Skip to main content

Table 1 Overview of the T. reesei transcriptome on wheat straw (W) and lactose (L)*

From: Comparative analysis of the Trichoderma reeseitranscriptome during growth on the cellulase inducing substrates wheat straw and lactose

    Wheat straw Lactose Wheat straw and lactose
      W > L L > W W = L
Transcript category    A B C D E
Gene category   FunCat      
All genes    1619 288 344 65 804
unknown genes    743 117 98 21 309
orphans    90 44 18 5 81
Metabolism   01      
  glycolysis 02.01 10   1   10
  PPP 02.07 1 2    1
  TCA cycle 02.10 4   2   5
  pentose catabolism NN** 1 1 1   2
  gluconeogenesis NN***    1 5  
  amino acids 01.01 17 8 6 3 15
  nucleotide 01.03 6   1 4  
  fatty acids 01.06.01 35 6 6 3 22
  phospholipids 01.06.03 15     6
  secondary metabolism 01.20 8 3    
Transport        
  MFS 20.01.03 28 7 28 3 46
  nitrogenous compounds 20.01.07, 20.01.09 4 5 2 3 8
  ions 20.01.01 6 1 1   5
  ABC transporters 20.03.25 4 2   1 4
  mitochondrial transport 20.09.04   1    1
  aquaporins 20.03.01    1   4
  iron transport and reduction 20.01.01.01 6   6   1
Transcription        
  transcription factors 11.02.03.04 98 16 18 3 57
  DNA 10.01 76   4   17
Cell cycle   10.03 13 2 2 1 9
Translation   12.04 7 1 1   1
Secretion   20.09.16 35 1 1   1
Signal transduction        
  G-protein signalling 30.01.05.05 6 1 4 3 9
  protein kinases/phosphatases 30.01.05 27 1 1   3
Extracellular products        
  SSCPs NN**** 39 6 12 1 18
  glycosyl transferases 14.07.02 5 1 2   1
Hydrolytic enzymes   01.25.01      
  CAZys   40 7 54 4 27
  proteases   26 6 8   8
  lipases   11 2 3 1 7
  nucleases   9   2 1  
  amidases and nitrilases   8 2 2   4
Oxidative enzymes   32.07      
  cytochrome P450 monooxygenases   11 1 5   12
  FAD-dependent monooxygenases   4   5   2
  dioxygenases   4 2 1   4
  multicopper oxidases   3   4   3
  peroxide/superoxide metabolism   7   1 1 4
  1. *Only genes that are at least 2-fold upregulated with respect to glucose (p < 0.05) are considered.
  2. **Not noted in FunCat; refers to enzymes involved in the fungal pentose catabolic pathway.
  3. ***FunCat combined gluconeogenesis and glycolysis; here we list genes specific only for gluconeogenesis (and which were consequently left out from glycolysis).
  4. ****Small secreted, cysteine-rich proteins; not listed in FunCat.