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. 2014 Feb;80(3):855–868. doi: 10.1128/AEM.02963-13

TABLE 3.

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

Enzyme and locus Protein Annotationb Lactate-sulfatec
 Pyruvated
Microarray Log2 R Proteomics
 Microarray log2 R Proteomics
I2 relative abundance G20 relative abundance Log2 R I2 relative abundance G20 relative abundance Log2 R
Cytoplasmic carbon metabolism enzymes
    Dde_1250 NfnA-2 Electron-bifurcating transhydrogenase 2, subunit A −1.61 4.61 6.67 −0.53 −3.16 NRe 3.77 Gf
    Dde_1251 NfnB-2 Electron-bifurcating transhydrogenase 2, subunit B −1.79 5.13 13.07 −1.35 −3.12 NDg 3.07 G
    Dde_1252 COG-CitT Malate/fumarate uptake transporter or antiporter with succinate −2.54 1.33 2.08 −0.62 −3.43 ND ND ND
    Dde_1253 COG-SfcA Malate:NADPH oxidoreductase, decarboxylating −2.74 0.40 40.38 −6.67 −3.71 2.41 55.18 −4.52
    Dde_1254 COG-FumA Fumarate hydratase, β subunit −2.39 ND 30.30 G −3.30 ND 28.20 G
    Dde_1255 COG-TtdA Fumarate hydratase, α region −2.41 ND 22.59 G −3.25 NR 30.78 G
    Dde_1256 FrdB Fumarate reductase, FeS protein −0.90 ND 26.64 G −2.46 NR 22.28 G
    Dde_1257 FrdA Fumarate reductase, flavoprotein unit −1.98 6.38 27.15 −2.09 −2.84 NR 27.28 G
    Dde_1258 FrdC Fumarate reductase, cytochrome b subunit −2.47 ND 12.55 G −3.01 ND 34.69 G
    Dde_3028 CooS Carbon monoxide dehydrogenase 0.07 4.88 1.21 2.02 2.24 97.48 5.38 4.18
    Dde_3029 CooC Carbon monoxide dehydrogenase 0.11 4.66 0.94 2.32 2.03 26.27 2.12 3.63
Periplasmic formate dehydrogenases
    Dde_0717 FdhA-1 Formate dehydrogenase, α subunit 0.72 46.97 2.04 4.53 3.76 119.82 0.33 8.57
    Dde_0718 FdhB-1 Formate dehydrogenase, β subunit 1.03 41.10 1.80 4.51 3.33 143.51 NR Ih
    Dde_0719 COG-MobB Molydopterin-guanine dinucleotide biosynthesis protein 0.58 19.39 2.83 2.78 1.61 66.07 3.07 4.42
Periplasmic hydrogenases
    Dde_2134 HysB [NiFeSe] hydrogenase, small subunit 0.13 17.86 18.67 −0.06 ND 29.76 4.86 2.62
    Dde_2135 HysA [NiFeSe] hydrogenase, large subunit 0.19 20.31 20.31 0.00 0.82 43.34 20.09 1.11
    Dde_2136 HysBA Maturation protease for hydrogenase 0.05 2.64 1.94 0.45 0.22 NR NR ND
    Dde_2137 HynB-1 [NiFe] hydrogenase, small subunit 0.18 43.00 33.83 0.35 ND NR NR ND
    Dde_2138 HynA-1 [NiFe] hydrogenase, large subunit 0.12 16.97 19.67 −0.21 0.15 32.02 9.38 1.77
Sulfate-reducing enzymes
    Dde_2265 Sat Sulfate adenylyltransferase 0.10i 347.34 427.86 −0.30 NRj 272.06 740.47 −1.44
    Dde_1778 PpaC Pyrophosphatase/inorganic diphosphatase −0.02 351.10 504.34 −0.52 −1.13 331.91 408.52 −0.30
    Dde_1109 ApsB Adenylyl sulfate reductase, β subunit −0.06 707.53 988.72 −0.48 NR 226.75 333.56 −0.56
    Dde_1110 AspA Adenylyl sulfate reductase, α subunit 0.50i 508.68 600.23 −0.24 NRj 340.12 534.26 −0.65
    Dde_1111 QmoA Quinone-interacting membrane-bound oxidoreductase 0.23 72.80 78.51 −0.11 −0.35 30.16 37.62 −0.32
    Dde_1112 QmoB Quinone-interacting membrane-bound oxidoreductase 0.20 65.97 71.95 −0.13 −0.25 31.01 23.18 0.42
    Dde_1113 QmoC Quinone-interacting membrane-bound oxidoreductase 0.05 54.56 58.67 −0.10 −0.28 16.57 21.76 −0.39
    Dde_2932 QrcA Type I cytochrome c3:menaquinone oxidoreductase hexaheme cytochrome c 0.38 NR NR ND 0.05 NR NR ND
    Dde_2933 QrcB Type I cytochrome c3:menaquinone oxidoreductase, molybdopterin-containing subunit 0.29 NR 204.68 G 0.41 42.57 13.59 1.65
    Dde_2934 QrcC Type I cytochrome c3:menaquinone oxidoreductase, periplasmic molybdopterin-containing subunit 0.25 45.16 44.34 0.03 0.21 52.63 21.10 1.32
    Dde_2935 QrcD Type I cytochrome c3:menaquinone oxidoreductase, integral membrane protein subunit −0.02 ND ND ND 0.31 NR ND ND
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.