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Table 1 Chromosomal genes differentially expressed in response to anaerobic conditions not previously published in E. coli and S. flexneri microarray analysis

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

Metabolism

     

Energy production and conversion

SF5M90T_1519

 

putative oxidoreductase, major subunit

3.80

-4.97

-3.30

SF5M90T_3856

yiaY

putative oxidoreductase

3.18

-2.73

-2.67

SF5M90T_1560

 

putative oxidoreductase, major subunit

3.06

 

-3.87

SF5M90T_3333

pckA

phosphoenolpyruvate carboxykinase

1.99

 

0.62

SF5M90T_3877

yiaK

putative dehydrogenase

1.93

1.22

0.93

SF5M90T_3374

ugpQ

glycerophosphodiester phosphodiesterase, cytosolic

1.89

  

SF5M90T_2534

hmpA

dihydropteridine reductase, ferrisiderophore reductase activity

1.47

5.38

5.85

SF5M90T_33

caiB

l-carnitine dehydratase

1.32

  

SF5M90T_3679

atpF

membrane-bound ATP synthase, F0 sector, subunit b

1.04

  

SF5M90T_3680

atpE

membrane-bound ATP synthase, F0 sector, subunit c

1.04

  

SF5M90T_3937

ppc

phosphoenolpyruvate carboxylase

0.91

 

0.64

SF5M90T_579

galT

galactose-1-phosphate uridylyltransferase

0.77

  

SF5M90T_1419

ydjA

predicted oxidoreductase

-1.17

1.69

1.52

SF5M90T_2771

ygaF

hydroxyglutarate oxidase

-1.31

4.12

2.99

SF5M90T_4044

gltP

glutamate-aspartate symport protein

-1.32

  

SF5M90T_1603

rnfB

electron transport complex protein

-1.46

  

SF5M90T_2869

fldB

flavodoxin 2

-1.56

  

SF5M90T_1602

rnfA

Na + -translocating NADH-quinone reductase subunit E

-1.75

  

SF5M90T_1011

rutA

pyrimidine monooxygenase

-3.07

  

Carbohydrate transport and metabolism

SF4250

treB

PTS system trehalose(maltose)-specific transporter subunits IIBC

3.66

  

SF5M90T_4160

treC

trehalase 6-P hydrolase

3.56

  

SF5M90T_1379

manX

PTS enzyme IIAB, mannose-specific

3.36

  

SF5M90T_1378

manY

PTS enzyme IIC, mannose-specific

3.11

  

SF5M90T_1377

manZ

PTS enzyme IID, mannose-specific

2.89

  

SF5M90T_3670

rbsD

high affinity ribose transport protein

2.71

  

SF5M90T_1101

ptsG

PTS system, glucose-specific IIBC component

2.27

  

SF5M90T_3491

treF

cytoplasmic trehalase

2.12

  

SF5M90T_2419

murP

PTS system N-acetylmuramic acid transporter subunits EIIBC

2.09

 

-0.71

SF5M90T_3499

pfkA

6-phosphofructokinase I

2.08

  

SF5M90T_2096

 

fructose-bisphosphate aldolase

2.02

2.08

1.86

SF5M90T_1001

agp

periplasmic glucose-1-phosphatase

2.00

1.40

1.57

SF5M90T_2887

rpiA

ribosephosphate isomerase, constitutive

1.84

  

SF5M90T_2898

pgk

phosphoglycerate kinase

1.84

  

SF5M90T_1403

gapA

glyceraldehyde-3-phosphate dehydrogenase A

1.83

  

SF5M90T_2097

yegT

putative nucleoside permease protein

1.74

  

SF5M90T_2897

fba

fructose-bisphosphate aldolase, class II

1.56

  

SF5M90T_2404

ptsH

PTS system protein HPr

1.56

  

SF5M90T_3850

mtlA

PTS system, mannitol-specific enzyme IIABC components

1.52

  

SF5M90T_1640

ydhC

putative transport protein

1.51

 

0.69

SF5M90T_2359

 

beta-fructosidase

1.49

 

0.72

SF5M90T_3496

tpiA

triosephosphate isomerase

1.45

  

