Additional Table S1: FunCat Categories of up-regulated genes in ∆gliT MeOH v ATCC46645 MeOH
FunCat ID
01.06.06
01.06.06.05
01.06.06.11
FunCat Category
isoprenoid metabolism
sesquiterpenes metabolism
tetracyclic and pentacyclic triterpenes (cholesterin,
steroids and hopanoids) metabolism
metabolism of phenylalanine
secondary metabolism
metabolism of eicosanoids
metabolism of alkaloids
metabolism of secondary products derived from Ltryptophan
No. of genes
9
5
5
p-value
0.000498
3.96E-07
0.02511
4
23
2
2
2
0.020364
1.59E-06
0.01226
0.039122
0.02148
10.03
10.03.01
14.07
16.01
16.03
16.21.01
20.01
20.01.01
20.01.01.01
20.01.01.01.01
20.01.01.01.01.01
20.01.01.07.07
20.01.11
20.01.13
20.01.15
20.01.26
20.01.27
20.03
20.03.02.02
20.03.25
20.09
20.09.16.01
cell cycle
mitotic cell cycle and cell cycle control
protein modification
protein binding
nucleic acid binding
heme binding
transported compounds (substrates)
ion transport
cation transport (H+, Na+, K+, Ca2+ , NH4+, etc.)
heavy metal ion transport (Cu+, Fe3+, etc.)
siderophore-iron transport
phosphate transport
amine / polyamine transport
lipid/fatty acid transport
electron transport
neurotransmitter transport
drug/toxin transport
transport facilities
symporter
ABC transporters
transport routes
Type I protein secretion system (ABC-type transport
systems)
1
1
4
4
2
6
37
11
10
9
7
2
4
5
11
3
9
17
3
10
24
5
0.000494
0.009208
0.014708
4.61E-07
0.001464
0.000882
1.52E-05
0.001083
0.000718
1.52E-06
3.08E-07
0.032776
0.015295
0.040613
0.006083
0.021951
0.00052
0.014017
0.048048
9.80E-07
0.023615
0.000304
20.09.18
32.05
32.05.01
32.05.05.01
32.07
32.07.01
32.07.05
34.01
34.01.01
34.01.01.01
cellular import
disease, virulence and defense
resistance proteins
toxins
detoxification
detoxification involving cytochrome P450
detoxification by export
homeostasis
homeostasis of cations
homeostasis of metal ions (Na, K, Ca etc.)
15
14
7
3
22
9
6
12
11
9
0.001044
0.000878
0.006809
0.034548
3.14E-08
7.69E-07
0.010986
0.000705
0.000707
0.00106
01.01.09.04
1.2
01.20.05.09
01.20.17.09
01.20.33
1
FunCat ID
34.01.03
34.01.03.03
41.01
41.01.03
41.01.03.01
FunCat Category
homeostasis of anions
homeostasis of phosphate
fungal/microorganismic development
tissue pattern formation
fruit body development (sexually or asexually
derived spores)
43.01
43.01.03
fungal/microorganismic cell type differentiation
fungal and other eukaryotic cell type differentiation
No. of genes
3
2
4
3
3
p-value
0.00723
0.014356
0.047098
0.001399
0.000928
2
2
0.04479
0.04479
Additional Table S2: FunCat Categories of down-regulated genes in ∆gliT MeOH v ATCC46645 MeOH
FunCat ID
01.01.06.04.02
01.01.09.02.02
01.02.02
1.05
01.05.06
01.05.06.07
01.20.17
01.20.17.03
01.25.03
2.01
02.16.01
16.01
16.17.01
16.17.09
16.21.01
20.01.01.01.01
20.09.18
20.09.18.07
32.05.03
FunCat Category
degradation of threonine
degradation of serine
nitrogen metabolism
C-compound and carbohydrate metabolism
C-2 compound and organic acid metabolism
C-2 compound and organic acid catabolism
metabolism of secondary products derived from
primary amino acids
metabolism of amines
extracellular protein degradation
glycolysis and gluconeogenesis
alcohol fermentation
protein binding
calcium binding
heavy metal binding (Cu, Fe, Zn)
heme binding
heavy metal ion transport (Cu+, Fe3+, etc.)
