Table 2.
List of the genes located in the GlnR-binding regions detected by ChIP-on-Chip
| Genes | Product |
|---|---|
| Common genes to GlnR and TnrA regulons | |
| glnR | Nitrogen sensing transcriptional regulator |
| tnrA | Nitrogen sensing transcriptional regulator |
| ureA | Urease |
| Genes in the TnrA primary regulon | |
| alsT* | Putative amino acid carrier protein; unknown |
| amtB* | Ammonium transporter |
| dtpT | Peptide transporter |
| nasA | Nitrate reductase |
| nasD | Assimilatory nitrite reductase subunit |
| oppA | Oligopeptide ABC transporter |
| pucI* | Allantoin permease |
| pucJ | Uric acid permease |
| pucR* | Transcriptional regulator of the purine degradation operon |
| ycsF | Putative nitrogen-containing heterocycle degradation enzyme |
| ycsI | Conserved hypothetical protein |
| yoyD | Putative exported protein |
| ysnD | Spore coat protein |
| yxkC | Unknown |
| yycC | Conserved hypothetical protein |
| Genes in the TnrA secondary regulon | |
| braB* | Branched-chain amino acid-Na+ symporter |
| codV* | Site-specific tyrosine recombinase |
| Genes containing a putative GlnR/TnrA box motif | |
| bceA* | Bacitracin ABC efflux transporter (ATP-binding protein) |
| yjcN* | Unknown |
| yraH* | Putative lyase |
| Other genes located in GlnR-binding regions | |
| bdhA | Acetoin reductase/2,3-butanediol dehydrogenase |
| cotY;cotX | Spore coat protein; spore coat protein |
| dhbF | Iderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester bacillibactin synthetase |
| gpsA | NAD(P)H-dependent glycerol-3-phosphate dehydrogenase |
| hmp | Flavohemoglobin |
| lysC | Aspartokinase II alpha and beta subunit |
| mmsA;iolR | Methylmalonate-semialdehyde dehydrogenase; transcriptional repressor |
| mntH | Manganese transporter |
| mutM | Formamidopyrimidine-DNA glycosidase |
| parA;yyaB | Chromosome partitioning protein; putative membrane protein |
| pksL | Polyketide synthase of type I |
| ppsA | Plipastatin synthetase |
| proS | Prolyl-tRNA synthetase |
| pucE | Xanthine dehydrogenase, iron-sulfur subunit |
| rghR | Transcriptional repressor in sporulation initiation |
| ylyB | Similar to pseudouridylate synthase |
| rocA | Delta-1-pyrroline-5 carboxylate dehydrogenase |
| rok | Transcriptional repressor of genetic competence |
| rasP | Control of cell division, and SigV and SigW activity |
| sinR | Transcriptional regulator for post-exponential-phase response |
| speE;speB | Spermidine synthase; polyamine metabolism; agmatinase |
| tyrS | Tyrosyl-tRNA synthetase |
| xlyB | N-acetylmuramoyl-l-alanine amidase; bacteriophage PBSX protein |
| ybxG | Putative amino acid permease |
| ycxD | Putative transcriptional regulator |
| yddJ | Putative lipoprotein |
| yddM | Putative helicase |
| yerO | Putative transcriptional regulator |
| yhdP | Potential magnesium efflux pump |
| yisK | Putative catabolic enzyme |
| yknU | Putative ABC transporter (ATP-binding protein) |
| ykoH | Two-component sensor histidine kinase [YkoG] |
| yktD | Conserved hypothetical protein |
| yobI | Putative NTPase with transmembrane helices |
| yobU | Putative effector of transcriptional regulator |
| yopQ | Conserved hypothetical protein; phage Spbeta |
| ypqP | C-terminal part of the split gene spsM |
| yrkK | Putative integral inner membrane protein |
In the ChIP-on-Chip experiments, 61 regions were detected as GlnR-binding targets. The GlnR-binding sites located near genes belonging to the GlnR and TnrA regulons are indicated. The asterisks indicate genes whose expression has been compared in the wild-type strain and in the ΔglnR mutant in this study