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Table 1 Chromosomal genes differentially expressed in response to anaerobic conditionsa

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

Gene ORF ID Rep 1b Rep 2 Definitionc Regulond
Small molecule biosynthesis
hda NGO0187 4.1 4.1 Histone deacetylase-like protein/acetoin utilization protein  
pdxH NGO0658 4.3 5.5 Pyridoxamine 5-phosphate oxidase MtrR
mobA NGO0754 3.5 4.6 Molybdopterin-guanine dinucleotide biosynthesis protein NsrR
leu1 NGO0848 6.6 4.5 2-isopropylmalate synthase  
folA NGO1694 3.8 2.8 Dihydrofolate reductase RpoH
Transport and binding proteins
fHBP NGO0033 3.5 4.2 Factor H binding protein  
hecA NGO0706 3.2 4.9 Filamentous hemagglutinin  
bfrA NGO0794 14.1 9.9 Bacterioferritin A  
bfrB NGO0795 9.7 10.1 Bacterioferritin B MtrR
pil NGO1177 3.5 3.5 Neisseria-specific type IV pilin-related protein  
  NGO1440 4.4 2.8 ABC-type amino acid transporter, periplasmic protein  
lecA NGO1981 5.0 3.9 Adhesin protein Lrp
Energy metabolism/Oxidation-Reduction
cybP NGO0805 3.2 2.8 Nickel-dependent hydrogenase, b-type cytochrome subunit  
npd NGO1024 9.6 7.9 2-Nitropropane dioxygenase-like MtrR
aniA NGO1276 28.4 28.0 Nitrite reductase NsrR, FNR
eftD NGO1396 5.2 5.1 Electron transfer flavoprotein-ubiquinone oxidoreductase  
Macromolecular biosynthesis
rl34 NGO2182 3.0 3. 1 50S ribosomal protein L34  
Regulation      
farR NGO0058 4.0 3.7 MarR family transcriptional regulator Lrp, MtrR
nmlR NGO0602 7.2 7.6 Transcriptional regulator nmlR NmlR, FNR
xre NGO0797 3.2 3.4 XRE family transcriptional regulator  
marR NGO1244 5.4 15.2 MarR-family transcriptional regulator RpoH, MtrR
nosR a NGO1401/1402 9.4 9.5 Regulator of nitrous oxide reductase pseudogenes FNR
lexA NGO1427 4.2 5.3 LexA-family repressor LexA
arsR NGO1562 6.1 2.2 ArsR-family transcriptional regulator  
Cell Structure
ompA NGO1559 3.7 3.4 Outer membrane protein  
lpcA NGO1986 4.2 6.1 Phosphoheptose isomerase  
Adaptation and stress response
grx3 NGO0114 3.3 6.6 Glutaredoxin 3 Fur
recN NGO0318 4.7 5.5 Repair protein RecN Fur, LexA
htpX NGO0399 11.8 8.6 Heat shock protein, Peptidase family M48 Lrp
dnrN NGO0653 8.9 12.3 Iron-sulfur cluster repair protein NsrR, FNR
  NGO0757 2.6 4.1 Putative periplasmic Cpx-family sensor kinase involved in P pilus formation  
hslR NGO0822 2.7 5.0 Heat shock protein HSP-15  
  NGO1022 3.8 3.4 DEDDh family exonuclease  
clpB NGO1046 4.9 9.4 Endopeptidase Clp ATP-binding chain B (HSP- F84.1) RpoH, MtrR
recX NGO1053 3.6 2.8 RecX-family regulator of RecA function  
tehB NGO1161 2.6 4.0 Tellurite resistance protein  
hsp33 NGO1189 6.1 5.2 Heat shock protein HSP-33 chaperonin MtrR
  NGO1245 4.0 8.5 ABC-type multidrug transport system, ATPase/permease  
hit NGO1273 2.3 5.5 Protein Kinase C Interacting protein belonging to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides  
nudH NGO1334 3.3 3.3 Nudix hydrolase, dinucleoside polyphosphate hydrolase  
