Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

EURASIP Journal on Bioinformatics and Systems Biology

Table 1 Alternative pathway classes from glycerol to pyruvate

Class	Characteristics	Max.	TFN	Microarray
		yield	prediction	LJ110 /	F41 malE::pyc /
				K98-62	K98-62
dihydroxyacetone-	dihydroxyaceton (toxic), dhaKLM operon is	0.0404	active	active	active
path	controlled by DhaR		(includes
			no DhaR)
Entner-Doudoroff-	eda and edd controlled by GntR	0.0365	repressed	active	active
path
serine biosynthesis	transamination step from 3-phosphoglycerate	0.0384	active	active	active
	to serine, various degenerating paths to		(via L-serine)
	pyruvate via L-serine, D-serine, L-cysteine
	and L-tryptophane
shikimate path	generates chorismate, pyruvate occurs as	0.0214	active	active	active
	a byproduct for tryptophan-, enterobactin-,
	tetrahydrofolate-, ubi/menaquinone-
	biosynthesis; secretion of enterobactin possible
methylglyoxal path	methylglyoxal (toxic) is formed from dhap	0.0365	active	active	active
	and detoxified in 3 different ways to lactate
acCoA synthesis	utilize deoxyribonucleotides as carbon shuttle	0.0344	repressed	active	active
	AMP, UMP and GMP are synthesized and
	degraded
murein path	via synthesis and degradation of murein	0.0297	repressed	(active)	active
CO₂ fixation	2 pyruvate are reinvested to form	0.0269	active	active	active
	2 oxaloacetate; carbon transfer between
	glycolysis/pentose phosphate pathway and
	TCA occurs only via CO₂

^aThe yields [gDCW mmol⁻¹] on glycerol were calculated for the experimentally determined maximal growth rate of the evolved strain K98-62 (μ = 0.25 h⁻¹). To compute the maximal yield for a single alternative pathway (AP) all other APs were restricted to their minimal value. For the prediction of the TFN, the environmental conditions of the chemostat (MM with glycerol) were used as an input. The APs have several important reactions for generating a yield. If the average expression level of genes for enzymes of those important reactions drops below a threshold of 7.0 units, we assumed that the enzymatic capacity to perform the reaction is not present.