TABLE 1

Genes with statistically significantly increased expression under nitrogen starvation conditionse

ClassLocus IDaOrtholog in J2315bDescriptioncGene nameFold change in expression (S vs N)d
TranscriptProtein
Amino acid metabolism and transportI35_0052BCAL0049Aspartate aminotransferase33.816.2
I35_0053BCAL0051Lysine-arginine-ornithine-binding periplasmic protein10.813.1
I35_0117BCAL0110Aminotransferase, DegT family7.10.3
I35_0766BCAL3107Urease accessory proteinureENA6.7
I35_0767BCAL3106Urease alpha subunitureC14.825.1
I35_0770BCAL3103Urease accessory proteinureD23.52.2
I35_0771BCAL3102Urea ABC transporter, ATPase proteinurtE14.617
I35_0772BCAL3101Urea ABC transporter, ATPase proteinurtD12.77.1
I35_0773BCAL3100Urea ABC transporter, permease proteinurtC14.25.2
I35_0774BCAL3099Urea ABC transporter, permease proteinurtB9.116.8
I35_0775BCAL3098Urea ABC transporter, urea binding protein58.959.2
I35_1698BCAL1782ABC transporter, periplasmic proteinNAND
I35_2151BCAL2224Glutamine synthetase type IglnA6.62.9
I35_2936BCAL0729Nitrogen regulatory protein PIIglnB14.95.8
I35_5082BCAM1235Protein containing transglutaminase-like domain17.923
I35_5083BCAM1236Large protein containing transglutaminase-like domain8.362.9
I35_7738BCAS0575Putative amino acid ABC transporter, permease protein62.3ND
I35_7740BCAS0577ABC-type amino acid transport40.739.1
I35_7810AminopeptidaseypdF30.9ND
Carbohydrate metabolism and transportI35_4472BCAM0577Sialic acid transporternanT7.516
Cell motilityI35_0121BCAL0114Flagellar biosynthesis proteinfliC12.70.2
I35_0148BCAL0141Flagellar biosynthesis proteinflhA7.5ND
I35_3097BCAL0567Flagellar hook proteinflgE18.30.2
I35_3098BCAL0566Flagellar basal body rod modification proteinflgD13.7ND
I35_3100BCAL0564Flagellar basal body rod proteinflgB20.0ND
I35_3140BCAL0525Flagellar M-ring proteinfliF11.60.1
Cell wall, membrane, envelope biogenesisI35_0757BCAL3115Glycosyltransferase, family 2wbxA13.00.8
I35_1705BCAL1790Ferric siderophore transport proteintonB50.3ND
I35_3288BCAL3508CidA-associated membrane proteincidB11.4ND
I35_4182BCAM0184LectinbclB9.80.4
I35_4183BCAM0185LectinbclC14.9ND
I35_4184BCAM0186LectinbclA10.41.2
I35_4616BCAM0717Outer membrane protein (porin)16.53.2
I35_4767BCAM0854Mannose-1-phosphate guanylyltransferase (GDP)bceA51.625
I35_4768Undecaprenyl phosphate galactosephosphotransferasebceB31.02.5
I35_4769BCAM0855UDP-glucose dehydrogenasebceC248.513.1
I35_4771BCAM0858Polysaccharide export lipoproteinbceE64.113.1
I35_4772BCAM0859Tyrosine protein kinasebceF43.523.6
I35_4773BCAM0860Glycosyltransferase, family 2bceG19.53.8
I35_4774BCAM0861GlycosyltransferasebceH51.83.4
I35_4776BCAM0863GlycosyltransferasebceJ98.44
I35_4777BCAM0864GlycosyltransferasebceK40.217.4
I35_4778BCAM0865Permeases of the major facilitator superfamilybceL14.5ND
I35_4922BCAM1003Nucleoside-diphosphate-sugar epimerases10.91.2
I35_4923BCAM1004GDP-mannose 4,6-dehydratasegca106.24.7
I35_4924BCAM1005O-antigen acetylase45.9ND
I35_4927BCAM1008Glycosyltransferase24.68.3
I35_4928BCAM1009O-antigen acetylase33.4ND
I35_4929BCAM1010UTP–glucose-1-phosphate uridylyltransferasegtaB110.420.4
I35_4930BCAM1011O-antigen acetylase8.9ND
I35_4934BCAM1015Outer membrane protein (porin)9.01.5
I35_5089BCAM1241O-antigen acetylase29.7ND
I35_5188BCAM1338GlycosyltransferaseNA1.4
Coenzyme metabolismI35_5550BCAM1687Uroporphyrinogen-III methyltransferase106.42.8
I35_7268BCAS02532-Dehydropantoate 2-reductase14.52.2
Energy production and conversionI35_2136BCAL2207Putative dihydrolipoamide dehydrogenase8.22
I35_2138BCAL2209Pyruvate dehydrogenase E1 componentaceE13.52
I35_5545BCAM1683Assimilatory nitrate reductase large subunit7.21
I35_5547BCAM1685Nitrite reductase [NAD(P)H] large subunitnirB12.411.2
I35_5712BCAM1833Aconitate hydratase (EC 4.2.1.3)acnB16.71
I35_6014BCAM21322-Aminomuconate semialdehyde dehydrogenasenbaE21.2ND
I35_6214BCAM2323Putative FMN oxidoreductase68.0ND
I35_6432BCAM2532Malate-sodium symporter11.20.4
Inorganic ion transport and metabolismI35_2276BCAL2352Carbonic anhydrase38.01.5
I35_2277BCAL2353Sulfate permease50.82.6
I35_2935BCAL0730Ammonium transporter12.910.6
I35_5548BCAM1686Nitrate/nitrite transporter13.52.6
I35_6210BCAM2319Phenylpropionate dioxygenase12.61.6