grpE NGO1422 3.6 2.7 Heat shock protein (HSP-70 cofactor; nucleotide exchange factor) RpoH, MtrR
erpA NGO1426 2.8 2.6 Putative iron-sulfur cluster insertion protein RpoH, Lrp
dnaK NGO1429 2.7 3.4 Heat shock protein, chaperone RpoH
  NGO1566 3.4 3.1 Nudix hydrolase, catalyzing the hydrolysis of nucleoside diphosphates  
ntrA NGO1702 3.5 20.1 Nitroreductase-like family containing uncharacterized proteins similar to nitroreductase  
ccp NGO1769 5.6 12.1 Cytochrome c peroxidase  
yhhF NGO1860 3.7 4.1 Probable DNA methylase  
dnaJ NGO1901 2.8 5.1 Heat shock protein HSP-40 RpoH
Hypothetical or Unassigned
  NGO0010 5.1 7.2 Neisseria-specific protein, uncharacterized  
  NGO0011 3.2 3.0 Conserved hypothetical protein  
  NGO0119 5.4 5.1 Neisseria-specific protein, uncharacterized; possible ribonuclease  
  NGO0165 3.2 5.9 Neisseria-specific protein, uncharacterized  
  NGO0569 3.8 2.1 Conserved hypothetical protein (possible transcriptional regulator)  
  NGO0570 3.5 3.4 Possible DNA-binding CreA protein RpoH
  NGO0618 3.3 2.7 Neisseria-specific protein, uncharacterized  
  DUF331 4.1 7.8 Uncharacterized protein family DUF331; the function of this family is unknown  
  NGO0802 3.7 4.0 Hypothetical protein (possible Neisseria-specific protein)  
  NGO0854 3.6 8.4 Hypothetical protein  
  NGO0895 6.4 4.6 Neisseria-specific protein, uncharacterized  
  NGO0896 4.1 5.0 Hypothetical protein  
  NGO0995 3.1 3.3 Neisseria-specific protein, uncharacterized  
  NGO1033 4.3 6.8 Probable transglycosylase  
  NGO1037 4.4 5.2 Hypothetical protein  
  NGO1191 3.5 2.7 Neisseria-specific protein, uncharacterized  
  NGO1277 6.6 7.0 Conserved hypothetical protein (NirV) FGE- sulfatase super family.  
  NGO1428 14.3 8.4 Neisseria-specific protein, uncharacterized LexA
  NGO1517 4.8 4.8 Neisseria-specific protein, uncharacterized NsrR
  NGO1793 6.4 4.3 Conserved hypothetical protein (probable integral membrane protein)  
  NGO1987 3.1 4.4 Uncharacterized protein family UPF0102; the function of this family is unknown  
  NGO2023 2.4 7.3 Conserved hypothetical protein  
Small RNA fnrS c   24.9 17.8 Probable small regulatory RNA FNR
Gene ORF ID Rep 1 Rep 2 Definition Regulon
Ngo Φ 1 phage
  NGO0463 9.2 5.9 Putative phage associated protein  
  NGO0464 12.3 9.0 Putative phage associated protein  
  NGO0465 15.4 7.3 Putative phage associated protein  
  NGO0467 23.6 29.8 Putative phage associated protein  
  NGO0472 94.6 19.7 Putative phage associated protein FNR
dnaB NGO0485 6.1 4.2 Replicative DNA helicase  
  NGO0488 4.2 10.0 Putative phage associated protein  
  NGO0489 10.2 16.9 Phage Holliday junction resolvase (RusA-like) protein  
  NGO0491 14.2 5.1 Putative phage associated protein  
  NGO0492 8.7 6.6 Putative phage associated protein  
  NGO0494 10.0 10.9 Putative phage associated protein  
  NGO0495 9.6 7.6 Putative phage associated protein  
  NGO0496 16.1 12.9 Putative phage associated protein  
  NGO0497 24.1 17.0 Putative phage associated protein  