SF5M90T_2405

ptsI

PEP-protein phosphotransferase system enzyme I

1.42

  

SF5M90T_2808

fucI

L-fucose isomerase

1.41

  

SF5M90T_2875

bglA

6-phospho-beta-glucosidase A

1.27

  

SF5M90T_3348

malP

maltodextrin phosphorylase

1.16

 

0.78

SF5M90T_1107

ycfO

beta-hexosaminidase

1.13

  

SF5M90T_8

talB

transaldolase B

1.10

  

SF5M90T_2033

gnd

gluconate-6-phosphate dehydrogenase

1.01

  

SF5M90T_581

galM

galactose-1-epimerase

1.01

1.41

1.00

SF5M90T_1805

eda

keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase

0.97

  

SF5M90T_580

galK

galactokinase

0.95

 

0.62

SF5M90T_2913

tktA

transketolase 1 isozyme

0.80

  

SF5M90T_2187

fruB

PTS system fructose-specific transporter subunit IIA/HPr protein

-1.33

  

SF5M90T_2186

fruK

fructose-1-phosphate kinase

-1.75

  

SF5M90T_3161

ptsO

phosphocarrier protein NPr

-1.76

  

SF5M90T_1637

 

putative transport protein

-1.93

1.58

 

SF5M90T_2185

fruA

PTS system, fructose-specific transport protein

-1.99

  

Aminoacid transport and metabolism

SF5M90T_2823

argA

N-acetylglutamate synthase

1.94

  

SF5M90T_1910

fliY

putative periplasmic binding transport protein

1.80

  

SF5M90T_625

ybgH

peptide transporter

1.64

-1.60

-1.21

SF5M90T_292

pepD

aminoacyl-histidine dipeptidase (peptidase D)

1.54

1.78

1.75

SF5M90T_2879

gcvT

aminomethyltransferase

1.53

 

1.44

SF5M90T_284

proA

gamma-glutamylphosphate reductase

1.48

  

SF5M90T_1121

potD

spermidine/putrescine periplasmic transport protein

1.44

 

-0.69

SF5M90T_2674

cysD

ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2

1.39

-2.30

-2.21

SF5M90T_1514

dcp

dipeptidyl carboxypeptidase II

1.35

 

0.63

SF5M90T_285

proB

gamma-glutamate kinase

1.26

 

-0.58

SF5M90T_2533

glyA

serine hydroxymethyltransferase

1.16

  

SF5M90T_2967

gsp

glutathionylspermidine synthetase/amidase

1.16

 

0.70

SF5M90T_1806

edd

6-phosphogluconate dehydratase

1.15

 

-0.72

SF5M90T_807

 

glutathione transporter ATP-binding protein

1.08

  

SF5M90T_2317

hisJ

histidine-binding periplasmic protein of high-affinity histidine transport system

1.05

  

SF5M90T_806

ybiK

putative asparaginase

1.02

  

SF5M90T_1122

potC

spermidine/putrescine transport system permease

0.97

-1.09

-0.92

SF5M90T_2882

pepP

proline aminopeptidase P II

0.94

  

SF5M90T_2877

gcvP

glycine decarboxylase

0.90

2.13

1.69

SF5M90T_3687

asnA

asparagine synthetase A

-1.23

 

-1.61

SF5M90T_4099

lysC

aspartokinase III, lysine sensitive

-1.33

1.37

1.14

SF5M90T_1253

trpE

anthranilate synthase component I

-1.57

  

SF5M90T_4187

cycA

transport of D-alanine, D-serine, and glycine

-1.69

  

SF5M90T_1946

yedA

putative transmembrane subunit

-1.79

  

SF5M90T_3626

yifK

putative amino acid/amine transport protein

-1.94

  

SF5M90T_3385

livJ

Leu/Ile/Val-binding protein precursor

-1.95

  

SF5M90T_2843

lysA

diaminopimelate decarboxylase

-2.11

2.44

 

SF5M90T_4029

proP

low-affinity transport system; proline permease II

-2.65

1.05

0.75

SF5M90T_4185

ytfF

putative transmembrane subunit

-3.70

2.71

 

