TABLE 2.
Functional classification of genes or operons differentially regulated by (p)ppGpp or DksA in H. ducreyi
| Functional category | No. of genes differentially expressed |
|||
|---|---|---|---|---|
| 35000HPΔrelAΔspoT/35000HPa |
35000HPΔdksA/35000HPb |
|||
| Upregulated | Downregulated | Upregulated | Downregulated | |
| Amino acid biosynthesis | 2 | 4 | 5 | 1 |
| Amino acid transport and metabolism | 6 | 6 | 5 | 2 |
| Amino sugar and nucleotide metabolism | 4 | 12 | 2 | 7 |
| Cellular carbohydrate biosynthetic process | 7 | 5 | 3 | 1 |
| Carbohydrate metabolism | 1 | 2 | 3 | 0 |
| Cell division | 2 | 5 | 1 | 2 |
| Cell membrane | 11 | 15 | 9 | 7 |
| Cellular homeostasis | 4 | 2 | 2 | 1 |
| Cellular response to stress | 0 | 2 | 3 | 0 |
| DNA binding | 3 | 1 | 4 | 2 |
| DNA metabolic process | 8 | 4 | 8 | 1 |
| Fatty acid biosynthesis and metabolism | 7 | 3 | 4 | 2 |
| Intracellular trafficking and secretion | 1 | 11 | 1 | 5 |
| Ion transport | 3 | 7 | 2 | 4 |
| Iron sulfur cluster binding | 2 | 6 | 0 | 3 |
| Lipid biosynthesis and metabolism | 3 | 4 | 5 | 2 |
| Metal ion binding | 10 | 8 | 7 | 5 |
| Nucleotide binding | 8 | 19 | 4 | 11 |
| Protein fate | 7 | 9 | 5 | 5 |
| RNA binding | 4 | 0 | 1 | 0 |
| RNA processing | 9 | 8 | 5 | 3 |
| Transcription | 10 | 9 | 2 | 3 |
| Translation | 15 | 27 | 12 | 6 |
| Transport of proteins and carbohydrates | 7 | 11 | 2 | 6 |
| Uncharacterized conserved protein | 6 | 10 | 7 | 1 |
| Hypothetical proteins | 75 | 89 | 30 | 92 |
a
Genes differentially expressed in 35000HPΔrelAΔspoT mutant versus 35000HP strain at stationary phase. Fifty-two percent of the genes were downregulated genes, and 48% were upregulated genes.
b
Genes differentially expressed in 35000HPΔdksA mutant versus 35000HP strain at stationary phase. Sixty-two percent of the genes were downregulated genes, and 38% were upregulated genes.