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Table 1 Transcriptional expression of pS88 and pAMM ORFs in different growth conditions compared to LB broth

From: Transcriptional analysis of the Escherichia coli ColV-Ia plasmid pS88 during growth in human serum and urine

Name

Gene

Function

LB with iron chelatorapS88

p b

Human serumex vivoapS88

p b

Human urineex vivoapS88

p b

Human urinein vivoapAMM

pS88001

int

Putative site-specific recombinase

0.85

0.775

0.59

0.427

0.73

0.505

0.84

pS88002

repA

RepFIB replication protein RepA

0.41

0.305

0.97

0.976

0.89

0.889

3.56

pS88003

 

Conserved hypothetical protein

1.67

0.496

1.26

0.758

3.09

0.159

7.26

pS88004

 

Conserved hypothetical protein

0.93

0.883

0.58

0.266

0.60

0.459

2.52

pS88006

 

Putative fragment of ImpB UV protection protein

0.48

0.578

0.77

0.550

1.51

0.367

1.17

pS88009

iutA

Ferric aerobactin receptor precursor IutA

4.12

0.007

4.23

0.006

4.01

0.048

9.02

pS88013

iucA

Aerobactin siderophore biosynthesis protein IucA

45.25

0.005

15.85

0.023

18.38

0.026

168.12

pS88014

shiF

Putative membrane transport protein ShiF

7.66

0.006

14.03

0.005

14.19

0.004

17.71

pS88015

 

Putative membrane protein; CrcB-like protein

2.40

0.105

0.82

0.807

4.19

0.051

6.08

pS88016

 

Conserved hypothetical protein

1.77

0.250

1.65

0.628

4.14

0.066

9.74

pS88017

 

Putative enolase

1.47

0.573

5.44

0.152

7.98

0.040

18.68

pS88019

sitD

SitD protein; iron transport protein

4.54

0.020

38.23

0.003

26.29

0.004

139.75

pS88022

sitA

SitA protein; iron transport protein

17.79

0.002

49.52

0.003

83.87

0.001

776.05

pS88026

 

Hypothetical protein

1.32

0.633

1.04

0.959

1.02

0.981

/ c

pS88027

 

Hypothetical protein; putative exported protein

0.70

0.626

1.04

0.956

0.31

0.187

/

pS88028

 

Conserved hypothetical protein

1.11

0.809

0.75

0.577

1.16

0.762

/

pS88029

 

Conserved hypothetical protein

1.30

0.712

1.22

0.751

2.20

0.260

/

pS88030

 

Conserved hypothetical protein

0.30

0.098

0.46

0.308

0.32

0.143

1.09

pS88031

 

Hypothetical protein

0.67

0.405

0.97

0.959

1.58

0.369

2.08

pS88037

sopA

SopA protein (Plasmid partition protein A)

0.60

0.227

0.47

0.147

1.12

0.847

0.98

pS88038

sopB

SopB protein (Plasmid partition protein B)

0.38

0.021

0.91

0.879

1.41

0.696

3.32

pS88039

 

Hypothetical protein

0.63

0.312

2.19

0.330

3.82

0.031

2.96

pS88040

 

Conserved hypothetical protein

0.73

0.510

2.74

0.240

3.61

0.031

3.61

pS88041

 

Hypothetical protein

1.39

0.295

0.42

0.174

1.77

0.092

1.47

pS88043

 

Hypothetical protein

0.89

0.782

1.47

0.378

2.00

0.188

1.83

pS88044

yubI

Putative antirestriction protein

1.35

0.720

1.13

0.890

0.99

0.991

3.38

pS88045

 

Conserved hypothetical protein

0.95

0.919

1.66

0.403

1.09

0.873

4.52

pS88046

 