Nucleotide transport and metabolism

   

SF5M90T_3587

udp

uridine phosphorylase

3.12

 

0.59

SF5M90T_2387

nupC

permease of transport system for 3 nucleosides

2.81

  

SF5M90T_2949

nupG

nucleoside permease

2.47

  

SF5M90T_674

ybeK

putative tRNA synthetase

1.60

  

SF5M90T_444

adk

adenylate kinase

1.51

 

-0.67

SF5M90T_2456

purC

phosphoribosylaminoimidazole-succinocarboxamidesynthetase

1.35

  

SF5M90T_4182

cpdB

2′:3′-cyclic-nucleotide 2′-phosphodiesterase

1.16

  

SF5M90T_291

gpt

guanine-hypoxanthine phosphoribosyltransferase

1.10

 

-0.89

SF5M90T_1598

add

adenosine deaminase

0.95

  

SF5M90T_478

purE

phosphoribosylaminoimidazole carboxylase

-1.41

  

Coenzyme transport and metabolism

SF5M90T_2274

menB

dihydroxynaphtoic acid synthetase

2.63

-1.75

-1.65

SF5M90T_2687

 

phenylacrylic acid decarboxylase-like protein

1.83

  

SF5M90T_2276

menD

2-oxoglutarate decarboxylase

1.76

-1.63

-1.75

SF5M90T_2273

menC

O-succinylbenzoate synthase

1.76

-1.72

-1.57

SF5M90T_3142

ispB

octaprenyl diphosphate synthase

1.06

  

SF5M90T_1613

pdxH

pyridoxinephosphate oxidase

1.06

  

SF5M90T_2880

visC

putative FAD-dependent oxidoreductase

0.89

  

SF5M90T_3011

ribB

3,4 dihydroxy-2-butanone-4-phosphate synthase

-1.10

  

SF5M90T_3577

yigC

putative oxidoreductase

-1.31

  

SF5M90T_2885

ygfA

putative ligase

-1.59

  

SF5M90T_3957

birA

biotin--protein ligase

-1.62

 

-0.51

SF5M90T_2103

thiM

hydoxyethylthiazole kinase

-1.95

  

Lipid transport and metabolism

SF5M90T_1094

acpP

acyl carrier protein

1.70

-3.04

 

SF5M90T_2272

menE

o-succinylbenzoate-CoA ligase

1.60

-1.54

-1.80

SF5M90T_2416

ucpA

putative oxidoreductase

1.45

 

-0.56

SF5M90T_339

sbmA

sensitivity to microcin B17, possibly envelope protein

-1.64

  

Inorganic ion transport and metabolism

SF5M90T_2903

 

hypothetical lipoprotein

3.41

  

SF5M90T_929

ycbO

alkanesulfonate transporter substrate-binding subunit

3.04

  

SF5M90T_2415

cysP

thiosulfate binding protein

2.81

-1.51

-1.88

SF5M90T_1636

sodB

superoxide dismutase

2.52

2.13

1.67

SF5M90T_1187

 

putative ATP-binding protein of ABC transporter

2.14

  

SF5M90T_454

copA

copper exporting ATPase

1.95

  

SF5M90T_1186

 

putative iron compound ABC transporter permease

1.69

  

SF5M90T_1185

 

iron ABC transporter ATP-binding protein

1.52

  

SF5M90T_4057

yjcE

predicted cation/proton antiporter

1.49

  

SF5M90T_2675

cysN

ATP-sulfurylase (ATP:sulfate adenylyltransferase), subunit 1

1.08

-2.08

-2.05

SF5M90T_448

ybaL

putative transport protein

-1.01

 

-0.50

SF5M90T_2386

mntH

divalent metal cation transporter

-1.93

1.61

1.68

SF5M90T_330

tauC

taurine transport system permease protein

-2.09

  

SF5M90T_3769

shiF

putative membrane transport protein

-2.16

  

SF5M90T_3054

ygjT

putative transport protein

-2.41

  

SF5M90T_1102

fhuE

outer membrane receptor for ferric iron uptake

-2.46

  

