up. #N/D. 119552 unique protein. 1.709135931. 1.25E-09. Sophorose up inositol oxygenase activity. 119790 myo-inositol oxygenase ,. 2.514687805. 1.70E-56.
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
i
Supplementary Material Trichoderma reesei CRE1-mediated Carbon Catabolite Repression in Response to Sophorose Through RNA Sequencing Analysis Amanda Cristina Campos Antoniêto1, Renato Graciano de Paula1, Lílian dos Santos Castro1, Rafael Silva-Rocha2, Gabriela Felix Persinoti3 and Roberto Nascimento Silva1,* 1
Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo 14049-900, Ribeirão Preto, SP, Brazil; 2Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo 14049-900, Ribeirão Preto, SP, Brazil; 3Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional, de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
Fig. (S1). CRE1 binding motif according to Silva-Rocha et al. (2014).
Fig. (S2). Quality assessment of biological replicates samples from T. reesei QM9414 and cre1 grown in sophorose used for RNA-seq analysis. Dispersion graphs were obtained through the DESeq package, Bioconductor.
ii Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
Fig. (S3). Principal Component Analysis of strains QM9414 and cre1 grown in sophorose. The analysis shows the distinction between the two different groups related to the samples QM9414 (blue) and cre1 (red). Representations were created through the DESeq package, Bioconductor.
Fig. (S4). Comparison of gene expression values assayed by qRT-PCR and RNA-seq. Comparison between the Log2 fold change values of cre1/QM9414 obtained by RNA-seq and qRT-PCR for 19 genes evaluated during growth of QM9414 and cre1 strains in presence of sophorose, showing a high correlation between the two techniques (r2 = 0.96).
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
iii
Table S1. Primers used in the validation of differentially expressed genes. Protein ID
Sequence 5’3’ (Foward)
Sequence 5’3’ (Reverse)
58475
ACTTCCAAGGTCACAGGTTG
AGTCCGTTCAACATGACCTG
120975
GTCGTTGTGAGAACTGCAATG
ACCCAGAAATGAAAGCCTCC
21876
GTCGGGTCGTTGACTATAACAC
ATTGCTCTTCACCGTCTTCC
104251
CATTTTGGGCTGGGACTCTAG
TTCAAAGTACTGCTCAGGGC
110267
TGGAATACAATCAGGCGGTG
CGGTTGGAATTCTGCTTTGG
76359
GGGCTAGAGAATTGGAAGACG
ATCTCGCCTCCAAATCCAAG
122792
TCTCGTCAACAGGCAATCAG
CAAGCCGTCCAGTTTTACATG
106314
GTGGTCGTGACTGAGATTGTC
AATTGCCTCTCCCTTGGTG
109945
CTGAAGCATGGATACGAGGTC
AGTAGATCCAAACCAAGGCAAG
72379
ACTCTGAATGCAAGTCTGGAC
TGGTCCTTTTCGCAGTATCC
82227
GCGTACAATGGCATCAATGG
ATCCCAACCCCATTCCTTTC
123232
AGATTGCCATTCCCCAGAAG
CCCGAGTACGTGACATGATTC
72567
ACAAGAATGCATCGTCTCCG
TGTTCCACCCGTTGTAGTTG
123989
CCGAGCTTGGTAGTTACTCTG
GGTAGCCTTCTTGACTGAGT
123992
CCAAACTATACGAGTAGCC
GAGTGAATGTCTTGATGG
73643
GCGCCACTGTTCCTGGAG
ACCGCTGCCACCACACTG
22197
CCATCTACATCACCGAGAACG
TCCAAGTGCGAGTCAAAGTAG
121735
CCAGGATAACTTCAACGAGGG
ATGTGGAGGTTGGAGAACTTG
64710
GTGTGATTTGCGATGCTTCTG
TCTAGGGAGGTTCTGAGGAAG
61470
TGAGAGCGGTGGTATCCACG
GGTACCACCAGACATGACAATGTT
Table S2. Summary of reads obtained by RNA Sequencing. Sample
Raw Reads
Quality Reads
Mapped Reads
% Mapped Read
Number of Nucleotides (GB)
QM9414 Soph1
14311488
12269998
8445229
68.83
1.69
QM9414 Soph2
17782393
16157814
11041736
68.34
2.21
QM9414 Soph3
19691061
17845732
12645886
70.86
2.53
cre1Soph1
24419114
20494637
14267543
69.62
2.9
cre1 Soph2
21562398
19687851
14888765
75.62
3.0
cre1Soph3
23733323
21554180
14371716
66.68
2.9
Total
121499777
108010212
75660875
69.99
15.13
iv Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
Table S3. Genes up- and down-regulated in the mutant cre1compared to QM9414 in presence of sophorose. Genes directly regulated by CRE1 are underlined in the table.
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
up
membrane
62285
unknown protein
1.083268973
3.17E-16
Sophorose
up
membrane
62172
amino acid permease (PotE?)
2.115123107
5.20E-44
Sophorose
up
integral to membrane
62488
MFS permease
2.388995134
1.58E-44
Sophorose
up
#N/D
54242
GH55 ?-1,3-glucanase
1.364187842
4.61E-18
Sophorose
up
metabolism
54667
acyl-CoA synthetase
1.54959194
2.24E-37
Sophorose
up
transferase activity, transferring groups other than amino-acyl groups
53372
acyltransferase 3
1.708602912
5.85E-36
Sophorose
up
#N/D
53401
unknown protein
1.101796594
4.46E-11
Sophorose
up
#N/D
54391
unknown protein
1.046974214
8.59E-12
Sophorose
up
amino acid metabolism
63919
Cys/Met metabolism PLP-dependent enzyme
1.093324201
2.76E-15
Sophorose
up
#N/D
63653
ankyrin
1.458367489
3.63E-27
Sophorose
up
#N/D
54768
unknown protein
1.587566593
4.39E-21
Sophorose
up
hydrolase activity
65162
GH18 endo-N-acetyl-ß-Dglucosaminidase Endo T
1.612469385
4.92E-42
Sophorose
up
hydrolase activity, acting on carbonnitrogen (but not peptide) bonds
65215
CE4 imidase
1.184328411
3.08E-18
Sophorose
up
oxidoreductase activity
65142
aldehyde dehydrogenase ALDH
1.055636779
1.81E-15
Sophorose
up
#N/D
64922
unknown protein, only present in Gibberella, Neurospora and Magnaporthe
1.555847442
1.26E-09
Sophorose
up
membrane
65191
MFS permease (maltose permease)
2.651082204
4.94E-77
Sophorose
up
catalytic activity
65677
Esterase/lipase/thioesterase
1.074127934
9.56E-11
Sophorose
up
integral to membrane
65915
MFS permease
1.846411462
1.31E-36
Sophorose
up
S-adenosylmethionine-dependent methyltransferase activity
65711
SAM-dependent methyltransferase
1.540004037
1.77E-23
Sophorose
up
metabolism
66294
ATP-NAD/AcoX kinase
1.058827672
6.96E-16
Sophorose
up
#N/D
66583
unknown protein
1.33801399
8.88E-21
Sophorose
up
#N/D
66788
unknown protein
1.470575658
2.58E-19
Sophorose
up
#N/D
67472
unknown protein
1.107637025
1.09E-17
Sophorose
up
#N/D
67324
unknown protein
1.01063305
7.80E-10
Sophorose
up
membrane
55077
MFS permease
1.338278769
2.27E-20
Sophorose
up
alpha-N-arabinofuranosidase activity
55319
GH54 ?-L-arabinofuranosidase ABF3
1.75621938
1.08E-49
Sophorose
up
#N/D
67902
unknown secreted protein
1.023430255
3.41E-05
Sophorose
up
protein kinase C activation
68412
Sphingoid long-chain base kinase
1.134427578
1.20E-07
Sophorose
up
membrane
68869
MFS permease
1.162285992
4.08E-14
Sophorose
up
oxidoreductase activity
69081
mitochondrial cytochrome b2, putative
1.076654903
1.93E-15
Sophorose
up
S-adenosylmethionine-dependent methyltransferase activity
68924
cyclopropane/fatty acid synthase; plant related
1.985506607
1.62E-57
