Biology Reference
In-Depth Information
Figure 5.
Interdependency between the metabolic network, the minimal set and the set of essential
reactions.
The set sizes are given for glucose growth conditions.
The sets of essential reactions consists of 259 and 274 reactions for glucose and ac-
etate conditions respectively, constituting 82 and 86% of the minimal set. These num-
bers indicate that most of the crucial metabolic routes are not duplicated at the level
of metabolic network structure. The set of essential reactions under glucose growth is
a subset of that under acetate, suggesting that the growth on glucose is more resistant
to perturbations (as the smaller number of reactions mean less fragility points in the
network). The reactions belonging exclusively to the acetate minimal set are mostly
members of glyconeogenic pathway, with ATP synthase, the reactions constituting the
glyoxylate shunt, and acetate transport reactions being the exceptions. The inessen-
tiality of ATP synthase under glucose and essentiality of the glyoxylate shunt under
acetate conditions are not surprising and similar effects have been reported in
E. coli
[55-57].
The reactions belonging to the non-essential part of the minimal set are mostly
members of central metabolic pathways (PPP, TCA cycle, and Pyruvate metabolism),
which emphasizes the importance of these pathways for the operation of the metabo-
lism and is in agreement with observations made in other bacteria [58].
Isoenzymes
The metabolic robustness of an organism may also be provided at the genetic level
through genes coding for isozymes. Data on gene and reaction essentiality provide
insights into this phenomenon. We utilized FBA to generate a list of
in silico
essential
gene predictions, including 153 and 159 genes under minimal glucose and acetate
growth respectively, in order to determine how gene/pathway redundancy affects net-
work robustness. These values may seem low when compared to the size of the pre-