I35_7455BCAS0413ABC-type nitrate/sulfonate/bicarbonate transporterNAND
Lipid metabolismI35_4672BCAM0774Poly-beta-hydroxyalkanoate depolymerase93.810.8
I35_5198BCAM1347Acyl carrier protein16.8ND
Nucleotide metabolism and transportI35_0014BCAL0012Adenylate cyclase15.61.3
I35_6180BCAM2289Purine nucleoside phosphorylase7.21
I35_7647Purine-cytosine permease and related proteinsNAND
Posttranslational modificationsI35_0690BCAL3171Molybdopterin insertion into xanthine dehydrogenasexdhC7.8ND
I35_4673BCAM0775Glutathione S-transferase86.78.8
I35_6232BCAM2339Putative protein; S-isoprenylcysteine methyltransferase9.4ND
Secondary structuresI35_2135BCAL2206Granule-associated proteinphaP48.11.6
I35_4023BCAM0023Acetoacetate decarboxylaseadc13.01.9
I35_4680BCAM0782Prolidase11.8ND
I35_4807BCAM0894Poly(3-hydroxybutyrate) depolymerase8.54
I35_6004BCAM2122Acetaldehyde dehydrogenaseNAND
Transcription and signal transductionI35_0200BCAL0209Histone acetyltransferase HPA215.3ND
I35_2150BCAL2223Nitrogen regulation proteinntrB7.94.3
I35_2608BCAL2749EAL domain protein7.73.2
I35_3013BCAL0652EAL domain protein15.616.5
I35_4015BCAM0015Hypothetical proteinNA1.4
I35_4612BCAM0714Heavy metal response transcriptional regulator10.91.3
I35_4613BCAM0715Signal transduction histidine kinase10.3ND
I35_4674BCAM0776Cyclic AMP-binding protein34.00.5
I35_4770BCAM0857Low-molecular-weight protein tyrosine phosphatase69.7ND
I35_5338BCAM1484Response regulator with CheY-like receiver domain10.9ND
I35_5551BCAM1688Response regulator NasT11.34.6
I35_6218BCAM2327AraC-type transcriptional regulator11.82.4
OtherI35_0759Hypothetical protein6.9ND
I35_1160BCAL1247Hypothetical protein12.50.7
I35_1483Hypothetical proteinNAND
I35_1518Hypothetical proteinNAND
I35_2235BCAL2308Hypothetical protein15.1ND
I35_3289BCAL3509Holin-like proteincidA259.5ND
I35_4096BCAM0087Hypothetical protein26.6ND
I35_4131BCAM0148Type VI secretion protein10.2ND
I35_4471BCAM0576Hypothetical protein8.81.4
I35_4614BCAM0716Hypothetical protein29.94.4
I35_4615Hypothetical protein9.1ND
I35_4617BCAM0718Hypothetical protein29.4ND
I35_4619BCAM0720Conserved integral membrane protein21.5ND
I35_4669BCAM0770Hypothetical protein214.11.7
I35_4765BCAM0852Hypothetical protein in rubrerythrin cluster8.7ND
I35_4766BCAM0853Transposase and inactivated derivatives26.98.3
I35_4775BCAM0862Unknown proteinbceI35.0ND
I35_4817Hypothetical protein9.6ND
I35_4862BCAM0942Hypothetical protein15.2ND
I35_4925BCAM1006Hypothetical protein10.83.3
I35_4926BCAM1007Protein involved in the export of O antigen and teichoic acid7.3ND
I35_5080BCAM1233Protein containing DUF404 and DUF407 domains10.412.9
I35_5081BCAM1234Protein containing DUF403 domain10.722.6
I35_5182BCAM1332Hypothetical protein17.8ND
I35_5345BCAM1491Hypothetical protein19.4ND
I35_5549Hypothetical protein460.0ND
I35_5753BCAM1927Membrane fusion protein18.6ND
I35_5959Choline dehydrogenaseNAND
I35_5976Paraquat-inducible protein BNAND
I35_5990BCAM2109Nonheme chloroperoxidase14.7ND
I35_6002BCAM2120Hypothetical proteinNAND
I35_6096BCAM2208Xanthine/uracil/thiamine/ascorbate permease family protein12.6ND
I35_6233BCAM23403-(3-Hydroxyalkanoyloxy)alkanoic acid synthaserhlA13.41.8
I35_6573BCAM2679Hypothetical protein9.4ND
I35_6578BCAM2684GCN5-related N-acetyltransferase13.6ND
I35_6579Hypothetical protein33.7ND
I35_6602BCAM2717Hypothetical protein8.7ND
I35_6638BCAM2752Putative secreted protein8.91.7
I35_7284BCAS0270Urea carboxylase-related aminomethyltransferase11.1ND
I35_7285BCAS0271Urea carboxylase-related aminomethyltransferase19.31
I35_7735BCAS0571Salicylate hydroxylase38.3ND
I35_7736BCAS0573Hypothetical proteinNAND
I35_7814FAD/FMN-containing dehydrogenasesNAND
  • a Nomenclature is given according to the 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 expression for comparison of the wild-type strain grown under nitrogen-limited (S) conditions and under nitrogen-replete conditions (N). NA, not applicable because the read number or spectral count for the wild type grown under nitrogen-replete conditions was 0; ND, the protein was not detected by the shotgun proteomic approach.

  • e According to DESeq analysis (P < 0.12). All genes with a σ54 box in the promoter region are indicated in bold.