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
v
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
up
#N/D
55887
unknown protein, secreted
2.854734813
7.63E-37
Sophorose
up
#N/D
55668
unknown protein
1.370872957
7.91E-24
Sophorose
up
#N/D
69692
Quinoprotein amine dehydrogenase beta chain-like protein
3.574257901
3.05E-136
Sophorose
up
deaminase activity
69753
ADA, Adenosine deaminase
2.027812419
2.25E-51
Sophorose
up
#N/D
69727
unknown protein
1.329717821
5.91E-11
Sophorose
up
integral to membrane
69834
MFS permease,
2.566553171
4.08E-72
Sophorose
up
#N/D
56499
N-acyl-phosphatidylethanolaminehydrolyzing phospholipase D, putative
1.389179297
0.034354025
Sophorose
up
#N/D
57098
unknown protein
1.302901515
3.44E-18
Sophorose
up
response to oxidative stress
70803
bifunctional catalase/peroxidase
1.063747535
1.36E-11
Sophorose
up
#N/D
70845
GH55 ?-1,3-glucanase
1.226730745
1.24E-16
Sophorose
up
integral to membrane
70860
allantoate permease, 10 TM domains
1.924273535
1.46E-55
Sophorose
up
integral to membrane
71029
Ctr copper transporter, putative
1.41603806
4.52E-21
Sophorose
up
zinc ion binding
58011
C2H2 conidiation transcription factor FlbC
1.394357416
9.64E-26
Sophorose
up
acid phosphatase activity
71092
phytase
1.771660688
2.05E-50
Sophorose
up
ATPase activity, coupled to transmembrane movement of substances
58899
MDR-type ABC transporters
1.23604581
0.029949005
Sophorose
up
response to antibiotic
58717
ß-lactamase class C
2.870563892
2.91E-19
Sophorose
up
fatty acid biosynthesis
59482
PKS
1.419470147
6.85E-19
Sophorose
up
#N/D
59368
unknown protein, Duf341
1.72109291
3.66E-41
Sophorose
up
#N/D
59515
MFS permease
1.020683247
7.22E-13
Sophorose
up
#N/D
71170
unknown protein, only in Gibberella
1.709449228
7.93E-32
Sophorose
up
hydrolase activity
60489
CE5 cutinase
2.342097038
1.49E-44
Sophorose
up
ubiquitin cycle
60000
ubiquitin-conjugating enzyme
1.043310014
1.92E-09
Sophorose
up
#N/D
22386
Epl1/Sm1
1.058952067
0.047104685
Sophorose
up
#N/D
22388
unknown protein
1.162605798
0.00609749
Sophorose
up
proteolysis and peptidolysis
22459
carboxypeptidase A
2.641669193
4.99E-36
Sophorose
up
#N/D
22564
HFBs
1.226479353
9.34E-27
Sophorose
up
proteolysis and peptidolysis
22637
ERCC8 (CSA, CKN1) involved in transcription-coupled nucleotideExcision repair
1.002396875
4.41E-16
Sophorose
up
hydrolase activity, acting on ester bonds
21960
phospholipase C
1.226095705
4.65E-24
Sophorose
up
#N/D
22129
GH61 polysaccharide monooxygenase
1.506465659
1.11E-36
Sophorose
up
cellulose binding
122081
GH7 Endo-?-1,4-glucanase EGL1/CEL7b
1.098435626
3.62E-05
Sophorose
up
metabolism
122110
4-coumarate:coenzyme A ligase
1.014431441
1.11E-11
vi Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
up
#N/D
119552
unique protein
1.709135931
1.25E-09
Sophorose
up
inositol oxygenase activity
119790
myo-inositol oxygenase ,
2.514687805
1.70E-56
Sophorose
up
#N/D
119857
unique protein
3.975982661
2.81E-78
Sophorose
up
#N/D
119963
HFBs
1.224904819
2.48E-25
Sophorose
up
#N/D
122197
unknown protein
1.075166365
1.38E-18
Sophorose
up
#N/D
122374
MRSP1/expansin-like
1.694402464
3.37E-09
Sophorose
up
oxidoreductase activity
122416
NADH:flavin oxidoreductase/NADH oxidase
1.190855041
7.59E-21
Sophorose
up
#N/D
122422
SSCRP
1.900730056
1.42E-49
Sophorose
up
oxidoreductase activity
122556
Short-chain dehydrogenase/reductase
1.811523749
9.60E-27
Sophorose
up
#N/D
122579
unknown protein, 4TM
1.675453939
1.79E-14
Sophorose
up
#N/D
122629
unique protein
2.721991998
1.74E-100
Sophorose
up
#N/D
122657
unknown protein
1.536400454
8.88E-21
Sophorose
up
oxidoreductase activity
122778
short chain dehydrogenase/reductase
1.045218173
0.002430328
Sophorose
up
carbohydrate metabolism
122780
GH28 exo-rhamnogalacturonase RGX1
2.2009423
1.07E-55
Sophorose
up
copper ion binding
122963
Cu_amine_oxidCopper amine oxidaseenzyme domain aligned
1.139794113
1.76E-21
Sophorose
up
electron transport
123079
short chain dehydrogenase/reductase
2.823422985
5.58E-116
Sophorose
up
#N/D
123199
SSCRP
1.465355326
1.31E-17
Sophorose
up
catalytic activity
123204
lipase/esterase
1.533280646
1.26E-37
Sophorose
up
alpha-N-arabinofuranosidase activity
123283
GH54 ?-L-arabinofuranosidase I ABF1
2.609209686
6.25E-09
Sophorose
up
ATPase activity, coupled to transmembrane movement of substances
123293
MDR-type ABC transporters
1.674288602
0.003535747
Sophorose
up
cell communication
119989
HFB2
1.267299616
1.13E-19
Sophorose
up
#N/D
123327
SWI-SNF chromatin-remodeling complex protein
1.053087318
1.91E-17
Sophorose
up
hydrogen-transporting ATPase activity, rotational mechanism
120156
cell morphogenesis protein PAG1
1.141933795
4.24E-08
Sophorose
up
#N/D
120160
unknown protein
1.328719309
2.79E-06
Sophorose
up
#N/D
123614
unknown protein
1.360701103
9.94E-30
Sophorose
up
#N/D
123616
short unique protein
1.185862663
2.20E-12
Sophorose
up
#N/D
123674
unique protein
1.311448461
1.64E-09
Sophorose
up
#N/D
123675
unknown protein
1.135067831
8.39E-15
Sophorose
up
#N/D
123713
transcriptional regulatorMedA, involved in fruiting body development
1.441144256
7.14E-27
Sophorose
up
membrane
123718
amino acid transporter, neutral 11 TM
3.326064571
2.71E-89
Sophorose
up
cellulose binding
123940
GH115 methylglurunoyl esterase CIP2
1.049830985
0.000140616
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
vii
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
up
#N/D
123955
Epl1/Sm1
3.392141431
1.76E-25
Sophorose
up
cell communication
123967
HFB3
1.044555783
6.43E-20
Sophorose
up
zinc ion binding
123968
unknown protein
1.023171897
5.50E-18
Sophorose
up
#N/D
120697
SSCRP
1.279683329
6.10E-26
Sophorose
up
glucan endo-1,3-alpha-glucosidase activity
120873
GH71 ?-1 3-glucanase
4.713358684
6.41E-245
Sophorose
up
copper ion binding
121098
Multicopper oxidases
1.129558625
1.05E-18
Sophorose
up
xylose isomerase activity
121308
PutA delta-1-pyrroline-5-carboxylate dehydrogenase
1.13617575
1.12E-15
Sophorose
up
#N/D
121415
Zn2Cys6 transcriptional regulator
1.97507616
5.89E-25
Sophorose
up
membrane
121482
MFS permease
2.423102861
4.37E-82
Sophorose
up
#N/D
121739
SSCRP
2.587593442
2.31E-30
Sophorose
up
hydrolase activity
48792
amidase
1.462837358
1.17E-27
Sophorose
up
cellulose binding
49976
GH5 endo-?-1,4-glucanase EGL5/CEL45a
1.000441331
4.93E-08
Sophorose
up
#N/D
50323
OOC1
3.120255694
7.93E-07
