Modeling and analysis provide biologists different opinions about metabolic network.
The findings in this study highlight the need for researchers to investigate the above issues and analysis for improving glycerol application in Escherichia coli especially.
Although the sample size in the study was small, the following recommendations could serve as general principles for researchers who would like to carry out glycerol anaerobic utilization in Escherichia coli.
We proposed that tryptone as the resource for biomass growing, so the tryptone’s carbon was excluded from metabolites poured out. During the biomass growing, reactions in
biological system may generate the redox factor that could improve the glycerol uptake and boost the glycerol dehydrogenase catalyzed reaction for fermentation.
Besides, we obviously found that glycerol fermentation in medium containing tryptone is prone to generate biomass and the experimental data showed the biomass grown most when the glycerol fermentation happened in tryptone added medium.
Moreover, these findings are parallel with previous studies .The FHL (formate hydrogen lyase) gene knocked out reduced the growing of biomass compared with FHL gene
complemented strain. The EFMs also reduced a big ratio when FHL gene knocked out. The model showed the tendency of E.coli prefers no formate in cell. When FHL gene was knocked out, the formate accumulated and hindered the metabolic pathway.
When comparing the high yields EFMs and EFMs with high coefficient of metabolites concentration, the later one was average yields predominates in E.coli. Although the gene modification resulted in relatively high ratio of high yields EFMs, deletion of average yields will decrease growing of biomass in cell.
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Appendix
Table 1 Reaction of elementary flux modes analysis
No. Reaction
34 FEM1 : PYR + CoASH = ACoA + FOR 66 GLYD1 : GLYCEROL_ext = GLYCEROL 67 GLYD2 : GLYCEROL + ATP = G3P + ADP 68 GLYD3 : GLYCEROL + NAD = DHA + NADH 69 GLYD4 : DHA + ATP = DHAP + ADP
70 TRYP : 4 TRYPTONE + 120000 NADH = 3 BIOMASS + 120000 NAD 71 GLYD6 : GLYCEROL = 3HPA
72 GLYD7 : 3HPA + NADH = 13PD + NAD
Table 2 Figures‘s detail EFMs
Figure Detail EFMs
Figure 2.6 1858: (37) 1.04797 GG4 3.54285 GG11 PPP2 0.0844116 TCA1 0.0844116 TCA2r 0.907776 FR3 0.223816 ANA1 4.31079 FEM1 4.15497 FEM5 4.15497 FEM6 4.31079 FEM4 EDP1 EDP2 6.10352e-005 BIO 0.907776 OPM4r 4.15497 TRA1 0.740051 TRA3 0.907776 TRA5 4.17145 TRA7 5.0556 GLYD1 5.0556 GLYD3 5.0556 GLYD4 -1.00293 GG2r -1.04797 GG5r -4.00763 GG6r 3.92065 GG7r 3.92065 GG8r 3.82349 GG9r 3.82349 GG10r PPP1 -0.0440674 PPP4r 0.0440674 PPP5r -0.00683594 PPP6r -0.00683594 PPP7r -0.0371704 PPP8r 0.0844116 TCA3r 0.0844116 TCA4 irreversible
Figure 2.7 111: (34) GG4 53.0358 GG11 1.7605 TCA1 1.7605 TCA2r 18.9333 FR3 4.66791 ANA1 48.1963 FEM1 44.9457 FEM5 44.9457 FEM6 48.1963 FEM4 0.0012207 BIO 18.9333 OPM4r 44.9457 TRA1 15.4346 TRA3 18.9333 TRA5 45.2889 TRA7 63.7296 GLYD1 63.7296 GLYD3 63.7296 GLYD4 -0.0604858 GG2r -GG5r -62.7296 GG6r 60.9161 GG7r 60.9161 GG8r 58.8889 GG9r 58.8889 GG10r -0.918518 PPP4r 0.918518 PPP5r -0.143188 PPP6r -0.143188 PPP7r -0.77533 PPP8r 1.7605 TCA3r 1.7605 TCA4 -20.8568 FC1r irreversible
Figure 2.8 1274: (40) 1.10956 GG4 1.14355 PPP2 0.143555 PPP3 0.108643 TCA1 0.108643 TCA2r 17.5392 FR1 9.10229 FR2 19.2469 FR3 17.8272 ANA1 8.43683 ANA2 9.13818 FEM1 4.32068 FEM7 4.32068 FEM8 4.61694 FEM5 4.61694 FEM6 9.13818 FEM4 EDP1 EDP2 6.10352e-005 BIO 4.61694 TRA1 4.32068 TRA2 0.952454 TRA3 19.2469 TRA5 19.2469 GLYD1 19.2469 GLYD2 19.2469 GLYD5 -1.14728 GG2r -1.10956 GG5r -18.1374 GG6r 18.0255 GG7r 18.0255 GG8r 17.9003 GG9r 17.9003 GG10r 1.14355 PPP1 0.0390015 PPP4r 0.104553 PPP5r 0.0390015 PPP6r 0.0390015 PPP7r 0.108643 TCA3r 0.108643 TCA4 irreversible
Figure 2.9 64: (33) GG4 53.0358 GG11 1.7605 TCA1 1.7605 TCA2r 4.66791 ANA1 48.1963 FEM1 44.9457 FEM5 44.9457 FEM6 2.90741 FEM4 0.0012207 BIO 44.9457 TRA1 15.4346 TRA3 45.2889 TRA6 82.663 GLYD1 63.7296 GLYD3 63.7296 GLYD4 18.9333 GLYD6 18.9333 GLYD7 -0.0604858 GG2r -GG5r -62.7296 GG6r 60.9161 GG7r 60.9161 GG8r 58.8889 GG9r 58.8889 GG10r -0.918518 PPP4r 0.918518 PPP5r -0.143188 PPP6r -0.143188 PPP7r -0.77533 PPP8r 1.7605 TCA3r 1.7605 TCA4 -20.8568 FC1r irreversible
Figure 2.10 1501: (36) 1.04797 GG4 3.54285 GG11 PPP2 0.0844116 TCA1 0.0844116 TCA2r 4.17145 TRA7 0.223816 ANA1 4.31079 FEM1 4.15497 FEM5 4.15497 FEM6 4.31079 FEM4 EDP1 EDP2 6.10352e-005 BIO 4.15497 TRA1 0.740051 TRA3 5.96338 GLYD1 5.0556 GLYD3 5.0556 GLYD4 0.907776 GLYD6 0.907776 GLYD7 -1.00293 GG2r -1.04797 GG5r -4.00763 GG6r 3.92065 GG7r 3.92065 GG8r 3.82349 GG9r 3.82349 GG10r PPP1 -0.0440674 PPP4r 0.0440674 PPP5r -0.00683594 PPP6r -0.00683594 PPP7r -0.0371704 PPP8r 0.0844116 TCA3r 0.0844116 TCA4 irreversible
Figure 2.11 135: (26) GG4 GG11 3 PPP2 3 PPP3 FEM6 FEM9 TRA1 4 TRA7 2 GLYD1 2 GLYD3 2 GLYD4 6.10352e-005 TRYP -3 GG2r -GG5r -GG6r GG7r GG8r GG9r GG10r 3 PPP1 2 PPP4r PPP5r PPP6r PPP7r PPP8r 6 FC1r irreversible
Figure 2.12 160: (21) GG4 GG11 PPP2 2 FEM6 2 FEM9 EDP1 EDP2 2 TRA1 2 TRA7 2 GLYD1 2 GLYD3 2 GLYD4 -GG2r -GG5r -GG6r GG7r GG8r GG9r GG10r PPP1 FC1r irreversible