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Table 4 Differential expression of secretory pathway genes.

From: Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway

ORF

gene name

homologous protein in S. cerevisiae

fold difference maltose/xylose

p

FDR

Translocation to ER:

An07g05800

 

SRP14 (YDL092w) – signal recognition particle SU

1.3

1.7·10-4

4.9·10-3

An15g06470*

 

signal sequence receptor, αSU ( Botryotinia fuckeliana )

1.7

1.6·10-5

1.1·10-3

An03g04340

 

SEC61 (YLR378c) – SEC61 complex SU

1.7

2.1·10-5

1.2·10-3

An01g11630*

 

SSS1 (YDR086c) – SEC61 complex SU

1.5

1.1·10-3

1.8·10-2

An01g13070*

 

SEC63 (YOR254c) – SEC63 complex SU

1.6

6.9·10-5

2.7·10-3

An02g01510

 

SEC62 (YPL094c) – SEC63 complex SU

1.7

1.5·10-3

2.3·10-2

An16g08830*

 

SEC66 (YBR171w) – SEC63 complex SU

1.8

3.5·10-4

8.3·10-3

Cleavage of signal sequence:

An16g07390

 

SPC2 (YML055w) – signal peptidase complex SU

1.7

2.5·10-5

1.4·10-3

An09g05420**

 

SPC3 (YLR066w) – signal peptidase complex SU

1.7

2.1·10-5

1.2·10-3

An01g00560*

 

SEC11 (YIR022w) – signal peptidase complex SU

1.7

1.7·10-3

2.5·10-2

Glycosylation:

An16g04330

 

DPM1 (YPR183w) – dolichol phosphate mannose synthase

1.6

2.3·10-5

1.3·10-3

An14g00270

 

dolichyl-phosphate mannosyltransferase (B. fuckeliana)

1.4

7.5·10-4

1.4·10-2

An03g04410**

 

ALG5 (YPL227c) – dolichyl-phosphate glucosyltransferase

1.6

2.8·10-4

7.2·10-3

An02g03240*

 

ALG7 (YBR243c) – N-acetyl-glucosaminephosphotransferase

1.7

2.2·10-4

6.0·10-3

An14g05910*

 

ALG2 (YGL065c) – mannosyltransferase

1.9

1.3·10-3

2.1·10-2

An04g03130

 

mannose-phosphate-dolichol utilization protein (Mus musculus)

1.6

2.1·10-4

5.7·10-3

An08g07020

 

ALG9 (YNL219c) – mannosyltransferase

1.4

4.2·10-3

4.6·10-2

An02g12630

 

ALG6 (YOR002w) – glucosyltransferase

1.3

1.7·10-3

2.5·10-2

An02g14940*

 

RFT1 (YBL020w) – flippase

1.5

7.6·10-5

2.8·10-3

An02g14560*

 

OST1 (YJL002c) – oligosaccharyltransferase complex, αSU

1.7

1.7·10-4

5.0·10-3

An07g04190*

 

WBP1 (YEL002c) – oligosaccharyltransferase complex, βSU

1.7

1.2·10-4

3.8·10-3

An18g03920*

 

OST2 (YOR103c) – oligosaccharyltransferase complex, εSU

1.5

1.4·10-4

4.4·10-3

An02g14930

 

OST3 (YOR085w) – oligosaccharyltransferase complex, γSU

1.5

9.7·10-5

3.4·10-3

An16g08570

 

STT3 (YGL022w) – oligosaccharyltransferase complex, SU

1.7

4.1·10-5

1.9·10-3

An04g06990

 

MNS1 (YJR131w) – class I α-mannosidase

1.3

2.0·10-3

2.8·10-2

An06g01510

 

class I α-mannosidase (Aspergillus fumigatus)

1.7

2.1·10-4

5.7·10-3

An12g00340

 

ER glucosyl hydrolase, Edem (A. fumigatus)

1.4

1.0·10-3

1.7·10-2

An07g04940

 

HOC1 (YJR075w) – α-1,6-mannosyltransferase

1.5

1.9·10-5

1.2·10-3

An16g08490

 

PMT4 (YJR143c) – O -mannosyltransferase

1.3

1.5·10-4

4.7·10-3

An15g04810

 

MNT2 (YGL257c) – α-1,3-mannosyltransferase

0.7

1.4·10-3

2.2·10-2

An08g04450

 

GDA1 (YEL024w) – guanosine diphosphatase

1.3

7.7·10-4

1.4·10-2

Folding:

An02g14800**

pdiA

PDI1 (YCL043c) – protein disulfide isomerase

1.8

1.1·10-5

3.6·10-3

An02g05890

epsA

thioredoxin domain protein, TXNDC5 (Homo sapiens)

