Fructose transport is represented as a symporter instead of facilitated diffusion

[davidhcsic]

Description of the issue:

In the current yeast-GEM, fructose transport is accompanied by a proton, implying it is a symport type of transport. Instead, glucose transport lacks this proton. IMM904 also has this proton.

Expected feature/value/output:

According to the literature, all hexoses are transported by facilitated diffusion transporters (HXT1/2/etc; no protons attached) in Sc. Furthermore, Sc lacks symport transporters for hexoses (see references below).

The growth of fructose should be slower than that of glucose. However, the yield should be similar. Currently, the proton associated with fructose transport consumes substantial amounts of ATP and decreases yield.

Anjos, J., de Sousa, H. R., Roca, C., Cássio, F., Luttik, M., Pronk, J. T., ... & Gonçalves, P. (2013). Fsy1, the sole hexose-proton transporter characterized in Saccharomyces yeasts, exhibits a variable fructose: H+ stoichiometry. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1828(2), 201-207.

Boles, Eckhard, and Cornelis P. Hollenberg. "The molecular genetics of hexose transport in yeasts." FEMS microbiology reviews 21.1 (1997): 85-111.

Current feature/value/output:

r_1134 D-fructose[e] + H+[e] => D-fructose[c] + H+[c]

Reproducing these results:

clear;
addpath(genpath(pwd));
load('model/yeast-GEM');

model=anaerobicModel(model);

%% glucose
model.lb(findRxnIDs(model,'r_1714'))=-3;
model.ub(findRxnIDs(model,'r_1714'))=-3;
model=changeObjective(model,{'r_4041'},1);
res=optimizeCbModel(model);
disp(res.full(findRxnIDs(model,'r_4041')));

load('model/yeast-GEM');
model=anaerobicModel(model);
%% Close glucose
model.lb(findRxnIDs(model,'r_1714'))=0;
model.ub(findRxnIDs(model,'r_1714'))=0;
%% fructose (same amount of hexose)
model.lb(findRxnIDs(model,'r_1709'))=-3;
model.ub(findRxnIDs(model,'r_1709'))=-3;
model=changeObjective(model,{'r_4041'},1);
res=optimizeCbModel(model);
disp(res.full(findRxnIDs(model,'r_4041')))

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Done this analysis in the develop branch of the repository
• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue