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Table 1 Genes differentially expressed in fnr+ and fnr strains of N. gonorrhoeae.

From: The small FNR regulon of Neisseria gonorrhoeae: comparison with the larger Escherichia coli FNR regulon and interaction with the NarQ-NarP regulon

fnr++ NO2-/fnr

fnr+- NO2-/fnr

      
    

Gene number

Gene name

 

FNR binding site upstream

ChIP enrichment

      

Product

Sequence

Location

 

Transcripts more abundant in the Ratio t-test Ratio t-test fnr+ strain

46.30

1.1 × 10 p value -5

73.06

7.3 × 10 p value -6

NMB1205

 

Transcript of unknown function

TTGAT TTGAATCAA

41.5

Yes

12.27

3.2 × 10 -4

6.60

7.3 × 10 -5

NGO1688

ompU

Putative iron uptake OMP

none

 

Yes

6.02

1.9 × 10 -5

3.56

8.2 × 10 -4

NGO1276

aniA

Nitrite reductase

TTGAC TTAAATTAA

88.5

Yes §

4.57

4.8 × 10 -4

3.52

3.2 × 10 -5

NGO1215

 

Conserved hypothetical protein (COG2847)

TTAAT CTACATCAA

73.5

NE

2.31

2.1 × 10 -3

2.88

5.2 × 10 -5

NGO0546

res

Type III restriction-modification system EcoPI enzyme

TTGAA TGTGATTAT

106.5

NE

4.21

1.9 × 10 -3

ND

 

XNG1301

nosR

Regulatory protein

TTGAT TTGCATCAA

20.5

NT

2.85

3.1 × 10 -3

0.72

0.06

NGO1621

 

Putative phage associated protein

none

 

NT

2.75

1.0 × 10 -3

0.83

0.28

NGO1622

 

Putative phage associated protein

none

 

NT

2.70

4.1 × 10 -3

0.86

0.47

NGO0472

 

Putative phage associated protein

none

 

NT

2.63

1.7 × 10 -4

1.00

0.51

NGO1455

 

Putative NRAMP family Manganese/Iron transporter

none

 

NE

2.56

5.1 × 10 -3

2.80

0.05

NGO0602

 

Putative MerR family transcriptional regulator

TTGTT TCATTTCCA

130.5

NT

2.20

9.5 × 10 -3

1.21

0.16

NGO0087

 

Hypothetical protein

none

 

NT

2.10

2.0 × 10 -3

1.02

0.83

NGO0473

 

Neisseria specific protein.

GTGAT TCTGACAAA

199.5

NE

2.01

1.4 × 10 -3

1.00

0.71

NGO1615

 

Putative phage associated protein

TTCAG CTGCTTCAA

CTGAT CAGCCTCAT

70.5

25.5

NT

Transcripts more abundant in the fnr strain

0.14

9.6 × 10 -6

0.18

8.1 × 10 -6

NGO1716

 

Putative phosphotransferase

TTGAG TGAAAATAA

85.5

Yes

0.29

7.3 × 10 -3

1.23

0.39

NGO0340

cysK

Cysteine synthetase

none

 

Yes

0.47

3.4 × 10 -4

1.47

0.04

NGO0374

glnQ

Amino acid ABC transporter

none

 

NT

0.37

0.12

0.19

8.4 × 10 -6

NGO0653

dnrN

Putative NO- response protein

ATGTT CAAAACCAA

36.5

NE

0.60

0.84

0.28

2.9 × 10 -3

NGO1275

norB

Nitric oxide reductase

TGAAT TTTAAACAA

33.5

Yes §

0.91

0.31

0.49

2.6 × 10 -4

NGO1428

 

Short Neisseria specific protein

none

 

NE

  1. The ratio of transcript intensity and Student's t-test p value are shown for each gene in each comparison; fnr+ + NO2 -/fnr and fnr+ - NO2 -/fnr. Predicted FNR binding sites with at most 3 mismatches to the consensus E. coli FNR binding site, TTGATNNNNATCAA, located up to 200 bases upstream of the translation start of the gene, are displayed. Note that positions 33.5, 88.5 etc indicate that the central bases of the inverted repeat sequence are located between bases 33 and 34, or between bases 88 and 89, upstream from the translation start. A ChIP enrichment of 60% or more is scored positive. ND, No data for this gene; NE, no enrichment; NT, not tested by ChIP. § The aniA and norB promoters are divergent; ChIP detected FNR binding to the aniA-norB region but cannot be used to resolve the two promoters.
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BMC Genomics

ISSN: 1471-2164

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