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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.
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Biotechnology for Biofuels and Bioproducts

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