yeast 8.3.3

ComplementaryData/modelCuration/Biomass_newRxnMatrix.tsv

@@ -0,0 +1,29 @@
+rxnID	coefficient	Metabolite standard name	Metabolite_type	compartment
+MNXR96437	1	Ca(2+)	reactant	extracellular
+MNXR96437	1	H+	reactant	extracellular
+MNXR96437	1	Ca(2+)	product	cytoplasm
+MNXR96437	1	H+	product	cytoplasm
+MNXR96797	1	chloride	reactant	extracellular
+MNXR96797	1	chloride	product	cytoplasm
+MNXR126350	1	Cu2(+)	reactant	extracellular
+MNXR126350	1	H+	reactant	extracellular
+MNXR126350	1	Cu2(+)	product	cytoplasm
+MNXR126350	1	H+	product	cytoplasm
+MNXR101669	1	Mn(2+)	reactant	extracellular
+MNXR101669	1	H+	reactant	extracellular
+MNXR101669	1	Mn(2+)	product	cytoplasm
+MNXR101669	1	H+	product	cytoplasm
+MNXR105278	1	Zn(2+)	reactant	extracellular
+MNXR105278	1	H+	reactant	extracellular
+MNXR105278	1	Zn(2+)	product	cytoplasm
+MNXR105278	1	H+	product	cytoplasm
+MNXR101553	1	Mg(2+)	reactant	extracellular
+MNXR101553	1	H+	reactant	extracellular
+MNXR101553	1	Mg(2+)	product	cytoplasm
+MNXR101553	1	H+	product	cytoplasm
+chloride exchange	1	chloride	reactant	extracellular
+Cu2(+) exchange	1	Cu2(+)	reactant	extracellular
+Mn(2+) exchange	1	Mn(2+)	reactant	extracellular
+Zn(2+) exchange	1	Zn(2+)	reactant	extracellular
+Mg(2+) exchange	1	Mg(2+)	reactant	extracellular
+Ca(2+) exchange	1	Ca(2+)	reactant	extracellular

ComplementaryData/modelCuration/Biomass_newRxnMet.tsv

@@ -0,0 +1,7 @@
+NewMetName	Charged formula	Charge	compartment	KEGG ID	CHEBI ID	Remark
+Ca(2+) [extracellular]	Ca	2	extracellular	C00076	CHEBI:29108
+chloride [extracellular]	Cl	-1	extracellular	C00698	CHEBI:17996
+Cu2(+) [extracellular]	Cu	2	extracellular	C00070	CHEBI:29036
+Mn(2+) [extracellular]	Mn	2	extracellular	C19610	CHEBI:29035
+Zn(2+) [extracellular]	Zn	2	extracellular	C00038	CHEBI:29105
+Mg(2+) [extracellular]	Mg	2	extracellular	C00305	CHEBI:18420		

ComplementaryData/modelCuration/Biomass_newRxnProp.tsv

@@ -0,0 +1,13 @@
+rxnID	rev	GPR	rxn_name_seed	EC	rxnID_kegg	Source;reason
+MNXR96437	1	YOL122C	Ca(2+) transport 			bigg:CAt4; gRrules come from TCDB, not included in the DBnewAnnotaiton update (PR #142)
+MNXR96797	1	YNL275W	chloride transport			bigg:Clt; gRrules come from TCDB, not included in the DBnewAnnotaiton update (PR #142)
+MNXR126350	1	YOL122C	Cu2(+) transport			rhea:28727; gRrules come from TCDB, not included in the DBnewAnnotaiton update (PR #142)
+MNXR101669	1	YGR191W	Mn(2+) transport			seed:rxn08946; gRrules come from TCDB, not included in the DBnewAnnotaiton update (PR #142)
+MNXR105278	1	( YGL255W or YLR130C )	Zn(2+) transport			bigg:ZN2t3pp; gRrules come from TCDB, not included in the DBnewAnnotaiton update (PR #142)
+MNXR101553	1	( GR191W or YOL130W )	Mg(2+) transport			bigg:MGt2pp; gRrules come from TCDB, not included in the DBnewAnnotaiton update (PR #142)
+chloride exchange	1		chloride exchange
+Cu2(+) exchange	1		Cu2(+) exchange
+Mn(2+) exchange	1		Mn(2+) exchange
+Zn(2+) exchange	1		Zn(2+) exchange
+Mg(2+) exchange	1		Mg(2+) exchange
+Ca(2+) exchange	1		Ca(2+) exchange