SF5M90T_1483

ydiE

hemin uptake protein

-2.93

-2.20

-1.55

SF5M90T_1572

mdtI

spermidine export protein

-3.61

  

Secondary metabolites biosynthesis, transport and catabolism

SF5M90T_1184

 

putative SAM-dependent methyltransferase

2.12

  

SF5M90T_331

tauD

taurine dioxygenase, 2-oxoglutarate-dependent

-2.97

1.94

 

Cellular processes and signalling

Cell cycle control, cell division, chromosome partitioning

SF5M90T_1243

yciB

probable intracellular septation protein A

0.93

 

-0.80

Defense mechanisms

SF5M90T_4215

ampC

beta-lactamase; penicillin resistance

1.55

 

-1.69

SF5M90T_3751

emrD

multidrug resistance protein D

1.41

  

SF5M90T_4273

 

putative restriction modification enzyme R subunit

1.41

-0.94

-0.99

SF5M90T_3781

shiA

virulence factor

1.30

  

SF5M90T_101

ampD

N-acetyl-anhydromuranmyl-L-alanine amidase

1.18

  

SF5M90T_772

ybhF

putative ABC-type multidrug transport system component

1.16

 

0.54

SF5M90T_771

ybhS

putative ABC-type multidrug transport system component

1.15

  

SF5M90T_770

ybhR

putative ABC-type multidrug transport system component

0.90

  

SF5M90T_418

mdlA

ATP-binding component of a transport system

-1.29

  

Signal transduction mechanisms

SF5M90T_2126

yehU

putative 2-component sensor protein

1.36

  

SF5M90T_3428

uspA

universal stress protein

0.86

  

SF5M90T_2388

yfeA

predicted diguanylate cyclase

-1.20

 

-0.81

SF5M90T_4339

creC

sensory histidine kinase

-1.63

1.43

 

Cell wall/membrane/envelope biogenesis

SF5M90T_1923

nmpC

outer membrane porin protein

2.04

-1.34

-1.13

SF5M90T_1618

slyB

putative outer membrane protein

1.82

-1.43

-0.92

SF5M90T_952

ompA

outer membrane protein 3a

1.59

  

SF5M90T_374

tsx

outer membrane protein

1.53

  

SF5M90T_256

gtrB

bactoprenol glucosyl transferase

1.36

-2.59

 

SF5M90T_2039

rfbC

dTDP-4-dehydrorhamnose 3,5-epimerase

1.20

-2.64

 

SF5M90T_4332

slt

soluble lytic murein transglycosylase

0.96

1.54

1.46

SF5M90T_3951

murI

glutamate racemase

0.93

 

-0.48

SF5M90T_3821

rfaD

ADP-L-glycero-D-mannoheptose-6-epimerase

0.82

  

SF5M90T_1241

tonB

transport protein

-1.72

  

SF5M90T_3956

murB

UDP-N-acetylenolpyruvoylglucosamine reductase

-2.23

 

-0.60

Cell motility

SF5M90T_1938

fliQ

flagellar biosynthetic protein

3.55

  

Intracellular trafficking, secretion and vesicular transport

   

SF5M90T_3964

secE

preprotein translocase

0.87

-1.06

-0.76

SF5M90T_3580

tatC

Sec-independent protein translocase

0.84

 

-0.57

SF5M90T_3501

yiiO

uncharacterized periplasmic protein

-4.72

 

2.64

Posttranslational modification, protein turnover, chaperones

SF5M90T_4204

mopB

co-chaperonin GroES

1.41

  

SF5M90T_3279

slyD

FKBP-type peptidyl-prolyl cis-trans isomerase

1.31

  

SF5M90T_462

ybbN

putative thioredoxin-like protein

0.90

  

SF5M90T_407

clpP

ATP-dependent proteolytic subunit of clpA-clpP serine protease

0.84

  

SF5M90T_3738

ibpA

heat shock protein

-1.17

  

SF5M90T_2074

yegD

putative heat shock protein

-2.80

 

-1.11

Information storage and processing

Translation, ribosomal structure and biogenesis

SF5M90T_2801

yfiA

translation inhibitor protein RaiA

2.70

  