cellular import
non-vesicular cellular import
defense related proteins
No. of genes
1
1
2
10
2
2
2
p-value
0.039609
0.043486
0.030127
0.044193
0.007604
0.004761
0.036082
2
1
3
2
1
2
5
2
2
5
3
2
0.006311
0.019996
0.010523
0.010002
0.015303
0.036082
0.034355
0.039675
0.039675
0.025931
0.044828
0.029312
2
Additional Table S3: KEGG Categories of up-regulated genes in ATCC46645 MeOH v ∆gliT MeOH
KEGG number
0.1.2
1
1.1
1.1.15
1.3
1.3.4
1.3.10
1.3.11
1.8.2
1.9
1.9.9
KEGG Pathway
Biosynthesis of secondary metabolites
Metabolism
Carbohydrate Metabolism
Inositol phosphate metabolism
Lipid Metabolism
Synthesis and degradation of ketone bodies
Glycerophospholipid metabolism
Ether lipid metabolism
Riboflavin metabolism
Metabolism of Terpenoids and Polyketides
Limonene and pinene degradation
No. of genes
12
27
12
2
9
2
3
2
4
8
7
p-value
0.020613
0.005372
0.045957
0.03607
0.005247
0.008389
0.021658
0.00659
0.000976
0.000542
0.001344
Additional Table S4: KEGG Categories of down-regulated genes in ATCC46645 MeOH v ∆gliT MeOH
KEGG number
0.1.2
1.1.1
1.1.7
1.3.3
1.5
1.5.2
1.5.9
1.5.10
1.5.11
1.6
1.6.1
1.11
1.11.18
KEGG Pathway
Biosynthesis of secondary metabolites
Glycolysis / Gluconeogenesis
Ascorbate and aldarate metabolism
Fatty acid metabolism
Amino Acid Metabolism
Glycine, serine and threonine metabolism
Histidine metabolism
Tyrosine metabolism
Phenylalanine metabolism
Metabolism of Other Amino Acids
beta-Alanine metabolism
Xenobiotics Biodegradation and Metabolism
Metabolism of xenobiotics by cytochrome P450
No. of genes
6
3
1
2
6
3
2
4
2
5
3
2
2
p-value
0.001579
0.001223
0.029675
0.007948
0.000529
0.000979
0.012132
0.000114
0.012132
3.77E-05
8.81E-05
0.004967
0.004967
3
Additional Table S5: FunCat Categories of up-regulated genes in ATCC46645 MeOH v ATCC46645
Gliotoxin
FunCat ID
FunCat Category
01.02.07
01.02.07.01
01.06.06
01.06.06.07
1.2
01.20.36
01.20.37
01.20.37.01
01.20.37.03
02.16.03.03
regulation of nitrogen, sulfur and selenium metabolism
regulation of nitrogen metabolism
isoprenoid metabolism
diterpenes metabolism
secondary metabolism
non-ribosomal peptide synthesis
metabolism of peptide derived compounds
metabolism of thioredoxin, glutaredoxin, glutathione
metabolism of peptide antibiotics
heterofermentative pathway and fermentaton of other
saccharides
protein binding
metal binding
transported compounds (substrates)
ion transport
cation transport (H+, Na+, K+, Ca2+ , NH4+, etc.)
heavy metal ion transport (Cu+, Fe3+, etc.)
siderophore-iron transport
drug/toxin transport
transport facilities
transport ATPases
ABC transporters
transport routes
cellular export and secretion
Type I protein secretion system (ABC-type transport
systems)
cellular import
non-vesicular cellular import
disease, virulence and defense
resistance proteins
defense related proteins
Detoxification
detoxification involving cytochrome P450
detoxification by export
oxygen and radical detoxification
glutathione conjugation reaction
Homeostasis
homeostasis of cations
homeostasis of metal ions (Na, K, Ca etc.)
