Table 1 Number of genes and proteins in COG classes up- and down-regulateda on various substrates compared to cellobiose
COG class | Description | Xylose vs cellobiose genes | Xylose vs cellobiose proteins | Xylose vs cellobiose (overlap of genes and proteins) | α-cellulose vs cellobiose genes | α-cellulose vs cellobiose proteins | α-cellulose vs cellobiose (overlap of genes and proteins) | Xylan vs cellobiose genes | Xylan vs cellobiose proteins | Xylan vs cellobiose (overlap of genes and proteins) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Down | Up | Down | Up | Down | Up | Down | Up | Down | Up | Down | Up | Down | Up | Down | Up | Down | Up | ||
C | Energy production and conversion | 3 | 1 | 1 | 2 | 1 | 3 | 1 | 2 | 2 | 3 | 1 | 2 | 0 | 1 | 1 | |||
D | Cell cycle control, cell division, chromosome partitioning | 2 | 0 | 1 | 2 | ||||||||||||||
E | Amino acid transport and metabolism | 8 | 14 | 2 | 4 | 1 | 4 | 4 | 8 | 0 | 3 | 1 | 1 | 4 | 0 | 2 | 0 | 2 | 1 |
F | Nucleotide transport and metabolism | 0 | 2 | ||||||||||||||||
G | Carbohydrate transport and metabolism | 11 | 32 | 3 | 23 | 7 | 27 | 5 | 28 | 3 | 20 | 1 | 33 | 7 | 40 | 5 | 24 | 7 | 40 |
H | Coenzyme transport and metabolism | 4 | 3 | 1 | 6 | 0 | 2 | 3 | 2 | 0 | 1 | 3 | |||||||
I | Lipid transport and metabolism | 7 | 1 | 2 | 0 | 1 | 1 | 3 | 1 | 2 | 1 | 1 | 4 | 0 | 4 | 0 | 3 | ||
J | Translation, ribosomal structure and biogenesis | 4 | 1 | 1 | |||||||||||||||
K | Transcription | 6 | 1 | 1 | 4 | 4 | 6 | 1 | 3 | 1 | 2 | 1 | 2 | 3 | 1 | 1 | 1 | ||
L | Replication, recombination and repair | 3 | 1 | 1 | |||||||||||||||
M | Cell wall/membrane/envelope biogenesis | 3 | 1 | 1 | 15 | 1 | 9 | 1 | 4 | 1 | 2 | ||||||||
N | Cell motility | 3 | 1 | 2 | 1 | 1 | |||||||||||||
O | Posttranslational modification, protein turnover, chaperones | 2 | 1 | 3 | 4 | 2 | 5 | 1 | 4 | ||||||||||
P | Inorganic ion transport and metabolism | 2 | 4 | 2 | 1 | 1 | 1 | 4 | 1 | 1 | 2 | 0 | |||||||
Q | Secondary metabolites biosynthesis, transport and catabolism | 19 | 1 | 6 | 0 | 5 | 1 | 7 | 2 | 0 | 1 | 1 | 15 | 0 | 7 | 0 | 5 | 2 | |
R | General function prediction only | 6 | 9 | 3 | 2 | 1 | 3 | 3 | 17 | 1 | 4 | 1 | 5 | 2 | 7 | 3 | 2 | 2 | 6 |
S | Function unknown | 6 | 0 | 0 | 3 | 1 | 11 | 3 | 4 | 2 | 1 | 3 | 0 | ||||||
T | Signal transduction mechanisms | 2 | 5 | 2 | 3 | 4 | 3 | 1 | 1 | 1 | 0 | 3 | 1 | ||||||
U | Intracellular trafficking, secretion, and vesicular transport | 2 | 0 | 2 | 0 | ||||||||||||||
V | Defense mechanisms | 2 | 3 | 2 | 0 | 1 | |||||||||||||
TOTAL | 86 | 74 | 18 | 33 | 17 | 42 | 38 | 122 | 28 | 56 | 14 | 59 | 43 | 56 | 29 | 27 | 22 | 55 | |