Using a reconstructed flavonoid subnetwork to study anthocyanin biosynthesis
Authors
Date
2007
Type
Conference Contribution - published
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Abstract
Flavonoids are ubiquitous secondary plant
metabolites that play a variety of roles in the reproduction and protection of plants. Anthocyanin
is a major subgroup of flavonoids that assist plants
in attracting pollinators and seed dispersers by
providing red to blue pigmentation in flowers and
fruits. The compounds are water soluble and occur
mostly as glucosylated pigments in fruits, leaves
and flowers.
A self-contained flavonoid subnetwork, consisting
of 137 metabolites and 117 reactions, is extracted
from the AraCyc database which contains
biochemical pathway information of the model
plant Arabidopsis thaliana (Arabidopsis).
Arabidopsis is used in this study because of the
vast metabolic information available for it as well
as the fact that it is very similar to most other
plants so should make a good representation of
flowering plants.
Using the stoichiometric matrix to mathematically
represent the connections between the reactions,
and convex analysis to identify all possible and
feasible metabolic routes at a steady state, 199
elementary modes (EMs) or pathways are derived
from the subnetwork. Eighty of these lead to the
formation of flavonoid compounds. The rest lead
to other compounds such as lignin and
phenylpropanoid esters, whose association and
interplay with flavonoid production is an
interesting result to be further investigated.
The study uses the subnetwork to investigate the
structural functionality of the anthocyanin
biosynthetic pathway (ABP). Two anthocyanin
compounds, pelargonidin and cyanidin glucosides,
are present in Arabidopsis and six EMs lead to
their formation. By identifying the enzymes related
to the reactions involved in the six EMs, the
structural functionality of the enzyme related genes
in the ABP are studied. Genes that play important
roles in multiple phenotypic traits are identified
and their relationship with other EMs in the flavonoid subnetwork investigated. Analysis is
also done to identify and study those genes which,
when deleted, would result in the non-production
of anthocyanin compounds. Emergent properties of
the anthocyanin biosynthetic pathway, such as
reaction participation and minimal cut sets are
used for the investigations.
The reaction participation looks at the multiple
phenotypic trait of the anthocyanin biosynthetic
pathway genes by determining the number of times
the enzyme product of each gene appears in the set
of 80 elementary modes responsible for the
formation of flavonoid compounds. The results
show that, in terms of their sequence in the
pathway, genes that occur early in the pathway are
involved in more EMs, and thus the formation of
other flavonoids, than those found later in the
ABP, which are more specific to the anthocyanin
compounds.
A general observation about the flavonoid
subnetwork is that it has a remarkably small
number of elementary modes compared to other
metabolic networks of similar size in other
organisms. This suggests a highly constrained
network, which could be due to fact that it deals
with secondary metabolites. The results are
discussed in more detail in the main paper.
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