homeostasis of anions
homeostasis of sulfate
16.01
16.17
20.01
20.01.01
20.01.01.01
20.01.01.01.01
20.01.01.01.01.01
20.01.27
20.03
20.03.22
20.03.25
20.09
20.09.16
20.09.16.01
20.09.18
20.09.18.07
32.05
32.05.01
32.05.03
32.07
32.07.01
32.07.05
32.07.07
32.07.07.03
34.01
34.01.01
34.01.01.01
34.01.03
34.01.03.01
No. of
genes
p-value
3
3
5
2
16
2
5
3
2
1
0.017385
0.002781
0.033215
0.004108
0.000226
0.020054
0.000183
0.000781
0.020054
0.021958
7
2
29
10
8
6
5
10
15
7
7
20
9
4
0.003838
0.020057
6.53E-05
0.000473
0.001876
0.000211
2.61E-05
1.00E-05
0.004936
9.55E-05
8.38E-05
0.015186
0.001148
0.001102
11
7
11
6
4
18
3
7
4
2
10
8
8
2
1
0.006834
0.006127
0.002563
0.007123
0.006148
2.04E-07
0.046189
0.000543
0.005223
0.018176
0.001026
0.005279
0.000763
0.037714
0.043442
4
Additional Table S6: FunCat Categories of down-regulated genes in ATCC46645 MeOH v ATCC46645
Gliotoxin
FunCat ID
FunCat Category
1.01
01.01.03
amino acid metabolism
assimilation of ammonia, metabolism of the glutamate
group
metabolism of arginine
metabolism of urea cycle, creatine and polyamines
metabolism of polyamines
metabolism of the cysteine - aromatic group
metabolism of phenylalanine
metabolism of tyrosine
nitrogen, sulfur and selenium metabolism
nitrogen metabolism
C-compound and carbohydrate metabolism
sugar, glucoside, polyol and carboxylate anabolism
C-2 compound and organic acid metabolism
C-2 compound and organic acid catabolism
aliphatic hydrocarbon metabolism
aliphatic hydrocarbon catabolism
metabolism of secondary products derived from primary
amino acids
metabolism of amines
glycolysis and gluconeogenesis
glycolysis methylglyoxal bypass
pyruvate dehydrogenase complex
respiration
aerobic respiration
fermentation
alcohol fermentation
mixed acid and butanediol fermentation
cell cycle
protein binding
metal binding
calcium binding
heavy metal binding (Cu, Fe, Zn)
complex cofactor/cosubstrate/vitamine binding
heme binding
electron transport
drug/toxin transport
transport ATPases
transport routes
01.01.03.05
01.01.05
01.01.05.01
01.01.09
01.01.09.04
01.01.09.05
1.02
01.02.02
1.05
01.05.02.04
01.05.06
01.05.06.07
01.05.10
01.05.10.07
01.20.17
01.20.17.03
2.01
02.01.01
2.08
2.13
02.13.03
2.16
02.16.01
02.16.09
10.03
16.01
16.17
16.17.01
16.17.09
16.21
16.21.01
20.01.15
20.01.27
20.03.22
20.09
No. of
p-value
genes
13
0.000154
3
0.044683
2
2
2
6
3
3
8
4
17
3
2
2
1
1
3
0.034001
0.042884
0.008585
0.005937
0.019408
0.006186
0.001192
0.001902
0.032987
0.037325
0.027495
0.017523
0.038822
0.038822
0.020843
3
6
1
2
4
3
4
3
1
1
5
14
4
12
12
4
8
4
3
3
0.001603
0.000252
0.046407
0.002628
0.032922
0.031565
0.005473
0.003187
0.015709
0.037294
0.017031
0.000681
0.002727
0.000173
0.000107
0.003295
0.003303
0.0393
0.042512
0.034473
5
Additional Table S7: FunCat Categories of up-regulated genes in A. fumigatus ∆gliT MeOH v A.
fumigatus ∆gliT Gliotoxin
FunCat ID
FunCat Category
01.01.06
01.01.06.04
01.01.06.05
01.01.09.01
01.01.09.02
01.01.09.03
01.02.03
01.02.03.01
01.03.01.03
01.03.16
1.04
1.05
01.05.02
01.05.02.07
metabolism of the aspartate family
metabolism of threonine
metabolism of methionine
metabolism of glycine
metabolism of serine
metabolism of cysteine
sulfur metabolism
sulfate assimilation
purine nucleotide/nucleoside/nucleobase anabolism
polynucleotide degradation
phosphate metabolism
C-compound and carbohydrate metabolism
sugar, glucoside, polyol and carboxylate metabolism
sugar, glucoside, polyol and carboxylate catabolism
01.05.03
polysaccharide metabolism
01.05.13.03
1.06
01.06.06
1.2
12.01
12.01.01
12.04
12.04.02
12.07
14.04
14.07
14.07.03
tetrahydrofolate-dependent C-1-transfer
lipid, fatty acid and isoprenoid metabolism
isoprenoid metabolism
secondary metabolism
ribosome biogenesis
ribosomal proteins
translation
translation elongation
translational control
protein targeting, sorting and translocation
protein modification
modification by phosphorylation, dephosphorylation,
autophosphorylation
protein binding
nucleic acid binding
RNA binding
metal binding
GTP binding
regulation by
regulation by modification
regulation of protein activity
transported compounds (substrates)
transport routes
nuclear transport
vesicular transport (Golgi network, etc.)
