feat: disable GCV except N-lim and Gly N-source

Author: edkerk

code/modelCuration/v9_1_0.m

@@ -294,11 +294,11 @@
 model = setParam(model,'eq','r_0501',0); %glycine cleavage, mitochondrion
 model = setParam(model,'eq','r_0507',0); %glycine cleavage complex (lipoylprotein), mitochondrion
 model = setParam(model,'eq','r_0509',0); %glycine cleavage complex (lipoamide), mitochondrion
-model.rxnNotes(ismember(model.rxns,{'r_0501','r_0507','r_0509'})) = {'Only active if glycine is nitrogen source'};
+model.rxnNotes(ismember(model.rxns,{'r_0501','r_0507','r_0509'})) = {'Only active if glycine is nitrogen source, or under nitrogen restriction'};
 
 % Glutamate synthase repressed in excess nitrogen
 model = setParam(model,'eq','r_0472',0);
-model.rxnNotes(ismember(model.rxns,{'r_0472'})) = {'Only active during nitrogen limitation'};
+model.rxnNotes(ismember(model.rxns,{'r_0472'})) = {'Only active during nitrogen restriction'};
 
 % The carnitine shuttle requires exogeneous carnitine, which is absent from
 % defined medium.
@@ -326,6 +326,14 @@
 currCoeff = full(model.S(metIdx,bioIdx)); % Gather the current coefficients
 model.S(metIdx,bioIdx) = currCoeff + [-DR; +DR; -DR];
 
+%% Enable glycine secretion to allow anaerobic growth
+% WORKAROUND: anaerobiosis is only allowed if a small amount of glycine
+% secretion is allowed, as overflow from THF produce by methionine synthase
+% if glycine cleavage system is inactive (= in nitrogen-excess and with
+% non-glycine nitrogen sources).
+model = setParam(model,'lb',{'r_1173'},-1000);
+
+
 %% ========================================================================
 
 %% DO NOT CHANGE OR REMOVE THE CODE BELOW THIS LINE.

code/modelTests/growth.m

@@ -96,7 +96,6 @@
     model_origin = setParam(model_origin,'ub','r_0472',1000);
     % Glycine cleavage system is derepressed under nitrogen limitation
     model_origin = setParam(model_origin,'ub',{'r_0501','r_0507','r_0509'},1000);
-
 end
 
 for i = 1:length(exp_data(:,1))

code/otherChanges/glycineNitrogenSource.m

@@ -1,6 +1,7 @@
 function model = glycineNitrogenSource(model)
 % glycineNitrogenSource
-%   Converts model to represent glycine as sole nitrogen source
+%   Converts model to represent glycine as sole nitrogen source: the
+%   glycine cleavage system is enabled.
 %
 %   Inputs: model           (struct) unmodified model
 %   Output: model           (struct) glycine model
@@ -11,10 +12,10 @@
 % source. See doi:10.1111/j.1567-1364.2002.tb00069.x; 
 % doi:10.1074/jbc.274.15.10523; doi:10.1128/EC.2.5.827-829.2003
 model.ub(strcmp(model.rxns,'r_0501'))=0; %glycine cleavage, mitochondrion
-model.lb(strcmp(model.rxns,'r_0501'))=0;
+model.lb(strcmp(model.rxns,'r_0501'))=1000;
 model.ub(strcmp(model.rxns,'r_0507'))=0; %glycine cleavage complex (lipoylprotein), mitochondrion
-model.lb(strcmp(model.rxns,'r_0507'))=0;
+model.lb(strcmp(model.rxns,'r_0507'))=1000;
 model.ub(strcmp(model.rxns,'r_0509'))=0; %glycine cleavage complex (lipoamide), mitochondrion
-model.lb(strcmp(model.rxns,'r_0509'))=0;
+model.lb(strcmp(model.rxns,'r_0509'))=1000;
 end
 

code/otherChanges/nitrogenLimitation.m

@@ -10,5 +10,7 @@
 % Glutamine synthase is repressed when nitrogen is in excess. See doi:10.1128/EC.2.5.827-829.2003
 model.ub(strcmp(model.rxns,'r_0472'))=1000;
 % Glycine cleavage system is repressed when nitrogen (non-glycine) is in excess
-model = setParam(model,'ub',{'r_0501','r_0507','r_0509'},1000);
+model.lb(strcmp(model.rxns,'r_0501'))=1000; %glycine cleavage, mitochondrion
+model.lb(strcmp(model.rxns,'r_0507'))=1000; %glycine cleavage complex (lipoylprotein), mitochondrion
+model.lb(strcmp(model.rxns,'r_0509'))=1000; %glycine cleavage complex (lipoamide), mitochondrion
 end