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Table 2 Differentially expressed proteins identified in P. putida UW4 wild-type (WT) and mutant strains, grouped by putative functional role.

From: Proteomic analysis of the response of the plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stress

Protein*

Accession number†

MW(kDa)/pI§

Score/Sequence coverage %¶

WT Ratio‡

Mut Ratio‡

Amino acid metabolism

     

1. ACC deaminase

Q4KK38_PSEF5

35.1/5.37

84.15/9.06

1.58

N/A

2. diaminopimelate decarboxylase

Q3K4R9_PSEPF

45.1/4.97

93.68/10.6

10.3

2.80

3. porphyromonas-type peptidyl-arginine deiminase

Q3KJM1_PSEPF

40.7/4.81

40.07/8.7

2.08

1.54

4. arginine biosynthesis protein

Q3K7U0_PSEPF

42.6/5.16

96.15/8.89

-3.05

-2.48

5. aminotransferase

Q3KG66_PSEPF

43.3/6.01

98.92/19.14

-2.32

-2.87

6. 3-isopropylmalate dehydratase

Q3KF23_PSEPF

24.2/5.39

87.37/35.98

N/S

-1.79

7. anthranilate synthase

Q4K4Z5_PSEF5

54.2/5.08

92.94/15.96

N/S

-3.25

General stress

     

8. universal stress protein

Q4KFC6_PSEF5

16.2/5.95

78.23/20.69

1.99

1.80

9. general stress protein CTC

Q3K6W3_PSEPF

21.2/5.99

98.62/16

3.56

2.08

Transport/efflux

     

10. major outer membrane protein

Q9X4L6_PSEFL

36.5/4.68

90.82/13.08

2.00

2.15

11. outer membrane protein OMP85

Q4KHG8_PSEF5

87.5/5.21

128/20 ¶

3.58

1.56

12. porin D

Q48FB5_PSE14

46.9/4.94

60.66/4.32

2.44

3.66

13. ArsA

Q89K44_BRAJA

63.5/5.81

99/4

1.89

1.68

Protein synthesis and folding

     

14. peptidyl-prolyl cis-trans isomerase B

Q87YQ0_PSESM

18.2/5.86

71.15/6.59

-1.62

1.55

15. ribosome recycling protein

Q886P0_PSESM

20.4/6.76

46.7/8.65

-2.16

-1.51

16. glutaminyl-tRNA synthetase

Q1IBQ0_9PSED

64.5/5.62

91.43/10.41

-2.29

N/S

Cell cycle and communication

     

17. MinD

Q3KFL9_PSEPF

33.7/5.55

99.17/29.7

-1.59

-1.51

18. DNA-binding protein

Q889U1_PSESM

20.9/5.88

46.84/16.93

-2.27

N/S

19. transcription regulator TraR/DksA family

Q3K6R3_PSEPF

16.8/5.21

62.4/20.41

-1.59

N/S

Anti-oxidative

     

20. thiol specific antioxidant

Q3KD94_PSEPF

17.6/4.99

87.21/30.72

3.38

N/S

21. ferredoxin NADP-reductase

Q48FA2_PSE14

29.6/5.32

97.54/29.73

1.69

1.77

22. GTP-binding protein TypA

Q3KJG5_PSEPF

67.0/5.40

95.1/9.9

2.32

1.5

23. superoxide dismutase

Q3K7N1_PSEPF

22.0/5.56

99.86/50.51

5.62

4.63

24. thioredoxin

Q3K4W0_PSEPF

11.7/5.06

95.81/44.04

19.8

3.41

25. 2-oxo-acid dehydrogenase

Q3KJ49_PSEPF

99.4/5.48

98.77/9.31

N/S

1.73

Other

     

26. ubiquinone dehydrogenase

Q3KA62_PSEPF

25.3/5.16

73.16/22.77

N/S

-1.93

27. thiolase

Q4ZY90_PSEU2

40.4/5.91

89.57/6.89

-1.82

N/S

28. similar to immunodominant antigen B

Q4L351_STAHJ

18.3/5.08

48.52/10.56

29.6

N/S

29. aldo/keto reductase

Q3K722_PSEPF

38.9/5.88

69.66/12.72

-1.61

N/S

30. pterin-4-alpha-carbinolamine dehydratase

Q3KG65_PSEPF

13.3/5.83

99.4/78.81

-2.91

2.08

31. isocitrate dehydrogenase

Q4K9U5_PSEF5

45.3/5.27

99.97/27.75

-1.77

N/S

32. transaldolase

Q3K9H0_PSEPF

33.7/5.66

96.25/15.26

-2.8

N/S

33. dihydrodipicolinate synthase

Q3KGJ2_PSEPF

31.3/5.77

97.86/39.04

-1.83

N/S

34. hypothetical protein

Q3KFH8_PSEPF

55.6/5.51

82.14/5.87

2.01

1.52

35. hypothetical protein

Q3KI45_PSEPF

25.7/5.36

83.22/12.61

N/S

-1.51

  1. * Protein numbering refer to numbers in Figure 2.
  2. † Accession number of top database match from the UniprotKB database.
  3. §MW and pI were calculated from amino acid sequence and compared with gel location.
  4. ¶Score and sequence coverage were calculated by PEAKS software except for the underlined value, which used MASCOT scores. All identifications were confirmed using MASCOT MS/MS ion search and/or peptide-fingerprinting and significant matches (p < 0.05) were retained.
  5. ‡ Ratios were calculated as R = (treated/control) or R = -(control/treated) for up-regulated and down-regulated proteins respectively. N/S, expression was not significantly altered; N/A, not applicable. All ratios shown are statistically significant (p < 0.05).