vacuolar/lysosomal transport
16.01
16.03
16.03.03
16.17
16.19.05
18.01
18.01.01
18.02
20.01
20.09
20.09.01
20.09.07
20.09.13
No. of
genes
p-value
21
4
16
6
7
5
4
4
5
2
25
55
8
5
4.34E-05
0.016958
8.06E-09
0.023326
0.019309
0.017006
0.010337
0.002668
0.046996
0.047423
0.02562
2.68E-05
0.002658
0.007245
4 0.000483
4
32
4
22
105
98
86
5
10
11
34
6
0.025738
0.008308
0.03403
0.010633
1.28E-61
3.40E-77
8.18E-49
0.027556
0.039614
0.040203
0.007761
0.00518
146
66
39
33
2
7
3
19
60
46
1
5
1
1.69E-08
0.00865
3.95E-05
0.040594
0.034046
0.006734
0.012856
0.009861
0.000723
0.000475
0.042961
0.002029
0.000691
6
FunCat ID
FunCat Category
20.09.18.09
30.01
30.01.05
30.01.05.01
30.01.09
32.01
32.01.01
32.01.07
32.05
32.07
34.11.03
40.01
40.01.03
42.01
42.04.03
42.16
43.01
43.01.03
43.01.03.05
vesicular cellular import
cellular signalling
enzyme mediated signal transduction
protein kinase
second messenger mediated signal transduction
stress response
oxidative stress response
unfolded protein response (e.g. ER quality control)
disease, virulence and defense
detoxification
chemoperception and response
cell growth / morphogenesis
directional cell growth (morphogenesis)
cell wall
actin cytoskeleton
mitochondrion
fungal/microorganismic cell type differentiation
fungal and other eukaryotic cell type differentiation
budding, cell polarity and filament formation
No. of
genes
p-value
2
14
6
3
1
29
2
10
13
14
2
8
1
7
2
27
15
15
9
0.033669
0.000329
0.000806
0.024907
0.030343
0.039761
0.046596
0.033292
0.009417
0.008595
0.008362
0.000427
0.009629
0.009139
0.047004
9.96E-07
0.000955
0.000955
0.039187
7
Additional Table S8: FunCat Categories of down-regulated genes A. fumigatus ∆gliT MeOH v A.
fumigatus ∆gliT Gliotoxin
FunCat ID
FunCat Category
1.01
01.01.03.03
01.01.05.01
01.01.09
01.01.09.04
01.01.11
amino acid metabolism
metabolism of proline
metabolism of polyamines
metabolism of the cysteine - aromatic group
metabolism of phenylalanine
metabolism of the pyruvate family (alanine, isoleucine, leucine,
valine) and D-alanine
metabolism of leucine
nitrogen, sulfur and selenium metabolism
nitrogen metabolism
catabolism of nitrogenous compounds
nucleotide/nucleoside/nucleobase metabolism
polynucleotide degradation
phosphate metabolism
C-compound and carbohydrate metabolism
sugar, glucoside, polyol and carboxylate metabolism
sugar, glucoside, polyol and carboxylate catabolism
polysaccharide metabolism
glycogen metabolism
C-2 compound and organic acid metabolism
C-2 compound and organic acid catabolism
C-4 compound metabolism
aminosaccharide catabolism
aliphatic hydrocarbon metabolism
aliphatic hydrocarbon catabolism
aromate metabolism
aromate catabolism
lipid, fatty acid and isoprenoid metabolism
fatty acid metabolism
sesquiterpenes metabolism
metabolism of hormones
secondary metabolism
metabolism of eicosanoids
metabolism of naphthoquinone, anthraquinone
non-ribosomal peptide synthesis
glycolysis and gluconeogenesis
glycolysis methylglyoxal bypass
accessory proteins of electron transport and membrane-associated
energy conservation
aerobic respiration
fermentation
alcohol fermentation
01.01.11.04
1.02
01.02.02
01.02.02.09
1.03
01.03.16
1.04
1.05
01.05.02
01.05.02.07
01.05.03
01.05.03.01
01.05.06
01.05.06.07
01.05.08
01.05.09.07
01.05.10
01.05.10.07
01.05.11
01.05.11.07
1.06
01.06.05
01.06.06.05
01.08.02
1.2
01.20.05.09
01.20.15.01
01.20.36
2.01
02.01.01
02.11.05
02.13.03
2.16
02.16.01
No. of
genes
93
5
6
35
16
15
10
57
17
8
28
5
52
211
50
40
45
4
12
10
3
7
3
3
15
11
119
29
6
3
103
4
2
6
23
4
1
p-value
5.67E-05
0.042464
0.014408
0.039198
0.015763
0.008954
0.007366
