Figure 1.
Overview of network properties.
(A) We distinguish between a core network and all remaining genes annotated with enzymatic function. (B) Distribution of pathway annotations across the 760 reactions. (C) The distribution of components that define the biomass objective function (BOF), excluding storage and maintenance (ATP). Abbreviations: Terpenoids (Terp.), Carotenoids (Carot.), Plastoquinone (PQ), Tocopherol (Toco.).
Figure 2.
A flux map for phototrophic growth under constant light.
The flux distribution was optimized for maximal biomass yield. Shown are flux values in units of . Flux values marked with an asterisk indicate non-unique values. The solution is characterized by a large flux through the CBB cycle and non-cyclic operation of the TCA cycle. Aerobic respiration and oxygenic photosynthesis share common components in the electron transport chain. During phototrophic growth, electrons originate from water splitting in PS II and are transferred to NADPH via PS I and FNR. Abbreviations are defined in the Materials and Methods.
Figure 3.
RuBisCO oxygenase and photorespiration.
Figure 4.
Experimental validation of the glyoxylate shunt.
(A) Enzymatic test to determine isocitrate lyase activity in cell-free extract of Synechocystis PCC 6803. Phenylhydrazon formation were measured as increase of A324 nm with time. Trace A - crude cell extract of Synechocystis cells, Trace B - crude cell extract passed over a PD-10 gel filtration column both corresponding to a protein concentration of reaction volume. Arrows mark the stepwise addition of phenylhydrazin (Phe, 5 mM), isocitrate (IC, 1 mM) and NADP (
mM), the latter as a control for isocitrate dehydrogenase activity. Increase in A324 nm in Trace A after adding of phenylhydrazin results from phenylhydrazine reactive metabolites, further increase after addition of IC results from internal NADP as a co-substrate of isocitrate dehydrogenase within the crude extract. Both traces show the same trend after addition of NADP, corresponding to the same isocitrate dehydrogenase activity. (B) The capability for utilization of acetate as sole carbon source was tested in spot assays in the presence of the photosystem II inhibitor DCMU (photoheterotrophic growth). Respective controls were conducted without the addition of DCMU (putative photomixotrophic growth) and without both sodium acetate and DCMU, respectively (photoautotrophic growth) to BG11 agar. 1∶1, 1.10 and 1∶100 represent dilution factors of the stock cell suspension of Synechocystis sp. PCC 6803 that contains
chlorophyll a per ml cell suspension.
Figure 5.
Alternative scenarios of flux through the TCA cycle.
(A) The conventional closed bacterial TCA cycle via the OGDH complex. (B) A bypass recently identified by Zhang and Bryant [49]. (C ) The glyoxylate shunt as a bypass of the TCA cycle, as utilized in the reconstruction of Shastri and Morgan [10]. (D) The GABA shunt as a bypass of the TCA cycle, as utilized in the reconstruction of Knoop et al. [13]. In terms of stoichiometric yield, the conventional cycle is most effective.
Figure 6.
A time-dependent biomass objective function.
The upper panel shows time-dependent objectives as inferred from literature and transcript data over a full diurnal cycle. The lower panel shows a simulation of the newly synthesized biomass components as a function of circadian time (CT). CT = 0 h marks sunrise.
Figure 7.
Selected metabolic fluxes over a full diurnal cycle.
Shown is (A) oxygen uptake, (B) phosphoglycerate kinase, (C) phosphoglucomutase, (D) carboxylation of RuBisCO, (E) CDP kinase and (F) succinic semialdehyde dehydrogenase (TCA bypass).