Figure 1.
Proposed oxidative phosphorylation pathway.
H. salinarum has analogs of all five respiratory complexes found in mitochondria and E. coli (complexes I to V). The boxes beneath each complex represent genes coding for specific subunits, which are often encoded adjacently in the genome (indicated by solid connections or by shared borders). Black broken lines are used to indicate that the connected genes, while not adjacent, are in the same genetic vicinity. The red broken line indicates that the cbaD and hcpB genes are fused in the archaeon. The proposed pathway has some notable differences from its more well-studied counterparts in E. coli or mitochondria. For example, genes coding for cytochrome c, which normally carries electrons to the terminal oxidase, could not be found in H. salinarum. Experimental evidence indicates that the function is likely performed by the copper protein halocyanin.
Figure 2.
Nutrient consumption and production data from aerobically grown cells.
Experimental data are shown using diamonds (average) with error bars provided. Model simulations are illustrated using red broken curves. The transport patterns of several metabolites qualitatively change during growth. For example, alanine and ornithine switch from production to consumption. For such metabolites, the piecewise Equation (3) was used to model utilization, and the corresponding parameter value, which represents a point near where the qualitative change occurs, is indicated with an inverted green triangle.
Table 1.
Comparison of transport equation forms.
Figure 3.
Arginine, proline and ornithine metabolism.
Prior to its depletion, arginine exhibits the highest uptake rate among the supplied nutrients. Most of it is deaminated to citrulline, which is then converted to ornithine and carbamoyl-phosphate (cbp). Most of the ornithine (≈95%) is transported outside through an arginine-ornithine antiporter. On the other hand, carbamoyl phosphate is primarily degraded to NH3 and CO2 in a reaction that produces ATP from ADP. Simulations show that at the beginning of growth this process produces most of the energy in the cells. The red broken arrows indicate connections to other parts of the network.
Figure 4.
Summary of nutrient uptake and incorporation rates under aerobic conditions.
The blue curves indicate the net amount of each amino acid that has been consumed (positive) or produced (negative) as a function of time. The red curves, on the other hand, show the total amount of each that has been incoporated into the biomass, whether integrated into proteins or as free metabolites. Clearly, for most of the supplied amino acids, the rate at which they are taken up from the medium far exceeds the rate at which they are directly incorporated. This implies that the pertinent amino acids are, in addition, significantly catabolized for energy, and/or are used to synthesize the other biomass constituents that are not supplied.
Figure 5.
Predicted fluxome during exponential phase (t = 30) that maximizes energy production.
Yellow ellipses represent compounds that are taken up from the medium, while light-red ellipses represent those that are accumulated in the medium. Larger fluxes are drawn with thicker arrows. Black and red arrows correspond to qualitatively invariable and qualitatively variable (see main text) fluxes, respectively. Side reactants, for the most part, are not depicted in the figure. Yellow rounded boxes represent biochemical pathways. Metabolite abbreviations: 3dhq - 3-dehydroquinate, 5,10mtthf - 5,10-methylenetetrahydrofolate, 6pglcn - 6-phosphogluconate, ac-CoA - acetyl-CoA, Ala - alanine, Asn - asparagine, Asp - aspartate, asp4sa - aspartate 4-semialdehyde, Arg - arginine, Cys - cysteine, dkfrcp - 6-deoxy-5-ketofructose 1-phosphate, gal - galactose, gap - glyceraldehyde 3-phosphate, cho - chorismate, glc - glucose, Gly - glycine, glyc - glycerol, Glu - glutamate, Gln - glutamine, His - histidine, hmg-CoA - 3-hydroxy-3-methyl-glutaryl-CoA, ipdp - isopenteny diphosphate, Ile - isolecuine, Leu - leucine, Lys - lysine, Met - methionine, mev - mevalonate, Orn - ornithine, Phe - phenylalanine, Pro - proline, prop-CoA - propanoyl-CoA, prpp - 5-phosphoribosyl diphosphate, pyr - pyruvate, Ser - serine, shk - shikimate, thf - tetrahydrofolate, Thr - threonine, Trp - tryptophan, Tyr - tyrosine, uppg-III - uroporphyrinogen III, Val - valine.