1.44E-05
0.002115
0.024727
0.006103
0.015934
0.029279
1.68E-06
0.017509
0.00538
0.003302
0.005114
0.000234
0.000463
0.01382
0.027922
0.01382
0.01382
0.027907
0.049486
0.000332
0.004169
0.001339
0.006062
1.01E-06
0.044562
0.038836
0.02449
0.012161
0.002418
0.025535
4 0.029733
21 0.002643
13 0.000262
8
FunCat ID
FunCat Category
2.19
10.01
10.01.02
10.01.03
10.01.05
10.01.05.01
10.01.05.03
10.01.09
10.01.09.05
10.03
10.03.01
10.03.01.01
10.03.01.03
metabolism of energy reserves (e.g. glycogen, trehalose)
DNA processing
DNA topology
DNA synthesis and replication
DNA recombination and DNA repair
DNA repair
DNA recombination
DNA restriction or modification
DNA conformation modification (e.g. chromatin)
cell cycle
mitotic cell cycle and cell cycle control
mitotic cell cycle
cell cycle checkpoints (checkpoints of morphogenesis, DNAdamage,-replication, mitotic phase and spindle)
cytokinesis (cell division) /septum formation and hydrolysis
nuclear and chromosomal cycle
chromosome segregation/division
cell cycle dependent cytoskeleton reorganization
spindle pole body/centrosome and microtubule cycle
RNA synthesis
mRNA synthesis
general transcription activities
transcriptional control
RNA processing
rRNA processing
tRNA processing
mRNA processing (splicing, 5'-, 3'-end processing)
splicing
RNA modification
tRNA modification
ribosome biogenesis
ribosomal proteins
translation
translation initiation
protein folding and stabilization
assembly of protein complexes
protein targeting, sorting and translocation
protein modification
modification with fatty acids (e.g. myristylation, palmitylation,
farnesylation)
modification by acetylation, deacetylation
modification by ubiquitination, deubiquitination
modification by ubiquitin-related proteins
proteasomal degradation (ubiquitin/proteasomal pathway)
10.03.03
10.03.04
10.03.04.05
10.03.05
10.03.05.01
11.02
11.02.03
11.02.03.01
11.02.03.04
11.04
11.04.01
11.04.02
11.04.03
11.04.03.01
11.06
11.06.02
12.01
12.01.01
12.04
12.04.01
14.01
14.1
14.04
14.07
14.07.01
14.07.04
14.07.05
14.07.07
14.13.01.01
No. of
genes
14
24
2
3
8
7
3
15
15
32
23
9
3
p-value
0.032019
2.49E-11
0.002266
1.56E-05
9.67E-09
3.27E-07
0.000212
0.000154
0.000275
6.83E-12
5.44E-09
9.66E-05
0.021885
5
2
2
1
1
51
50
9
50
9
2
2
6
4
2
1
2
1
5
2
5
5
9
70
1
0.000106
0.000108
0.020358
0.003755
0.026401
2.59E-10
2.32E-08
0.002961
4.00E-05
3.40E-14
2.61E-08
0.041973
2.72E-08
4.64E-07
0.020358
0.03752
6.10E-12
2.67E-08
4.29E-07
0.029035
0.001611
2.07E-08
3.55E-08
0.006125
0.039313
2
7
1
6
0.014199
0.005774
0.037562
0.000162
9
FunCat ID
FunCat Category
14.13.04
14.13.04.02
16.01
16.03
16.03.01
16.03.03
16.07
16.17
16.17.05
16.17.09
16.19
16.19.03
16.19.05
16.21
16.21.01
18.01
18.01.01
18.02
18.02.01
18.02.01.01
20.01
20.01.01
20.01.01.01
20.01.01.01.01
20.01.01.01.01.01
20.01.03
20.01.07
20.01.09
20.01.10
20.01.11
20.01.13
20.01.15
20.01.17
20.01.23
20.01.25
20.01.26
20.01.27
20.03
20.03.02
20.03.02.02
20.03.02.03
20.03.25
20.09.01
20.09.04
lysosomal and vacuolar protein degradation
vacuolar protein degradation
protein binding
nucleic acid binding
DNA binding
RNA binding
structural protein binding
metal binding
sodium binding
heavy metal binding (Cu, Fe, Zn)
nucleotide/nucleoside/nucleobase binding
ATP binding
GTP binding
complex cofactor/cosubstrate/vitamine binding
heme binding
regulation by
regulation by modification
regulation of protein activity
enzymatic activity regulation / enzyme regulator
enzyme activator
transported compounds (substrates)
ion transport
cation transport (H+, Na+, K+, Ca2+ , NH4+, etc.)
heavy metal ion transport (Cu+, Fe3+, etc.)
