Supplementary Material Trichoderma reesei CRE1 ...

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


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).



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


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


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


69081

mitochondrial cytochrome b2, putative

1.076654903

1.93E-15

Sophorose

up


68924

cyclopropane/fatty acid synthase; plant related

1.985506607

1.62E-57



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


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


70860

allantoate permease, 10 TM domains

1.924273535

1.46E-55

Sophorose

up


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


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



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


122416

NADH:flavin oxidoreductase/NADH oxidase

1.190855041

7.59E-21

Sophorose

up

#N/D

122422

SSCRP

1.900730056

1.42E-49

Sophorose

up


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


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


123293


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



vii


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


45445

tyrosinase

1.025984035

2.29E-06

Sophorose

up

#N/D

52476

unknown protein

2.483339586

1.05E-59

Sophorose

up


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


73924


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


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


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



Condition

Regulation

GO

Protein ID

Description

FC

p-value

Sophorose

up


81096

ferric reductase

1.575837578

1.59E-07

Sophorose

up

#N/D

81383

GPCR , contains RGS domain

1.598856647

3.77E-44

Sophorose

up


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


76672

GH3 ?-glucosidase BGL1/CEL3a

1.663342629

1.42E-08

Sophorose

up

ATP binding

76682


6.034239874

2.04E-05

Sophorose

up


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


5836

GH2 ?-mannosidase

2.486307762

1.04E-26

Sophorose

up

zinc ion binding

3449


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


1.015979202

4.99E-13

Sophorose

up

#N/D

109643

autophagy protein (Atg22), putative

1.187317237

3.16E-14



ix


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


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


41617

lae1

1.825223426

9.37E-34

Sophorose

up

zinc ion binding

26871


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


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


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



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


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


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


-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


68813

MFS permease

-1.464249503

1.48E-19

Sophorose

Down


68803

RTA1 like protein

-4.890884301

3.12E-82

Sophorose

Down

electron transport

68705


-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


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



xi


Condition

Regulation

GO

Protein ID

Description

FC

p-value

Sophorose

Down


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


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


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


-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


60890

L-galactose dehydrogenase (LGalDH), putative

-1.019291072

6.08E-06

Sophorose

Down


60987


-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


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



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


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


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


122505

aryl-alcohol dehydrogenase

-1.608339359

1.19E-25

Sophorose

Down


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


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



xiii


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


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


-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


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


-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


123946

dehydrogenase associated with cellulase signal transduction (PMID: 15288024)

-2.102745032

7.70E-22

Sophorose

Down


123979

peptide transporter MTD1

-1.925820071

4.28E-10

Sophorose

Down

zinc ion binding

120430


-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



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


-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


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


-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



xv


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


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


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


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


-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


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



Condition

Regulation

GO

Protein ID

Description

FC

p-value

Sophorose

Down


46936

2-deoxy-D-gluconate 3-dehydrogenase

-1.149111943

8.81E-14

Sophorose

Down


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


-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


73536

NADP-glutamate dehydrogenase

-1.690019971

5.80E-13

Sophorose

Down


73618

PKS

-3.525276562

3.41E-41

Sophorose

Down


73621

PKS

-4.030888199

3.29E-37

Sophorose

Down


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


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


74194

mannitol dehydrogenase LXR1

-1.903410877

3.96E-09

Sophorose

Down


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


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


79510


-1.239883859

1.12E-13



xvii


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


79738


-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


-1.502199969

3.14E-22

Sophorose

Down

ATP binding

80142

HSP104 and related ATP-dependent Clp proteases

-1.500261028

0.005343511

Sophorose

Down


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


80875

MFS permease

-1.197970446

0.000936272

Sophorose

Down

ATP binding

80973


-1.210745682

7.55E-17

Sophorose

Down


75105

unknown protein

-1.267735371

5.26E-15

Sophorose

Down

membrane

81082

aquaglyceroporin

-2.476881124

2.61E-47

Sophorose

Down


81102

unknown protein

-1.079560557

0.001277813

Sophorose

Down


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



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


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


76784

sorbitol dehydrogenase

-2.461679581

3.18E-34

Sophorose

Down


76852

GH2 ?-galactosidase/?-glucuronidase

-2.109783643

2.70E-22

Sophorose

Down


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


-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



xix


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


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


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


-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


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


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


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


111932

PutA delta-1-pyrroline-5-carboxylate dehydrogenase

-1.10958591

1.81E-15

xx Current Genomics, 2016, Vol. 17, No. 2



Condition

Regulation

GO

Protein ID

Description

FC

p-value

Sophorose

Down


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


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


106626

unknown protein, SWIFT domain

-2.30334091

5.25E-21

Sophorose

Down


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


27689

MFS permease

-1.07658044

1.36E-14

Sophorose

Down

#N/D

42848

unknown protein

-2.674429534

1.51E-83

Sophorose

Down


39535

mannitol-1-phosphate dehydrogenase

-1.103826646

1.25E-13

Sophorose

Down


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


31134

isoprenylcysteine carboxyl methyltransferase

-1.999437339

3.69E-38

Sophorose

Down


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


72321

subtilisin-like serine protease

-1.274371259

1.01E-15

Sophorose

Down


73119

unknown protein

-1.898316932

8.03E-42



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


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


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


Table S5. Transporter proteins used in the phylogenetic analysis. Organism

Access Portal

Identification

Description

Saccharomyces cerevisiae

Saccharomyces Genome Database

YHR094C

Hexose transporter



YHR092C

Hexose transporter



YDR343C

Hexose transporter

Neurospora crassa

Neurospora crassa Database

NCU00821

Sugar transporter

Neurospora crassa


NCU04963

Glucose transporter

Neurospora crassa


NCU08114

Cellodextrin transporter

Neurospora crassa


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


GenBank

EFY97396.1

MFS transporter


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



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


-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