Table 1

Differentially expressed proteins identified in Cr(VI)-challenged LB-grown F1

Gene ID

Functional category

Protein function

Poisson regression coefficient

FDR


Pput 4553

Inorganic ion transport and metabolism

periplasmic binding protein

26.59

3.89E-17

Pput 0942

Coenzyme transport and metabolism

Methyltransferase type 11

26.54

2.60E-16

Pput 1043

Inorganic ion transport and metabolism

TonB-dependent hemoglobin/transferrin/lactoferrin family receptor

25.63

1.59E-06

Pput 4550

Unknown Function

protein of unknown function DUF399

25.29

9.88E-05

Pput 0984

Energy production and conversion

fumarate lyase

25.06

3.01E-27

Pput 1680

Secondary metabolites biosynthesis, transport and catabolism

amino acid adenylation domain

24.97

1.82E-03

Pput 1675

Secondary metabolites biosynthesis, transport and catabolism

amino acid adenylation domain

24.84

6.16E-08

Pput 1968

Inorganic ion transport and metabolism

periplasmic solute binding protein

24.76

2.34E-07

Pput 1678

Inorganic ion transport and metabolism

TonB-dependent siderophore receptor

24.38

4.17E-05

Pput 1640

Amino acid transport and metabolism

2,4-diaminobutyrate 4-transaminase

23.81

9.88E-08

Pput 1961

Unknown Function

MbtH domain protein

23.60

2.47E-06

Pput 5216

Intracellular trafficking, secretion and vesicular transport

TonB system transport protein ExbD type-1

23.42

2.62E-05

Pput 0892

Unknown Function

2OG-Fe(II) oxygenase

23.24

1.54E-04

Pput 5104

Energy production and conversion

Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family

22.97

1.82E-03

Pput 3040

Cell Motility

hypothetical protein

22.78

1.55E-07

Pput 0943

none

lipopolysaccharide kinase

22.76

7.08E-03

Pput 0603

Unknown Function

hypothetical protein

22.76

7.08E-03

Pput 1679

Unknown Function

protein of unknown function DUF323

22.76

7.08E-03

Pput 3610

Cell wall membrane and envelope biogenesis

Lytic transglycosylase, catalytic

22.76

7.08E-03

Pput 1973

Secondary metabolites biosynthesis, transport and catabolism

Lysine/ornithine N-monooxygenase-like protein

22.76

2.34E-07

Pput 0636

Coenzyme transport and metabolism

aminotransferase class-III

-0.73

9.20E-03

Pput 3436

Carbohydrate transport and metabolism

methylisocitrate lyase

-0.74

6.72E-03

Pput 0936

Energy production and conversion

hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha subunit

-0.76

2.05E-12

Pput 2460

Post translational modification and protein turnover chaperones

heat shock protein Hsp20

-0.80

1.67E-03

Pput 1617

Energy production and conversion

cytochrome c oxidase, cbb3-type, subunit II

-0.90

1.30E-05

Pput 1610

Energy production and conversion

cytochrome c oxidase, cbb3-type, subunit III

-0.92

4.85E-05

Pput 1615

Energy production and conversion

cytochrome c oxidase, cbb3-type, subunit III

-0.92

2.47E-06

Pput 1123

Inorganic ion transport and metabolism

bacterioferritin

-1.06

9.58E-03

Pput 2593

Lipid transport and metabolism

3-oxoacid CoA-transferase, B subunit

-1.16

3.81E-03

Pput 4498

Lipid transport and metabolism

acetyl-CoA acetyltransferase

-1.23

3.34E-07

Pput 4329

Amino acid transport and metabolism

thiamine pyrophosphate enzyme TPP binding domain protein

-1.25

4.49E-03

Pput 1388

Amino acid transport and metabolism

putative agmatinase

-1.82

8.75E-11

Pput 0143

Energy production and conversion

cytochrome c, class I

-1.84

5.95E-09

Pput 2061

Inorganic ion transport and metabolism

catalase/peroxidase HPI

-2.01

8.74E-07

Pput 3734

Energy production and conversion

NADH:flavin oxidoreductase/NADH oxidase

-2.60

1.37E-04

Pput 2594

Lipid transport and metabolism

3-oxoacid CoA-transferase, A subunit

-3.14

7.15E-09

Pput 2025

Transcription

transcriptional regulator, GntR family

-19.95

9.31E-03

Pput 1948

none

cytochrome c, class I

-22.49

1.37E-04

Pput 1559

Transcription

putative transcriptional regulator, AsnC family

-22.95

9.31E-03

Pput 2382

Energy production and conversion

Gluconate 2-dehydrogenase

-23.20

1.83E-03

Pput 3735

Transcription

AraC-type transcriptional regulator domain protein

-24.08

4.39E-03

Pput 1496

Signal transduction mechanisms

Two-component, sigma54 specific, transcriptional regulator, Fis family

-24.95

9.31E-03


FDR: False Discovery Rate

Table 1 lists top 20 up-regulated and down-regulated proteins in LB-grown chromate shocked cells of P. putida when compared to unstressed LB grown cells. Poisson regression coefficient score and False Discovery Rate (FDR) of 1% were used for analyzing expression levels of the proteins.

Thompson et al. BMC Genomics 2010 11:311   doi:10.1186/1471-2164-11-311

Open Data