Limits...
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.

Gille C, Bölling C, Hoppe A, Bulik S, Hoffmann S, Hübner K, Karlstädt A, Ganeshan R, König M, Rother K, Weidlich M, Behre J, Holzhütter HG - Mol. Syst. Biol. (2010)

Bottom Line: It is based on the manual evaluation of >1500 original scientific research publications to warrant a high-quality evidence-based model.The final network is the result of an iterative process of data compilation and rigorous computational testing of network functionality by means of constraint-based modeling techniques.Taking the hepatic detoxification of ammonia as an example, we show how the availability of nutrients and oxygen may modulate the interplay of various metabolic pathways to allow an efficient response of the liver to perturbations of the homeostasis of blood compounds.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biochemistry, University Medicine Charité Berlin, Berlin, Germany.

ABSTRACT
We present HepatoNet1, the first reconstruction of a comprehensive metabolic network of the human hepatocyte that is shown to accomplish a large canon of known metabolic liver functions. The network comprises 777 metabolites in six intracellular and two extracellular compartments and 2539 reactions, including 1466 transport reactions. It is based on the manual evaluation of >1500 original scientific research publications to warrant a high-quality evidence-based model. The final network is the result of an iterative process of data compilation and rigorous computational testing of network functionality by means of constraint-based modeling techniques. Taking the hepatic detoxification of ammonia as an example, we show how the availability of nutrients and oxygen may modulate the interplay of various metabolic pathways to allow an efficient response of the liver to perturbations of the homeostasis of blood compounds.

Show MeSH
Functional flux mode for the detoxification of NH3 with low oxygen demand. Flux distribution obtained for ammonia detoxification into the nitrogen compounds urea (17.3%), alanine (40%) and glutamine (42.7%). The setting is detailed in the result section (detoxification of ammonia). Presentation is similar to Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2964118&req=5

f4: Functional flux mode for the detoxification of NH3 with low oxygen demand. Flux distribution obtained for ammonia detoxification into the nitrogen compounds urea (17.3%), alanine (40%) and glutamine (42.7%). The setting is detailed in the result section (detoxification of ammonia). Presentation is similar to Figure 1.

Mentions: The decreased oxygen demand in flux distributions using higher proportions of glutamine and alanine is accompanied by increased uptake of the substrates glucose and palmitate (Figure 2B). This is due to an increased demand of energy and carbon for the amidation and transamination of glutamate and pyruvate to discharge nitrogen in the form of glutamine and alanine, respectively. A detailed analysis of the flux modes obtained at high oxygen (89.3% urea, 5.3% glutamine, 5.3% alanine) and low oxygen (17.3% urea, 42.7% glutamine, 40.0% alanine) demand settings (Figures 3 and 4, respectively) revealed that both solutions rely on glycolysis, the oxidative pentose pathway, fatty-acid β-oxidation and the Krebs cycle for substrate entry and breakdown. In both simulations, non-zero fluxes through a complex part of the central metabolism occur consisting of (i) reactions and intermediates attributable to a single pathway; for instance, the urea cycle or Krebs cycle, (ii) reactions and intermediates interconnecting these traditionally perceived pathways (e.g. transaminase reactions, pyruvate) and (iii) transport processes for the flow and balancing of substrates, energy and redox equivalents between compartments. However, there are considerable differences between the two scenarios: the flux solution for high urea production, which is characterized by high oxygen demand, carries a high flux through the urea cycle and the recovery pathway of aspartate as a precursor for argininosuccinate synthesis. A sequence of reactions transports fumarate into mitochondria, produces and transaminates oxaloacetate (using Krebs cycle enzymes and aspartate transaminase) and transports aspartate to the cytosol. These reactions carry a considerably lower flux in the low oxygen demand solution, which is, conversely, characterized by a marked increase in glycolytic flux and exclusive use of pyruvate for transamination to alanine and formation of malate. In the high urea setting, pyruvate is primarily transported to the mitochondria and converted to acetyl-CoA and fed into the Krebs cycle. Intriguingly, in the low oxygen setting, not only is the flux through the complexes of the respiratory chain diminished, but the F0/F1-ATPase reaction does not carry any flux at all, indicating that in this solution the ATP demand can be satisfied entirely by substrate-level phosphorylation and that the respiratory chain and oxygen uptake is needed solely to drive secondary active transport processes. This finding is consistent with the observations that the proton motive force in hepatocytes is used only partly for ATP synthesis as approximately 20% of respiratory oxygen consumption can be attributed to proton-driven mitochondrial transport (Brand et al, 1991). With regard to the inversely correlated demand for oxygen and organic substrates, we observe several combinations of the chosen nitrogen compounds, which appear equally optimal with respect to effective substrate usage: high proportions of urea require high oxygen uptake, but lower quantities of glucose and palmitate, whereas flux distributions with proportions of nitrogen compounds as 17% urea, 43% glutamine and 40% alanine use considerably less oxygen at the expense of a higher substrate intake. For other nitrogen compound ratios, notably settings with very high flux into alanine, the reduction in oxygen consumption is accompanied by an even higher increase in substrate demand. Taken together, this analysis reveals strong dependencies between the available level of oxygen and variations in the substrate demand of hepatocytes required for effective ammonia detoxification by the liver.


HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.

Gille C, Bölling C, Hoppe A, Bulik S, Hoffmann S, Hübner K, Karlstädt A, Ganeshan R, König M, Rother K, Weidlich M, Behre J, Holzhütter HG - Mol. Syst. Biol. (2010)

Functional flux mode for the detoxification of NH3 with low oxygen demand. Flux distribution obtained for ammonia detoxification into the nitrogen compounds urea (17.3%), alanine (40%) and glutamine (42.7%). The setting is detailed in the result section (detoxification of ammonia). Presentation is similar to Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2964118&req=5

f4: Functional flux mode for the detoxification of NH3 with low oxygen demand. Flux distribution obtained for ammonia detoxification into the nitrogen compounds urea (17.3%), alanine (40%) and glutamine (42.7%). The setting is detailed in the result section (detoxification of ammonia). Presentation is similar to Figure 1.
Mentions: The decreased oxygen demand in flux distributions using higher proportions of glutamine and alanine is accompanied by increased uptake of the substrates glucose and palmitate (Figure 2B). This is due to an increased demand of energy and carbon for the amidation and transamination of glutamate and pyruvate to discharge nitrogen in the form of glutamine and alanine, respectively. A detailed analysis of the flux modes obtained at high oxygen (89.3% urea, 5.3% glutamine, 5.3% alanine) and low oxygen (17.3% urea, 42.7% glutamine, 40.0% alanine) demand settings (Figures 3 and 4, respectively) revealed that both solutions rely on glycolysis, the oxidative pentose pathway, fatty-acid β-oxidation and the Krebs cycle for substrate entry and breakdown. In both simulations, non-zero fluxes through a complex part of the central metabolism occur consisting of (i) reactions and intermediates attributable to a single pathway; for instance, the urea cycle or Krebs cycle, (ii) reactions and intermediates interconnecting these traditionally perceived pathways (e.g. transaminase reactions, pyruvate) and (iii) transport processes for the flow and balancing of substrates, energy and redox equivalents between compartments. However, there are considerable differences between the two scenarios: the flux solution for high urea production, which is characterized by high oxygen demand, carries a high flux through the urea cycle and the recovery pathway of aspartate as a precursor for argininosuccinate synthesis. A sequence of reactions transports fumarate into mitochondria, produces and transaminates oxaloacetate (using Krebs cycle enzymes and aspartate transaminase) and transports aspartate to the cytosol. These reactions carry a considerably lower flux in the low oxygen demand solution, which is, conversely, characterized by a marked increase in glycolytic flux and exclusive use of pyruvate for transamination to alanine and formation of malate. In the high urea setting, pyruvate is primarily transported to the mitochondria and converted to acetyl-CoA and fed into the Krebs cycle. Intriguingly, in the low oxygen setting, not only is the flux through the complexes of the respiratory chain diminished, but the F0/F1-ATPase reaction does not carry any flux at all, indicating that in this solution the ATP demand can be satisfied entirely by substrate-level phosphorylation and that the respiratory chain and oxygen uptake is needed solely to drive secondary active transport processes. This finding is consistent with the observations that the proton motive force in hepatocytes is used only partly for ATP synthesis as approximately 20% of respiratory oxygen consumption can be attributed to proton-driven mitochondrial transport (Brand et al, 1991). With regard to the inversely correlated demand for oxygen and organic substrates, we observe several combinations of the chosen nitrogen compounds, which appear equally optimal with respect to effective substrate usage: high proportions of urea require high oxygen uptake, but lower quantities of glucose and palmitate, whereas flux distributions with proportions of nitrogen compounds as 17% urea, 43% glutamine and 40% alanine use considerably less oxygen at the expense of a higher substrate intake. For other nitrogen compound ratios, notably settings with very high flux into alanine, the reduction in oxygen consumption is accompanied by an even higher increase in substrate demand. Taken together, this analysis reveals strong dependencies between the available level of oxygen and variations in the substrate demand of hepatocytes required for effective ammonia detoxification by the liver.

Bottom Line: It is based on the manual evaluation of >1500 original scientific research publications to warrant a high-quality evidence-based model.The final network is the result of an iterative process of data compilation and rigorous computational testing of network functionality by means of constraint-based modeling techniques.Taking the hepatic detoxification of ammonia as an example, we show how the availability of nutrients and oxygen may modulate the interplay of various metabolic pathways to allow an efficient response of the liver to perturbations of the homeostasis of blood compounds.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biochemistry, University Medicine Charité Berlin, Berlin, Germany.

ABSTRACT
We present HepatoNet1, the first reconstruction of a comprehensive metabolic network of the human hepatocyte that is shown to accomplish a large canon of known metabolic liver functions. The network comprises 777 metabolites in six intracellular and two extracellular compartments and 2539 reactions, including 1466 transport reactions. It is based on the manual evaluation of >1500 original scientific research publications to warrant a high-quality evidence-based model. The final network is the result of an iterative process of data compilation and rigorous computational testing of network functionality by means of constraint-based modeling techniques. Taking the hepatic detoxification of ammonia as an example, we show how the availability of nutrients and oxygen may modulate the interplay of various metabolic pathways to allow an efficient response of the liver to perturbations of the homeostasis of blood compounds.

Show MeSH