TABLE 5.

Predicted motifs for individual genesa

Putative functional categoryORFGene productAnaerobicAerobicPosbPredicted binding sitecProbdPutative operon
nMean (FUR2/WT)nMean (FUR2/WT)
Cellular processes
    Adaptations to atypical conditionsSO2355Universal stress protein family110.43110.13−65atcggTTTTGAAAAGAGTTTTGATCTagaac0.82
Energy metabolism
    Electron transportSO1779Decaheme cytochrome c (omcA)120.21110.17−43acgacTAATGAGATTTGTTCTTATTTgatat0.97
SO1782Decaheme cytochrome c MtrD41.5143.90−349actggTAACGATAATAGTTTTCAATTgtgtt0.99SO1782-81-80
SO4062Polysulfide reductase; subunit A (psrA)121.0880.03−234acgatTTTTTAGAACAATTTTAACTTttagt0.78SO4062-61-60
    SugarsSO1755Phosphoglucomutase/phosphomannomutase family protein83.5645.47−9aaggtAATTGAAAATGATTTTCACTGaggca0.99
Hypothetical proteinsSO0447Hypothetical protein810.41814.81−126aatctTATTGCGAACTATTCTCATCAgtgct0.99SO0447-48-49
SO0798Conserved hypothetical protein6103.11026.73−41aaatcAAATAATAACAATTCTCATTTacata0.98SO0798-97
SO0799Conserved hypothetical protein53.0552.19−87tatgtAAATGAGAATTGTTATTATTTgattt0.98
SO1188Conserved hypothetical protein10165.71036.96−164atactTTTTGATAATAAATATCATTTactat0.93SO1188-89-90
SO2039Conserved domain protein812.7882.87−23ccattAAATGCGAATAATTAGCAATTaattc0.99
SO3025Conserved hypothetical protein1118.8888.3−199ttggtAAATGACAATAGTTGTCATTTgagag1.00
SO3027Hypothetical protein72.9771.23−316ctctcAAATGACAACTATTGTCATTTaccaa1.00
SO3406Hypothetical protein710.82721.45−252aatgcAAATGATATTGTTTATCATTTaaatt1.00SO3406-07-08
SO3062Hypothetical protein967.721055.82−46aatttTGTTGAGAACAATTCTCATCTaaatt1.00
SO3344Hypothetical protein726.15728.9−23actttAAATGATAATGATTATCAGTTaaggc1.00
SO4700Hypothetical protein118.67119.33−65atcgcAAATCAAATCCATTCTCATTAatgat0.98
SO4740Conserved hypothetical protein913.15377.83−39aatttTAATGAGAATTGTTATCATCTaatta1.00
Protein fate
    Degradation of proteins, peptides, and glycopeptidesSO0445HflC protein, putative51.3852.41−186agcacTGATGAGAATAGTTCGCAATAagatt0.99
Transport and binding proteins
    CationsSO0139Ferritin (ftn)109.286.41−112tgaacAAATGAAAATCATTTTTATCAactaa0.99
SO0583Bacterioferritin-associated ferredoxin (bfd)1028.611111.22−34attgcATTTGATAAGCGTTTTCATTTagaat0.99
SO1111Bacterioferritin subunit 281.6480.16−104agcgaTAATGAGAATGCTTTTAATTAttaag0.98SO1111-12
SO1482TonB-dependent receptor; putative1243.71025.81−28aaagaGGATGGAAATCATTATCATTCgcaac0.93
SO1580TonB-dependent heme receptor66.3642.48−6aaactATGTGAGAATTATTCTCATCTttggc0.99
SO1783Ferrous iron transport protein A (feoA)75.04411.19−100aacacAATTGAAAACTATTATCGTTAccagt0.99feoAB
SO3030Siderophore biosynthesis protein (alcA)1010.44107.93−187cctgcAGATGAGAACGATTTGCATTTataat1.00alcA-SO3031-32
SO3669Heme transport protein (hugA)1074.96625.45−148atcgcAAATGATAATGATTTCTATTTgatca0.92SO3669-68-67
SO3670TonB1 protein (tonB1)1133.161019.02−76tgatcAAATAGAAATCATTATCATTTgcgat0.92tonB1-exbB1-exbD1
SO4516Ferric vibriobactin receptor (viuA)68.7788.21−79aatgtAAATGATATTGGTTATCAATTgcgat0.99
SO4523Iron-regulated outer membrane virulence protein (irgA)1243.8365.61−23tccggTATTGAAAATTATTATCATTTagaaa1.00
SO4743TonB-dependent receptor; putative1236.231026.20−95accttAAATAAAAACAATTCTTATTTatatt0.98
Additional genes with sites that match the motif
SO4196Hypothetical protein41.8461.72−236accgtGATTGATAACACTTTTCTTTTcaggae0.90
SO4197S-adenosylmethionine 2-demethylmenaquinone methyltransferase (menG-2)120.91120.72−69
SO3714Putative sugar-binding protein80.70100.67−318tttgaAACTGATAACCGTTTTGATCAcattge0.88
SO3715Oxygen-insensitive NAD(P)H nitroreductase120.79121.16−73
SO0230Ribosomal protein S1091.34120.86−119gaattAAATGATAAGTCTTTGAACTTatcate0.84
SO0744Iron(III) ABC transporter; periplasmic iron(III)-binding protein54.1390.96−55ttcgaAACTGATAACTATTATCATTAatagtf
SO2841Hypothetical protein111.39112.03−39tagttGACTGATAATAGTTTTCATTTagaatf
  • a Upstream sequences of genes exhibiting ≥5-fold change in expression were analyzed for putative regulatory motifs using Gibbs Recursive Sampler.

  • b Position of the putative regulatory site relative to the translation start codon of the gene.

  • c Binding site is capitalized.

  • d Posterior probability that the site is described by the motif model.

  • e Additional sites predicted by Gibbs sampling in randomly chosen negative control sequences during the Wilcoxon test. Intergenic sequences upstream of SO4196-SO4197, SO3714-SO3715, and SO0230 were included during Gibbs sampling as negative controls for the Wilcoxon signed-rank test, because these genes did not exhibit ≥2-fold change in expression as determined by microarray analysis.

  • f Additional sites predicted (P < 0.05) by using the motif model in Fig. 3 to SCAN the set of intergenic sequences upstream of genes that exhibit an expression ratio of ≥2-fold.