TABLE 3

Genes downregulated in the σ54 mutant compared to the H111 wild-type strain (DESeq P < 0.12) and harboring σ54 binding sites in their promoter regions

Locus IDaOrtholog in J2315bDescriptioncGene nameFold change in expression
σ54 mutant vs wtdComplemented σ54 mutant vs wte
I35_0068BCAL0066Ethanolamine operon regulatory protein0.0081.4
I35_0764BCAL3109Urease accessory protein UreGureG0.050.6
I35_0765BCAL3108Urease accessory protein UreFureF0.020.8
I35_0766BCAL3107Urease accessory protein UreEureE0.021.1
I35_0767BCAL3106Urease alpha subunitureC0.031.2
I35_0768BCAL3105Urease beta subunitureBNA3.0
I35_0769BCAL3104Urease gamma subunitureA0.071.6
I35_0770BCAL3103Urease accessory protein UreDureD0.030.7
I35_0771BCAL3102Urea ABC transporter, ATPase proteinurtE0.021.1
I35_0772BCAL3101Urea ABC transporter, ATPase proteinurtD0.030.7
I35_0773BCAL3100Urea ABC transporter, permease proteinurtC0.070.6
I35_0774BCAL3099Urea ABC transporter, permease proteinurtB0.020.9
I35_0775BCAL3098Urea ABC transporter, urea binding protein0.021.3
I35_1214BCAL1319Nitrite transporter0.121.1
I35_1215BCAL1320Regulator of cell morphogenesis and NO signalingNA1.2
I35_1420BCAL1523PE_PGRS family protein0.050.5
I35_1421BCAL1524PE_PGRS family protein0.020.3
I35_1734BCAL1818Zn-dependent hydrolases, including glyoxylases0.041.0
I35_1735BCAL1819Oxidoreductase (flavoprotein)0.0050.7
I35_1736Oxidoreductase (flavoprotein)0.0020.5
I35_2149BCAL2222Nitrogen regulation protein NR(I)ntrC0.091.0
I35_2150BCAL2223Nitrogen regulation protein NR(II)ntrB0.071.3
I35_2151BCAL2224Glutamine synthetase type IglnA0.102.0
I35_2727BCAL0940Membrane carboxypeptidase0.160.8
I35_2935BCAL0730Ammonium transporteramtB0.021.3
I35_4051BCAM0050aHypothetical protein0.101.4
I35_4450BCAM0555Alkanesulfonate-binding proteinNA1.2
I35_4452BCAM0557Alkanesulfonate monooxygenase0.042.3
I35_4669BCAM0770Hypothetical protein0.024.2
I35_4672BCAM0774Poly-beta-hydroxyalkanoate depolymerase0.0040.7
I35_5080BCAM1233Protein containing DUF404 and DUF407 domains0.011.7
I35_5081BCAM1234Protein containing DUF403 domain0.0041.0
I35_5082BCAM1235Protein containing transglutaminase-like domain0.0022.2
I35_5083BCAM1236Large protein containing transglutaminase-like domain0.010.9
I35_5084BCAM1237Protein containing DUF404, DUF407, and DUF403 domains0.110.8
I35_5085BCAM1238Protein containing transglutaminase-like domain0.120.6
I35_5335BCAM1481Hypothetical proteinNA0.1
I35_5545BCAM1683Assimilatory nitrate reductase large subunit0.013.9
I35_5546BCAM1684Nitrite reductase [NAD(P)H] small subunitNA4.4
I35_5547BCAM1685Nitrite reductase [NAD(P)H] large subunitnirB0.045.2
I35_5548BCAM1686Nitrate/nitrite transporter0.014.1
I35_5874BCAM2039Two-component response regulator0.020.3
I35_6218BCAM2327Transcriptional regulator0.041.3
I35_7023BCAS0024Transcriptional regulator GabR of GABA utilization0.081.6
I35_7622d-Glycero-d-manno-heptose 1,7-bisphosphate phosphatase0.071.3
I35_7626Conserved domain protein0.061.6
  • a Nomenclature is given according to data in GenBank (accession no. HG938370, HG938371, and HG938372).

  • b Orthologs were identified as described in Materials and Methods.

  • c According to EggNOG classification.

  • d Fold change in transcript expression for comparison of the σ54 mutant and the wild type (wt) grown under nitrogen-limited conditions. NA, not applicable because the read number for the mutant strain was 0.

  • e Fold change in transcript expression for comparison of the complemented σ54 mutant and the wild type (wt) grown under nitrogen-limited conditions.