SF5M90T_2392

gltX

glutamate tRNA synthetase, catalytic subunit

1.65

  

SF5M90T_155

frr

ribosome releasing factor

1.21

  

SF5M90T_650

glnS

glutamine tRNA synthetase

1.08

  

SF5M90T_3893

glyQ

glycine tRNA synthetase, alpha subunit

1.06

 

-0.50

SF5M90T_4220

yjeA

putative lysyl-tRNA synthetase

0.95

-1.75

-1.72

SF5M90T_3894

glyS

glycine tRNA synthetase, beta subunit

0.81

  

Transcription

SF5M90T_3025

ygiP

putative transcriptional regulator/nucleoid-associated protein

3.04

-4.57

-2.45

SF5M90T_2417

murR

HTH-type transcriptional regulator

2.35

  

SF5M90T_3510

rhaR

positive regulator for rhaRS operon

2.33

  

SF5M90T_1595

malI

repressor of malX and Y genes

1.98

  

SF5M90T_2125

yehT

putative two-component response regulator

1.80

  

SF5M90T_1373

cspC

cold shock protein

1.59

-1.38

 

SF5M90T_3349

malT

positive regulator of mal regulon

1.58

 

0.58

SF5M90T_3335

ompR

osmolarity response regulator

1.42

  

SF5M90T_3453

yiaG

putative transcriptional regulator

1.38

 

3.65

SF5M90T_2089

gatR

galactitol utilization operon repressor

1.33

  

SF5M90T_71

cra

transcriptional repressor of fru operon and others

1.16

  

SF5M90T_4197

yjdC

putative transcriptional regulator

1.15

 

1.37

SF5M90T_1370

 

putative regulator

1.09

  

SF5M90T_3578

rfaH

transcriptional activator

-1.57

 

-0.96

SF5M90T_4242

yjeB

HTH-type transcriptional repressor

-1.95

  

SF5M90T_984

cspH

cold shock-like protein

-3.35

  

Replication, recombination and repair

SF5M90T_2925

endA

DNA-specific endonuclease I

1.42

-3.26

-2.74

SF5M90T_3034

ygjF

G/U mismatch-specific DNA glycosylase

1.23

 

1.10

SF5M90T_410

hupB

DNA-binding protein HU-beta

1.08

  

SF5M90T_775

rhlE

putative ATP-dependent RNA helicase

-1.16

  

SF5M90T_3117

deaD

inducible ATP-independent RNA helicase

-1.20

  

SF5M90T_1769

dbpA

ATP-dependent RNA helicase

-1.86

  

Poorly characterized

General function prediction only

SF5M90T_2762

stpA

DNA-binding protein

3.51

-3.00

-2.60

SF5M90T_275

 

putative crossover junction endodeoxyribonuclease

2.84

  

SF5M90T_2418

muQ

N-acetylmuramic acid 6-phosphate etherase

2.77

 

-0.93

SF5M90T_1724

 

putative acetyltransferase

2.06

-2.41

 

SF5M90T_2435

 

putative amino acid antiporter

2.03

1.90

1.58

SF5M90T_2301

yfbT

putative phosphatase

2.00

  

SF5M90T_773

ybhG

putative membrane protein

1.78

1.02

 

SF5M90T_1227

hns

DNA-binding protein

1.69

-1.24

 

SF5M90T_2275

yfbB

putative enzyme

1.62

-1.90

-1.85

SF5M90T_3225

yrdA

putative transferase

1.51

  

SF5M90T_4236

hfq

RNA-binding protein

1.45

-2.10

 

SF5M90T_3315

gph

phosphoglycolate phosphatase

1.25

  

SF5M90T_2192

yeiR

putative GTPases

1.03

  

SF5M90T_1919

yedE

putative transport system permease protein

1.03

-1.83

-1.96

SF5M90T_3295

yhfC

putative transport

0.97

-1.30

-1.25

SF5M90T_2205

yejK

nucleoid-associated protein

0.95

  

SF5M90T_2066

yegH

putative transport protein

0.84

  

SF5M90T_3344

yhgH

putative gluconate periplasmic binding protein

0.81

  

SF5M90T_3102

yraM

putative glycosylase

0.73

  