Sophorose
up
hydrolase activity
50390
5' nucleotidase
1.18292409
4.24E-19
Sophorose
up
calcium ion binding
45112
serine/threonine protein kinase
1.059609884
1.92E-13
Sophorose
up
oxidoreductase activity
45445
tyrosinase
1.025984035
2.29E-06
Sophorose
up
#N/D
52476
unknown protein
2.483339586
1.05E-59
Sophorose
up
proteolysis and peptidolysis
47127
peptidase M18
1.670302821
3.50E-45
Sophorose
up
#N/D
47733
SSCRP
1.192089413
2.34E-24
Sophorose
up
cellulose binding
73643
GH61 polysaccharide monooxygenase CEL61a
1.183973354
2.05E-09
Sophorose
up
hydrogen-transporting ATPase activity, rotational mechanism
73924
MDR-type ABC transporters
1.365486691
5.94E-19
Sophorose
up
#N/D
78576
unknown protein
1.021497315
4.59E-14
Sophorose
up
#N/D
78639
Serine/threonine protein kinase
1.227336553
1.15E-25
Sophorose
up
#N/D
79726
unknown protein
1.556222463
1.50E-21
Sophorose
up
proteolysis and peptidolysis
79921
GH92 ?-1,2-mannosidase
1.105124624
3.65E-21
Sophorose
up
membrane
79960
GH47 ?-1,2-mannosidase
1.04414929
9.94E-17
Sophorose
up
oxidoreductase activity
80019
short-chain dehydrogenase/reductase
1.715371901
1.09E-48
Sophorose
up
membrane
80058
MFS permease
2.157423656
1.36E-19
Sophorose
up
#N/D
80149
unknown protein,
1.386734811
1.82E-31
Sophorose
up
membrane
80639
iron transporter
1.399282384
7.65E-11
Sophorose
up
74807
GH76 GPI-anchored ?-1,6-mannanase
1.453286854
3.26E-33
Sophorose
up
80980
peptidyl arginine deiminase
1.412719446
2.66E-34
protein amino acid dephosphorylation #N/D
viii Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
up
oxidoreductase activity
81096
ferric reductase
1.575837578
1.59E-07
Sophorose
up
#N/D
81383
GPCR , contains RGS domain
1.598856647
3.77E-44
Sophorose
up
proteolysis and peptidolysis
81517
unknown protein
1.856633265
1.82E-56
Sophorose
up
ATP binding
82105
PDR-type ABC transporters
2.436468257
0.028615017
Sophorose
up
calcium- and calmodulin-responsive adenylate cyclase activity
82153
unknown protein
1.011624382
1.07E-11
Sophorose
up
fatty acid biosynthesis
82208
PKS
2.805781961
5.87E-23
Sophorose
up
hydrolase activity, acting on ester bonds
76155
acid phosphatase-like protein
1.280344908
2.75E-14
Sophorose
up
electron transport
76230
Flavin-containing monooxygenase
2.666711276
3.17E-13
Sophorose
up
carbohydrate metabolism
76672
GH3 ?-glucosidase BGL1/CEL3a
1.663342629
1.42E-08
Sophorose
up
ATP binding
76682
PDR-type ABC transporters
6.034239874
2.04E-05
Sophorose
up
integral to membrane
76897
MFS permease
1.081366052
1.79E-14
Sophorose
up
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
76971
SSCRP
2.899353523
2.91E-44
Sophorose
up
electron transport
77512
cytochrome P450
1.017403635
1.08E-16
Sophorose
up
nucleus
4124
myb transcriptional regulator
2.401264146
2.70E-28
Sophorose
up
electron transport
4999
cytochrome P450 monooxygenase
2.10946303
1.90E-65
Sophorose
up
#N/D
5319
unknown protein
1.83903255
2.08E-29
Sophorose
up
#N/D
5607
unknown protein
1.051787071
3.63E-11
Sophorose
up
carbohydrate metabolism
5836
GH2 ?-mannosidase
2.486307762
1.04E-26
Sophorose
up
zinc ion binding
3449
Zn2Cys6 transcriptional regulator
3.113965619
1.62E-36
Sophorose
up
DNA repair
107680
DNA photolyase, class I, rapidly regulated by blue light in T. harzianum
1.130547429
0.022951247
Sophorose
up
#N/D
102851
SSCRP
3.333279109
1.29E-74
Sophorose
up
#N/D
102904
unknown protein
1.342154709
0.000894948
Sophorose
up
#N/D
102908
SSCRP
1.069345258
0.019447524
Sophorose
up
#N/D
103205
unknown protein
1.635487409
2.40E-21
Sophorose
up
#N/D
103273
RNA polymerase II Elongator subunit
1.141392533
7.67E-13
Sophorose
up
phospholipase D activity
108157
unique protein
1.140882906
4.85E-20
Sophorose
up
#N/D
108261
SSCRP
1.089807915
3.92E-15
Sophorose
up
zinc ion binding
108357
C2H2 transcriptional regulator
1.49538455
9.26E-07
Sophorose
up
#N/D
108586
unknown protein
2.074745748
3.17E-06
Sophorose
up
#N/D
108663
SSCRP
1.032588483
4.41E-15
Sophorose
up
#N/D
108929
unique protein
1.974424746
5.42E-37
Sophorose
up
zinc ion binding
109328
Zn2Cys6 transcriptional regulator
1.015979202
4.99E-13
Sophorose
up
#N/D
109643
autophagy protein (Atg22), putative
1.187317237
3.16E-14
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
ix
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
up
electron transport
109746
cytochrome P450 monooxygenase, putative
1.56980101
0.002943803
Sophorose
up
N-acetyltransferase activity
103537
GCN5-N-acetyltransferase
1.570810317
6.65E-32
Sophorose
up
#N/D
111253
unknown protein
1.498372332
1.28E-14
Sophorose
up
lysosome organization and biogenesis
111849
GH30 endo-?-1,4-xylanase XYN4
1.84212069
2.68E-26
Sophorose
up
#N/D
111915
SSCRP
1.714970236
5.14E-21
Sophorose
up
membrane
104072
xylose transporter
2.640000013
1.06E-73
Sophorose
up
#N/D
104277
cell wall protein, distantly related to A. niger CwpA.
2.670177695
4.99E-81
Sophorose
up
#N/D
104320
MFS permease
1.413171724
4.67E-11
Sophorose
up
hydrogen-transporting ATPase activity, rotational mechanism
111990
unknown protein
1.181445758
6.45E-14
Sophorose
up
#N/D
105196
unknown protein
1.037968748
1.05E-12
Sophorose
up
#N/D
106051
unknown protein
1.830252903
3.23E-31
Sophorose
up
cell communication
106538
HFB4
2.460883311
3.54E-14
Sophorose
up
amidase activity
106645
unknown protein
1.20282065
5.27E-16
Sophorose
up
S-adenosylmethionine-dependent methyltransferase activity
41617
lae1
1.825223426
9.37E-34
Sophorose
up
zinc ion binding
26871
Zn2Cys6 transcriptional regulator
1.284476557
3.58E-15
Sophorose
up
#N/D
30250
N-acetylglucosaminyltransferase
1.050524997
3.82E-11
Sophorose
up
#N/D
32798
unknown protein
1.359381611
5.97E-09
Sophorose
up
#N/D
33827
unknown protein
2.867753691
1.29E-13
Sophorose
up
#N/D
37525
GPCR , contains RGS domain
1.573054459
1.31E-36
Sophorose
up
#N/D
28353
unknown protein
1.257373414
3.31E-19
Sophorose
up
#N/D
41761
iron transporter
1.192573589
1.53E-14
Sophorose
up
#N/D
27992
PTH11 GPCR
1.109291321
5.41E-15
Sophorose
up
#N/D
43115
SSCRP
1.339240889
9.51E-05
Sophorose
up
serine-type endopeptidase inhibitor activity
72379
conidiospore surface protein cmp1
1.839655583
5.24E-12
Sophorose
up
carbohydrate metabolism
72704
GH27 ?-galactosidase AGL3
1.600557339
1.30E-16
Sophorose
up
#N/D
72788
GT 31 glycosyltransferase
2.430546429
4.85E-44
Sophorose
Down
#N/D
62380
MFS permease (galactose permease ?)
