Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Castillo, Sandra; Barth, Dorothee; Arvas, Mikko; Pakula, Tiina M.; Pitkänen, Esa; Blomberg, Peter; Seppanen-Laakso, Tuulikki; Nygren, Heli; Sivasiddarthan, Dhinakaran; Penttilä, Merja; Oja, Merja

doi:10.1186/s13068-016-0665-0

Biotechnology for Biofuels and Bioproducts

Table 3 The coefficients (mmol/g CDW) used in the biomass equation of the T. reesei model

From: Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Kegg Id	Compound name	Coefficient
C00133	Alanine	−0.382^a
C00062	Arginine	−0.253^a
C00152	Asparagine	−0.141^a
C00049	Aspartate	−0.233^a
C00097	Cysteine	−0.053^a
C00064	Glutamine	−0.161^a
C00025	Glutamate	−0.248^a
C00037	Glycine	−0.289^a
C00135	Histidine	−0.098^a
C00407	Isoleucine	−0.193^a
C00123	Leucine	−0.362^a
C00047	Lysine	−0.202^a
C00073	Methionine	−0.092^a
C00079	Phenylalanine	−0.151^a
C00148	Proline	−0.243^a
C00065	Serine	−0.322^a
C00188	Threonine	−0.233^a
C00078	Tryptophan	−0.061^a
C00082	Tyrosine	−0.113^a
C00183	Valine	−0.254^a
C06424	Myristic acid	−0.00015^b
C08362	Palmitoleic acid	−0.00043^b
C06427	\(\alpha\)−Linolenic acid	−0.01^b
C00219	Arachidic acid	−0.00013^b
C08320	Lignoceric acid	−0.00014^b
C00249	Palmitic acid	−0.026^c
C01530	Stearic acid	−0.003^c
C00712	Oleic acid	−0.008^c
C01595	Linoleic acid	−0.061^c
C01694	Ergosterol	−0.007^d
C00093	Glycerol−3−P	−0.04^e
C00588	Phosphocholine	−0.014^e
C00346	Phosphoethanolamine	−0.007^e
C00031	d−Glucose	−0.385^f
C00140	N-acetyl-d-glucosamine	−0.948^f
C00360	Deoxyadenosine monophosphate	−0.007^g
C00239	Deoxycytidine monophosphate	−0.008^g
C00362	Deoxyguanosine monophosphate	−0.008^g
C00364	Deoxythymidine monophosphate	−0.007^g
C00020	Adenosine-monophosphate	−0.047^h
C00055	Cytidine monophosphate	−0.045^h
C00144	Guanosine monophosphate	−0.053^h
C00105	Uridine monophosphate	−0.045^h
C00001	Water	−59.276ⁱ
C00002	Adenosine triphosphate	−59.276ⁱ
C00008	Adenosine diphosphate	59.276ⁱ
C00009	Organic phosphorous	59.305ⁱ
C00059	Sulfate	−0.02ⁱ
C00255	Riboflavin	−0.001ⁱ
C00010	Coenzyme A	−0.000001^j
C00003	Nicotinamide adenine dinucleotide (NAD)	−0.000001^j
C00016	Flavin adenine dinucleotide (FAD)	−0.000001^j
C00051	Glutathione	−0.000001^j
C00101	tetrahydrofolate	−0.000001^j
C00575	3′,5′-cyclic AMP	−0.000001^j
C00096	GDP-mannose	−0.000001^j
C01083	\(\alpha\),\(\alpha\)-Trehalose	−0.000001^j

The coefficients correspond to the measured or estimated molar amounts of the compound in the cells, as described in "Methods" section
^aThe amount of amino acids calculated based on the measured cellular protein and the ratio of amino acids in cellular proteins calculated based on the codon abundancy in the RNAseq data of transcriptome
^b Esterified fatty acid measured using GC-MS
^c Sum of measured esterified and free fatty acid measured using GC-MS
^d Measured using GC-MS
^e The amount estimated to be needed for synthesis of triacylglycerols, phophatidylethanolamines or phosphatidylcholines (1 mol of glycerol-3-P, phosphoethanolamine or phosphocholine per 1 mol of triacylglycerol, phosphatidylethanolamine or phosphatidylcholine, respectively)
^f The measured total carbohydrate was assumed to consist of polymers of d-glucose subunits (glucan) and polymers of N-acetyl-d-glucosamine (chitin). Chitin content of the cells was estimated based on the amount of chitin in Aspergillus oryzae [8], and the rest of the measured carbohydrate as glucan
^g The amount of deoxyribonucleotides in DNA calculated based on the cellular DNA amount and the GC content of the genome
^h The amount of ribonucleotides in RNA was estimated based on the measured total RNA amount the nucleotide ratio in genome region encoding ribosomal 18S-28S pre-rRNA
ⁱ As in S. cerevisiae model iMM904 [42]
^j Trace amount of the compound was added

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