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PNNL-CompBio / CONCERTO

Continuous integration and validation for genome-scale metabolic model consortia
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Get binary azo-rhodo working with a carbon source that only rhodo grows on #93

Open djinnome opened 1 year ago

djinnome commented 1 year ago

for example, xylose, but you can use any biolog carbon compound that is + for rhodo and - for azo.

mcnaughtonadm commented 1 year ago

Using Xylose as the carbon source, we can grow the binary between azo and rhodo.

compartments abundance growth_rate reactions metabolites
Azotobacter 0.5 0.371855 2469 2003
Rhodosporidium 0.5 1.037279 2398 2051
medium NaN NaN 449 449

The default media provides glc__D_m at a flux value of 5 which when optimizing the binary, doesn't lead to growth. When adding xyl__D_m at a flux of 5, there is growth in both organisms. When using just xyl__D_m at a flux value of 5, there is not community growth. When using xyl__D_m with a flux value of 10, there is community growth. Seems like there is not enough carbon in the model to grow under the model provided 'Default'. Should we make modifications to the model until we can grow with xyl__D_m using a flux value of 5, or consider growing with 10 a success of binary growth?

djinnome commented 1 year ago

Binary growth where only Rhodo can consume an external carbon source is the goal. Can you confirm that Azo is not consuming xyl__D_m and can you tell me what internal carbon source(s) Azo is consuming?

mcnaughtonadm commented 1 year ago

In this instance with 10 xyl__D_e, it is the sole carbon source (there are some minor trna SRC reactions acting as uptake but 97.72% of carbon is provided by xylose). All of that is being used by Rhodo so Azo is not consuming it.

Internally, just by briefly viewing the fluxes (more may pop up with a visualization), Azo is importing EX_glcn_e (D-gluconate) from Rhodosporidium's export (table below).

Organism Flux
Azotobacter -11.84127256
Rhodosporidium 11.84127256
djinnome commented 1 year ago

Congratulations, this counts as success! As a bonus round, do we know if Rhodo actually excretes gluconate under xylose conditions? And if so, does Azo really eat it? i.e. can we check the Azo Biolog and the Rhodo-Cyano metabolite exchange data to see if gluconate is in there?

djinnome commented 1 year ago

Lastly, do we know if Cyano is capable of secreting xylose if we were to replace the engineered sucrose transporter with a xylose transporter?

djinnome commented 1 year ago

@PBohutskyi ?