ComplementaryData/modelCuration/Metabolomics_newRxnProp.tsv

@@ -15,7 +15,7 @@ MNXR137279	0	Ketol-acid reductoisomerase, mitochondrial			seed:rxn13008
 MNXR95271	0	pyruvate:pyruvate acetaldehydetransferase (decarboxylating); (S)-2-acetolactate pyruvate-lyase (carboxylating)	2.2.1.6	R00226	rhea:25249
 MNXR97523	1	(R)-2,3-dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing)	1.1.1.383;1.1.1.86	R04439	rhea:22068
 MNXR106779	0	(2R,3S)-3-methylmalate:NAD+ oxidoreductase	1.1.1.-;1.1.1.85	R00994	rhea:32715
-MNXR121603	0	malate/β-methylmalate synthase	2.3.3.-		metacyc:RXN-18333
+MNXR121603	0	malate/beta-methylmalate synthase	2.3.3.-		metacyc:RXN-18333
 MNXR99136	0	palmitoyl-CoA hydrolase	3.1.2.-;3.1.2.2		rhea:40143
 MNXR99175	0	long-chain-fatty-acid---CoA ligase	6.2.1.3		rhea:33651
 MNXR100010	0	a-galactosidase (stachyose)	3.2.1.22		seed:rxn02596

ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv

@@ -0,0 +1,21 @@
+model_id	name	abundance_mmol/gDW	MW_g/mol	group	reference
+s_3880[c]	Ca(2+) 	2.17E-04	40.08	ion	DOI: 10.22161/ijeab/2.2.2
+s_3778[c]	chloride 	1.29E-03	35.45	ion	DOI: 10.3103/S106836741702015X
+s_4019[c]	Cu2(+) 	6.59E-04	63.55	ion	DOI: 10.22161/ijeab/2.2.2
+s_0924[c]	iron(2+) 	3.04E-05	55.84	ion	DOI: 10.22161/ijeab/2.2.2
+s_3801[c]	Mn(2+) 	2.73E-03	54.94	ion	DOI: 10.22161/ijeab/2.2.2
+s_3822[c]	Zn(2+) 	7.48E-04	65.39	ion	DOI: 10.22161/ijeab/2.2.2
+s_1373[c]	potassium 	3.63E-03	39.1	ion	DOI: 10.22161/ijeab/2.2.2
+s_1437[c]	sodium 	3.97E-03	22.99	ion	DOI: 10.22161/ijeab/2.2.2
+s_4013[c]	Mg(2+) 	0.001242543	24.3	ion	DOI: 10.22161/ijeab/2.2.2
+s_1467[c]	sulphate	0.02	96.06	ion	Forster2003
+s_1203[c]	NADH 	1.5E-04	663.43	cofactor	DOI: 10.1016/j.ymben.2013.11.005; Supplementary file
+s_1198[c]	NAD 	2.65E-03	662.43	cofactor	DOI: 10.1016/j.ymben.2013.11.005; Supplementary file
+s_1212[c]	NADPH 	2.7E-03	745.4209	cofactor	DOI: 10.1016/j.ymben.2013.11.005; Supplementary file
+s_1207[c]	NADP(+) 	5.7E-04	744.4129	cofactor	DOI: 10.1016/j.ymben.2013.11.005; Supplementary file
+s_0529[c]	coenzyme A 	1.90E-04	767.5341	cofactor	DOI: 10.1016/j.ymben.2013.11.005; Supplementary file
+s_1487[c]	THF 	6.34E-05	445.4292	cofactor	DOI: 10.1021/jf048083g
+s_1475[c]	TDP 	0.0000012	425.3144	cofactor	DOI:10.1002/jib.293; Figure 6B
+s_0687[c]	FAD 	0.00001	785.5497	cofactor	DOI: 10.1002/yea.1897
+s_1405[c]	riboflavin	0.00099	376.36	cofactor	Forster2003
+s_3714[c]	heme a	0.000001	852.83	cofactor	Forster2003