  NGO0498 18.0 9.5 Putative phage associated protein  
  NGO0499 17.4 12.9 Putative phage associated protein  
  NGO0500 17.6 6.6 Putative phage associated protein  
  NGO0501 27.4 9.1 Putative phage associated protein  
  NGO0502 47.2 6.8 Putative phage associated protein  
  NGO0503 6.0 4.8 Putative phage associated protein  
  NGO0504 14.4 5.2 Putative phage associated protein  
  NGO0506 15.9 11.3 Putative phage associated protein  
  NGO0507 22.3 12.1 Putative phage associated protein  
  NGO0508 15.6 11.1 Putative phage associated protein  
  NGO0509 3.5 3.6 Putative phage associated protein  
  NGO0510 7.1 5.6 Putative phage associated protein  
  NGO0512 9.4 13.2 Putative phage associated protein  
  NGO0513 4.9 5.2 Putative phage associated protein  
  NGO0514 9.8 6.2 Putative phage associated protein  
  NGO0522 9.4 5.6 Putative phage associated protein  
Ngo Φ2 phage
  NGO1100 4.1 5.0 Putative phage associated protein  
  NGO1120 75.5 16.0 Putative phage associated protein  
  NGO1131 19.4 16.8 Putative phage associated protein  
  NGO1132 11.3 16.2 Putative phage associated protein  
Ngo Φ3 phage
  NGO1614 8.2 11.0 Putative phage associated protein  
  NGO1615 10.3 7.2 Conserved hypothetical protein (type I restriction enzyme related) FNR
  NGO1624 34.0 16.0 Putative phage associated protein  
  NGO1627 6.6 4.4 Conserved hypothetical protein (probable phage origin)  
  NGO1628 7.6 4.9 Putative phage associated protein  
  NGO1633 26.9 137.3 Putative phage associated protein  
  NGO1634 27.4 18.8 Putative phage associated protein  
  NGO1635 58.1 5.4 Putative phage associated protein  
  NGO1636 26.4 10.0 Putative phage associated protein  
  NGO1637 16.6 5.5 Putative phage associated protein  
  NGO1640 22.4 10.6 Putative phage associated protein  
Ngo Φ5 phage
  NGO0731 5.1 7.3 Putative phage associated protein  
  NGO0732 3.3 2.2 Putative phage associated protein  
Gene ID Rep 1 Rep 2 Definition Regulon
Small molecule biosynthesis
cysK NGO0340 -2.8 -6.7 Cysteine synthase FNR
hesB NGO0632 -3.8 -4.0 Iron-sulfur cluster biosynthesis  
iscU NGO0633 -4.8 -5.3 Iron-sulfur cluster assembly scaffold protein  
iscS NGO0636 -4.8 -5.6 Cysteine desulferase  
hisD NGO1240 -3.3 -3.2 Histidinol dehydrogenase  
pgsA NGO1247 -3.8 -7.1 CDP-alcohol phosphatidyltransferase  
asd NGO1997 -3.3 -5.0 Aspartate-semialdehyde dehydrogenase  
Transport and binding proteins
gluP NGO0142 -3.1 -4.3 Glucose/galactose transporter  
nhaC NGO0143 -2.8 -3.3 Na+/H+ antiporter (NhaC)  
amtB NGO0198 -3.7 -5.3 Ammonium Transporter Family  
fbp NGO0217 -4.8 -5.6 ABC-type iron transporter, periplasmic binding protein Fur, Lrp
oxiA NGO0372 -6.7 -20.0 Bacterial extracellular solute-binding protein FarR
  NGO0373 -3.7 -11.1 ABC-type arginine transport system, permease component FarR
glnQ NGO0374 -2.9 -11.1 ABC-type amino acid transporter, ATP-binding protein FarR, FNR
citT NGO0377 -5.6 -9.1 Di- and tri-carboxylate transporters (inorganic ion transport)  
