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Table 3 Genes repressed in the "Energy metabolism" category in anaerobic cultures of EtrA7-1 grown on lactate and nitrate relative to the wild type (reference strain).

From: Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensisMR-1

Gene ID Gene name Relative expressiona Predicted EtrA binding sitesc COG Annotation
SO0274 ppc 0.48 (± 0.19)   phosphoenolpyruvate carboxylase
SO0398 frdA 0.30 (±0.16)b   fumarate reductase flavoprotein subunit
SO0399 frdB 0.39 (± 0.06)   fumarate reductase iron-sulfur protein
SO0845 napB 0.15 (± 0.04)   cytochrome c-type protein NapB
SO0846 napH 0.18 (± 0.11)   iron-sulfur cluster-binding protein napH
SO0847 napG 0.14 (± 0.07)   iron-sulfur cluster-binding protein NapG
SO0848 napA 0.18 (± 0.13) periplasmic nitrate reductase
SO0849 napD 0.30 (± 0.04) GTCGATCGGGATCAAA CGTGATCTAACTCTCA napD protein
SO0903 nqrB-1 0.34 (± 0.15) TTTGCTGTAAAGCAAA TGTGCATGGAATCGCC NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrB
SO0904 nqrC-1 0.28 (± 0.09) NADH:ubiquinone oxidoreductase, Na translocating, gamma subunit
SO0905 nqrD-1 0.27 (± 0.14) NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrD
SO0906 nqrE-1 0.23 (± 0.07) NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrE
SO0907 nqrF-1 0.23 (± 0.08)   NADH:ubiquinone oxidoreductase, Na translocating, beta subunit
SO0970 fccA 0.31 (±0.17)   Periplasmic fumarate reductase, FccA
SO1018 nuoE 0.44 (± 0.17)   NADH dehydrogenase I, E subunit
SO1019 nuoCD 0.35 (± 0.13)   NADH dehydrogenase I, C/D subunits
SO1020 nuoB 0.40 (± 0.10)   NADH dehydrogenase I, B subunit
SO1363 hcp 0.13 (± 0.08)   prismane protein
SO1364 hcr 0.12 (± 0.07)   iron-sulfur cluster-binding protein
SO1429 dmsA-1 0.43 (± 0.09) TGTGATACAATTCAAA anaerobic dimethyl sulfoxide reductase, A subunit
SO1430 dmsB-1 0.29 (± 0.04) anaerobic dimethyl sulfoxide reductase, B subunit
SO1490 adhB 0.28 (± 0.12) TGTGATCTAGATCGGT TTGGAACTAGATAACT alcohol dehydrogenase II
SO1776 mtrB 0.22 (± 0.04)   outer membrane protein precursor MtrB
SO1777 mtrA 0.25 (± 0.06)   decaheme cytochrome c MtrA
SO1778 mtrC 0.30 (± 0.09)   decaheme cytochrome c MtrC
SO1779 omcA 0.30 (± 0.05) GTGGAATTAGATCCCA TGTGATTGAGATCTGA TTTGAGGTAGATAACA decaheme cytochrome c
SO2097 hyaC 0.07 (± 0.04)   quinone-reactive Ni/Fe hydrogenase, cytochrome b subunit
SO2098 hyaB 0.11 (± 0.10)   quinone-reactive Ni/Fe hydrogenase, large subunit
SO2099 hyaA 0.07 (± 0.11)   quinone-reactive Ni/Fe hydrogenase, small subunit precursor
SO2136 adhE 0.40 (± 0.10)   aldehyde-alcohol dehydrogenase
SO2912 pflB 0.18 (± 0.11) TTTGAGCTGAAACAAA formate acetyltransferase
SO2913 pflA 0.20 (± 0.13)   pyruvate formate-lyase 1 activating enzyme
SO2915 ackA 0.23 (±0.16)   acetate kinase
SO2916 pta 0.23 (± 0.14)   phosphate acetyltransferase
SO3144 etfA 0.36 (± 0.13)   electron transfer flavoprotein, alpha subunit
SO3285 cydB 0.21 (± 0.06) cytochrome d ubiquinol oxidase, subunit II
SO3286 cydA 0.22 (± 0.10) TTTGATTCAAATCAAT cytochrome d ubiquinol oxidase, subunit I
SO3980 nrfA 0.18 (± 0.06) TTTGCGCTAGATCAAA cytochrome c552 nitrite reductase
SO4513 fdhA-2 0.06 (± 0.02) ACTGTTCTAGATCAAA formate dehydrogenase, alpha subunit
SO4515 fdhC-2 0.07 (± 0.01)   formate dehydrogenase, C subunit, putative
SO4591 cymA 0.39 (± 0.27)   tetraheme cytochrome c
  1. a The relative expression is presented as the ratio of the dye intensity of the anaerobic cultures with 2 mM KNO3 of EtrA7-1 to that of MR-1 (reference).
  2. bThe standard deviation was calculated from six data points, which included three independent biological samples and two technical samples for each biological sample.
  3. c The arrows indicate that the gene is regulated by the binding site that follows. The direction of the arrow indicates the location of the gene. An arrow pointing down indicates the gene or operon is in the plus or sense strand and the arrow pointing up indicates the gene or operon is in the minus or anti-sense strand.