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Table 1 Transcriptional characteristics of the genes within the nitrogen fixation island of P. stutzeri A1501

From: Global transcriptional analysis of nitrogen fixation and ammonium repression in root-associated Pseudomonas stutzeri A1501

 

Gene name

Functional description

Ammonium shocka

Nitrogen fixationb

Consensus sequencec

     

NifA

RpoN

PST1302

 

glutaredoxin-related protein

0.06

16.83

  

PST1303

 

thiosulfate sulfurtransferase glpE

0.03

53.99

  

PST1304

nifQ

nitrogen fixation protein NifQ

0.03

46.56

  

PST1305

 

arsenate reductase related protein

0.03

38.67

  

PST1306

nifB

FeMo cofactor biosynthesis protein NifB

0.06

21.46

Yes

Yes

PST1307

 

conserved hypothetical protein

0.57

1.87

No

Yes

PST1308

 

transcriptional regulator, LysR family

0.43

2.22

No

No

PST1309

 

conserved hypothetical protein

0.84

1.12

No

No

PST1310

 

transcriptional regulator, AraC family

1.03

1.02

No

No

PST1311

 

fosmidomycin resistance protein

0.81

1.34

No

Yes

PST1312

tpmA

thiopurine s-methyltransferase

0.34

2.65

No

Yes

PST1313

nifA

positive regulatory protein

0.15

6.95

  

PST1314

nifL

negative regulatory protein

0.12

7.68

Yes

Yes

PST1315

rnfA

electron transport complex, A subunit

0.37

2.66

Yes

Yes

PST1316

rnfB

electron transport complex, B subunit

0.10

9.94

  

PST1317

rnfC

electron transport complex, C subunit

0.49

2.22

  

PST1318

rnfD

electron transport complex, D subunit

0.13

7.67

  

PST1319

rnfG

electron transport complex, G subunit

0.16

7.47

  

PST1320

rnfE

electron transport complex, E subunit

0.15

8.80

  

PST1321

rnfH

electron transport complex, H subunit

0.21

17.55

  

PST1322

nifY2

iron-molybdenum cofactor biosynthesis protein

0.10

21.74

  

PST1323

 

nitrogen fixation-related protein

0.18

13.73

  

PST1324

 

conserved hypothetical protein

0.15

25.99

  

PST1325#

 

conserved hypothetical protein

0.15

9.68

Yes

Yes

PST1326

nifH

Fe protein

0.32

94.05

Yes

Yes

PST1327

nifD

MoFe protein, alpha subunit

0.56

54.16

  

PST1328

nifK

MoFe protein, beta subunit

0.62

38.22

  

PST1329

nifT

nitrogen fixation protein

1.70

7.82

  

PST1330

nifY

iron-molybdenum cofactor biosynthesis protein

0.33

8.51

  

PST1331

 

conserved hypothetical protein

0.41

12.55

  

PST1332

 

leucine-rich repeat domain protein

0.57

3.27

No

Yes

PST1333

nifE

iron-molybdenum cofactor biosynthesis protein

0.05

35.82

Yes

Yes

PST1334

nifN

iron-molybdenum cofactor biosynthesis protein

0.07

13.32

  

PST1335

nifX

iron-molybdenum cofactor biosynthesis protein

0.10

37.97

  

PST1336

 

protein of unknown function DUF269

0.29

5.06

  

PST1337

 

protein of unknown function DUF683

0.05

63.84

  

PST1338

 

ferredoxin, 4Fe-4S

0.08

31.07

Yes

Yes

PST1339

 

ferredoxin, 2Fe-2S

0.76

2.94

  

PST1340

 

conserved hypothetical protein

0.82

1.28

  

PST1341

 

conserved hypothetical protein

0.85

1.28

  

PST1342

 

conserved hypothetical protein

0.43

3.69

  

PST1343

 

conserved hypothetical protein

0.70

2.56

  

PST1344

 

conserved hypothetical protein

0.21

7.16

Yes

Yes

PST1345

modC

molybdenum transport protein ModC

0.79

1.59

  

PST1346

modB

molybdate ABC transporter

0.48

2.05

  

PST1347

modA

molybdenum ABC transporter

0.20

4.12

  

PST1348

 

putative molybdenum-binding protein

0.22

3.88

Yes

Yes

PST1349

hesB

Fe-S cluster assembly protein

0.07

20.92

Yes

Yes

PST1350

nifU

Fe-S cluster assembly protein NifU

0.11

10.77

  

PST1351

nifS

nitrogenase metalloclusters biosynthesis protein

0.11

16.21

  

PST1352

nifV

homocitrate synthase

0.05

24.55

  

PST1353

cysE

serine acetyltransferase (cysE-like)

0.05

32.98

  

PST1354

 

conserved hypothetical protein

0.10

11.11

  

PST1355

nifW

nitrogenase stabilizing/protective protein

0.16

26.04

  

PST1356

nifZ

Fe-S cofactor synthesis protein

0.17

18.17

  

PST1357

nifM

putative peptidyl-prolyl cis/trans isomerase

0.19

18.78

  

PST1358

 

ATP-dependent Clp protease

0.56

8.42

  

PST1359

nifF

flavodoxin for electron transfer

0.86

14.91

Yes

Yes

  1. aInduction ratio (ammonium shock conditions/nitrogen fixation conditions) after exposure of bacteria to 20 mM ammonia for 10 min.
  2. bInduction ratio (nitrogen fixation conditions/nitrogen-excess conditions).
  3. cORF(s) preceded by a consensus sequence that resembles the NifA or RpoN consensus sequence for A1501. The predicted NifA-σ54-dependent operons are shown in Figure 2B.
  4. #Also designated pnfA in this study.
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BMC Genomics

ISSN: 1471-2164

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