cysA NGO0445 -5.6 -9.1 ABC-type sulfate transporter, ATP-binding protein Lrp
sbp NGO0877 -4.8 -25.0 ABC-related sulfate-binding protein  
  NGO1290 -3.8 -3.3 Putative sodium/alanine symport protein  
hemO NGO1318 -7.1 -12.5 Heme oxygenase/iron starvation protein Fur
lldP NGO1361 -9.1 -8.3 L-lactate permease (partial only)  
exbD NGO1377 -3.4 -3.6 Membrane bound biopolymer transport protein ExbD/TolR  
exbB NGO1378 -3.1 -5.0 Transport protein  
lctP NGO1449 -4.0 -14.3 L-lactate permease  
potF NGO1494 -7.7 -20.0 ABC-type spermidine/putrescine transporter, solute binding protein MtrR
putP NGO1552 -5.6 -11.1 Sodium/proline symport protein  
ompU NGO1688 -2.6 -3.7 Putative iron uptake protein FNR
yaaJ NGO1787 -3.3 -4.3 Sodium/alanine symport protein  
  NGO1807 -2.7 -3.8 Amino-acid symport protein  
gltS NGO1890 -3.1 -5.0 Sodium/glutamate symport protein MtrR
  NGO1954 -3.6 -6.3 Di- and tri-peptide permease, PRT2  
sstT NGO1957 -4.5 -11.1 Sodium/serine symport protein  
glnM NGO2011 -6.7 -12.5 ABC-type amino acid transport system, permease component MtrR, FarR
glnP NGO2012 -10.0 -10.0 ABC-type amino acid transport system, permease component FarR
glnQ NGO2013 -6.3 -11.1 ABC-type amino acid transporter, ATP-binding protein MtrR, FarR
apaA NGO2014 -6.3 -16.7 Bacterial extracellular solute-binding proteins, family 3 MtrR, FarR
  NGO2016 -3.6 -3.3 Predicted permease  
  NGO2096 -6.3 -12.5 SNF family sodium-dependent transporter  
Energy metabolism/Oxidation-Reduction
  NGO0108 -4.0 -5.9 NADPH-dependent FMN reductase Fur, Lrp
lldD NGO0639 -7.1 -11.1 L-lactate dehydrogenase  
eda NGO0713 -3.0 -5.6 KHG-KDPG bifunctional aldolase  
rpeC NGO0758 -4.8 -3.8 Ribulose-phosphate 3-epimerase  
fdx NGO0825 -5.3 -5.3 Ferredoxin  
cisY NGO0918 -3.6 -3.8 Type II citrate synthase Lrp
sdhB NGO0920 -2.9 -4.2 Succinate dehydrogenase, iron-sulfur protein Lrp
sdhA NGO0921 -3.7 -3.4 Succinate dehydrogenase, flavoprotein subunit Lrp
sdhD NGO0922 -2.9 -3.4 Succinate dehydrogenase, membrane anchor protein  
sdhC NGO0923 -1.8 -4.2 Succinate dehydrogenase, cytochrome b556 chain  
fumC NG01029 -2.9 -6.3 Fumarate hydratase Fur, MtrR
gpmA NGO1258 -4.0 -5.6 Phosphoglyceromutase Lrp
nqrA NGO1413 -4.0 -7.7 Na(+)-translocating NADH-quinone reductase subunit A  
nqrB NGO1414 -5.0 -8.3 Na(+)-translocating NADH-quinone reductase subunit B  
nqrC NGO1415 -4.2 -8.3 Na(+)-translocating NADH-quinone reductase subunit C  
nqrD NGO1416 -3.8 -16.7 Na(+)-translocating NADH-quinone reductase subunit D  
nqrE NGO1417 -4.3 -12.5 Na(+)-translocating NADH-quinone reductase subunit E  
nqrF NGO1418 -3.7 -9.1 Na(+)-translocating NADH-quinone reductase subunit F MtrR
dadA NGO1808 -3.6 -5.3 D-amino acid dehydrogenase small subunit  
mqo NGO1980 -3.7 -5.0 Malate:quinone oxidoreductase  
Macromolecular biosynthesis
greB NGO0262 -3.7 -5.3 Transcription elongation factor  
parC NGO1259 -3.8 -2.9 DNA topoisomerase IV subunit A  
  NGO1261 -6.3 -7.1 S-adenosylmethionine-dependent methyltransferase  
