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Table 1 Alternative pathway classes from glycerol to pyruvate

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

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     
  1. 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.