siderophore-iron transport
C-compound and carbohydrate transport
amino acid/amino acid derivatives transport
peptide transport
protein transport
amine / polyamine transport
lipid/fatty acid transport
electron transport
nucleotide/nucleoside/nucleobase transport
allantoin and allantoate transport
vitamine/cofactor transport
neurotransmitter transport
drug/toxin transport
transport facilities
carrier (electrochemical potential-driven transport)
symporter
antiporter
ABC transporters
nuclear transport
mitochondrial transport
No. of
genes
17
11
78
32
24
6
2
100
4
76
48
39
5
86
25
18
9
35
26
5
220
49
46
22
12
42
23
6
7
24
27
69
7
11
16
15
42
121
35
15
21
19
1
4
10
p-value
6.11E-07
1.86E-06
8.24E-24
1.81E-14
2.58E-06
8.12E-11
0.041317
0.039709
0.022913
0.002646
5.41E-09
3.07E-06
0.008471
1.60E-06
2.20E-06
0.008169
0.016078
0.000273
0.047686
0.002299
5.20E-09
0.000752
2.44E-05
0.000125
0.000234
0.015267
0.001485
0.02449
1.36E-06
2.69E-07
0.003886
5.13E-07
0.033968
0.046105
0.003346
5.02E-05
8.60E-07
2.50E-07
9.89E-07
0.002761
5.64E-05
0.025255
0.000516
0.004171
FunCat ID
FunCat Category
20.09.07
20.09.18
20.09.18.07
30.01
30.01.05
30.01.05.01
30.01.05.05
32.01.04
32.01.07
32.01.09
32.05
32.05.01
32.05.03
32.05.05
32.05.05.01
32.07
32.07.01
32.07.03
32.07.05
34.01
34.01.01
34.01.01.01
34.01.03
34.11
34.11.13
34.11.13.07
40.01
40.02
40.02.03
40.10.02.01
41.01.03
41.01.03.01
42.1
42.04
42.04.03
42.04.05
42.10.03
42.27
43.01
43.01.03
43.01.03.05
vesicular transport (Golgi network, etc.)
cellular import
non-vesicular cellular import
cellular signalling
enzyme mediated signal transduction
protein kinase
G-protein mediated signal transduction
pH stress response
unfolded protein response (e.g. ER quality control)
DNA damage response
disease, virulence and defense
resistance proteins
defense related proteins
virulence, disease factors
toxins
detoxification
detoxification involving cytochrome P450
detoxification by modification
detoxification by export
homeostasis
homeostasis of cations
homeostasis of metal ions (Na, K, Ca etc.)
homeostasis of anions
cellular sensing and response to external stimulus
gas and metabolite distribution
circulation (e.g. blood pressure)
cell growth / morphogenesis
activity of intercellular mediators
anti-apoptosis
tissue pattern formation
fruit body development (sexually or asexually derived spores)
nucleus
cytoskeleton/structural proteins
actin cytoskeleton
microtubule cytoskeleton
organization of chromosome structure
extracellular / secretion proteins
fungal/microorganismic cell type differentiation
fungal and other eukaryotic cell type differentiation
budding, cell polarity and filament formation
No. of
genes
p-value
9
78
35
30
14
8
2
4
3
7
85
36
14
32
13
90
22
11
29
61
56
42
7
47
4
4
27
4
4
8
6
6
15
10
4
2
15
6
40
40
15
11
6.86E-06
9.66E-05
0.018662
1.85E-05
3.61E-05
0.013121
5.00E-05
0.015146
0.02153
0.014162
1.74E-09
7.17E-05
0.033645
0.000761
0.006216
1.31E-09
2.14E-05
0.041021
0.000841
3.12E-06
8.46E-07
1.17E-05
0.040824
0.026046
0.044562
0.032698
0.012945
0.022913
0.022913
0.010649
0.007644
0.00353
3.49E-05
1.33E-06
0.004171
0.004758
0.00084
0.046962
0.00999
0.00999
0.00084
Additional Table S9: KEGG Categories of up-regulated genes in ATCC46645 MeOH v ATCC46645
Gliotoxin
KEGG number
KEGG Pathway
1.11
1.11.18
Xenobiotics Biodegradation and Metabolism
Metabolism of xenobiotics by cytochrome
P450
No. of
genes
p-value
2 0.011312
2 0.011312
Additional Table S10: KEGG Categories of down-regulated genes in ATCC46645 MeOH v ATCC46645
Gliotoxin
KEGG number
KEGG Pathway
0.1.1
0.1.2
1
1.1.1
1.1.7
1.5
1.5.2
1.5.4
1.5.8
1.5.10
1.5.11
1.6
1.6.1
Metabolic pathways
Biosynthesis of secondary metabolites
Metabolism
Glycolysis / Gluconeogenesis
Ascorbate and aldarate metabolism
Amino Acid Metabolism
Glycine, serine and threonine metabolism
Valine, leucine and isoleucine degradation
Arginine and proline metabolism
Tyrosine metabolism
Phenylalanine metabolism
Metabolism of Other Amino Acids
beta-Alanine metabolism
No. of
genes
19
12
20
3
2
17
4
4
3
9
6
4
4
p-value
6.48E-05
0.00029
0.003936
0.022129
0.00245
2.39E-10
0.002102
0.000834
0.017141
1.80E-08
3.29E-06
0.035241
9.15E-05
12
Additional Table S11: KEGG Categories of up-regulated genes in A. fumigatus ∆gliT MeOH v A.