rplP NGO1831.1 -3.2 -6.3 50S ribosomal protein L16 Lrp
rpsC NGO1832 -3.2 -7.7 30S ribosomal protein S3 Lrp
rplV NGO1833 -2.9 -10.0 50S ribosomal protein L22  
rpsS NGO1834 -2.8 -12.5 30S ribosomal protein S19  
rplD NGO1837 -2.2 -7.1 50S ribosomal protein L4  
rspJ NGO1841 -2.7 -7.1 30S ribosomal protein S10 Lrp
rpoC NGO1850 -3.3 -5.0 DNA-directed RNA polymerase subunit beta'  
rpoB NGO1851 -2.1 -4.5 DNA-directed RNA polymerase subunit beta  
Cell Structure
nspA NGO0233 -3.1 -3.7 Outer membrane protein (Probable Opa protein)  
GNA2132 NGO1958 -5.3 -8.3 Predicted lipoprotein GNA2132  
lgtG NGO2072 -7.7 -6.3 Probable lipooligosaccharide glycosyl transferase G  
Adaptation and stress response
cspA NGO0410 -3.8 -3.3 Cold shock protein  
trxB NGO0580 -2.6 -4.8 Thioredoxin reductase NmlR
trx1 NGO0652 -5.3 -6.3 Thioredoxin I Fur
cstA NGO1064 -3.8 -12.5 Putative carbon starvation protein  
mtrF NGO1368 -7.7 -25.0 Antibiotic resistance efflux pump component MtrR, FarR
sspB NGO2131 -4.5 -3.6 Protease specificity-enhancing factor  
Hypothetical or unassigned
  NGO0554 -4.5 -5.0 Hypothetical protein Fur
  NGO0635 -4.8 -3.6 Hypothetical protein  
  NGO1065 -4.8 -7.7 Hypothetical protein  
  NGO2097 -3.7 -3.1 Conserved hypothetical protein  
Small RNA
nrrF e   -4.8 -7.7 Fur-repressed small regulatory RNA Fur
  1. a Gonococci grown in an anaerobe chamber on plates containing 5 mM nitrite.
  2. b The fold change for each replicate was calculated by comparing RPKM values of anaerobically grown gonococci to RPKM values of aerobically grown gonococci. A positive value represents an induction of gene expression anaerobically, and a negative value represents a repression of gene expression anaerobically
  3. c Protein definitions are derived from the annotated FA1090 genome (NCBI), and/or the NCBI conserved domain database [33].
  4. d (Fur) Genes that have been shown to be directly regulated by Fur in Sebastian et al., (2002) [95] and/or Jackson et al., (2010) [75]. (RpoH) Genes reported to be upregulated during RpoH overexpression in Gunesekere et al., (2006) [23]. (LexA) Genes reported to be in the LexA regulon by Schook et al., (2010) [50]. (Lrp) Genes found to be differentially expressed in a N. meningitidis Δlrp mutant (NMB0573, closest gonococcal homolog is NGO1407, NCBI) by microarray analysis in Ren et al., (2007) [46]. (MtrR) Genes found to be differentially expressed in a gonococcal ΔmtrR mutant by microarray analysis in FolsterΔ et al., (2009) [56]. (FarR) Genes reported to be in the FarR regulon by Friedrich et al., (2007) [54]. (NmlR) Genes reported to be in the NmlR regulon by Kidd et al., (2005) [47]. (FNR) Genes found to be differentially expressed microaerobically in a Δfnr mutant with and without nitrite by microarray analysis in Whitehead et al., (2007) [7]. (NsrR) Genes reported to be in the NsrR regulon by Isabella et al., (2007) [3] and Isabella, (2010) [19].
  5. e Fur-repressed small regulatory RNA described by Ducey et al., (2009) [96].