-2.767841236
3.10E-67
Sophorose
Down
ATPase activity, coupled to transmembrane movement of substances
62693
ABC-transporter Ste6p
-2.392795507
9.66E-35
Sophorose
Down
cell adhesion
62213
unknown protein with fasciclin domain
-1.000630266
2.63E-17
Sophorose
Down
#N/D
62462
PTH11 GPCR
-1.798009704
5.18E-30
Sophorose
Down
protein biosynthesis
62611
MRP-type ABC transporter
-2.317454767
5.20E-31
x Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
malate metabolism
62153
malate dehydrogenase
-1.603150582
4.42E-08
Sophorose
Down
#N/D
63240
HET-E-1, putative
-1.789044237
1.34E-26
Sophorose
Down
#N/D
62871
unknown protein
-2.354002819
1.19E-34
Sophorose
Down
#N/D
53893
unknown protein
-1.402089903
0.000418829
Sophorose
Down
structural molecule activity
63687
ankyrin
-1.84100035
1.00E-28
Sophorose
Down
ATP binding
63568
SNF2-like helicase, ATPase domain
-1.458531534
6.36E-17
Sophorose
Down
integral to membrane
53475
MFS permease
-1.050942308
7.49E-10
Sophorose
Down
nucleoside-triphosphatase activity
64710
AAA+-type ATPase
-3.190858615
3.27E-135
Sophorose
Down
cell adhesion
65522
unknown protein
-2.971702048
4.16E-30
Sophorose
Down
#N/D
65695
unknown protein
-1.149737238
0.012698982
Sophorose
Down
carbohydrate metabolism
66041
GH18 chitinase CHI18-18
-2.1128963
4.21E-17
Sophorose
Down
glucan 1,4-alpha-glucosidase activity
66280
unknown protein
-1.626049875
2.56E-21
Sophorose
Down
zinc ion binding
66828
Zn2Cys6 transcriptional regulator
-1.009312221
3.06E-16
Sophorose
Down
protein amino acid phosphorylation
66521
unknown protein
-1.039602586
3.76E-13
Sophorose
Down
#N/D
66865
unknown protein
-1.234161502
0.007734579
Sophorose
Down
#N/D
53722
unknown protein
-1.06629325
1.28E-15
Sophorose
Down
#N/D
66804
GH69: candidate a-glycosyltransferase
-1.065329413
1.81E-14
Sophorose
Down
#N/D
67133
unknown protein
-1.473927794
4.13E-14
Sophorose
Down
intracellular
67117
3'-5' exonuclease
-1.184630027
1.78E-12
Sophorose
Down
#N/D
55041
unknown protein
-1.130925062
1.03E-13
Sophorose
Down
#N/D
67717
unknown protein, ß-lactamase HMMPfam
-1.29981209
1.36E-07
Sophorose
Down
#N/D
67971
MYND-type Zn-finger protein
-1.362842485
1.28E-21
Sophorose
Down
#N/D
68086
unknown protein
-1.592814935
0.000413617
Sophorose
Down
glucan 1,4-alpha-glucosidase activity
67983
nuclear migration protein, ami1, of N. crassa
-1.342546067
3.83E-26
Sophorose
Down
thiamin biosynthesis
68608
Thiazole biosynthetic enzyme (Stressinducible protein sti35)
-1.262758779
4.13E-27
Sophorose
Down
integral to membrane
68813
MFS permease
-1.464249503
1.48E-19
Sophorose
Down
integral to membrane
68803
RTA1 like protein
-4.890884301
3.12E-82
Sophorose
Down
electron transport
68705
cytochrome P450 monooxygenase
-2.426714632
3.81E-50
Sophorose
Down
metabolism
55631
phospholipase
-1.072841496
1.46E-18
Sophorose
Down
membrane
69141
neutral amino acid permeasde
-1.48847658
1.39E-25
Sophorose
Down
integral to membrane
69611
MFS permease
-1.368974612
6.29E-19
Sophorose
Down
#N/D
55375
unknown protein
-1.148589192
1.53E-20
Sophorose
Down
#N/D
56863
unknown protein
-1.272770168
1.13E-20
Sophorose
Down
catalytic activity
56830
dipeptidyl peptidase 5
-1.039696905
0.00017171
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
xi
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
nucleoside-triphosphatase activity
56396
unknown protein
-1.105971194
8.81E-16
Sophorose
Down
#N/D
56215
26S proteasome non-ATPase regulatory subunit 9, putative
-1.512211066
4.64E-30
Sophorose
Down
proteolysis and peptidolysis
56853
unknown protein
-1.410387071
0.007648014
Sophorose
Down
protein folding
56434
FKBP-type peptidyl-prolyl isomerase, putative
-1.098646456
4.29E-15
Sophorose
Down
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
56470
LdhA Lactate dehydrogenase and related dehydrogenases
-1.534604073
4.22E-30
Sophorose
Down
amidase activity
70859
amidase
-1.112686079
4.81E-14
Sophorose
Down
#N/D
70961
dienelactone hydrolase
-1.702546057
1.09E-11
Sophorose
Down
hydrolase activity
59082
GH18, chitinaseCHI18-2
-2.622043806
4.55E-05
Sophorose
Down
proteolysis and peptidolysis
58698
subtilisin like protease (SUB2)
-1.275039372
1.78E-06
Sophorose
Down
#N/D
58381
unknown protein
-1.351404545
1.45E-22
Sophorose
Down
#N/D
59137
unknown protein
-1.435912339
0.001034224
Sophorose
Down
electron transport
58333
FAD binding protein
-1.426302042
1.81E-05
Sophorose
Down
electron transport
58772
cytochrome P450 monooxygenase
-1.079378619
3.10E-13
Sophorose
Down
zinc ion binding
58475
unknown protein
-4.160740563
0.008071254
Sophorose
Down
membrane
58584
aquaglyceroporin
-2.50455634
5.99E-44
Sophorose
Down
#N/D
59778
GPCR, related to A nidulans GprC
-1.324195176
9.74E-21
Sophorose
Down
#N/D
59151
SSCRP
-2.57740842
2.42E-50
Sophorose
Down
#N/D
59801
unknown protein
-1.9865893
0.031211597
Sophorose
Down
oxidoreductase activity
60890
L-galactose dehydrogenase (LGalDH), putative
-1.019291072
6.08E-06
Sophorose
Down
ATPase activity, coupled to transmembrane movement of substances
60987
MRP-type ABC transporter
-1.002753947
4.47E-09
Sophorose
Down
#N/D
60761
transcriptional regulator Grainyhead/CP2
-1.188197769
5.37E-10
Sophorose
Down
zinc ion binding
60981
unknown protein
-2.353521773
2.52E-69
Sophorose
Down
S-adenosylmethionine-dependent methyltransferase activity
61284
methyltransferase
-1.16264474
5.06E-16
Sophorose
Down
metabolism
61750
Sur2 sphinganine C4-hydroxylase of Saccharomyces cerevisiae
-1.062489028
8.13E-06
Sophorose
Down
#N/D
62100
Hsp30
-2.576636582
1.81E-12
Sophorose
Down
#N/D
21270
CAP20 virulence factor
-1.306765245
8.63E-28
Sophorose
Down
glycolysis
21406
phosphoglycerate kinase
-1.234394295
1.11E-14
Sophorose
Down
electron transport
22464
Bifunctional P-450:NADPH-P450 reductase
-1.033947397
1.70E-11
Sophorose
Down
#N/D
22590
unknown protein
-2.290253011
2.76E-35
Sophorose
Down
#N/D
23015
unknown protein
-1.011590695
0.010646748
xii Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
phosphotransferase activity, carboxyl group as acceptor
21716
Acetate kinase
-1.357416371
0.003605764
Sophorose
Down
oxidoreductase activity
21876
Zinc-binding oxidoreductase
-7.977537629
3.30E-125
Sophorose
Down
protein amino acid prenylation
22093
Protein farnesyltransferase, alpha subunit
-1.339761606
4.31E-27
Sophorose
Down
protein amino acid ADP-ribosylation
22115
poly polymerase (Poly[ADP-ribose] synthetase)
-1.050294091
3.12E-13
Sophorose
Down
nucleus
119530
RNA polymerase III RPC4.