1.3

1.3·10-3

2.1·10-2

An18g02020*

tigA

protein disulfide isomerase

1.6

2.3·10-4

6.1·10-3

An01g04600**

prpA

MPD1 (YOR288c) – protein disulfide isomerase

1.9

6.0·10-4

1.2·10-2

An16g07620**

 

ERO1 (YML130c) – thiol oxidase

1.5

3.1·10-3

2.1·10-2

An18g04260**

 

HUT1 (YPL244c) – UDP-galactose transporter

1.6

1.5·10-4

4.6·10-3

An08g07810

 

FAD1 (YDL045c) – FAD synthase

1.3

1.3·10-3

2.1·10-2

An11g04180**

bipA

KAR2 (YJL034w) – ER chaperone

2.2

5.0·10-5

2.2·10-3

An18g06470

 

ERJ5 (YFR041c) – ER located DNA-J protein

1.5

3.4·10-4

8.2·10-3

An01g13220**

 

LHS1 (YKL073w) – ER lumen Hsp70 chaperone

1.9

2.8·10-4

7.1·10-3

An01g06670

 

FPR2 (YDR519w) – peptidyl-prolyl isomerase

1.7

1.9·10-3

2.7·10-2

Trimming and quality control of N-glycosylated folded proteins:

An15g01420*

 

CWH41 (YGL027c) – alpha glucosidase I

1.7

3.3·10-6

3.8·10-4

An09g05880

 

ROT2 (YBR229c) – glucosidase II, αSU

1.5

1.1·10-5

8.5·10-4

An13g00620*

 

GTB1 (YDR221w) – glucosidase II, βSU

1.7

2.6·10-5

1.4·10-3

An01g08420**

clxA

CNE1 (YAL058w) – calnexin

2.3

6.5·10-6

5.8·10-4

Vesicular transport of proteins between ER and Golgi:

An04g00360

 

SEC13 (YLR208w) – COPII complex SU

1.4

2.2·10-5

1.3·10-3

An02g01690

 

SEC31 (YDL195w) – COPII complex SU

1.6

2.7·10-4

7.0·10-3

An08g10650

 

SEC24 (YIL109c) – COPII complex SU

1.5

1.6·10-3

2.3·10-2

An01g04730

 

SEC23 (YPR181c) – COPII complex SU

1.6

1.4·10-4

4.3·10-3

An08g03590

 

EMP24 (YGL200c) – COPII vesicle membrane component

1.4

2.8·10-3

3.4·10-2

An04g01780

 

ERP1 (YAR002c-a) – COPII vesicle component

1.5

1.3·10-3

2.1·10-2

An09g05490

 

ERP3 (YDL018c) – p24 family protein

1.5

1.3·10-4

4.1·10-3

An04g08830

 

EMP47 (YFL048c) – COPII vesicle membrane component

1.4

1.2·10-5

8.9·10-4

An08g03960

 

ERV29 (YGR284c) – glycoprotein cargo receptor

1.5

2.1·10-5

1.2·10-3

An02g04250*

 

vesicular integral-membrane protein ( Pyrenophora tritici-repentis )

1.6

7.6·10-5

2.8·10-3

An07g09960

 

BET1 (YIL004c) – v-SNARE

1.3

5.0·10-3

5.1·10-2

An07g02170

 

BOS1 (YLR078c) – v-SNARE

1.4

1.8·10-3

2.6·10-2

An08g06780*

 

USO1 (YDL058w) – SNARE complex assembly protein

1.8

2.2·10-4

6.0·10-3

An02g06870

 

RAD50-interacting protein 1 (M. musculus)

1.2

2.3·10-3

3.0·10-2

An04g01990

 

centromere protein ZW10 (Gallus gallus)

1.3

1.1·10-3

1.8·10-2

An04g08690

 

GSG1 (YDR108w) – TRAPP complex SU

1.3

4.9·10-3

5.0·10-2

An04g06090

 

BET4 (YJL031c) – geranylgeranyltransferase, α SU

1.5

8.1·10-6

6.8·10-4

An03g04940**

 

ERV41 (YML067c) – involved in COPII vesicle fusion

2.1

1.2·10-5

9.0·10-4

An01g04320*

 

ERV46 (YAL042w) – involved in COPII vesicle fusion

1.8

1.7·10-5

1.1·10-3

An08g00290

 

RUD3 (YOR216c) – Golgi-matrix protein

1.4

2.8·10-5

1.5·10-3

An08g03690

 

ARF2 (YDL137w) – ADP-ribosylation factor

1.3

1.8·10-5

1.1·10-3

An07g02190

 

SEC7 (YDR170c) – guanine nucleotide exchange factor

1.3

2.7·10-3

3.4·10-2

An18g02490

 

GEA2 (YEL022w) – guanine nucleotide exchange factor on ARF

1.3

6.8·10-4

1.3·10-2

An16g02460

 

COP1 (YDL145c) – COPI complex, α SU

1.4

3.5·10-5

1.7·10-3

An07g06030

 

