal production of the twelve biosynthetic precursors and the metabolic cofactors.

Compound	μmol/g DW	Compound	μmol/g DW
Amino Acids		Phospholipids
Alanine	488	Phosphatidyl serine	2.58
Arginine	281	Phosphatidyl ethanolamine	96.75
Asparagine	229	Phosphatidyl glycerol	23.22
Aspartate	229	Cardiolypin	6.45
Cysteine	87	Fatty acid composition (% of total fatty acid)
Glutamate	250	Myristic acid (2.68)
Glutamine	250	Myristoleic acid (7.70)
Glycine	582	Palmitic acid (38.23)
Histidine	90	Palmitoleic acid (10.74)
Isoleucine	276	Heptadecenoic acid (16.11)
Leucine	428	cis-Vaccenic acid (0.90)
Lysine	326	Oleic acid (17.91)
Methionine	146	Nonadecenoic acid (5.73)
Phenylalanine	176	Cell Wall Sructures
Proline	210	Lipopolysaccharide	8.4
Serine	205	Peptidoglycan	27
Threonine	241	Cofactors and other molecules
Tryptophan	54	5-Methyl-THF	50.0
Tyrosine	131	Putrescine	35.0
Valine	402	Spermidine	7.0
Protein synthesis/processing (ATP/ Amino Acid)	4.306	NAD	2.15
Ribonucleotides		NADH	0.05
ATP	165	NADP	0.13
GTP	203	NADPH	0.4
CTP	126	UDP-Glucose	3.0
UTP	136	ATP	4.0
RNA synthesis/processing (ATP/Nucleotide)	0.40	ADP	2.0
Deoxyribonucleotides		AMP	1.0
dATP	24.7	CoA	0.03
dTTP	24.7	Acetyl-CoA	0.04
dGTP	25.4	Succinyl-CoA	0.01
dCTP	25.4	Glycogen	154
DNA synthesis/processing (ATP/Nucleotide)	1.372

The optimal production was calculated for the wild-type strain and the deletion strains. The constraints are set as defined in Figure 1. The color code quantitatively defines effect of the in silico deletion; red corresponds to 0.0, yellow corresponds to 0-50% of the wild-type production, blue corresponds to 50-100% of the wild-type, and no color coding is illustrated when the production is unchanged from the wild-type. Data for other carbon sources is available online. G6P, glucose-6-phosphate; F6P, fructose-6-phosphate; R5P, ribose-5-phosphate; E4P,erythrose 4-phosphate; T3P1, glyceraldehyde 3-phosphate; 3PG, 3-phosphoglycerate; PEP, phosphoenolpyruvate; PYR, pyruvate; ACCOA, acetyl-CoA; AKG, α-ketoglutarate; SUCCOA, succinyl-CoA; OA, oxaloacetate.

ISSN: 1471-2105