Table 2.
Putative FabR targets identified using ChIP-chip
| Gene IDa | Namea | Possible FabR Targetb | Functiona | Functional Classb |
|---|---|---|---|---|
| STM1100 | hpaR (<) | IR hpaR-hpaG | 4-Hydroxyphenylacetate catabolism | 1 |
| STM1101 | hpaG (>) | 4-Hydroxyphenylacetate catabolism | 1 | |
| STM1336 | rplT (>) | P pheS | 50S ribosomal protein L20 | 2 |
| STM1337 | pheS (>) | Phenylalanyl-tRNA synthetase subunit alpha | 3 | |
| STM2378 | fabB (<) | IR fabB-STM2379 | 3-Oxoacyl-(acyl carrier protein) synthase I | 4 |
| STM2379 | STM2379 (>) | 5-Methylaminomethyl-2-thiouridine methyltransferase | 5 | |
| STM2401 | ddg (>) | DR ddg-yfdZ | Lipid A biosynthesis palmitoleoyl acyltransferase | 6 |
| STM2402 | yfdZ (<) | Aminotransferase | 7 | |
| STM2415 | gltX (<) | IR gltX-valU | Glutamyl-tRNA synthetase | 3 |
| STM2416 | valU (>) | tRNA | 3 | |
| STM2615 | STM2615 (<) | P STM2615 | tRNA | 3 |
| STM2616 | STM2616 (<) | Antirepressor-like protein | 8 | |
| STM2616 | STM2616 (<) | P STM2616 | Antirepressor-like protein | 8 |
| STM2617 | STM2617 (<) | Antiterminator-like protein | 8 | |
| STM2989 | metZ (>) | P metW | tRNA | 3 |
| STM2990 | metW (>) | tRNA | 3 | |
| STM3049 | yqfA (<) | P yqfA | Putative hemolysin | 6 |
| STM3050 | yqfB (<) | Hypothetical protein | 5 | |
| STM3289 | metY (<) | IR metY-argG | tRNA | 3 |
| STM3290.S | argG (>) | Argininosuccinate synthase | 7 | |
| STM4148 | nusG (>) | P rplK | Transcription antitermination protein | 8 |
| STM4149 | rplK (>) | 50S ribosomal protein L11 | 2 | |
| STM4150 | rplA (>) | P rplJ | 50S ribosomal protein L1 | 2 |
| STM4151 | rplJ (>) | 50S ribosomal protein L10 | 2 |
aSTM numbers, gene names, genomic orientation (< and > indicating minus and positive strand, respectively) and gene functions are taken from NCBI Refseq NC_003197 [86] and results are sorted according to their STM numbers
bThe mentioned genes belong to the following functional classes: (1) Carbon compound degradation, (2) Ribosomal protein synthesis and modification, (3) Aminoacyl tRNA metabolism, (4) Fatty acid metabolism, (5) Conserved hypothetical protein, (6) Membrane homeostasis, (7) Amino acid biosynthesis, (8) RNA synthesis, RNA modification and DNA transcription
bIR indicates that both genes are possible FabR targets since the FabR binding region was situated in the intergenic region between the two mentioned divergently transcribed genes and hence contains the (putative) promoters of both genes. P points at the (putative) promoter region of the mentioned gene since the intergenic region identified during the ChIP-chip analysis was situated between two genes transcribed in the same direction and hence only contains the (putative) promoter of this gene. DR indicates that probably none of the identified genes is a putative FabR target since both adjacent genes are convergently transcribed respective to the retained intergenic FabR binding region