Closed djinnome closed 1 year ago
By setting the EX_glc__D_e
reaction to 0 in the RT CobraPy medium, the FBA solution returns infeasible. If we then add the EX_sucr_e
reaction into the RT medium at a flux of 1 (what the EX_glc__D_e
is normally at). The RT model will grow.
The objective values are:
EX_glu__D_e
: 0.0733EX_sucr_e
: 0.149Reactions that sucr_e
is involved in:
SUCRe: h2o_e + sucr_e --> fru_e + glc__D_e
EX_sucr_e: sucr_e -->
Reactions that glc__D_e
is involved in:
MLTG1e: h2o_e + malttr_e --> glc__D_e + malt_e
TREHe: h2o_e + tre_e --> 2.0 glc__D_e
AMY2e: glygn2_e + 8.0 h2o_e --> 8.0 glc__D_e + glygn4_e
EX_glc__D_e: glc__D_e <=>
BG_CELLB: cellb_e + h2o_e --> 2.0 glc__D_e
BG_MBDG: h2o_e + mbdg_e --> glc__D_e + meoh_e
SALCNHe: h2o_e + salcn_e --> 2hxmp_e + glc__D_e
AMY1e: 8.0 h2o_e + strch1_e --> 8.0 glc__D_e + strch2_e
MALTe: h2o_e + malt_e --> 2.0 glc__D_e
ARBTHe: arbt_e + h2o_e --> glc__D_e + hqn_e
GLCt1: glc__D_e --> glc__D_c
13BGHe: 13BDglcn_e + h2o_e --> glc__D_e
SUCRe: h2o_e + sucr_e --> fru_e + glc__D_e
hey. I have a real sucrose export data from batch experiment if want to validate or constrain the model
You have exported metabolite data for axenic Rhodosporidum toruloides growing on sucrose? If so, that would be awesome, as we currently only have exported metabolite data for Rhodo in a co-culture
It is content (g/L) of sucrose in axenic S.elongatus when it is growing alone and content in S.elongatus-Rhodo co-culture when they grow together mixed, or when they are separated by membranes
Got it. At what point in time after inoculation was the measurement taken for each condition (axenic, co-culture mixed, co-culture separated)? Do we also have measurements of biomass (or a proxy such as OD) taken at the same time as sucrose was measured?
https://github.com/PNNL-CompBio/CONCERTO/issues/20#issuecomment-1451435609
@mcnaughtonadm getting Rhodo to grow on sucrose solves half the problem. The other half is adding sucrose export to cyano, and ensuring it secretes it.
As a point of reference towards this, here is the base optimization through CobraPy of the cyano model.
We have an objective value of: 0.0539 with the following Uptake
and Secretion
Metabolite | Reaction | Flux | C-Number | C-Flux |
---|---|---|---|---|
co2_e | EX_co2_e | 0.7191 | 1 | 30.67% |
cobalt2_e | EX_cobalt2_e | 2.758E-07 | 0 | 0.00% |
fe3_e | EX_fe3_e | 8.635E-05 | 0 | 0.00% |
h_e | EX_h_e | 1.882 | 0 | 0.00% |
hco3_e | EX_hco3_e | 1.455 | 1 | 62.07% |
leu__L_e | EX_leu__L_e | 0.02836 | 6 | 7.26% |
mg2_e | EX_mg2_e | 0.0006043 | 0 | 0.00% |
nh4_e | EX_nh4_e | 0.0031 | 0 | 0.00% |
no3_e | EX_no3_e | 0.4029 | 0 | 0.00% |
photon650_e | EX_photon650_e | 0.0006043 | 0 | 0.00% |
photon670_e | EX_photon670_e | 11.7 | 0 | 0.00% |
photon690_e | EX_photon690_e | 18.2 | 0 | 0.00% |
pi_e | EX_pi_e | 0.023 | 0 | 0.00% |
so4_e | EX_so4_e | 0.008394 | 0 | 0.00% |
amylose_c | SK_amylose_c | 0.02769 | 0 | 0.00% |
Metabolite | Reaction | Flux | C-Number | C-Flux |
---|---|---|---|---|
5drib_c | DM_5drib_c | -5.6E-06 | 5 | 26.10% |
amob_c | DM_amob_c | -1.411E-06 | 15 | 19.73% |
co_c | DM_co_c | -5.701E-05 | 1 | 53.14% |
dialurate_c | DM_dialurate_c | -2.758E-07 | 4 | 1.03% |
pho_loss_c | DM_pho_loss_c | -0.5849 | 0 | 0.00% |
o2_e | EX_o2_e | -3.151 | 0 | 0.00% |
The current state of sucr
within the model is as follows:
SUCR: h2o_c + sucr_c --> fru_c + glc__D_c
SPP: h2o_c + suc6p_c --> pi_c + sucr_c
Current Pull Request waiting for Review and Approval by either @JamesPino or @djinnome introducing Jupyter Notebook showing how to generate a Synechococcus model capable of exporting sucrose. Moving this task to done, but not closing the issue until PR goes through.
Issue solved with #33 , closing issue.
Make sure that cyano excretes sucrose under co2 + light inputs Make sure that rhodosporidum is capable of growth on sucrose