Strain design ec yeast

ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMatrix.tsv

@@ -0,0 +1,7 @@
+rxnID	coefficient	Metabolite standard name	Metabolite_type	compartment
+MNXR111232	1	farnesyl diphosphate	reactant	cytoplasm
+MNXR111232	1	diphosphate	product	cytoplasm
+MNXR111232	1	amorphadiene	product	cytoplasm
+Amorphadiene transport	1	amorphadiene	reactant	cytoplasm
+Amorphadiene transport	1	amorphadiene	product	extracellular
+Amorphadiene exchange	1	amorphadiene	reactant	extracellular

ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMetAnnotation.tsv

@@ -0,0 +1,3 @@
+NewMetName	Charged formula	Charge	compartment	KEGG ID	CHEBI ID	Remark
+amorphadiene [cytoplasm]	C15H24	0	cytoplasm		CHEBI:52026	MNXM3912
+amorphadiene [extracellular]	C15H24	0	extracellular		CHEBI:52026	MNXM3912

ComplementaryData/Amorphadiene_GEM/newpathway_newRxnProp.tsv

@@ -0,0 +1,4 @@
+rxnID	rev	GPR	rxn_name_seed	EC	rxnID_kegg	Source;reason
+MNXR111232	0		amorphadiene synthase	4.2.3.24	R07630	rhea:26446
+Amorphadiene transport	0		Amorphadiene transport			NA
+Amorphadiene exchange	0		Amorphadiene exchange			NA

