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Aspergillus nidulans is a model organism for aspergilli, which are an important …


Biology Articles » Mycology » Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans » Tables

Tables
- Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans

Table 1
Biochemical conversions and transport processes, and number of ORFs associated with the metabolic reactions
Part of metabolism
Number of metabolic reactions
Number of previously annotated ORFsa
Number of newly annotated ORFs
Total number of ORFs
Biochemical reactions
1,095 (681b)
188
468
656
      C-compound metabolism
463 (220)
96
166
262
      Energy metabolism
20 (17)
14
40
54
      Aminoacid metabolism
238 (171)
40
125
165
      Nucleotide metabolism
144 (114)
10
44
54
      Lipid metabolism
175 (122)
13
97
110
      Secondary metabolism
42 (25)
16
14
30
      Nitrogen and sulphur metabolism
8 (7)
2
3
5
      Polymerization, assembly and maintenance
5 (5)



Transport processes
118 (113)
6
3
9
Total
1,213 (794)
194
472
666
Shown are the total number of biochemical conversions and transport processes included in the metabolic reconstruction for A. nidulans (number of unique reactions are given in parenthesis), and the number of ORFs (previously and newly annotated) associated with the metabolic reactions. The total number of unique ORFs in the metabolic network may be different from the sum of the number of ORFs in the different parts of the metabolism, because there are ORFs that encode functions in several parts of the metabolism. aAspergillus nidulans Database [9]. bSix nonenzymatic steps are included. ORF, open reading frame.
Table 2
Genes that are differentially expressed in the different pair-wise comparisons possible between the categories
Comparison
Total genes (up/down)
Metabolic genes (%)
Ethanol versus glucose
418 (249/169)
103 (25%)
Ethanol versus glycerol
206 (92/114)
58 (28%)
Glycerol versus glucose
71 (57/14)
12 (17%)
Shown are the number of genes that are differentially expressed in the different pair-wise comparisons possible between the categories, for a cutoff P value in the logit-t test of 0.01. The total number of genes is presented along with the number of upregulated (up) and downregulated (down) genes (shown in parenthesis). The number (and percentage) of metabolic genes identified within the differentially expressed genes is also shown.
Table 3
Classification of the genes in each cluster into GO categories
Cluster
Number of genes in cluster
Biological processes
Molecular functions
Cluster 1
280
Ribosome biogenesis
Cytoplasm organization and biogenesis
Ribosome biogenesis and assembly
RNA binding
SnoRNA binding
Nucleic acid binding
Cluster 2
146
Alcohol metabolism
Monosaccharide metabolism
Monosaccharide catabolism
Translation elongation factor activity
Carbohydrate kinase activity
Thryptophan synthase activity
Cluster 3
184
Karyogamy
Karyogamy during conjugation with cellular fusion
Glucan metabolism
DNA binding
Protein kinase regulator activity
Kinase regulator activity
Cluster 4
206

Peroxidase activity
Oxidoreductase activity, acting on peroxide as acceptor
Cluster 5
92

Oxidoreductase activity
Pyruvate dehydrogenase activity
Pyruvate dehydrogenase (acetyl transferring) activity
Cluster 6
125
Generation of precursor metabolites and energy
Energy derivation by oxidation of organic compounds
Fatty acid β-oxidation
Oxidoreductase activity
Triose-phosphate isomerase activity
Allophanate hydrolase activity
Cluster 7
254
Cofactor metabolism
Coenzyme metabolism
Generation of precursor metabolites and energy
Hydrogen ion transporter activity
Monovalent inorganic cation transporter activity
Lyase activity
Cluster 8
212
Protein biosynthesis
Cellular biosynthesis
Macromolecule biosynthesis
Structural constituent of ribosome
Structural molecule activity
Peptidyltransferase activity
The genes in each cluster are classified into GO categories (provided by CADRE), according to the three most important biological processes and molecular functions. The fields with fewer than three categories correspond to cases in which the P values were above the cutoff selected in the GO term analysis. The sum of the number of genes in each cluster is not equal to the total number of differentially expressed genes (1,534) because 35 genes were discarded in the clustering analysis (see Analysis of transcriptome data, under Materials and methods).
Table 4
Highly regulated or reporter metabolites for the three possible pair-wise comparisons between the different carbon sources
Ethanol versus glucose
Ethanol versus glycerol
Glycerol versus glucose
Reporter metabolite
n
P
Reporter metabolite
n
P
Reporter metabolite
n
P
Acetyl coenzyme A (mitochondrial)
12
2.1E-06
Oxaloacetate
13
7.6E-05
N-Carbamoyl-L-aspartate
3
1.0E-03
Coenzyme A (mitochondrial)
14
2.6E-06
Coenzyme A (mitochondrial)
14
1.2E-04
Carbamoyl phosphate
5
1.7E-03
Glyoxylate (glyoxysomal)
3
1.8E-05
Glyoxylate (glyoxysomal)
3
2.1E-04
2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine
2
2.8E-03
Oxaloacetate
13
9.4E-05
Acetyl coenzyme A (mitochondrial)
12
2.7E-04
Glycogen
2
2.8E-03
Acetyl coenzyme A (glyoxysomal)
2
1.1E-04
Acetyl coenzyme A (glyoxysomal)
2
4.2E-04
Maltose
6
2.9E-03
Coenzyme A (glyoxysomal)
2
1.1E-04
Coenzyme A (glyoxysomal)
2
4.2E-04
Maltose (extracellular)
6
2.9E-03
Oxaloacetate (mitochondrial)
11
4.4E-04
Oxaloacetate (mitochondrial)
11
4.3E-04
L-glutamine
16
3.1E-03
Carnitine
2
4.9E-04
2-Oxoglutarate (mitochondrial)
9
4.9E-04
α-D-glucose 1-phosphate
4
3.4E-03
O-acetylcarnitine
2
4.9E-04
Citrate
1
5.6E-04
ATP
94
3.7E-03
Propanoyl-coenzyme A
3
6.1E-04
Phosphoenolpyruvate
6
8.5E-04
(R)-3-Hydroxy-3-methyl-2-oxobutanoate (mitochondrial)
2
4.4E-03
Maltose
6
7.0E-04
Fumarate (mitochondrial)
3
8.6E-04
(R)-2,3-dihydroxy-3-methylbutanoate (mitochondrial)
2
4.4E-03
Maltose (extracellular)
6
7.0E-04
α-D-glucose 1-phosphate
4
9.5E-04
Carbon dioxide
42
4.7E-03
O-acetylcarnitine (mitochondrial)
2
9.0E-04
Citrate (mitochondrial)
5
1.3E-03
S-acetyldihydrolipoamide (mitochondrial)
2
5.1E-03
Carnitine (mitochondrial)
2
9.0E-04
Carnitine
2
1.9E-03
Carbon dioxide (mitochondrial)
16
6.0E-03
O-acetylcarnitine (glyoxysomal)
2
9.0E-04
O-acetylcarnitine
2
1.9E-03
ADP
64
1.2E-02
Shown are highly regulated or reporter metabolites for the three possible pair-wise comparisons between the different carbon sources, according to Patil and Nielsen [23]. 'n' denotes the number of neighbors of the reporter metabolite (the number of reactions in which it participates).
Table 5
Enzymes and transporters in subnetworks
Ethanol versus glucose (26 reactions)
Ethanol versus glycerol (33 reactions)
Glycerol versus glucose (34 reactions)
6-Phosphofructokinase
1,3-β-Glucan synthase
5'-Phosphoribosylformyl glycinamidine synthetase
Acetyl-CoA hydrolase
Acetyl-CoA hydrolase
8-Amino-7-oxononanoate synthase
Aconitate hydratase (mitochondrial)
Acetyl-CoA synthase
Aldehyde dehydrogenase
Alcohol dehydrogenase
Aconitate hydratase (mitochondrial)
α,α-Trehalase
Aldehyde dehydrogenase
Adenylate kinase
α-Glucosidase
α-Glucosidase
Alanine-glyoxylate transaminase
α-Glucosidase
α-Glucosidase
Alcohol dehydrogenase
Aspartate-carbamoyltransferase
α-Glucosidase
Aldehyde dehydrogenase
Aspartate-carbamoyltransferase
Aspartate transaminase (mitochondrial)
Aspartate transaminase (mitochondrial)
B-ketoacyl-ACP synthase
Aspartate transaminase (mitochondrial)
Aspartate transaminase (mitochondrial)
Carbamoyl-phophate synthetase
ATP:citrate oxaloacetate-lyase
ATP:citrate oxaloacetate-lyase
Citrate synthase (mitochondrial)
Carnitine O-acetyltransferase
Carnitine O-acetyltransferase
Dihydrolipoamide S-acetyltransferase (mitochondrial)
Carnitine O-acetyltransferase (mitochondrial)
Carnitine O-acetyltransferase (mitochondrial)
Dihydroxy acid dehydratase (mitochondrial)
Carnitine/acyl carnitine carrier
Citrate synthase (mitochondrial)
Fatty-acyl-CoA synthase
Citrate synthase (mitochondrial)
Citrate synthase (mitochondrial)
Fatty-acyl-CoA synthase
Formate dehydrogenase
Formate dehydrogenase
Fructose-bisphosphatase
Fructose-bisphosphatase
Fumarate dehydratase (mitochondrial)
Glucan 1,3-β-glucosidase (extracellular)
Gluconolactonase (extracellular)
Glucose 6-phosphate 1-dehydrogenase
Glucose 6-phosphate 1-dehydrogenase
Glucose 6-phosphate 1-dehydrogenase
Glucose-6-phosphate isomerase
Glycerol 3-phosphate dehydrogenase (FAD dependent)
Glyceraldehyde 3-phosphate dehydrogenase
Glycerol 3-phosphate dehydrogenase (FAD dependent)
Glycerol dehydrogenase
Isocitrate lyase (glyoxysomal)
Glycerol dehydrogenase
Glycerol kinase
Glycerol kinase
Isocitrate lyase (glyoxysomal)
GTP cyclohydrolase I
Mannose-6-phosphate isomerase
Malate dehydrogenase (malic enzyme; NADP+)
Ketol-acid reductoisomerase (mitochondrial)
Phosphoenolpyruvate carboxykinase
Malate synthase (glyoxysomal)
Malate dehydrogenase (malic enzyme; NADP+)
Pyruvate kinase
Mannitol 2-dehydrogenase (NAD+)
Mannitol 2-dehydrogenase (NAD+)
Transketolase
Phosphoenolpyruvate carboxykinase
Mannitol 2-dehydrogenase (NADP+)

Phosphoglucomutase
Phosphoenolpyruvate carboxykinase

Phosphogluconate dehydrogenase (decarboxylating)
Phosphoribosylamine-glycine ligase

Phosphorylase
Phosphorylase

Pyruvate kinase
Pyruvate dehydrogenase (lipoamide) (mitochondrial)

Transketolase
Pyruvate kinase

UTP-glucose-1-phosphate uridylyltransferase
Ribulokinase


UTP-glucose-1-phosphate uridylyltransferase
Shown is a list of the enzymes and transporters that participate in the 'small', highly correlated subnetworks for each pair-wise comparison between the three carbon sources investigated. Enzymes common to all reactions are highlighted in bold. Some enzymes appear more than once in the table, which means that they are isoenzymes and are encoded by different genes. CoA, coenzyme A.

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