Table 2

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

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


a average of RPKM ratios from replicates in Table 1.

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.

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.

† Data from Ducey, et al., (2009) [96].

Isabella and Clark BMC Genomics 2011 12:51   doi:10.1186/1471-2164-12-51

Open Data