fumigatus ∆gliT gliotoxin
KEGG
number
0.1.1
1
1.1
1.1.9
1.2.9
1.3
1.5.3
1.6.4
1.7
1.8.3
1.8.9
1.9
1.9.9
2
2.2.1
2.2
4
4.1
KEGG Pathway
Metabolic pathways
Metabolism
Carbohydrate Metabolism
Amino sugar and nucleotide sugar
metabolism
Sulfur metabolism
Lipid Metabolism
Cysteine and methionine metabolism
Selenoamino acid metabolism
Glycan Biosynthesis and Metabolism
Vitamin B6 metabolism
One carbon pool by folate
Metabolism of Terpenoids and Polyketides
Limonene and pinene degradation
Genetic Information Processing
Ribosome
Translation
Cellular Processes
Transport and Catabolism
No. of
p-value
genes
58 6.74E-05
75 8.25E-12
20 4.67E-05
2 0.028819
7
8
12
9
2
3
4
3
3
94
67
70
8
1
0.000198
0.001172
2.08E-05
0.001556
0.042004
0.021708
0.036031
0.002402
0.010487
7.13E-17
3.30E-68
2.55E-49
0.026965
0.002435
13
Additional Table S12: KEGG Categories of down-regulated genes in A. fumigatus ∆gliT MeOH v A.
fumigatus ∆gliT gliotoxin
KEGG
number
0.1.1
0.1.2
1
1.1
1.1
1.1.1
1.1.8
1.1.11
1.1.12
1.1.13
1.2.1
1.3
1.3.3
1.3.4
1.4.2
1.5
1.5.4
1.5.10
1.5.11
1.5.12
1.6
1.6.1
1.6.5
1.6.7
1.7.15
1.8.2
1.9
1.9.9
1.10.11
1.10.15
2
2.1
2.2
2.3
2.4
4
4.3
4.3.2
KEGG Pathway
Metabolic pathways
Biosynthesis of secondary metabolites
Metabolism
Carbohydrate Metabolism
Biosynthesis of Other Secondary
Metabolites
Glycolysis / Gluconeogenesis
Starch and sucrose metabolism
Glyoxylate and dicarboxylate metabolism
Propanoate metabolism
Butanoate metabolism
Oxidative phosphorylation
Lipid Metabolism
Fatty acid metabolism
Synthesis and degradation of ketone
bodies
Pyrimidine metabolism
Amino Acid Metabolism
Valine, leucine and isoleucine degradation
Tyrosine metabolism
Phenylalanine metabolism
Tryptophan metabolism
Metabolism of Other Amino Acids
beta-Alanine metabolism
Cyanoamino acid metabolism
D-Arginine and D-ornithine metabolism
Other glycan degradation
Riboflavin metabolism
Metabolism of Terpenoids and Polyketides
Limonene and pinene degradation
Caffeine metabolism
Penicillin and cephalosporin biosynthesis
Genetic Information Processing
Transcription
Translation
Folding, Sorting and Degradation
Replication and Repair
Cellular Processes
Cell Growth and Death
Cell cycle - yeast
No. of
p-value
genes
124 0.000226
62 0.001578
186 3.55E-15
84 5.28E-09
5 9.21E-05
11
15
5
13
20
2
40
9
4
0.047858
0.027631
0.042527
0.00066
0.00198
0.013538
0.000795
0.008109
0.012232
2
57
13
18
10
10
21
7
7
2
4
8
23
22
2
3
6
1
1
2
2
9
1
1
0.039747
0.000136
0.000231
0.000628
0.01954
0.005708
0.020068
0.010189
0.020421
0.0347
0.048468
0.011536
0.012106
0.004694
0.012492
0.005089
2.77E-20
3.89E-06
3.37E-05
7.48E-07
0.004471
0.007314
0.000981
0.005251
14
Additional Table S13: Summary statistics of the illumina RNA-Seq. The number of mapped reads is
computed from the TopHat alignments to the CADRE 3a Aspergillus fumigatus Af293 reference
genome.
