TABLE 3.
Number of (A) upregulated and (B) downregulated differentially expressed genes in Lysobacter capsici AZ78 in response to diffusible communication signals.
| Class name | IND | LeDSF3 | GLY | BUT | 3HBA | 4HBA | AHL |
| (A) | |||||||
| Global metabolism | 42 | 34 | 21 | 17 | 2 | 4 | 1 |
| Carbohydrate metabolism | 17 | 24 | 8 | 4 | 2 | 2 | 0 |
| Energy metabolism | 9 | 17 | 7 | 6 | 6 | 2 | 2 |
| Lipid metabolism | 5 | 10 | 3 | 2 | 1 | 0 | 0 |
| Nucleotide metabolism | 8 | 11 | 2 | 1 | 1 | 0 | 0 |
| Amino acid metabolism | 25 | 29 | 10 | 7 | 5 | 3 | 0 |
| Protein metabolism | 10 | 15 | 10 | 8 | 3 | 1 | 0 |
| Secondary metabolism | 19 | 8 | 3 | 4 | 2 | 1 | 1 |
| DNA metabolism | 6 | 7 | 3 | 1 | 4 | 0 | 0 |
| RNA transcription and degradation | 37 | 20 | 14 | 14 | 1 | 2 | 4 |
| Translation | 14 | 21 | 5 | 2 | 5 | 2 | 0 |
| Growth | 28 | 20 | 9 | 10 | 2 | 3 | 1 |
| Oxidative stress | 5 | 3 | 1 | 0 | 1 | 0 | 0 |
| Antagonistic activity | 9 | 10 | 5 | 3 | 3 | 1 | 1 |
| Defense | 13 | 13 | 5 | 3 | 2 | 7 | 7 |
| Transport, phosphotransferase systems, and secretion | 35 | 48 | 14 | 11 | 10 | 4 | 7 |
| Signal transduction and receptors | 6 | 7 | 3 | 4 | 1 | 1 | 1 |
| Kinase/phosphatase | 10 | 8 | 5 | 4 | 0 | 0 | 0 |
| Quorum sensing | 1 | 0 | 0 | 0 | 0 | 0 | 1 |
| Motility, chemotaxis, and biofilm | 5 | 11 | 4 | 5 | 1 | 0 | 0 |
| Unknown | 76 | 62 | 54 | 42 | 15 | 17 | 3 |
| (B) | |||||||
| Global metabolism | 12 | 17 | 2 | 7 | 5 | 2 | 0 |
| Carbohydrate metabolism | 2 | 5 | 3 | 0 | 1 | 0 | 0 |
| Energy metabolism | 12 | 9 | 7 | 7 | 0 | 0 | 0 |
| Lipid metabolism | 5 | 3 | 1 | 0 | 0 | 0 | 0 |
| Nucleotide metabolism | 1 | 4 | 1 | 0 | 0 | 0 | 0 |
| Amino acid metabolism | 3 | 5 | 0 | 2 | 0 | 0 | 0 |
| Protein metabolism | 3 | 5 | 1 | 3 | 2 | 0 | 0 |
| Secondary metabolism | 1 | 6 | 1 | 0 | 0 | 0 | 0 |
| DNA metabolism | 21 | 23 | 11 | 11 | 1 | 1 | 1 |
| RNA transcription and degradation | 4 | 15 | 3 | 3 | 1 | 1 | 0 |
| Translation | 13 | 14 | 18 | 10 | 2 | 0 | 1 |
| Growth | 12 | 14 | 6 | 4 | 3 | 0 | 0 |
| Oxidative stress | 1 | 4 | 1 | 0 | 1 | 0 | 0 |
| Antagonistic activity | 25 | 15 | 5 | 8 | 1 | 0 | 0 |
| Defense | 9 | 9 | 5 | 4 | 5 | 0 | 0 |
| Transport, phosphotransferase systems, and secretion | 20 | 20 | 5 | 4 | 6 | 3 | 0 |
| Signal transduction and receptors | 3 | 2 | 1 | 2 | 0 | 0 | 0 |
| Kinase/phosphatase | 2 | 3 | 2 | 0 | 0 | 0 | 0 |
| Quorum sensing | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Motility, chemotaxis, and biofilm | 7 | 0 | 0 | 0 | 1 | 0 | 0 |
| Unknown | 81 | 100 | 35 | 29 | 13 | 3 | 2 |
LeDSF3, 13-methyltetradecanoic acid 50 μM; IND, indole 500 μM; GLY, glyoxylic acid 0.01 μM; BUT, 2,3-butanedione 0.01 μM; 3HBA, 3-hydroxybenzoic acid 30 μM; 4HBA, 4-hydroxybenzoic acid 50 μM; AHL, mix of N-acyl-homoserine lactones 20 μM.