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Table 2 Genes induced in the "Energy Metabolism" category in anaerobic cultures of EtrA7-1 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

SO0162

pckA

2.21 (± 0.48)b

TGTGAGCTGGATCATT

phosphoenolpyruvate carboxykinase (ATP)

SO0747

fpr

2.17 (± 1.01)

 

ferredoxin--NADP reductase

SO1103

nqrA-2

2.25 (± 0.54)

TCTGCGCTAGCTCAAT CGTGATTGCGATCGCA

NADH:ubiquinone oxidoreductase, Na translocating, alpha subunit

SO1104

nqrB-2

2.70 (± 1.01)

NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrB

SO1105

nqrC-2

3.15 (± .080)

NADH:ubiquinone oxidoreductase, Na translocating, gamma subunit

SO1106

nqrD-2

4.65 (± 2.07)

NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrD

SO1107

nqrE-2

3.63 (± 1.61)

NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrE

SO1108

nqrF-2

4.21 (± 2.05)

NADH:ubiquinone oxidoreductase, Na translocating, beta subunit

SO1891

scoB

3.77 (± 1.80)

 

Acetyl-CoA:acetoacetate CoA transferase, alpha subunit AtoA

SO1892

scoA

3.21 (± 2.14)

 

acetate CoA-transferase, beta subunit AtoD

SO1927

sdhC

2.47 (± 1.26)

 

succinate dehydrogenase, cytochrome b556 subunit

SO1930

sucA

3.02 (± 1.22)

 

2-oxoglutarate dehydrogenase, E1 component

SO1931

sucB

3.60 (± 1.58)

 

2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase

SO1932

sucC

3.29 (± 0.98)

 

succinyl-CoA synthase, beta subunit

SO1933

sucD

3.28 (± 1.24)

 

succinyl-CoA synthase, alpha subunit

SO2361

ccoP

2.30 (± 0.92)

cytochrome c oxidase, cbb3-type, subunit III

SO2362

ccoQ

3.44 (± 1.16)

cytochrome c oxidase, cbb3-type, CcoQ subunit

SO2364

ccoN

2.76 (± 1.07)

CTTGAGCCATGTCAAA GTTGATCTAGATCAAT

cytochrome c oxidase, cbb3-type, subunit I

SO4509

fdhA-1

2.33 (± 0.56)

 

formate dehydrogenase, alpha subunit

SO4510

fdhB-1

4.03 (± 1.57)

 

formate dehydrogenase, iron-sulfur subunit

SO4511

fdhC-1

2.53 (± 0.31)

 

formate dehydrogenase, C subunit, putative

  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. b The 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.