-1.035110232
4.32E-08
Sophorose
Down
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
122010
LdhA Lactate dehydrogenase and related dehydrogenases
-1.586459834
3.06E-33
Sophorose
Down
protein binding
122069
SSCRP
-1.975926156
2.97E-19
Sophorose
Down
extracellular region
122087
unknown protein
-2.454946409
3.93E-48
Sophorose
Down
#N/D
122089
unknown protein
-1.642874514
7.41E-25
Sophorose
Down
#N/D
122103
unknown protein
-1.296731614
3.06E-25
Sophorose
Down
hydrogen-transporting ATPase activity, rotational mechanism
122124
AAA ATPase
-2.808432317
1.96E-41
Sophorose
Down
#N/D
122147
unique protein
-1.325572231
3.74E-19
Sophorose
Down
#N/D
119556
unknown protein, secreted
-1.042853159
8.69E-12
Sophorose
Down
#N/D
119568
unknown protein
-1.003870595
6.32E-17
Sophorose
Down
#N/D
119694
unknown protein
-1.5237897
0.008857059
Sophorose
Down
NAD binding
119735
Glyceraldehyde-3-phosphate dehydrogenase, isozyme 2
-1.089753952
2.18E-20
Sophorose
Down
#N/D
119864
unknown protein
-2.411185681
1.42E-47
Sophorose
Down
#N/D
119902
unique protein
-2.125132349
3.33E-33
Sophorose
Down
#N/D
122242
unknown protein, 1 TM
-1.822785673
2.64E-40
Sophorose
Down
amino acid metabolism
122301
Cystathionine betalyases/cystathionine gamma-synthases
-1.199942414
2.99E-05
Sophorose
Down
#N/D
122487
DNAse
-2.835743333
1.51E-60
Sophorose
Down
oxidoreductase activity
122505
aryl-alcohol dehydrogenase
-1.608339359
1.19E-25
Sophorose
Down
carbohydrate metabolism
122511
glucan endo-1,3(4)-?-D-glucosidase
-2.868793834
1.79E-54
Sophorose
Down
#N/D
122569
unknown protein
-1.584605386
1.59E-39
Sophorose
Down
#N/D
122792
unknown protein
-2.937490174
3.97E-35
Sophorose
Down
#N/D
122879
bHLH transcriptional regulator
-1.16348888
0.021730679
Sophorose
Down
#N/D
123009
glutamine synthetase
-1.534187875
6.25E-21
Sophorose
Down
oxidoreductase activity
123084
chloroperoxidase
-1.346670221
0.013829743
Sophorose
Down
trehalose metabolism
123226
GH37 ?,?-trehalase
-1.317674583
1.51E-19
Sophorose
Down
catalytic activity
123238
epoxide hydrolase
-1.711961191
2.99E-32
Sophorose
Down
#N/D
123260
unknown protein
-3.118207944
7.51E-38
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
xiii
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
#N/D
123261
unknown protein
-2.394313756
2.78E-64
Sophorose
Down
amidase activity
123262
unique protein, HTG, amidase domain, 1 TM
-1.10582537
5.40E-13
Sophorose
Down
oxidoreductase activity
123274
Aldehyde dehydrogenase
-1.02504861
0.00092319
Sophorose
Down
#N/D
120030
unique protein
-1.193752614
5.26E-10
Sophorose
Down
#N/D
120057
unknown protein
-2.387965812
1.93E-76
Sophorose
Down
zinc ion binding
120117
C2H2 transcriptional regulator
-3.263902663
2.20E-142
Sophorose
Down
#N/D
120193
unknown protein
-1.486964305
5.75E-14
Sophorose
Down
#N/D
120257
unknown protein
-1.086323223
1.76E-11
Sophorose
Down
isoprenoid biosynthesis
120290
thiamine pyrophosphokinase
-1.544180547
4.86E-31
Sophorose
Down
porphyrin biosynthesis
123382
Coproporphyrinogen III oxidase
-1.711268278
2.88E-05
Sophorose
Down
catalytic activity
123471
Subtilisin like protease, related to S. cerevisiae Kex2 protease
-1.039059363
2.06E-08
Sophorose
Down
#N/D
123475
cell wall Thr-rich mannoprotein. Distantly related to S. cerevisiae Dan4p.
-1.808373102
2.82E-54
Sophorose
Down
#N/D
123476
unknown protein
-2.386051778
6.98E-51
Sophorose
Down
#N/D
123636
unknown protein
-1.152658384
1.53E-20
Sophorose
Down
#N/D
123648
unknown protein
-2.164155892
5.55E-29
Sophorose
Down
#N/D
123659
cell wall protein, istantly related to S. cerevisiae Pir3p.
-1.133402081
2.03E-11
Sophorose
Down
transport
123673
Ankyrin
-2.037863477
2.33E-08
Sophorose
Down
#N/D
123687
unknown protein
-1.149807229
0.044063629
Sophorose
Down
#N/D
123697
Unknown protein
-1.60832151
3.39E-06
Sophorose
Down
integral to membrane
123702
MFS permease
-1.734332873
1.82E-20
Sophorose
Down
molecular function unknown
123732
unique protein
-1.656944073
7.52E-20
Sophorose
Down
#N/D
123733
HET protein
-1.433130464
1.65E-27
Sophorose
Down
zinc ion binding
123881
Zn2Cys6 transcriptional regulator
-1.332864906
1.64E-30
Sophorose
Down
#N/D
123888
unknown protein
-1.680047995
1.15E-13
Sophorose
Down
#N/D
123914
unique protein
-1.77759558
2.34E-30
Sophorose
Down
oxidoreductase activity
123946
dehydrogenase associated with cellulase signal transduction (PMID: 15288024)
-2.102745032
7.70E-22
Sophorose
Down
oxidoreductase activity
123979
peptide transporter MTD1
-1.925820071
4.28E-10
Sophorose
Down
zinc ion binding
120430
Zn2Cys6 transcriptional regulator
-1.113130253
2.16E-15
Sophorose
Down
#N/D
124059
SSCRP
-1.109266738
2.52E-11
Sophorose
Down
biosynthesis
124097
phenazine biosynthesis protein phzF
-1.861521081
4.51E-23
Sophorose
Down
phosphate transport
124157
unknown protein
-1.344289287
1.67E-21
Sophorose
Down
#N/D
124177
unknown protein
-1.074588217
0.003804376
xiv Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
cathepsin F activity
124222
CaaX-protease, related to E. nidulans rce1, involved in signal transduction
-2.671293033
5.09E-61
Sophorose
Down
#N/D
120570
tRNA splicing endonuclease SEN15 of yeast.
-1.170131968
0.01033963
Sophorose
Down
#N/D
120751
unknown protein
-1.215482774
0.002874977
Sophorose
Down
phosphopantetheine binding
120821
phytase
-2.414070168
1.98E-42
Sophorose
Down
#N/D
120851
HET domain protein, related to N. crassa pin-c3
-1.100646652
4.56E-13
Sophorose
Down
#N/D
124282
unknown protein, SET and MYND domain
-2.497920228
7.25E-60
Sophorose
Down
hydroxyacylglutathione hydrolase activity
120877
Zn-dependent ß-lactamase
-1.359082504
1.51E-20
Sophorose
Down
#N/D
120975
unknown protein
-3.832585626
0.000221395
Sophorose
Down
#N/D
121088
unknown protein, secreted 1 TM
-1.972777392
9.36E-36
Sophorose
Down
zinc ion binding
121107
Zn2Cys6 transcriptional regulator
-1.256141516
2.68E-25
Sophorose
Down
#N/D
124293
unknown protein
-1.297147185
3.19E-12
Sophorose
Down
#N/D
121126
unknown protein
-1.710855996
3.67E-36
Sophorose
Down
membrane
121139
Amino acid transporters
-1.010875283
1.80E-08
Sophorose
Down
amidase activity
121154
Amidase
-1.106393511
1.53E-16
Sophorose
Down
#N/D
121178
unknown protein
-1.447936226
8.29E-30
Sophorose
Down
aromatic compound metabolism
121230
unique protein
-1.412555945
0.004260527
Sophorose
Down
#N/D
121294
glucan endo-1,3(4)-?-D-glucosidase
-1.3732885
3.33E-14
Sophorose
Down
dihydroneopterin triphosphate pyrophosphohydrolase activity
121336
unique protein
-1.492818362
7.40E-20
Sophorose
Down
#N/D
121396
unique protein
-1.088278373
8.59E-10
Sophorose
Down
#N/D
121416
unknown protein
-4.585171815
1.33E-135
Sophorose
Down
#N/D
121427
unknown protein
-2.009257388
2.61E-44
Sophorose
Down
integral to membrane
121441
carbounknown proteinlic acid transporter
-2.816493633
7.62E-18
Sophorose
Down
#N/D
121471
SSCRP
-2.256336834
1.73E-74
Sophorose
Down
zinc ion binding
121474
Zn2Cys6 transcriptional regulator
-1.027709813
3.77E-10
Sophorose
Down
membrane
121486
unknown protein
-3.617403681
5.72E-34
Sophorose
Down
biosynthesis
121491
-2.930725401
7.23E-10
Sophorose
Down
pyruvate decarboxylase activity
121534
pyruvate decarboxylase
-3.164522375
5.42E-44
Sophorose
Down
#N/D
121620
NMT1 thiamine biosynthesis protein
-1.313179672
2.09E-18
Sophorose
Down
L-serine metabolism
121686
Serine hydroxymethyltransferase
-1.27371705
5.11E-19
Sophorose
Down
carbon-sulfur lyase activity
121693
Glutathione-dependent formaldehydeactivating, GFA
-1.032603778
1.17E-14
GT4 ?,?'-trehalose phosphorylase/synthase
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
xv
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
DNA-directed RNA polymerase III activity
121818
unknown secreted protein
-1.586580545
1.53E-08
Sophorose
Down
ATP binding
121839
HSP70
-2.041995095
3.54E-62
Sophorose
Down
#N/D
121843
C6HC zinc finger protein
-1.696583407
9.86E-46
Sophorose
Down
membrane
43671
ammonium permease MEA1
-1.82315335
2.04E-10
Sophorose
Down
integral to membrane
43701
MFS multidrug transporter
-3.900233698
5.86E-195
Sophorose
Down
#N/D
48852
unknown protein
-1.269069722
6.22E-22
Sophorose
Down
calcium-mediated signaling
48924
calcipressin
-1.062246642
0.0017132
Sophorose
Down
#N/D
49048
RNA-dependent RNA-polymerase
-1.091111342
0.022951247
Sophorose
Down
#N/D
44178
unknown protein
-1.681013087
9.80E-19
Sophorose
Down
#N/D
44278
Rab geranyl transferase escort protein
-1.834877778
3.42E-14
Sophorose
Down
#N/D
49589
unknown protein
-3.013384979
4.15E-66
Sophorose
Down
N-acetylglucosamine metabolism
49898
glucosamine-6-phosphate isomerase
-2.968212168
5.95E-31
Sophorose
Down
#N/D
50212
GT Glycosyltransferases not yet assigned to a family
-1.744280996
4.56E-29
Sophorose
Down
carbohydrate metabolism
50215
GH16 endo-1,3-?-D-glucosidase/1,3glucan binding protein
-2.101177882
7.17E-45
-1.000499823
2.24E-11
Sophorose
Down
tRNA aminoacylation for protein translation
50583
Guanine deaminase (GDEase), an aminohydrolase responsible for the conversion ofGuanine to xanthine and ammonia, the first step to utilizeGuanine as a nitrogen source.
