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Table 2 Microarray results for known, predicted, and novel σ 54 -dependent operons and sRNA genes of S . Typhimurium

From: Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ54 (RpoN) regulon of Salmonella Typhimurium LT2

Locus taga

Gene symbolb

Function

bEBPc

WT/ΔrpoNd

Ref.e

Known σ54- dependent operons and sRNA genes:

   

STM0368-71

prpBCDE

Proprionate catabolism (putative)

PrpR

45

[4]

STM0830-28

glnHPQ

Glutamine high-affinity transporter

NtrC

7.1

[27]

STM2355

argT

Lysine/arginine/ornithine transport protein

NtrC

3.5

[2]

STM_R0152

glmY

GlmY sRNA

GlrR

0.9

[28]

STM_R0167

glmZ

GlmZ sRNA

GlrR

1.1

[28]

STM4007-05

glnALG

Glutamine synthetase

NtrC

48

[29]

Predicted σ54- dependent operons:

   

STM0462-63

glnK amtB

hypothetical protein

NtrC

3.6

[22]

STM0577-72

 

PTS (putative)

STM0571

67

[18]

STM0649.S-53

 

Hydrolase (putative)

STM0652

11

[18]

STM0665-62

gltIJKL

Glutamate/aspartate transporter

NtrC

1.8

[18, 30]

STM1285-84

yeaGH

Serine protein kinase (putative)

NtrC

2.5

[18, 30]

STM1303-07

astCABDE

Arginine/ornithine/glutamine metabolism

NtrC

2.4 f

[31, 32]

STM1690-86

pspABCDE

Phage shock proteins

PspF

17

[5]

STM2360-56

------ ubiX

Amino acid transport (putative)

STM2361

100

[18]

STM2840-41

norV ygbD

Nitric oxide reductase

NorR

16

[18, 33]

STM2843-42

hydN hypF

Hydrogenase maturation proteins

FhlA

13

[34]

STM2853-44

hycABCDEFGHI -

Hydrogenase 3

FhlA

26

[35]

STM2854-58

hypABCDE

Formate-hydrogen lyase system

FhlA

5.6

[35]

STM3521-18

- rtcBA

RNA repair system (putative)

RtcR

71

[23]

STM3568

rpoH

Heat shock sigma factor (σ32)

 

1.7

[36, 37]

STM3772-66

 

PTS (putative)

STM3773

39

[18]

STM4172

zraP

Zinc resistance-associated protein

ZraR

16

[3, 18]

STM4173-74

hydHG

Zinc resistance two-component system

ZraR

3.7

[3]

STM4244

pspG

Phage shock protein

PspF

1.4

[38]

STM4285

fdhF

Formate dehydrogenase

FhlA

29

[39]

STM4535-40.s

 

PTS (putative)

STM4534

16

[18]

Novel σ54- dependent operon:

   

STM2944-2937

 

CRISPR-associated genes

 

1.6 f

--

  1. aLocus tags for genes within operons or sRNA genes are grouped by those previously shown to be σ54-dependent in Salmonella, previously predicted to be σ54-dependent, or identified in this study as encoded in a novel σ54-dependent transcript. Locus tags for operons that are not up-regulated are in bold type.
  2. bGenes that have not been assigned a gene symbol are represented by a dash (−).
  3. cKnown or predicted bacterial enhancer-binding protein (bEBP) that activates the σ54-dependent operon.
  4. dSignal ratio for the first gene in the operon in WT and ΔrpoN strains expressing DctD250 from pPHBP92. Operons with at least one gene with a signal ratio >3 and p-value <0.02 are considered up-regulated by RpoN; signal ratios above the 3-fold cut off are in bold type. Data for all genes in these operons can be found in Additional file1.
  5. eReferences for operons shown to be σ54-dependent in Salmonella and for operons either determined to be σ54-dependent in other bacterial genera or predicted to be regulated by σ54 in Salmonella are listed.
  6. fThe first gene in the operon was <3-fold up-regulated, but other genes in the operon were >3-fold up-regulated.
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BMC Genomics

ISSN: 1471-2164

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