The metabolic annotation of protein sequences was performed
with the
E2P2 software (version 3.0) which is used to
build
Plant
Metabolic Network Pathway Databases . To be more stringent when
inferring homology between proteins, we decreased the Blast e-value
cutoff in the E2PE code from 1e-2 to 1e-5. We used the
pathway-tools
software to infer biochemical reactions and metabolic pathways
from the protein annotations (pathway-prediction-score-cutoff=0.3)
and create a Pathway-Genome Database (PGDB) which can be browsed at
this
url. A MetExplore instance was also created to
facilitate the visualization of the metabolic network and the
mapping of omics data and is available at this
url. .
First, we removed 26 metabolic pathways from the initial set of 501
automatically inferred metabolic pathways. Then, we created a
superpathway of sunflower’s oil metabolism on the basis of the main
composition of the oil (refs) in the sunflower by merging 16
pathways:
- superpathway of fatty acid biosynthesis II (plant)
- fatty acid biosynthesis initiation I
- linoleate biosynthesis I (plants)
- oleate biosynthesis I (plants)
- stearate biosynthesis II (bacteria and plants)
- palmitate biosynthesis II (bacteria and plants)
- fatty acid elongation – saturated
- Vitamin E biosynthesis
- diacylglycerol biosynthesis (PUFA enrichment in oilseed)
- plant sterol biosynthesis
- diacylglycerol and triacylglycerol biosynthesis
- fatty acid biosynthesis (plant mitochondria)
- gamma-linolenate biosynthesis I (plants)
- long-chain fatty acid activation
- monoacylglycerol metabolism (yeast)
- very long chain fatty acid biosynthesis II
The
oil biosynthesis pathway thus created involves
125 reactions, 160 metabolites and 429 genes.
We checked also the
links between genes and reactions by browsing literature about 40
metabolic genes (essentially identified in the oil metabolism).