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Table 2 Comparison of the anaerobic stimulon with the iron and hydrogen peroxide responsive stimulon

From: Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae

Gene ORF designation     Definition
Common elements of the anaerobic and iron responsive stimulon
   -O2/+O2a -Fe/+Feb   
farR NGO0058 3.9 -2.0   MarR family transcriptional regulator
gluP NGO0142 -3.7 2.9   Glucose/galactose transporter
nhaC NGO0143 -3.1 -2.3   Na+/H+ antiporter (NhaC)
amtB NGO0198 -4.3 -14.2   Ammonium transporter AmtB
nspA NGO0233 -3.4 2.6   Outer membrane protein
greB NGO0262 -4.5 -1.8   Transcription elongation factor
  NGO0373 -7.4 -2.5   Amino acid ABC transporter, permease protein
  NGO0377 -7.4 -150.4   Probable transmembrane transport protein
cspA NGO0410 -3.6 3.2   Cold shock protein A
  NGO0492 7.7 1.8   Putative phage associated protein
  NGO0506 13.6 -3.2   Putative phage associated protein
  NGO0635 -4.2 4.2   Hypothetical protein
lldD NGO0639 -9.1 3.9   L-lactate dehydrogenase
pdxH NGO0658 4.9 1.8   Pyridoxamine 5-phosphate oxidase
eda NGO0713 -4.3 6.9   KHG-KDPG bifunctional aldolase
  NGO0732 2.8 2.7   Neisseria-specific protein
mobA NGO0754 4.1 3.2   Molybdopterin-guanine dinucleotide biosynthesis protein
  NGO0757 3.4 2.2   Putative periplasmic Cpx-family sensor kinase
bfrA NGO0794 12.0 -2.8   Bacterioferritin A
bfrB NGO0795 9.9 -1.9   Bacterioferritin B
hslR NGO0822 3.9 2.4   Heat shock protein (Hsp15)
  NGO0895 5.5 1.8   Neisseria-specific protein, uncharacterized
sdhA NGO0921 -3.6 -2.3   Succinate dehydrogenase flavoprotein subunit
sdhC NGO0923 -3.0 -2.3   Succinate dehydrogenase, cytochrome b556 chain
  NGO0995 3.2 1.9   Neisseria-specific protein, uncharacterized
hsp33 NGO1189 5.7 -2.9   Heat shock protein Hsp33 chaperonin
  NGO1261 -6.7 3.4   S-adenosylmethionine-dependent methyltransferase
lldP NGO1361 -8.7 -3.2   L-lactate permease
nqrB NGO1414 -6.7 -2.7   Sodium-translocating NADH-ubiquinone reductase subunit B
nqrC NGO1415 -6.3 -2.1   Sodium-translocating NADH-ubiquinone reductase subunit C
nqrE NGO1417 -8.4 -5.5   Sodium-translocating NADH-ubiquinone reductase subunit E
nqrF NGO1418 -6.4 -3.1   Sodium-translocating NADH-ubiquinone reductase subunit F
putP NGO1552 -8.3 -5.3   Sodium/proline symporter PutP
ompA NGO1559 3.6 2.5   Probable outer membrane protein
arsR NGO1562 4.2 -2.3   ArsR family transcriptional regulator
  NGO1628 6.3 2.1   Conserved hypothetical protein
  NGO1633 82.1 2.1   Putative phage associated protein
  NGO1688 -3.1 3.7   Conserved hypothetical protein
folA NGO1694 3.3 -2.0   Dihydrofolate reductase (FolA)
  NGO1807 -3.3 -3.0   Amino-acid transporter
dadA NGO1808 -4.4 -2.9   D-amino acid dehydrogenase small subunit (DadA)
yhhF NGO1860 3.9 2.2   Probable DNA methylase Symport protein (possible sodium/dicarboxylate
  NGO1957 -7.8 -2.0   symporter)
  NGO2023 4.9 1.9   Conserved hypothetical protein
sspB NGO2131 -4.1 3.3   Stringent starvation protein B
  nrrF -6.2 170†   Fur regulated small regulatory RNA
Common elements of the anaerobic and hydrogen peroxide responsive stimulon
   -O2/+O2 +HP/-HPc   
recN NGO0318 5.1 3.0   DNA repair protein RecN (recombination protein N)
dnaB NGO0485 5.2 6.5   Replicative DNA helicase
nmlR NGO0602 7.4 -4.8   Transcriptional regulator MerR-family
nifU NGO0633 -5.0 4.6   Fe-S scaffold protein
iscS NGO0636 -5.2 4.1   Cysteine desulferase
leu1 NGO0848 5.6 3.3   2-isopropylmalate synthase
aniA NGO1276 28.2 -3.6   Copper-containing dissimilatory nitrite reductase
grpE NGO1422 3.2 5.8   Heat shock protein (HSP-70 cofactor)
lexA NGO1427 4.8 6.3   Transcriptional regulator, repressor
  NGO1428 11.4 3.9   Neisseria-specific protein, uncharacterized
dnaK NGO1429 3.1 10.8   Heat shock protein (HSP-70 chaperone)
ccp NGO1769 8.9 2.7   Probable cytochrome c peroxidase
dnaJ NGO1901 4.0 3.0   Heat shock protein HSP-40/chaperone DnaJ
Common elements of the anaerobic, iron, and hydrogen peroxide responsive stimulon
   -O2/+O2 -Fe/+Fe +HP/-HP  
  NGO0108 -4.9 4.7 6.8 Conserved hypothetical protein (possible oxidoreductase)
glr3 NGO0114 5.0 4.7 4.8 Glutaredoxin 3
fbpA NGO0217 -5.2 8.7 5.5 Periplasmic iron-binding protein
  NGO0554 -4.8 24.5 70.6 Hypothetical protein
trx1 NGO0652 -5.8 3.2 13.5 Thioredoxin I
fumC NGO1029 -4.6 6.4 8.4 Fumarate hydratase (fumarase C)
clpB NGO1046 7.2 4.3 23.8 Endopeptidase ClpB (heat shock protein)
pgm NGO1258 -4.8 2.0 2.8 Phosphoglycerate mutase
hemO NGO1318 -9.8 8.4 9.8 Heme oxygenase/iron starvation protein
exbD NGO1377 -3.5 3.9 4.4 Transport protein (ExbD)
exbB NGO1378 -4.1 6.5 4.7 Transport protein (ExbB) Sodium-translocating NADH-ubiquinone reductase
nqrA NGO1413 -5.8 -2.3 -2.6 subunit A
      Sodium-translocating NADH-ubiquinone reductase
nqrD NGO1416 -10.3 -4.0 -2.8 subunit D
lecA NGO1981 4.5 2.5 2.5 Adhesin protein
  1. a average of RPKM ratios from replicates in Table 1.
  2. b Data from Jackson et al., (2010) [75], taken from time point where iron depletion had the biggest effect on gene expression. A positive value represents an induction of gene expression under iron depleted conditions, and a negative value represents a repression of gene expression under iron depleted conditions.
  3. c Hydrogen peroxide (HP); Data from Stohl et al., (2005) [74]. A positive value represents induction of gene expression in the presence of hydrogen peroxide, and a negative value represents a repression in gene expression in the presence of hydrogen peroxide.
  4. † Data from Ducey, et al., (2009) [96].