strain_design_ecYeast/Strain_design_Amor.m

@@ -0,0 +1,152 @@
+% Pathway construction of Amorphadiene (Amor) in yeastGEM model
+
+% Add new reactions to the model
+cd ../ComplementaryScripts
+model = loadYeastModel;
+
+% Load stoichiometry data:
+fid = fopen('../ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMatrix.tsv');
+newreaction = textscan(fid,'%s %s %s %s %s','Delimiter','\t','HeaderLines',1);
+matrix.rxnIDs  = newreaction{1};
+matrix.metcoef = cellfun(@str2num, newreaction{2});
+matrix.metIDs  = newreaction{3};
+matrix.mettype = newreaction{4};
+matrix.metcompartments = newreaction{5};
+fclose(fid);
+
+% Load rxn properties data:
+fid  = fopen('../ComplementaryData/Amorphadiene_GEM/newpathway_newRxnProp.tsv','r');
+rev = textscan(fid,'%s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1);
+newrxn.ID  = rev{1};
+newrxn.Rev = cellfun(@str2num, rev{2});
+newrxn.GPR = rev{3};
+newrxn.rxnNames      = rev{4};
+newrxn.rxnECNumbers  = rev{5};
+newrxn.rxnKEGGID     = rev{6};
+newrxn.rxnNotes      = rev{7};
+newrxn.rxnMetaNetXID = newrxn.ID;
+for i = 1:length(newrxn.rxnMetaNetXID)
+    if ~startsWith(newrxn.rxnMetaNetXID{i},'MNXR')
+        newrxn.rxnMetaNetXID{i} = '';
+    end
+end
+newrxn.rxnMetaNetXID = regexprep(newrxn.rxnMetaNetXID,'_cv','');
+fclose(fid);
+
+% Change coefficients for reactants:
+for i=1:length(matrix.rxnIDs)
+    if strcmp(matrix.mettype(i),'reactant')
+        matrix.metcoef(i) = matrix.metcoef(i)*-1;
+    end
+end
+
+% Change compartments:
+CONValldata = cat(2,model.compNames,model.comps);
+lbracket    = ' [' ;
+llbracket   = '[';
+rbrackets   = ']';
+space       = ' ';
+[m, n]      = size(CONValldata);
+for i = 1:m
+    aa = CONValldata(i,1);
+    aa = char(aa);
+    for j=1:length(matrix.rxnIDs)
+        bb = matrix.metcompartments(j,1);
+        bb = char(bb);
+        if strcmp(bb,aa)
+            matrix.Newcomps(j,1) = CONValldata(i,2);
+        end
+    end
+end
+for i=1:length(matrix.rxnIDs)
+    matrix.metnames(i) = strcat(matrix.metIDs(i),lbracket,matrix.metcompartments(i),rbrackets);
+    matrix.Newcomps(i) = strcat(llbracket,matrix.Newcomps(i),rbrackets);
+end
+
+% Map mets to model.metnames, get s_index for new mets:
+cd otherChanges
+for j = 1:length(matrix.metnames)
+    [~,metindex] = ismember(matrix.metnames(j),model.metNames);
+    if metindex ~= 0
+        matrix.mets(j) = model.mets(metindex);
+    elseif metindex == 0
+        newID = getNewIndex(model.mets);
+        matrix.mets(j) = strcat('s_',newID,matrix.Newcomps(j));
+        model = addMetabolite(model,char(matrix.mets(j)), ...
+            'metName',matrix.metnames(j));
+    end
+end
+
+% Add metabolite data:
+fid = fopen('../../ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMetAnnotation.tsv');
+newmet_annot         = textscan(fid,'%s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1);
+newmet.metNames      = newmet_annot{1};
+newmet.metFormulas   = newmet_annot{2};
+newmet.metCharges    = cellfun(@str2num, newmet_annot{3});
+newmet.metKEGGID     = newmet_annot{5};
+newmet.metChEBIID    = newmet_annot{6};
+newmet.metMetaNetXID = newmet_annot{7};
+
+fclose(fid);
+for i = 1:length(newmet.metNames)
+    [~,metID] = ismember(newmet.metNames(i),model.metNames);
+    if metID ~= 0
+        model.metFormulas{metID}   = newmet.metFormulas{i};
+        model.metCharges(metID)    = newmet.metCharges(i);
+        model.metKEGGID{metID}     = newmet.metKEGGID{i};
+        model.metChEBIID{metID}    = newmet.metChEBIID{i};
+        model.metMetaNetXID{metID} = newmet.metMetaNetXID{i};
+        model.metNotes{metID}      = 'NOTES: added after the heterologous update';
+    end
+end
+
+% Add new reactions according to rev ID: Met Coef needs to be a column, not
+% a row. Coef should be a double, which was converted at the import section
+EnergyResults     = {};
+MassChargeresults = {};
+RedoxResults      = {};
+if ~isfield(model,'rxnMetaNetXID')
+    model.rxnMetaNetXID = cell(size(model.rxns));
+end
+for i = 1:length(newrxn.ID)
+    cd ../otherChanges
+    newID = getNewIndex(model.rxns);
+    j     = find(strcmp(matrix.rxnIDs,newrxn.ID{i}));
+    Met   = matrix.mets(j);
+    Coef  = transpose(matrix.metcoef(j));
+    [model,rxnIndex] = addReaction(model, ['r_' newID],...
+        'reactionName', newrxn.ID{i},...
+        'metaboliteList',Met,...
+        'stoichCoeffList',Coef,...
+        'reversible',newrxn.Rev(i,1),...
+        'geneRule',newrxn.GPR{i},...
+        'checkDuplicate',1);
+    cd ../modelexpansion/
+    [EnergyResults,RedoxResults] = CheckEnergyProduction(model,{['r_' newID]},EnergyResults,RedoxResults);
+    [MassChargeresults] = CheckBalanceforSce(model,{['r_' newID]},MassChargeresults);
+    if isempty(rxnIndex)
+        rxnIndex = strcmp(model.rxns,['r_' newID]);
+    end
+    % Add rxn annotation:
+    model.rxnNames{rxnIndex}      = newrxn.rxnNames{i};
+    model.rxnECNumbers(rxnIndex)  = newrxn.rxnECNumbers(i);
+    model.rxnKEGGID(rxnIndex)     = newrxn.rxnKEGGID(i);
+    model.rxnMetaNetXID(rxnIndex) = newrxn.rxnMetaNetXID(i);
+    model.rxnConfidenceScores(rxnIndex) = 1;   %reactions without gene but needed for modelling
+    model.rxnNotes{rxnIndex} = ['NOTES: heterologous pathway; ',newrxn.rxnNotes{i}];
+end
+
+% Set constraints of pathway
+model=changeRxnBounds(model,'r_1714',-1000,'l'); % minimal glucose uptake rate
+model=changeRxnBounds(model,'r_2111',0.1,'l'); % maximum growth rate
+model=changeObjective(model,'r_4603'); % RxnID of new product's exchange reaction
+model=changeRxnBounds(model,'r_0458',0,'u'); % delete GAL1
+model=changeRxnBounds(model,'r_0459',0,'u'); % delete GAL7
+model=changeRxnBounds(model,'r_1071',0,'l'); % delete GAL7
+model=changeRxnBounds(model,'r_1071',0,'u'); % delete GAL7
+model=changeRxnBounds(model,'r_1070',0,'u'); % delete GAL10
+model=changeRxnBounds(model,'r_1070',0,'l'); % delete GAL10
+
+% Save model:
+cd ../../result_ecYeast/ecModels
+save Amor_GEM.mat model