Sophorose
Down
extracellular region
50616
Coenzyme A transferase
-4.057586417
1.28E-40
Sophorose
Down
#N/D
50996
unknown protein, C2 domain
-1.337928033
0.000574865
Sophorose
Down
integral to membrane
44956
MFS permease
-2.219981597
3.65E-69
Sophorose
Down
#N/D
44967
unknown protein,
-2.658364916
2.58E-35
Sophorose
Down
metabolism
44987
ERG25 methylsterol desaturase, SUR2-type hydroxylase/desaturase, catalytic region
-1.862748971
1.52E-31
Sophorose
Down
#N/D
51415
unknown protein
-1.270471321
1.74E-13
Sophorose
Down
sulfuric ester hydrolase activity
52073
sulfatase
-1.016876839
2.60E-16
Sophorose
Down
#N/D
52165
unknown protein, 1 TM
-2.203645864
6.50E-10
Sophorose
Down
#N/D
52206
#N/D
-3.936782714
4.84E-209
Sophorose
Down
#N/D
45573
PTH11 GPCR
-1.120414144
8.26E-05
Sophorose
Down
#N/D
45971
mismatched base pair and cruciform DNA recognition protein
-1.923328783
0.000553423
Sophorose
Down
protein amino acid phosphorylation
45998
serine threonine protein kinase SNF1
-2.122829828
1.17E-71
Sophorose
Down
one-carbon compound metabolism
46238
S-adenosylmethionine synthetase
-1.264775341
5.03E-13
Sophorose
Down
#N/D
46764
unknown protein
-2.832883066
1.39E-67
Sophorose
Down
membrane
46794
oligopeptide transporter
-1.643768409
2.95E-44
xvi Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
oxidoreductase activity
46936
2-deoxy-D-gluconate 3-dehydrogenase
-1.149111943
8.81E-14
Sophorose
Down
proteolysis and peptidolysis
47286
unknown protein
-1.903264848
1.68E-29
Sophorose
Down
#N/D
47424
unknown protein
-1.95843203
9.67E-29
Sophorose
Down
membrane
47710
MFS permease
-1.356936119
1.10E-15
Sophorose
Down
prenylcysteine oxidase activity
47814
prenylcysteine lyase, putative
-1.371997831
3.02E-29
Sophorose
Down
#N/D
48211
unknown protein, intracellular
-1.20082135
0.002891791
Sophorose
Down
sulfuric ester hydrolase activity
78320
Sulfatase
-1.275585955
7.69E-17
Sophorose
Down
#N/D
73516
Grg1 Glucose repressible protein
-2.838402457
2.63E-67
Sophorose
Down
#N/D
78391
unknown protein
-1.074792285
2.90E-10
Sophorose
Down
#N/D
73519
unknown protein, 4 TM
-3.263272076
2.51E-48
Sophorose
Down
response to oxidative stress
73523
unknown protein with WSC domains
-1.504006157
1.28E-33
Sophorose
Down
disulfide oxidoreductase activity
78496
Flavin-containing monooxygenase Fmo1 like
-1.07081994
4.94E-09
Sophorose
Down
oxidoreductase activity
73536
NADP-glutamate dehydrogenase
-1.690019971
5.80E-13
Sophorose
Down
S-adenosylmethionine-dependent methyltransferase activity
73618
PKS
-3.525276562
3.41E-41
Sophorose
Down
S-adenosylmethionine-dependent methyltransferase activity
73621
PKS
-4.030888199
3.29E-37
Sophorose
Down
aromatic compound metabolism
73623
flavoprotein monooxygenase
-3.562551868
1.67E-20
Sophorose
Down
electron transport
73631
isoamyl alcohol oxidase
-4.692759247
1.52E-67
Sophorose
Down
nucleic acid binding
74017
unknown protein
-1.329118187
1.44E-16
Sophorose
Down
proteolysis and peptidolysis
78542
cytosolic phospholipase A2, putative
-1.242569667
1.83E-23
Sophorose
Down
metabolism
78611
phospholipase D
-1.551797859
0.003760523
Sophorose
Down
metabolism
78732
6-phosphofructo-2-kinase
-1.583701514
4.11E-36
Sophorose
Down
#N/D
78792
unknown protein
-1.073519867
1.45E-13
Sophorose
Down
oxidoreductase activity
74194
mannitol dehydrogenase LXR1
-1.903410877
3.96E-09
Sophorose
Down
oxidoreductase activity
74278
Pyridine nucleotide-disulphide oxidoreductase, class-II
-1.654942167
6.31E-25
Sophorose
Down
proprotein convertase activity
74282
QI74 orthologue
-2.330190727
8.70E-15
Sophorose
Down
#N/D
74515
unknown protein
-1.10309265
3.42E-14
Sophorose
Down
glycine catabolism
78864
GcvTGlycine cleavage system T protein
-1.778518912
7.58E-38
Sophorose
Down
#N/D
78956
unknown protein
-1.478371558
5.91E-11
Sophorose
Down
membrane
78970
mitochondrial (phosphate) carrier
-1.095867368
1.78E-19
Sophorose
Down
proteolysis and peptidolysis
79111
unknown protein
-1.201489665
1.02E-16
Sophorose
Down
#N/D
79396
GT2 ß-glycosyltransferase, related to hyaluronan synthases
-1.516718079
1.24E-38
Sophorose
Down
ATPase activity, coupled to transmembrane movement of substances
79510
MRP-type ABC transporter
-1.239883859
1.12E-13
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
xvii
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
#N/D
79598
unknown protein
-1.744550844
1.42E-26
Sophorose
Down
hydrolase activity
79671
N-acetyl-glucosamine-6-phosphate deacetylase
-4.415871401
2.97E-85
Sophorose
Down
oxidoreductase activity
79738
Zinc-binding oxidoreductase
-1.735304098
7.43E-34
Sophorose
Down
membrane
79741
ER-bound Farnesyl-diphosphate farnesyltransferase
-1.769263923
3.12E-19
Sophorose
Down
RNA processing
79823
DCL2, Dicer-like protein, involved in quelling
-1.024167397
1.20E-05
Sophorose
Down
#N/D
80007
Like Rad54; interacts with Dmc1
-1.210159832
2.91E-21
Sophorose
Down
#N/D
80026
MFS permease
-1.035338503
2.68E-17
Sophorose
Down
ATP binding
80028
MRP-type ABC transporter
-1.502199969
3.14E-22
Sophorose
Down
ATP binding
80142
HSP104 and related ATP-dependent Clp proteases
-1.500261028
0.005343511
Sophorose
Down
oxidoreductase activity
80425
unknown protein
-1.493281718
2.87E-29
Sophorose
Down
membrane
74854
stearic acid desaturase Sde1
-1.054740597
2.07E-11
Sophorose
Down
#N/D
80863
unknown protein
-1.134279763
5.87E-23
Sophorose
Down
integral to membrane
80875
MFS permease
-1.197970446
0.000936272
Sophorose
Down
ATP binding
80973
PDR-type ABC transporters
-1.210745682
7.55E-17
Sophorose
Down
hydrogen-transporting ATPase activity, rotational mechanism
75105
unknown protein
-1.267735371
5.26E-15
Sophorose
Down
membrane
81082
aquaglyceroporin
-2.476881124
2.61E-47
Sophorose
Down
oxidoreductase activity
81102
unknown protein
-1.079560557
0.001277813
Sophorose
Down
integral to membrane
81136
serine/threonine phosphatase 2 C, PTC2
-1.820260549
1.78E-17
Sophorose
Down
#N/D
81183
unknown protein
-1.097085923
1.76E-06
Sophorose
Down
#N/D
81328
unknown protein, only in fungi
-1.037152333
3.57E-12
Sophorose
Down
#N/D
81329
unknown protein
-1.273913685
7.30E-22
Sophorose
Down
glycine metabolism
81339
glycine dehydrogenase
-1.160518396
1.68E-22
Sophorose
Down
hydrolase activity, acting on carbonnitrogen (but not peptide) bonds, in linear amides
81511
formamidase
-1.199249769
4.30E-15
Sophorose
Down
membrane
81536
cation transporting ATPase
-1.136815131
1.62E-12
Sophorose
Down
hydrolase activity
81598
GH18, chitinase CHI18-7
-1.202211553
1.01E-10
Sophorose
Down
electron transport
81652
unknown protein
-1.510393828
8.62E-25
-1.79535933
1.51E-17
Sophorose
Down
#N/D
81690
ß-arrestin protein, shares similarity with Aspergillus idulans CreD, possible inhibitor of G-protein coupled receptors
Sophorose
Down
#N/D
81756
unknown protein
-1.351114871
2.21E-29
Sophorose
Down
#N/D
81803
mitochondrial protein sorting (Msf1)
-1.164266507
0.00029119
xviii Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
#N/D
81819
unknown protein
-5.12186971
2.50E-43
Sophorose
Down
tRNA aminoacylation for protein translation
81822
mitochondrial leucyl-tRNA synthetase.