Sample Name
Accession
Total Reads
Mapped Reads
Rate
A. fumigatus wild-type_MeOH_Dup1
ERS132604
24504538
22855107
0.93
A. fumigatus wild-type_MeOH_Dup2
ERS132605
21976034
20477250
0.93
A. fumigatus wild-type_MeOH_Dup3
ERS149278
20072230
19089952
0.95
A. fumigatus wild-type_gliotoxin_Dup1 ERS132606
20480420
19279500
0.94
A. fumigatus wild-type_gliotoxin_Dup2 ERS132607
18348804
17334037
0.94
A. fumigatus wild-type_gliotoxin_Dup3 ERS149279
20327620
19328531
0.95
A. fumigatus ∆gliT_MeOH_Dup1
ERS132608
19801840
18713743
0.95
A. fumigatus ∆gliT_MeOH_Dup2
ERS132609
3636850
3438830
0.95
A. fumigatus ∆gliT_MeOH_Dup3
ERS149280
19494792
18529853
0.95
A. fumigatus ∆gliT_gliotoxin_Dup1
ERS132610
20170690
19206707
0.95
A. fumigatus ∆gliT_gliotoxin_Dup2
ERS132611
18974974
17964194
0.95
15
Additional Table S14: Primers used for qRT-PCR analysis
Primer Name
ogliZ_F
ogliZ_R
ogliA_F
ogliA_R
oosc3_F
oosc3_R
olaeA_F
olaeA_R
ogliT_F
ogliT_R
oAFUA_3G13700_F
oAFUA_3G13700_R
oftmA_F
oftmA_R
opsoA_F
opsoA_R
ooptB_F
ooptB_R
ofma-PKS_F
ofma-PKS_R
osidH_F
osidH_R
Primer Sequence
CTCCGATTCCGACCTTTCTT
GTTAGGCTGCTGAGGGTCTG
GTATGGGTCCGCCTTCTTTC
TGTAGGAGCCCGAGGAGAT
AATTCTGGCTGTGCGTTCTC
CTGCTGATAGGGGATGTCGT
AGGCCGCTCAAGAAACAAC
TCGTCCGTTCTCCTGATAGC
CCGAGTCCGTCACCATCTAC
GCCAAAGATCCCATCGACAC
TTGTTTTCGGAACTGGGAAG
GTTGGCCTGTTGGACTGTTT
CTGCCTGGTTCTAGCCGCAAGG
TGCGGAGGTATTCCAGCGCAGT
TGGTGGCGGCCTGATCTACCTT
TGCCCGAATCACTCCCTTGGAC
TGTCCTTCTGGCTCGCAGGT
ATCCACCATCCGCGGAAACG
ATCATCGGATCGGTGAAGAG
GCTGGATTTGGGTTGAGAAA
CCTCACATTCTCCTCCTCACA
CGTTGAGGTCGTTCCATTCT
Reference
This study
This study
This study
This study
This study
This study
This study
This study
This study
This study
This study
This study
(Cramer et al., 2006)
(Cramer et al., 2006)
(Cramer et al., 2006)
(Cramer et al., 2006)
(Hartmann et al., 2011)
(Hartmann et al., 2011)
This study
This study
This study
This study
16
120
**
% survival
100
80
60
40
20
in
lio
to
x
eO
H
g
liT
G
M

gl
iT
C
TC
A
A
TC
C
46
6
45
46
6
G
45
M
lio
to
x
eO
H
in
0
Figure S1: Viability assay. There was 85 % survival of ∆gliT following gliotoxin treatment
compared to 97 % survival in the control group. There was 100 % survival of wild-type both
with and without gliotoxin treatment.
References
Cramer, R. A, Stajich, J. E., Yamanaka, Y., Dietrich, F. S., Steinbach, W. J., & Perfect, J. R.
(2006). Phylogenomic analysis of non-ribosomal peptide synthetases in the genus
Aspergillus. Gene, 383, 24–32. doi:10.1016/j.gene.2006.07.008
Hartmann, T., Cairns, T. C., Olbermann, P., Morschhäuser, J., Bignell, E. M., & Krappmann,
S. (2011). Oligopeptide transport and regulation of extracellular proteolysis are required
for growth of Aspergillus fumigatus on complex substrates but not for virulence.
Molecular Microbiology, 82(4), 917–35. doi:10.1111/j.1365-2958.2011.07868.x
17