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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.