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Table 2 Virulence plasmid genes differentially expressed in response to anaerobic conditions

From: RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri

ORF IDab

Gene

Description

RNA-seqclog2FC

RNA-seqclog2FC

FRT-seqclog2FC

   

WT no O2/O2

Δfnr/WT no O2

Δfnr/WT no O2

pWR501_0265

yigB

hypothetical protein

2.56

  

pWR501_0225

ospI

T3SS effector

2.00

-2.21

 

pWR501_0250

shf

peptidoglycan deacetylase

1.24

-3.42

-1.30

pWR501_0251

rfbU

glycosiltransferase

1.21

-1.65

-1.16

pWR501_0252

virK

virulence protein

1.15

-2.16

-1.03

pWR501_0039

parA

plasmid segregation protein

1.13

  

pWR501_0253

msbB

acyltransferase

1.07

-3.03

-1.08

pWR501_0074

sepA

secreted protease

-1.12

1.34

1.52

pWR501_0177

 

hypothetical protein

-1.55

 

1.04

pWR501_0283

ipaH1.4

T3SS effector

-1.56

  

pWR501_0175

 

hypothetical protein

-1.58

 

2.29

pWR501_0176

 

hypothetical protein

-1.76

 

2.02

pWR501_0015

 

hypothetical protein

-2.00

1.52

1.05

pWR501_0002

 

putative resolvase

-2.04

1.97

 

pWR501_0007

 

hypothetical protein

-2.25

1.63

 

pWR501_0014

 

hypothetical protein

-2.25

1.60

1.27

pWR501_0192

virG

invasion protein

-2.25

 

2.36

pWR501_0144

ipgF

unknown function

-2.38

 

3.20

pWR501_0051

virF

transcriptional activator of virulence

-2.47

  

pWR501_0006

 

hypothetical protein

-2.54

  

pWR501_0143

ipgE

chaperon

-2.55

 

3.39

pWR501_0146

mxiH

T3SS component

-2.56

1.55

4.10

pWR501_0122

 

hypothetical protein

-2.58

1.53

1.95

pWR501_0121

 

hypothetical protein

-2.65

  

pWR501_0191

virA

T3SS effector

-2.66

 

2.42

pWR501_0147

mxiI

T3SS component

-2.80

2.00

4.01

pWR501_0013

mkaD

mouse killing factor

-2.81

1.97

3.33

pWR501_0145

mxiG

T3SS component

-3.02

 

3.45

pWR501_0148

mxiJ

T3SS component

-3.06

2.17

4.33

pWR501_0031

 

hypothetical protein

-3.14

  

pWR501_0005

 

hypothetical protein

-3.14

 

2.49

pWR501_0292

sopA

VirG-specific protease

-3.25

 

2.49

pWR501_0291

 

hypothetical protein

-3.31

  

pWR501_0138

ipgB

invasion protein

-3.34

 

3.66

pWR501_0157

spa15

chaperon

-3.34

3.52

4.43

pWR501_0012

shET2-2

enterotoxin

-3.38

 

3.41

pWR501_0156

mxiA

T3SS component

-3.44

 

4.67

pWR501_0160

spa32

invasion protein

-3.45

1.34

4.63

pWR501_0141

 

hypothetical protein

-3.50

 

3.71

pWR501_0004

phoN2

apyrase

-3.52

2.38

3.25

pWR501_0150

mxiL

hypothetical protein

-3.59

2.07

4.64

pWR501_0132

acp

hypothetical protein

-3.62

 

5.19

pWR501_0166

spa-orf10

hypothetical protein

-3.64

1.97

4.52

pWR501_0158

spa47

T3SS component

-3.65

3.19

4.69

pWR501_0140

icsB

T3SS effector

-3.65

2.16

4.43

pWR501_0162

spa24

T3SS component

-3.70

2.28

3.71

pWR501_0159

spa13

T3SS component

-3.75

 

5.13

pWR501_0161

spa33

T3SS component

-3.75

1.99

4.03

pWR501_0151

mxiM

T3SS component

-3.81

2.40

4.25

pWR501_0155

mxiC

T3SS component

-3.86

2.43

4.95

pWR501_0290

 

hypothetical protein

-3.86

 

2.00

pWR501_0030

 

putative enterotoxin fragment

-3.90

2.20

4.54

pWR501_0163

spa9

T3SS component

-3.92

1.93

3.56

pWR501_0137

ipgC

chaperon

-3.93

1.86

4.04

pWR501_0135

ipaC

T3SS effector

-3.93

2.65

5.01

pWR501_0165

spa40

T3SS component

-3.94

 

4.02

pWR501_0139

ipgA

chaperon

-3.95

2.45

4.25

pWR501_0153

mxiD

T3SS component

-3.98

2.33

4.81

pWR501_0152

mxiE

transcriptional activator

-4.06

2.51

4.48

pWR501_0154

mxiD

T3SS component

-4.08

2.66

4.54

pWR501_0134

ipaD

T3SS effector

-4.16

2.99

4.92

pWR501_0167

spa-orf11

hypothetical protein

-4.19

2.85

4.07

pWR501_0136

ipaB

T3SS effector

-4.24

2.97

4.59

pWR501_0133

ipaA

T3SS effector

-4.24

3.09

4.98

pWR501_0003

 

hypothetical protein

-4.57

 

3.29

pWR501_0164

spa29

T3SS component

-5.06

2.36

3.32

pWR501_0131

virB

transcriptional activator

-5.17

2.40

4.26

  1. aS. flexneri 5a str. M90T pWR501 virulence plasmid sequence was used as reference GenBank accession numbers AF348706.
  2. bGenes are arranged in descending order in relation to Log2 of Fold Change values of WT no O2/WT O2 comparison.
  3. cLog2 of Fold Change values of WT no O2/WT O2 and Δfnr no O2/WT no O2 comparisons are presented. Only values considered differentially expressed are shown (p adjust <0.05).
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BMC Genomics

ISSN: 1471-2164

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