TABLE 3

Comparison of gene expression and relative protein abundance differences between D. alaskensis G20 and CycA mutant I2a

Enzyme and locusProteinAnnotationbLactate-sulfatecPyruvated
Microarray Log2RProteomicsMicroarray log2RProteomics
I2 relative abundanceG20 relative abundanceLog2 RI2 relative abundanceG20 relative abundanceLog2R
Cytoplasmic carbon metabolism enzymes
    Dde_1250NfnA-2Electron-bifurcating transhydrogenase 2, subunit A−1.614.616.67−0.53−3.16NRe3.77Gf
    Dde_1251NfnB-2Electron-bifurcating transhydrogenase 2, subunit B−1.795.1313.07−1.35−3.12NDg3.07G
    Dde_1252COG-CitTMalate/fumarate uptake transporter or antiporter with succinate−2.541.332.08−0.62−3.43NDNDND
    Dde_1253COG-SfcAMalate:NADPH oxidoreductase, decarboxylating−2.740.4040.38−6.67−3.712.4155.18−4.52
    Dde_1254COG-FumAFumarate hydratase, β subunit−2.39ND30.30G−3.30ND28.20G
    Dde_1255COG-TtdAFumarate hydratase, α region−2.41ND22.59G−3.25NR30.78G
    Dde_1256FrdBFumarate reductase, FeS protein−0.90ND26.64G−2.46NR22.28G
    Dde_1257FrdAFumarate reductase, flavoprotein unit−1.986.3827.15−2.09−2.84NR27.28G
    Dde_1258FrdCFumarate reductase, cytochrome b subunit−2.47ND12.55G−3.01ND34.69G
    Dde_3028CooSCarbon monoxide dehydrogenase0.074.881.212.022.2497.485.384.18
    Dde_3029CooCCarbon monoxide dehydrogenase0.114.660.942.322.0326.272.123.63
Periplasmic formate dehydrogenases
    Dde_0717FdhA-1Formate dehydrogenase, α subunit0.7246.972.044.533.76119.820.338.57
    Dde_0718FdhB-1Formate dehydrogenase, β subunit1.0341.101.804.513.33143.51NRIh
    Dde_0719COG-MobBMolydopterin-guanine dinucleotide biosynthesis protein0.5819.392.832.781.6166.073.074.42
Periplasmic hydrogenases
    Dde_2134HysB[NiFeSe] hydrogenase, small subunit0.1317.8618.67−0.06ND29.764.862.62
    Dde_2135HysA[NiFeSe] hydrogenase, large subunit0.1920.3120.310.000.8243.3420.091.11
    Dde_2136HysBAMaturation protease for hydrogenase0.052.641.940.450.22NRNRND
    Dde_2137HynB-1[NiFe] hydrogenase, small subunit0.1843.0033.830.35NDNRNRND
    Dde_2138HynA-1[NiFe] hydrogenase, large subunit0.1216.9719.67−0.210.1532.029.381.77
Sulfate-reducing enzymes
    Dde_2265SatSulfate adenylyltransferase0.10i347.34427.86−0.30NRj272.06740.47−1.44
    Dde_1778PpaCPyrophosphatase/inorganic diphosphatase−0.02351.10504.34−0.52−1.13331.91408.52−0.30
    Dde_1109ApsBAdenylyl sulfate reductase, β subunit−0.06707.53988.72−0.48NR226.75333.56−0.56
    Dde_1110AspAAdenylyl sulfate reductase, α subunit0.50i508.68600.23−0.24NRj340.12534.26−0.65
    Dde_1111QmoAQuinone-interacting membrane-bound oxidoreductase0.2372.8078.51−0.11−0.3530.1637.62−0.32
    Dde_1112QmoBQuinone-interacting membrane-bound oxidoreductase0.2065.9771.95−0.13−0.2531.0123.180.42
    Dde_1113QmoCQuinone-interacting membrane-bound oxidoreductase0.0554.5658.67−0.10−0.2816.5721.76−0.39
    Dde_2932QrcAType I cytochrome c3:menaquinone oxidoreductase hexaheme cytochrome c0.38NRNRND0.05NRNRND
    Dde_2933QrcBType I cytochrome c3:menaquinone oxidoreductase, molybdopterin-containing subunit0.29NR204.68G0.4142.5713.591.65
    Dde_2934QrcCType I cytochrome c3:menaquinone oxidoreductase, periplasmic molybdopterin-containing subunit0.2545.1644.340.030.2152.6321.101.32
    Dde_2935QrcDType I cytochrome c3:menaquinone oxidoreductase, integral membrane protein subunit−0.02NDNDND0.31NRNDND
  • a Log2 R, where R is the transcript expression measured by microarray analysis for I2 protein-coding genes compared with that obtained for G20 or relative protein abundance values obtained from proteomic data. Log2 (I2/G20) values in bold are for those genes or proteins with at least a 2-fold difference in expression or abundance between I2 and G20. Relative abundance is derived from the number of spectra acquired for a protein.

  • b Gene annotations were was obtained from http://www.microbesonline.org, http://genome.ornl.gov/microbial/ddes/, and M. Price (personal communication; see Table S2 in the supplemental material).

  • c Lactate-sulfate was MO basal salts with 60 mM lactate and 30 mM sulfate providing medium for sulfate respiration.

  • d Pyruvate medium was MO basal salts containing 60 mM pyruvate for growth by fermentation.

  • e NR, data do not meet the criteria for reproducibility.

  • f G, log2 R was not meaningful since protein was detected only in the G20 culture.

  • g ND, no protein was detected in either G20 or I2.

  • h I, log2 R was not meaningful since protein was detected only in the I2 culture.

  • i Microarray data for Dde_2265 and Dde_1110 were reevaluated by qRT-PCR, and log2 ratios of I2/G20 transcripts from lactate-sulfate (60 mM/30 mM) cultures were found to be −0.004 and 0.017, respectively, indicating no change.

  • j Microarray data for Dde_2265 and Dde_1110 were reevaluated by qRT-PCR, and log2 ratios of I2/G20 transcripts from pyruvate (60 mM) cultures were found to be −0.083 and −0.077, respectively, indicating no change.