TABLE 4.

Comparison of transcriptome and proteome data

ORFaGene productProteomicsMicroarray (meand [FUR/WT])
FUR2WT
5 m/zb1 m/zb2 m/zbPeptidesc5 m/zb1 m/zb2 m/zbPeptidesc
Upregulated in FUR2
    SO0314Ornithine decarboxylase; inducible (speF)36.518.523.52016.14.74.780.41e
    SO0401Alcohol dehydrogenase; zinc containing69.463.554.31403.601NAf
    SO0442Phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase (purH)17.316.819.594.64.6010.92e
    SO0453Peptidyl-prolyl cis-trans isomerase FkbP (fkbP-1)011.742.3400001.17e
    SO0520Heavy-metal efflux pump; CzcA family2.29.912.762.20010.77e
    SO0798Conserved hypothetical protein10.418.518.19000026.7
    SO0958Alkyl hydroperoxide reductase; C subunit (ahpC)39.746.046.610009.510.5e
    SO1190Conserved hypothetical protein37.958.558.5135.5205.1315.47
    SO1482TonB-dependent receptor; putative37.934.826.522000026.81
    SO1580TonB-dependent heme receptor14.712.924.81203.1012.48
    SO20015′-nucleotidase (ushA)13.216.014.186.74.24.221.11e
    SO3667Conserved hypothetical protein37.342.731.4107.000159.66
    SO3668Conserved hypothetical protein17.218.318.33000037.5
    SO3669Heme transport protein (hugA)53.541.643.83015.49.89.8725.45
    SO3914TonB-dependent receptor; putative19.511.024.11610.40042.83
    SO4133Uridine phosphorylase (udp)42.143.343.366.79.521.430.75
    SO4516Ferric vibriobactin receptor (viuA)10.810.825.3800008.21
    SO4523Iron-regulated outer membrane virulence protein (irgA)69.056.754.43417.84.26.845.61
    SO4743TonB-dependent receptor; putative27.833.241.61906.46.4126.2
    SO2304gAlanine dehydrogenase25.931.725.9911.6001NA
    SO4422gTonB-dependent receptor; iron-siderophore receptor44.642.535.511013132NA
    SO4422gSimilar to ferric aerobactin receptor3511.315.880000NA
Downregulated in FUR2
    SO1377Conserved hypothetical protein000023.326.725.5151.47e
    SO1778Decaheme cytochrome c (omcB)00009.815.517.7110.19
    SO1779Decaheme cytochrome c (omcA)00004.212.513.660.17
    SO2363Cytochrome c oxidase; cbb3-type; subunit II (ccoO)08.719.7222.147.639.480.94e
    SO2907TonB-dependent receptor domain protein4.510.54.3429.637.140.2281.32e
    SO3733Hypothetical protein000021.58.013.1120.94e
    SO4077TonB-dependent receptor, putative000011.915.417.480.97e
    SOA0048Prolyloligopeptidase family protein00006.310.66.071.24e
  • a ORFs are presented that show a 30% change in sequence coverage or a difference of four or more unique peptides.

  • b 5 m/z refers to the percent sequence coverage from a five-part LC-MS/MS experiment covering the entire mass spectrum in five separate steps; 1 m/z refers to the percent sequence coverage from a single 2D LC-MS/MS experiment that involved one injection and 11 subsequent salt steps analyzed by MS; 2 m/z refers to the percent sequence coverage from two 2D LC-MS/MS experiments, which included two injections each with eight subsequent salt steps analyzed using MS over two m/z ranges.

  • c Total number of unique peptides detected per gene product by triplicate LC-MS/MS analysis.

  • d Relative gene expression is presented as the mean ratio of the fluorescence intensity of the FUR2 strain to that of the parental strain (WT).

  • e Change in expression was <2-fold.

  • f NA, not available.

  • g ORFs originally annotated by TIGR as pseudogenes whose expression was verified by proteomics.