Export sucrose from Synechococcus

[djinnome]

Make sure that cyano excretes sucrose under co2 + light inputs Make sure that rhodosporidum is capable of growth on sucrose

[mcnaughtonadm]

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:

• With EX_glu__D_e : 0.0733
• With EX_sucr_e : 0.149
• With both: 0.225

Reactions 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

[PBohutskyi]

hey. I have a real sucrose export data from batch experiment if want to validate or constrain the model

[djinnome]

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

[PBohutskyi]

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

[djinnome]

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?

[djinnome]

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.

[mcnaughtonadm]

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

Uptake

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%

Secretion

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

[mcnaughtonadm]

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.

[mcnaughtonadm]

Issue solved with #33 , closing issue.