Conserved hypothetical protein

0.80

0.717

1.38

0.661

1.25

0.735

2.07

pS88047

ydbA

Conserved hypothetical protein

1.71

0.542

0.99

0.987

1.33

0.739

4.18

pS88048

ydcA

Putative adenine-specific DNA methylase

1.44

0.652

1.09

0.917

1.52

0.606

3.98

pS88050

ssb

Single-stranded DNA-binding protein

1.56

0.383

2.42

0.152

1.96

0.211

2.91

pS88051

yubL

Conserved hypothetical protein

0.90

0.832

1.21

0.842

2.13

0.203

2.05

pS88054

ycjA

Putative DNA-binding protein involved in plasmid partitioning (ParB-like partition protein)

1.31

0.260

2.60

0.392

3.45

0.007

2.30

pS88055

psiB

Plasmid SOS inhibition protein B

0.74

0.414

5.34

0.094

3.26

0.026

4.03

pS88056

psiA

Plasmid SOS inhibition protein A

1.67

0.321

13.06

0.048

6.44

0.016

3.02

pS88057

flmC

Putative F-plasmid maintenance protein C

2.27

0.144

0.55

0.346

0.65

0.401

2.21

pS88059

yubN

Conserved hypothetical protein

2.01

0.441

0.90

0.902

1.20

0.826

3.52

pS88060

yubO

Conserved hypothetical protein

1.13

0.781

1.79

0.211

2.24

0.075

3.89

pS88061

yubP

Conserved hypothetical protein

1.43

0.397

2.40

0.109

1.72

0.408

4.27

pS88062

yubQ

X polypeptide (P19 protein); Putative transglycosylase

0.94

0.948

0.88

0.910

1.20

0.852

4.90

pS88063

traM

Protein TraM (Conjugal transfer protein M)

0.77

0.313

0.94

0.866

0.92

0.769

0.25

pS88064

traJ

Protein TraJ (Positive regulator of conjugal transfer operon)

0.39

0.212

2.86

0.310

1.08

0.898

1.98

pS88066

traA

Fimbrial protein precursor TraA (Pilin)

1.59

0.053

0.54

0.188

0.19

0.004

0.21

pS88092

traT

Complement resistance and surface exclusion outer membrane protein TraT

0.27

0.265

0.54

0.573

0.82

0.847

0.35

pS88095

traX

F pilin acetylase TraX

0.56

0.157

0.54

0.409

0.72

0.389

0.88

pS88096

finO

Fertility inhibition protein FinO (Conjugal transfer repressor)

0.49

0.127

0.98

0.968

0.88

0.732

1.21

pS88097

yigA

Conserved hypothetical protein YigA

1.22

0.803

2.08

0.427

0.95

0.953

0.50

pS88098

yigB

Putative nuclease YigB

0.46

0.241

0.47

0.463

1.34

0.648

2.34

pS88099

repA2

Replication regulatory protein RepA2 (Protein CopB)

1.27

0.340

1.43

0.199

2.24

0.071

1.93

pS88100

repA1

Replication initiation protein RepA1

0.56

0.120

1.14

0.702

2.18

0.072

1.53

pS88101

yacA

Conserved hypothetical protein YacA. possible repressor

0.49

0.344

0.96

0.961

0.41

0.293

4.30

pS88102

yacB

Putative plasmid stabilization system protein YacB

0.31

0.169

0.64

0.502

0.32

0.227

1.57

pS88103

yacC

Putative exoribonuclease YacC

0.38

0.209

0.56

0.461

0.50

0.369

0.95

pS88104

cia

Colicin-Ia

5.11

0.105

21.06

0.023

6.03

0.087

70.36

pS88105

imm

Colicin-Ia immunity protein

1.10

0.944

5.58

0.048

3.46

0.106

3.17

pS88106

ybaA

Conserved hypothetical protein YbaA

5.25

0.197

4.87

0.189

8.90

0.096

3.27

pS88108

ydeA

Conserved hypothetical protein YdeA

0.45

0.247

0.31

0.165

0.41

0.222

0.51

pS88109

ydfA

Conserved hypothetical protein YdfA

0.17

0.119

0.69

0.733

0.36

0.284

0.58

pS88110

 

Putative acetyltransferase

0.71

0.606

0.98

0.983

0.77

0.684

1.57

pS88111

 

