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gregmedlock / psy_recon

Metabolic network reconstruction and analysis of Pseudomonas syringae
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Curate synthesis of lipid A core #9

Open gregmedlock opened 5 years ago

gregmedlock commented 5 years ago

In order to represent LPS, we'll use lipid A core (http://modelseed.org/biochem/compounds/cpd15432)

The pathway for synthesis in e. coli is mostly worked out, and syringae is known to synthesize it.

phtuber commented 5 years ago

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121216

phtuber commented 5 years ago

done, save for one issue, which may not even be an issue: In the above paper they have lipid A, final product before adornment with sugars and amino sugars, being trafficked to the exterior side of the cell wall; do you think this is a necessary step for us to include (if being energy accurate then yes as it is an ATP demand)

gregmedlock commented 5 years ago

I think it makes sense--we could either explicitly include it in the "generation" of lipid A, or factor it into the calculation for growth-associated or non-growth-associated maintenance (i.e. ATP demand). As a cell wall component, we would suspect LPS synthesis is proportional to biomass production, thus ATP production required for LPS trafficking should be factor into growth-associated maintenance--make sense?