SEC21 (YNL287w) – COPI complex, γ SU

1.4

2.9·10-5

1.5·10-3

An08g06330

 

SEC28 (YIL076w) – COPI complex, ε SU

1.5

3.2·10-5

1.6·10-3

An08g03270

 

SEC26 (YDR238c) – COPI complex, β SU

1.4

1.8·10-4

5.3·10-3

An02g05870

 

SEC27 (YGL137w) – COPI complex, β ' SU

1.5

5.4·10-4

1.1·10-2

An02g02830

 

RER1 (YCL001w) – retention of ER membrane proteins

1.3

1.1·10-4

3.8·10-3

An04g05250*

 

RER2 (YBR002c) – retention of ER membrane proteins

1.2

3.7·10-3

4.2·10-2

An07g07340

 

ERD2 (YBL040c) – ER retention HDEL-receptor

1.4

1.1·10-4

3.8·10-3

Other processes in the secretory pathway:

An11g02650

 

AGE2 (YIL044c) – ARF GTPase activating protein effector

1.1

3.6·10-3

4.0·10-2

An16g03590

 

SEC14 (YMR079w) – phosphatidylinositol/-choline transfer protein

1.2

3.3·10-3

3.8·10-2

An04g02070

 

CHC1 (YGL206c) – clathrin, heavy chain

1.2

2.7·10-3

3.4·10-2

An16g02490

 

APL2 (YKL135c) – β-adaptin

1.5

3.3·10-3

3.8·10-2

An16g03010

 

VPS4 (YPR173c) – vacuolar protein sorting AAA-ATPase

0.8

3.1·10-3

3.7·10-2

An02g05380

 

VPS33 (YLR396c) – vacuolar protein sorting

1.3

2.5·10-4

6.5·10-3

An14g05130

 

VPS16 (YPL045w) – vacuolar protein sorting

0.8

4.0·10-3

4.4·10-2

An01g02910

 

VPS52 (YDR484w) – vacuolar protein sorting

1.4

4.2·10-3

4.6·10-2

An02g11720

 

AMS1 (YGL156w) – vacuolar α-mannosidase

0.8

2.3·10-3

3.0·10-2

An06g01200

 

EMP70 (YLR083c) – conserved endosomal membrane protein

1.3

3.2·10-4

7.8·10-3

An03g06900

 

SEC10 (YLR166c) – exocyst complex SU

1.2

3.5·10-4

8.3·10-3

An02g04030

 

EXO70 (YJL085w) – exocyst complex SU

1.3

3.7·10-3

4.1·10-2

An01g11960

 

BFR1 (YOR198c) – component of mRNP complex

1.4

2.3·10-4

6.1·10-3

An04g01950

 

STE24 (YJR117w) – zinc metalloprotease

1.3

2.7·10-4

6.9·10-3

An07g10050

 

microtubule binding protein HOOK3 (A. fumigatus)

1.2

2.7·10-3

3.4·10-2

Protein misfolding (UPR and ER associated degradation):

An08g01480

 

TRL1 (YJL087c) – tRNA ligase

0.7

1.1·10-4

3.7·10-3

An01g07900

cpcA

GCN4 (YEL009c) – bZIP transcription factor

0.8

2.6·10-3

3.3·10-2

An11g11250*

 

protein kinase inhibitor p58 ( Rattus norvegicus )

1.6

4.7·10-5

2.1·10-3

An01g08980

 

ORM1 (YGR038w) – conserved ER protein

0.7

3.8·10-4

8.8·10-3

An15g00640

 

DER1 (YBR201w) – involved in ER associated protein degradation

1.4

2.2·10-3

3.0·10-2

An16g07970

 

HRD1 (YOL013c) – ubiquitin-protein ligase

1.3

8.3·10-4

1.5·10-2

An01g12720

 

HRD3 (YLR207w) – ubiquitin-protein ligase

1.6

6.4·10-5

2.5·10-3

An09g06110

 

UBC7 (YMR022w) – ubiquitin conjugating enzyme

1.2

3.0·10-3

3.6·10-2

An04g01720

 

HLJ1 (YMR161w) – DnaJ co-chaperone

1.3

2.6·10-4

6.8·10-3

  1. ORF = identifier for open reading frame in A. niger CBS513.88 genome sequence [3]; gene name in A. niger; protein encoded by ORF-homolog in S. cerevisiae and yeast protein function if available; fold difference reflects ratio of normalized transcript levels on maltose compared to xylose (maltose/xylose); significance of each observation is given by p-value (p) and the Benjamini-Hochberg false discovery rate (FDR).
  2. Bold indicates observations with very high significance (FDR ≤ 0.005).
  3. * and ** denote genes with increased transcription during ER-stress with 2/3 or 3/3 types of protein folding stress [15], repectively.
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BMC Genomics

ISSN: 1471-2164

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