strain_design_ecYeast/Strain_design_FFAs.m

@@ -149,7 +149,7 @@
 
 % Pathway construction of FFAs in ecYeast model
 
-% Add new reactions of asp pathway to the model
+% Add new reactions of FFA pathway to the model
 cd ../../../ModelFiles/mat
 load('ecYeastGEM_batch.mat');
 model = ecModel_batch;

strain_design_ecYeast/Untitled2.m

@@ -0,0 +1,45 @@
+Kcat1=115*3600;
+MW1=27.249;
+model = addReaction(model,'3HP_newRxn1','metaboliteList',{'s_0794','s_1212','s_4184','prot_P39831','s_1207','s_4207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false);
+model = addReaction(model,'3HP_newRxn7','metaboliteList',{'prot_pool','prot_P39831'},'stoichCoeffList',[-MW1 1],'reversible',false);
+% Add rxns of gene bcere0029_32090
+model = addReaction(model,'3HP_newRxn4','metaboliteList',{'s_0441','s_1399','s_0955','s_4184'},'stoichCoeffList',[-1 -1 1 1],'reversible',false);
+% Add rxns of gene A7U8C7
+Kcat2=7.03*3600;
+MW2=61.24;
+model = addReaction(model,'3HP_newRxn5','metaboliteList',{'s_0794','s_0973','prot_A7U8C7','s_0441','s_0456'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false);
+model = addReaction(model,'3HP_newRxn8','metaboliteList',{'prot_pool','prot_A7U8C7'},'stoichCoeffList',[-MW2 1],'reversible',false);
+% Add rxns of gene YGR019Wly
+Kcat3=0.1324*3600;
+MW3=52.946;
+model = addReaction(model,'3HP_newRxn6','metaboliteList',{'s_0180','s_0441','prot_P17649ly','s_0991','s_4184'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1],'reversible',false);
+model = addReaction(model,'3HP_newRxn9','metaboliteList',{'prot_pool','prot_P17649ly'},'stoichCoeffList',[-MW3 1],'reversible',false);
+% Add transport and exchange rxns of 3HP
+model = addReaction(model,'3HP_newRxn2','metaboliteList',{'s_4207','s_4208'},'stoichCoeffList',[-1 1],'reversible',false);
+model = addReaction(model,'3HP_newRxn3','metaboliteList',{'s_4208'},'stoichCoeffList',[-1],'reversible',false);
+
+% Add gene rules to the reaction
+model=changeGeneAssociation(model,'3HP_newRxn1','fdyG');
+model=changeGeneAssociation(model,'3HP_newRxn4','bcere0029_32090');
+model=changeGeneAssociation(model,'3HP_newRxn5','A7U8C7');
+model=changeGeneAssociation(model,'3HP_newRxn6','YGR019Wly');
+
+% Normalization of geneShortNames, metComps, enzymes, and enzGenes
+model.geneShortNames(1128)={'fdyG'};
+model.geneShortNames(1129)={'bcere0029_32090'};
+model.geneShortNames(1130)={'A7U8C7'};
+model.geneShortNames(1131)={'YGR019Wly'};
+
+model.metComps(4147)=1;
+model.metComps(4148)=1;
+model.metComps(4149)=1;
+model.metComps(4150)=1;
+model.metComps(4151)=3;
+
+model.enzymes(964)={'P39831'};
+model.enzymes(965)={'A7U8C7'};
+model.enzymes(966)={'P17649ly'};
+
+model.enzGenes(964)={'fdyG'};
+model.enzGenes(965)={'A7U8C7'};
+model.enzGenes(966)={'YGR019Wly'};

strain_design_ecYeast/scripts_metEngFinders/lymetEng_TargetsFinder.m

@@ -100,7 +100,7 @@
 metList    = [metList,'Growth'];
 Rows       = ['WT_yields';model.genes];
 ResultsTable = cell2table(resultsMat,'VariableNames',metList,'RowNames',Rows);
-writetable(ResultsTable,['../../result_ecYeast/' filename],'WriteVariableNames',true,'WriteRowNames',true,'Delimiter','\t')
+writetable(ResultsTable,['../../result_ecYeast/results_Findtargets' filename],'WriteVariableNames',true,'WriteRowNames',true,'Delimiter','\t')
 end
 
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