ComplementaryScripts/missingFields/addSBOterms.m

@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % model = addSBOterms(model)
 %
-% Benjamín J. Sánchez
+% Benjamin J. Sanchez. Last update: 2018-11-26
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = addSBOterms(model)
@@ -13,7 +13,7 @@
 model.metSBOTerms = cell(size(model.mets));
 for i = 1:length(model.mets)
     metName = model_r.metNames{i};
-    if ismember(metName,{'biomass','DNA','RNA','protein','carbohydrate','lipid'}) ...
+    if ismember(metName,{'biomass','DNA','RNA','protein','carbohydrate','lipid','cofactor','ion'}) ...
             || endsWith(metName,' backbone') || endsWith(metName,' chain')
         model.metSBOTerms{i} = 'SBO:0000649';     %Biomass
     else

ComplementaryScripts/modelCuration/addBiomassUpdate.m

@@ -0,0 +1,237 @@
+function model = addBiomassUpdate(model,data)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% addBiomassUpdate
+% Adds rxns and metabolites for BiomassUpdate.
+% Input: model, Biomass_newRxnMatrix.tsv, Biomass_newRxnProp.tsv,
+%        Biomass_newRxnMet.tsv.
+%
+% NOTE: changeGeneAssociation.m is a function from COBRA
+%
+% Feiran Li     2018-10-23
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+% Load stoichiometry data:
+cd ..
+fid = fopen('../ComplementaryData/modelCuration/Biomass_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/modelCuration/Biomass_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   = ']';
+[m, ~]      = 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/modelCuration/Biomass_newRxnMet.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 for BiomassUpdate (PR #174)';
+    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 ../modelCuration    
+    [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.rxnNotes{rxnIndex} = 'NOTES:added for BiomassUpdate (PR #174)';
+    if ~isempty(model.rules{rxnIndex})
+        model.rxnConfidenceScores(rxnIndex) = 2;   %reactions has GPR rules
+    elseif contains(model.rxnNames(rxnIndex),'exchange')
+        model.rxnConfidenceScores(rxnIndex) = NaN; %exchange rxns
+    else
+        model.rxnConfidenceScores(rxnIndex) = 1;   %reactions without gene but needed for modelling
+    end
+end
+
+% add gene standard name for new genes
+fid = fopen('../../ComplementaryData/databases/SGDgeneNames.tsv');
+yeast_gene_annotation = textscan(fid,'%s %s','Delimiter','\t','HeaderLines',1);
+fclose(fid);
+
+geneIndex = zeros(1,1);
+for i = 1: length(model.genes)
+    geneIndex = strcmp(yeast_gene_annotation{1}, model.genes{i});
+    if sum(geneIndex) == 1 && ~isempty(yeast_gene_annotation{2}{geneIndex})
+        model.geneNames{i} = yeast_gene_annotation{2}{geneIndex};
+    else
+        model.geneNames{i} = model.genes{i};
+    end
+end
+
+% Add protein name for genes
+for i = 1:length(model.genes)
+    model.proteins{i} = strcat('COBRAProtein',num2str(i));
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Introduce two PseudoRxn for cofactors and ions
+group = unique(data.groups);
+for i = 1:length(group)
+%get new metID for pseudo mets :ion and cofactor
+    cd ../otherChanges
+    metname = [group{i} ' [cytoplasm]'];
+    [~,index] = ismember(metname,model.metNames);
+    if index ~= 0
+        metID = model.mets(index);
+    elseif index == 0
+        metID  = ['s_' getNewIndex(model.mets) '[c]'];
+        model = addMetabolite(model,metID, ...
+            'metName',metname);
+    end
+    [~,index] = ismember(metID,model.mets);
+    model.metNotes{index}      = 'NOTES:added for BiomassUpdate (PR #174)';
+
+% Get coefficients for pseudo rxns: ion pseudoreaction, cofactor pseudoreaction
+    newps.rxnName = {[group{i},' pseudoreaction']};
+    index = strcmp(group{i},data.groups);
+    newps.metIDs = data.mets(index);
+    newps.metcoef = data.abundances(index)*-1;
+
+% introduce two pseudo mets ion [cytoplasm], cofactor [cytoplasm] into the reaction
+    newps.metIDs = [newps.metIDs;metID];
+    newps.metcoef = [newps.metcoef;1];
+    [~,index] = ismember(newps.rxnName,model.rxnNames);
+    if index == 0
+        rxnID = ['r_' getNewIndex(model.rxns)];
+    else
+        rxnID = model.rxns{index};
+    end
+    [model,rxnIndex] = addReaction(model, rxnID,...
+                       'reactionName', char(newps.rxnName),...
+                       'metaboliteList',newps.metIDs,...
+                       'stoichCoeffList',newps.metcoef,...
+                       'reversible',false,...
+                       'checkDuplicate',1);
+     cd ../modelCuration/
+    [EnergyResults,RedoxResults] = CheckEnergyProduction(model,{['r_' newID]},EnergyResults,RedoxResults);
+    [MassChargeresults] = CheckBalanceforSce(model,{['r_' newID]},MassChargeresults);
+    if isempty(rxnIndex)
+        rxnIndex = strcmp(model.rxns,rxnID);
+    end
+    model.rxnNotes{rxnIndex} = 'NOTES:added for BiomassUpdate (PR #174)';
+    model.rxnConfidenceScores(rxnIndex) = 1; %needed for modeling
+    model = rmfield(model,'grRules');
+end
+
+% Change original biomass equation
+UnusedMets = {'sulphate [cytoplasm]','riboflavin [cytoplasm]', 'heme a [cytoplasm]'};
+[~,UnusedMets_index] = ismember(UnusedMets,model.metNames);
+AddMets = {'cofactor [cytoplasm]','ion [cytoplasm]'};
+[~,AddMets_index] = ismember(AddMets,model.metNames);
+biomassRxn = 'r_4041';
+[~,biomassRxn_index] = ismember(biomassRxn,model.rxns);
+model.S(UnusedMets_index,biomassRxn_index) = 0;
+model.S(AddMets_index,biomassRxn_index) = -1;
+
+% Save model:
+if isfield(model,'grRules')
+model = rmfield(model,'grRules');
+end
+model = minimal_Y6(model);
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ComplementaryScripts/modelCuration/minimal_Y6.m