-1.891032158
1.40E-52
Sophorose
Down
#N/D
82017
siderophore transporter
-2.060195964
6.67E-47
Sophorose
Down
#N/D
82032
unknown protein
-1.893886236
0.000263058
Sophorose
Down
#N/D
75262
unknown protein
-2.162222438
9.34E-50
Sophorose
Down
#N/D
75394
unknown protein
-4.471277122
3.72E-106
Sophorose
Down
catalytic activity
82360
lipase/serine esterase, putative
-1.302879684
1.52E-20
Sophorose
Down
zinc ion binding
82512
26S proteasome regulatory complex subunit Rpn4
-1.792203497
3.01E-14
Sophorose
Down
transport
75884
unknown protein
-2.209450362
7.25E-61
Sophorose
Down
antibiotic biosynthesis
76034
Iron/ascorbate family oxidoreductases
-1.27173866
3.25E-13
Sophorose
Down
#N/D
76065
unknown protein
-1.040991814
1.74E-09
Sophorose
Down
acid phosphatase activity
76117
unknown protein
-1.034157328
2.02E-13
Sophorose
Down
carbohydrate metabolism
82616
GH5 membrane bound endoglucanase CEL5b
-2.06777336
1.43E-54
Sophorose
Down
arginine biosynthesis
82619
arginosuccinate synthetase
-2.80121372
5.36E-101
Sophorose
Down
regulation of oxidoreductase activity
76215
sulfide:quinone oxidoreductase/flavobinding protein
-1.914103776
1.23E-36
Sophorose
Down
#N/D
76359
unknown protein, only present in ascomycota
-2.702149576
2.41E-24
Sophorose
Down
electron transport
76617
FAD-binding dehydrogenase
-1.091971332
0.000255577
Sophorose
Down
glycerol-3-phosphate dehydrogenase complex
76620
Glycerol-3-phosphate dehydrogenase
-4.146611247
2.31E-209
Sophorose
Down
transport
76722
flavohemoglobin
-1.538886525
5.17E-07
Sophorose
Down
#N/D
76763
PTH11 GPCR
-1.293557919
6.67E-14
Sophorose
Down
oxidoreductase activity
76784
sorbitol dehydrogenase
-2.461679581
3.18E-34
Sophorose
Down
hydrogen-transporting ATPase activity, rotational mechanism
76852
GH2 ?-galactosidase/?-glucuronidase
-2.109783643
2.70E-22
Sophorose
Down
oxidoreductase activity
77288
Thioredoxin reductase
-5.234679235
1.89E-196
Sophorose
Down
#N/D
77547
GT1 glycosyltransferase
-2.438244435
3.62E-17
Sophorose
Down
#N/D
77557
GT glycosyltransferases not yet assigned to a family, 3 TMs
-2.411689663
9.53E-22
Sophorose
Down
#N/D
77699
unknown protein
-2.144601628
4.23E-08
Sophorose
Down
#N/D
77795
LIMPET, E3-ubiquitin ligase SCON-2
-1.134644682
4.28E-20
Sophorose
Down
zinc ion binding
77878
C2H2 transcriptional regulator
-1.004235754
5.55E-14
Sophorose
Down
chromate transport
77969
chromate transporter
-1.21439621
8.81E-14
Sophorose
Down
#N/D
1818
unknown protein
-1.171913135
0.00727734
Sophorose
Down
metabolism
1925
fatty acid hydroxylase, Cytb5, SUR2type hydroxylase/desaturase, catalytic region
-2.154949353
2.69E-59
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
xix
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
regulation of transcription, DNAdependent
4231
GATA type transcriptional regulator
-2.245162673
5.81E-51
Sophorose
Down
catalytic activity
4626
unknown protein, C2 domain
-1.399038891
0.000899332
Sophorose
Down
methyltransferase activity
4860
Siroheme synthase CysG
-1.11096463
9.53E-12
Sophorose
Down
proteolysis and peptidolysis
2648
Fe(II)/2-oxoglutarate-dependent diounknown proteingenase
-1.132598935
0.001121597
Sophorose
Down
mRNA processing
2721
unknown protein
-1.128812755
3.18E-18
Sophorose
Down
oxidoreductase activity
3327
NADH:flavin oxidoreductase/NADH oxidase
-1.010201835
3.61E-13
Sophorose
Down
#N/D
107639
unknown protein
-1.442138989
2.01E-05
Sophorose
Down
#N/D
107715
SSCRP
-1.327111978
0.005910596
Sophorose
Down
exo-alpha-sialidase activity
102437
unique protein, secreted
-1.134286003
8.46E-18
Sophorose
Down
zinc ion binding
102497
Zn2Cys6 transcriptional regulator
-1.618242913
4.21E-34
Sophorose
Down
hydrolase activity, acting on glycosyl bonds
102998
ADP-ribosylglycohydrolase-like protein
-1.755028016
5.03E-29
Sophorose
Down
nucleoside-triphosphatase activity
103149
AAA ATPase
-2.948228823
1.02E-110
Sophorose
Down
#N/D
108583
unknown protein
-1.957515334
9.52E-40
Sophorose
Down
#N/D
108818
unknown protein
-1.089407062
4.98E-05
Sophorose
Down
#N/D
108852
unique protein
-2.386218528
1.10E-21
Sophorose
Down
catalytic activity
109078
prenyltransferase, related to E. nidulans CaaX farnesyltransferase beta subunit ram1
-1.063251025
2.18E-19
Sophorose
Down
electron transport
109201
FAD binding domain-containing protein
-1.315077138
2.07E-19
Sophorose
Down
#N/D
109850
unknown protein
-1.830309543
2.72E-35
Sophorose
Down
#N/D
109945
unique protein
-2.69763337
1.76E-25
Sophorose
Down
one-carbon compound metabolism
110171
S-adenosyl-L-homocysteine hydrolase
-1.011015486
3.50E-08
Sophorose
Down
proteolysis and peptidolysis
110267
unknown protein
-5.045104916
1.14E-141
Sophorose
Down
#N/D
110452
unknown protein
-1.50261635
1.57E-32
Sophorose
Down
#N/D
103822
unknown protein
-2.004150213
4.09E-32
Sophorose
Down
#N/D
110593
unknown protein
-1.339076646
5.83E-06
Sophorose
Down
electron transport
110620
unknown protein
-1.663292087
1.48E-35
Sophorose
Down
#N/D
110879
unknown protein
-1.849537056
0.001199519
Sophorose
Down
S-adenosylmethionine-dependent methyltransferase activity
111082
glutathione S transferase, 2 TM
-1.065260442
4.64E-08
Sophorose
Down
catalytic activity
111357
FAD-dependent oxidoreductase
-2.288274264
8.99E-58
Sophorose
Down
catalytic activity
111382
ankyrin
-1.310248886
3.92E-15
Sophorose
Down
#N/D
111494
HET protein
-3.407008458
1.17E-76
Sophorose
Down
oxidoreductase activity
111932
PutA delta-1-pyrroline-5-carboxylate dehydrogenase
-1.10958591
1.81E-15
xx Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
(Table S3) contd….