Predicted dehydrogenase

1.41

0.562

0.31

0.126

0.88

0.801

1.48

pS88112

 

Predicted dehydrogenase

1.25

0.691

0.63

0.416

1.19

0.736

0.87

pS88113

 

Predicted dehydrogenase

0.92

0.893

1.13

0.850

1.65

0.509

3.02

pS88114

cvi

Microcin V immunity protein

0.84

0.735

1.13

0.846

2.17

0.203

4.48

pS88115

cvaC

Microcin V precursor (Microcin V bacteriocin)

21.96

0.007

17.27

0.010

29.58

0.016

61.11

pS88116

cvaB

Microcin V secretion/processing ATP-binding protein CvaB

12.88

0.010

17.55

0.001

19.43

0.006

162.02

pS88117

cvaA

Microcin V secretion protein CvaA

26.23

0.012

44.02

0.005

43.81

0.019

215.77

pS88118

 

Conserved hypothetical protein

3.99

0.095

4.66

0.066

3.32

0.219

7.46

pS88123

 

Putative Phospho-2-dehydro-3-deoxyheptonatealdolase

354.6

0.000

190.9

0.001

109.6

0.006

144.67

pS88124

iroN

IroN. Salmochelin siderophore receptor

2.94

0.137

2.14

0.465

1.95

0.394

28.97

pS88128

iroB

IroB. Putative glucosyltransferase

72.17

0.001

48.95

0.002

37.97

0.014

69.71

pS88130

 

Conserved hypothetical protein

1.84

0.336

3.36

0.198

10.36

0.029

3.10

pS88131

 

Conserved hypothetical protein

2.43

0.318

9.11

0.031

13.83

0.039

14.66

pS88132

 

Hypothetical protein

0.20

0.013

0.95

0.871

0.63

0.482

0.40

pS88133

iss

Iss (Increased serum survival)

0.28

0.083

0.48

0.282

0.36

0.151

0.66

pS88136

 

Hypothetical protein

0.93

0.896

1.51

0.618

1.71

0.391

0.65

pS88137

 

Conserved hypothetical protein; Putative GTPase

0.40

0.263

0.52

0.504

0.64

0.580

1.59

pS88142

 

Conserved hypothetical protein

0.51

0.096

0.48

0.134

0.77

0.458

/

pS88143

 

Conserved hypothetical protein

0.57

0.090

0.70

0.646

0.84

0.750

/

pS88146

etsC

Putative type I secretion outer membrane protein EtsC

1.05

0.893

0.42

0.208

0.78

0.478

0.61

pS88148

etsA

Putative type I secretion membrane-fusion protein EtsA

0.49

0.126

0.34

0.211

0.36

0.050

0.31

pS88154

 

Hypothetical protein

0.47

0.330

4.44

0.163

1.25

0.790

3.00

pS88155

ompT

Outer membrane protease (omptin)

0.48

0.178

0.43

0.092

0.42

0.137

0.37

pS88156

hlyF

Hemolysin HlyF

1.02

0.981

0.44

0.402

0.72

0.507

0.14

pS88157

 

Conserved hypothetical protein; putative Mig-14 protein

1.11

0.921

0.47

0.376

0.94

0.942

0.11

S88-1832

gapA d

Glyceraldehyde-3-phosphate dehydrogenase

1.70

0.396

0.46

0.254

1.15

0.789

0.90

S88-0266

dinB d

DNA polymerase IV

0.69

0.343

2.36

0.131

0.69

0.317

0.90

S88-4457

yjaD d

NADH pyrophophatase

0.85

0.586

0.91

0.698

1.26

0.344

1.24

  1. a Fold changes of transcription levels relative to reference condition (growth in LB). Fold change > 4 are in bold print.
  2. b p value in Student’s t test for the comparison of the three biological replicates for each experiment in different growth conditions and the reference condition. p < 0.05 are in bold print.
  3. c ORFs present in plasmid pS88 but absent from plasmid pAMM. d Housekeeping genes.
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BMC Microbiology

ISSN: 1471-2180

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