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Table 1 Up-regulated genes in K3 strain

From: Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant

Functional class and gene namea,b,c,d,e,f,g

Operonc,d,e,f,h

Known or predicted function

Fold change

Transport and binding protein

artI

art P IQM d

Arginine-binding periplasmic protein 1

1.74

artJ c

 

Arginine-binding periplasmic protein 2

1.78

feoB

feo A c B

Ferrous iron transport protein

2.19

glnH c

glnHPQ d

Glutamine ABC transporter periplasmic-binding protein

1.57

mdtE e

mdtE F

Multidrug resistance efflux transporter

1.64

oppA c

oppABC DF

Periplasmic oligopeptide-binding protein

2.66

phnC b,c

phnCDEFGHIJKLMNOP

Phosphonates transport ATP-binding protein

145.81

phoE b,c

 

Outer membrane phosphoporin protein

85.15

potE

speF-potE

Putrescine-ornithine antiporter

2.56

pstS b,c

pstS CA B - phoU

High-affinity phosphate-specific transport system

60.97

srlA c

srlAEBD - gutM - srlR c - gutQ

PTS system, glucitol/sorbitol-specific IIC2 component

4.61

ugpB b,c,d

ugpBAEC d Q

sn-glycerol 3-phosphate transport system periplasmic binding protein

40.00

yeaN

yeaN O

Putative amino acid/amine transport protein

2.91

yhiD d,e

 

Predicted Mg(2+) transport ATPase inner membrane protein

2.35

Energy metabolism

dhaK

dhaKL M

Dihydroxyacetone kinase

1.85

grxB

 

Glutaredoxin 2

1.85

hcp

hcp - hcr

Hydroxylamine reductase

1.63

melA

melAB

Alpha-galactosidase

3.24

nagB

nagB ACD

Glucosamine-6-phosphate deaminase

1.83

napH

nap FDAG HB C-ccmABCDEFGH

Quinol dehydrogenase membrane component

2.56

nrfA

nrfABCD EFG

Cytochrome c552/nitrite reductase, formate-dependent

3.74

talA c,d

 

Transaldolase

1.57

treA c,d

 

Periplasmic trehalase

1.67

ulaB

ula A B c C DE F

L-ascorbate-specific enzyme IIB component of PTS

2.46

ulaG

 

Predicted L-ascorbate 6-phosphate lactonase

2.04

Protein fate

hdeA d,e

hdeAB d,e

Acid-resistance protein

2.10

iraP c,d

 

Anti-adaptor protein for σS stabilization

4.42

Cellular processes

amn b,c

 

AMP nucleosidase

6.08

katE d

 

Catalase HPII/hydroperoxidase HPII(III)

1.95

sodC f

 

Superoxide dismutase (Cu-Zn)

1.75

ycgV

 

Predicted adhesin

4.01

Transcription

chaB

chaB C

Cation transport regulator

1.75

gadE e

 

DNA-binding transcriptional activator

3.60

gadX d,e

 

DNA-binding transcriptional dual regulator

2.15

gadW d,e

 

DNA-binding transcriptional activator

6.84

iciA b,c

 

Chromosome replication initiation inhibitor protein

2.00

phoB b,c

phoBR

DNA-binding response regulator in two-component regulatory system with PhoR (or CreC)

36.23

yhiF e

 

Predicted transcriptional regulator

1.66

Central intermediary metabolism

gadA c,d,e

 

Glutamate decarboxylase alpha

2.57

gadB c,d,e

gadBC

Glutamate decarboxylase beta

4.91

phoA b,c

phoA - psiF

Alkaline phosphatase

112.67

sufA e

sufABCDSE

Iron-sulfur cluster assembly scaffold protein

1.91

Cell enveloppe

yibD b

 

Putative glycosyl transferase

45.95

Fatty acid and phospholipid metabolism

cdh

 

CDP-diacylglycerol phosphotidylhydrolase

4.28

hdhA d

 

7-alpha-hydroxysteroid dehydrogenase

1.52

Unknown function

c0754 g

 

Hypothetical protein

2.12

c0778 g

c0778-speF-potE

Hypothetical protein

2.43

c0902

 

Hypothetical protein

1.65

c1013

 

Hypothetical protein

1.83

c1153 c,g

 

Hypothetical protein

2.35

c1435 g

 

Hypothetical protein

2.26

c2837 g

 

Hypothetical protein

1.53

c4182

 

Hypothetical protein

1.76

phoH b,c

 

Conserved protein with nucleoside triphosphate hydrolase domain

5.95

psiE b,c

 

Phosphate-starvation-inducible protein

1.84

ytfK b

 

Hypothetical protein

6.65

z0950 g

 

Unknown

1.58

Biosynthesis of cofactors, prosthetic groups and carriers

iucD g

iucABC D -iutA

Lysine/ornithine N-monooxygenase

1.76

Regulatory function

dps d,f

 

DNA protection during starvation conditions

1.87

isrA

 

Small antisense RNA

1.64

sgrS

 

Small antisense RNA

1.98

rybA

 

Small antisense RNA

1.59

rygC

 

Small antisense RNA

1.50

yddV

yddV - dos

Predicted diguanylate cyclase

1.80

  1. a The first up-regulated gene of the operon is shown, b Members of the Pho regulon c Indicates the presence of Pho box in the gene promoter, d Genes belonging to RpoS regulon, e Genes involved in acid stress response, f Genes involved in oxidative stress response, g Pathogen-associated ORF, h Genes in bold are up-regulated in K3 strain.