SF5M90T_794

ybiP

putative enzyme

-1.14

  

SF5M90T_2207

yejM

putative sulfatase

-1.36

  

SF5M90T_3139

yhbE

putative permeases of drug/metabolite transporter superfamily

-1.36

 

-0.90

SF5M90T_966

yccA

putative carrier/transport protein

-1.38

 

-1.18

SF5M90T_2742

yqaB

putative phosphatase

-1.51

  

SF5M90T_3882

bax

putative ATP-binding protein

-1.70

 

-0.77

SF5M90T_3370

yhhX

putative regulator

-1.97

 

1.30

SF5M90T_3621

aslB

putative arylsulfatase regulator

-2.73

  

SF5M90T_2516

 

putative enzyme

-3.91

  

Function unknown

SFxv_3833

 

conserved hypothetical protein

3.59

-4.23

 

SF5M90T_2431

 

conserved hypothetical protein

2.89

  

SF5M90T_2432

 

conserved hypothetical protein

2.69

  

SF5M90T_11

 

uncharacterized protein

2.57

  

SF5M90T_1402

yeaD

conserved hypothetical protein

2.45

  

SF5M90T_828

ybjO

conserved hypothetical protein

2.23

 

-2.52

SF5M90T_1941

dsrB

conserved hypothetical protein

2.03

-2.43

 

SF5M90T_2302

yfbU

conserved hypothetical protein

1.87

  

SF5M90T_451

ybaK

conserved hypothetical protein

1.86

-1.21

-1.10

SSJG_00311

 

conserved hypothetical protein

1.75

 

-1.60

SF5M90T_5

yaaA

conserved hypothetical protein

1.54

  

SF5M90T_1387

 

conserved hypothetical protein

1.51

  

SF5M90T_3911

yiiU

conserved hypothetical protein

1.45

-2.49

 

SF5M90T_957

 

conserved hypothetical protein

1.37

  

SF5M90T_4146

yjgD

conserved hypothetical protein

1.28

-2.30

 

SF5M90T_2622

 

conserved hypothetical protein

1.24

-1.46

 

SF5M90T_3155

yhbN

conserved hypothetical protein

0.81

  

SF5M90T_479

ybbF

conserved hypothetical protein

-1.19

  

SF5M90T_2195

rtn

conserved hypothetical protein

-1.50

  

SF5M90T_438

ybaN

conserved hypothetical protein

-1.73

  

SF5M90T_1853

 

conserved hypothetical protein

-2.03

-2.58

 

SF5M90T_1647

 

conserved hypothetical protein

-2.11

  

SF5M90T_983

ymcD

conserved hypothetical protein

-2.34

  

SF5M90T_4094

yjbA

P-starvation inducible protein PsiE

-2.51

1.69

 

SF5M90T_1110

ycfJ

conserved hypothetical protein

-2.52

 

0.99

SF2861

 

hypothetical protein remnant

-2.64

  

SF5M90T_2146

yohO

membrane protein

-2.96

  

SF5M90T_1952

 

putative outer membrane pore protein

-2.98

  

SF5M90T_4307

 

putative inner membrane protein

-3.40

  

SF1231

 

conserved hypothetical protein

-3.71

 

-1.60

SF5M90T_427

ybaA

conserved hypothetical protein

-3.88

  

Phage related

    

S1668

relF

prophage maintenance protein

1.75

  

SF5M90T_1793

 

putative phage integrase protein

1.45

-1.60

 

SF5M90T_1056

 

hypothetical bacteriophage protein

1.14

  

SF5M90T_740

 

putative bacteriophage protein

-1.93

  
  1. aGenomes used as reference are: S. flexneri 5a str. M90T, S. flexneri 2a str. 301, S. flexneri 2002017, Shigella sp. D9 and S. flexneri 2457 T with GenBank accession numbers AGNM00000000, NC_004337, NC_017328, NZ_GG657384 and NC_004741 respectively.
  2. bGenes are classified in functional categories based on the database of Clusters of Orthologous Groups (COGs). http://www.ncbi.nlm.nih.gov/COG/. Inside each subgroup, genes 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

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