Condition
Regulation
GO
Protein ID
Description
FC
p-value
Sophorose
Down
oxidoreductase activity
104180
Ankyrin
-3.900561446
2.91E-24
Sophorose
Down
#N/D
104251
unknown protein
-6.106890976
8.17E-105
Sophorose
Down
glutathione transferase activity
104390
glutathione S-transferase
-2.156648999
2.12E-36
Sophorose
Down
#N/D
112001
unknown protein
-1.435442424
6.75E-10
Sophorose
Down
#N/D
112390
unknown protein
-1.26559824
1.06E-21
Sophorose
Down
#N/D
105106
unique protein
-1.222937746
0.001275035
Sophorose
Down
oxidoreductase activity
112567
taurine catabolism dioxygenase
-3.455268704
2.54E-59
Sophorose
Down
#N/D
105533
SSCRP
-3.567685699
1.24E-112
Sophorose
Down
#N/D
106181
unique protein
-1.704538625
8.04E-20
Sophorose
Down
#N/D
106314
Ankyrin
-3.285726623
3.55E-86
Sophorose
Down
nucleoside-triphosphatase activity
106626
unknown protein, SWIFT domain
-2.30334091
5.25E-21
Sophorose
Down
integral to membrane
107294
RTA1-like protein, 7 TM, responds to xenobiotic stimuli
-1.156657634
4.51E-12
Sophorose
Down
glucan 1,3-beta-glucosidase activity
39942
GH17 glucan endo-1,3-?-glucosidase
-1.264895071
0.008957459
Sophorose
Down
zinc ion binding
35552
C2H2 transcription factor
-1.829172319
6.50E-28
Sophorose
Down
#N/D
37783
unknown protein
-1.671963106
1.23E-26
Sophorose
Down
#N/D
36608
unknown protein
-1.027988925
2.74E-17
Sophorose
Down
#N/D
38812
iron transporter
-1.298018597
5.09E-09
Sophorose
Down
integral to membrane
27689
MFS permease
-1.07658044
1.36E-14
Sophorose
Down
#N/D
42848
unknown protein
-2.674429534
1.51E-83
Sophorose
Down
aromatic compound metabolism
39535
mannitol-1-phosphate dehydrogenase
-1.103826646
1.25E-13
Sophorose
Down
integral to membrane
28409
MFS permease
-2.842962259
7.22E-68
Sophorose
Down
#N/D
41895
glutathione-S-transferase
-2.35565863
7.06E-55
Sophorose
Down
#N/D
36267
unknown protein, 3TM
-1.322469939
6.43E-20
Sophorose
Down
integral to membrane
31134
isoprenylcysteine carboxyl methyltransferase
-1.999437339
3.69E-38
Sophorose
Down
carbohydrate metabolism
39755
GH16 glucan endo-1,3(4)-?-Dglucosidase
-1.108468586
9.19E-12
Sophorose
Down
#N/D
71851
#N/D
-1.066908073
9.86E-13
Sophorose
Down
signal transducer activity
72259
RgsA, regulator of G-protein signaling
-1.722692869
1.44E-34
Sophorose
Down
proteolysis and peptidolysis
72321
subtilisin-like serine protease
-1.274371259
1.01E-15
Sophorose
Down
protein amino acid phosphorylation
73119
unknown protein
-1.898316932
8.03E-42
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
xxi
Table S4. CAZy genes up-regulated in the mutant cre1 compared to QM9414 in the presence of sophorose. Gene expression values are represented as Log2 fold change. Protein ID
Name
Class
Family
Annotation
FC
p-value
GH*
71
Candidate -1 3-glucanase
4.71
6.4E-245
GH
54
-L-arabinofuranosidase I
2.61
6.3E-09
5836
GH
2
Candidate -mannosidase
2.49
1.0E-26
60489
CE**
5
Candidate cutinase
2.34
1.5E-44
120873 123283
abf1
122780
rgx1
GH
28
Candidate exo-rhamnogalacturonase
2.20
1.1E-55
111849
xyn4
GH
30
Endo--1,4-xylanase
1.84
2.7E-26
55319
abf3
GH
54
Candidate -L-arabinofuranosidase
1.76
1.1E-49
76672
bgl1/cel3a
GH
3
-glucosidase
1.66
1.4E-08
65162
Endo T
GH
18
Endo-N-acetyl--D-glucosaminidase
1.61
4.9E-42
72704
agl3
GH
27
-galactosidase
1.60
1.3E-16
22129
GH
61
Candidate copper-dependent polysaccharide monooxygenase
1.51
1.1E-36
74807
GH
76
Candidate -1,6-mannanase
1.45
3.3E-33
54242
GH
55
Candidate -1,3-glucanase
1.36
4.6E-18
57098
GH
92
Candidate -1,2-mannosidase
1.30
3.4E-18
70845
GH
55
Candidate -1,3-glucanase
1.23
1.2E-16
65215
CE
4
Candidate imidase
1.18
3.1E-18
GH
61
Candidate copper-dependent polysaccharide monooxygenase/endo--1,4-glucanase
1.18
2.1E-09
GH
92
Candidate -1,2-mannosidase
1.11
3.7E-21
73643
egl4/cel61a
79921 122081
egl1/cel7b
GH
7
Endo--1,4-glucanase
1.10
3.6E-05
123940
cip2
CE
15
Glucuronoyl esterase
1.05
1.4E-04
GH
47
Candidate -1,2-mannosidase
1.04
9.9E-17
GH
45
Endo--1,4-glucanase
1.00
4.9E-08
79960 49976 *Glycoside hydrolase **Carbohydrate esterase.
egl5/cel45a
xxii Current Genomics, 2016, Vol. 17, No. 2
Supplementary Material
Table S5. Transporter proteins used in the phylogenetic analysis. Organism
Access Portal
Identification
Description
Saccharomyces cerevisiae
Saccharomyces Genome Database
YHR094C
Hexose transporter
Saccharomyces cerevisiae
Saccharomyces Genome Database
YHR092C
Hexose transporter
Saccharomyces cerevisiae
Saccharomyces Genome Database
YDR343C
Hexose transporter
Neurospora crassa
Neurospora crassa Database
NCU00821
Sugar transporter
Neurospora crassa
Neurospora crassa Database
NCU04963
Glucose transporter
Neurospora crassa
Neurospora crassa Database
NCU08114
Cellodextrin transporter
Neurospora crassa
Neurospora crassa Database
NCU10021
Glucose transporter
Aspergillus nidulans
AspGD
AN3199
Sugar transporter MFS
Aspergillus nidulans
AspGD
AN6831
Sugar transporter putative
Aspergillus oryzae
AspGD
AO090103000130
Maltose permease
Aspergillus oryzae
AspGD
AO090038000233
Maltose permease
Aspergillus niger
GenBank
XP_001397059.2
ABC transporter
Escherichia coli
GenBank
YP006127731.1
Sugar transporter
Metarhizium anisopliae
GenBank
GQ167043.1
Oligosaccharide transporter
Metarhizium anisopliae
GenBank
EFY97396.1
MFS transporter
Metarhizium anisopliae
GenBank
EFY94560.1
ABC transporter
Talaromyces marneffei
GenBank
XP002152585.1
Maltose permease
Talaromyces stipitatus
GenBank
XP002484658.1
Sugar transporter
Candida albicans
Candida Genome Database
19.13383
Glucose sensor
Ogataea angusta
GenBank
ACA58225.1
Glucose sensor
Beauveria bassiana
GenBank
EJP62811.1
Potassium channel
Togninia mínima
GenBank
EOO00826.1
ABC transporter
Colletotrichum gloeosporioides
GenBank
EQB50276.1
ABC transporter
Fusarium fujikuroi
GenBank
CCT62487.1
Cation transporter
Supplementary Material
Current Genomics, 2016, Vol. 17, No. 2
xxiii
Table S6. Comparison of gene expression values obtained by RNA-seq and qRT-PCR when the strains were grown in sophorose. Gene expression values are represented as Log2 fold change. Protein ID
Description
qRT-PCR
RNA-seq
58475
unknown protein
-4.33
-4.160740563
120975
unknown protein
-4.57
-3.832585626
21876
Zinc-binding oxidoreductase
-9.95
-7.977537629
104251
unknown protein
-6.85
-6.106890976
110267
unknown protein
-4.62
-5.045104916
76359
unknown protein, only present in ascomycota
-3.16
-2.702149576
122792
unknown protein
-3.09
-2.937490174
106314
Ankyrin
-4
-3.285726623
64710
AAA+-type ATPase
-3.22
-3.190858615
109945
unique protein
-3.19
-2.69763337
72379
conidiospore surface protein cmp1
1.82
1.839655583
82227
GH3 -glucosidase CEL3c
-0.27
-0.068762013
123232
GH12 endo-ß-1,4-glucanase
-1.3
-0.008740619
72567
GH6 Cellobiohydrolase CEL6A/CBH2
0.58
0.492458157
123989
GH7 Cellobiohydrolase CBH1/CEL7a
0.65
0.448688197
123992
swollenin
0.59
0.093914481
73643
GH61 polysaccharide monooxygenase CEL61a
1.87
1.183973354
22197
GH1 ß-glucosidase CEL1b
-0.94
0.143325507
121735
GH3 -glucosidase CEL3b
0.94
0.019351069