@@ -20,7 +20,15 @@
                     'r_2060'; ... % sulphate exchange
                     'r_1861'; ... % iron exchange, for test of expanded biomass def
                     'r_1832'; ... % hydrogen exchange
-                    'r_2100'};    % water exchange
+                    'r_2100'; ... % water exchange
+                    'r_4593'; ... % chloride exchange
+                    'r_4595'; ... % Mn(2+) exchange
+                    'r_4596'; ... % Zn(2+) exchange
+                    'r_4597'; ... % Mg(2+) exchange
+                    'r_2049'; ... % sodium exchange
+                    'r_4594'; ... % Cu(2+) exchange
+                    'r_4600'; ... % Ca(2+) exchange
+                    'r_2020' };   % potassium exchange
 
 blockedExchanges = {'r_1663'; ... % bicarbonate exchange
                     'r_4062'; ... % lipid backbone exchange
@@ -32,11 +40,11 @@
 glucoseExchangeIndex = findRxnIDs(model,glucoseExchange);
 BlockedRxnIndex      = findRxnIDs(model,blockedExchanges);
 
-if length(uptakeRxnIndexes) ~= 7
-    error('Not all exchange reactions were found.')
+if length(find(uptakeRxnIndexes~= 0)) ~= 15
+    warning('Not all exchange reactions were found.')
 end
 
-model.lb(uptakeRxnIndexes)     = -1000;
+model.lb(uptakeRxnIndexes(uptakeRxnIndexes~=0))     = -1000;
 model.lb(glucoseExchangeIndex) = -1;
 
 model.lb(BlockedRxnIndex) = 0;