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Table 4 Change in protein expression in response to nitrogen and carbon-nitrogen limitation in comparison with carbon-limitation

From: The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach

 

Locus tag

Gene symbol

Protein

Transcript

    

D.E

Peptides No.a

Fold change

P -value

Differential protein expression of CN vs. C

   

Energy metabolism

       

ATP synthase F1, α-sub

PP5415

AtpA

only in CN

12

ND

ND

Glycogen debranching

PP4055

GlgX

4.5

20

1.9

0.05

Acetolactate synthase

PP3365

  

3.5

15

-1.0

n.s.

Isocitrate dehydrogenase

PP4011

ICD

-5.0

28

-1.4

n.s.

Acetoin dehydrogenase ¥ α-sub

PP0555

AcoA

-4.0

 

7

-8.3

0

Acetoin dehydrogenase β-sub

PP0554

AcoB

-5.6

23

-4.2

0

Acetoin dehydrogenase

PP0553

AcoC

-3.7

10

-4.0

0

Nitrogen metabolism

       

Nitrogen regulatory protein P-II

PP5234

GlnK

only in CN

6

10.4

0

Protein synthesis

       

Elongation factor Tu

PP0452

TUF-2

only in CN

16

-1.6

n.s.

Amino acid transport and biosynthesis

       

Branched-chain amino acid ABC trans

PP4841

LivK

26.4

22

4.5

0

Glutamine synthetase

PP5046

GlnA

2.2

28

1.0

n.s.

Signal transduction

       

Response regulator

PP5048

NtrC

6.7

43

1.7

n.s.

Transport and binding protein

       

Outer membrane porin

PP1206

OprD

2.7

11

-1.1

n.s.

Outer membrane porin

PP2089

OprF

2.6

21

1.2

n.s.

Purine ribonucleotide biosynthesis

       

adenylosuccinate synthetase

PP4889

PurA

-4.4

16

-1.1

n.s.

Hypothetical protein

PP2384

  

-2.8

6

1.5

n.s.

Protein fate

PP0980

PepA

-2.3

30

1.0

n.s.

Differential protein expression of N vs. C

    

Energy metabolism

       

Succinyl-CoA synthetase

PP4185

SucD

only in N

8

1.2

n.s.

ATP synthase F1, alpha sub

PP5415

AtpA

only in N

13

ND

ND

Glycogen debranching

PP4055

GlgX

12.3

31

2.4

n.s.

Electron transfer flavoprotein

PP4203

  

4.5

36

0.90

n.s.

Succinate dehydrogenase

PP4191

SdhA

3.9

23

2.8

n.s.

NADH dehydrogenase I

PP4123

NuoF

2.9

15

2.4

n.s.

Glycosyl hydrolase

PP4053

  

2.6

21

3.0

n.s.

Phosphoenolpyruvate synthase

PP2082

PpsA

2.4

24

1.5

n.s.

Acetoin dehydrogenase β-sub

PP0554

AcoB

only in C

23

-4.0

0

Acetoin dehydrogenase

PP0553

AcoC

only in C

10

-5.3

0

Malate synthase

PP0356

GlcB

-9.1

9

-1.2

n.s.

Aldehyde dehydrogenase

PP0545

GlcB

-5.9

19

-1.9

n.s.

thioredoxin reductase

PP0786

TrxB

-5.6

11

1.3

n.s.

Isocitrate lyase

PP4116

AceA

-4.2

19

1.3

n.s.

Isocitrate dehydrogenase

PP4011

ICD

-2.1

14

1.1

n.s.

Fatty acid metabolism

       

3-hydroxyacyl-CoA dehydrogenase

PP2047

  

only in N

18

20.9

0

Acetyl-CoA acetyltransferase

PP2051

AtoB

only in N

20

27.9

0

acetyl-CoA carboxylase

PP0558

AccC-1

8.3

27

1.3

n.s.

Fatty oxidation complex α-sub

PP2136

FadB

3.1

13

2.3

n.s.

3-oxoacyl-CoA thiolase

PP2137

FadA

3.0

23

2.4

n.s.

Fatty-acid CoA ligase

PP0763

  

-2.9

15

-1.1

n.s.

Transport and binding protein

       

Outer membrane porin

PP2089

OprF

5.4

17

1.4

n.s.

ABC transporter

PP1726

  

-25.0

15

1.2

n.s.

Amino acid transport and biosynthesis

       

Branched-chain amino acid ABC

PP4864

  

only in N

9

-1.1

n.s.

Amino acid biosynthesis

PP5046

GlnA

16.0

17

1.5

n.s.

Hydantoin racemase

PP4310

  

8.8

15

1.2

n.s.

General amino acid ABC transporter

PP1300

AapP

4.0

16

1.1

n.s.

amino acid ABC transporter

PP1071

  

only in C

23

-2.0

n.s.

amino acid ABC transporter

PP0282

  

-33.3

15

-1.2

n.s.

Branched-chain amino acid ABC

PP4867

  

-16.7

11

1.8

n.s.

Dipeptide ABC transporter

PP0885

  

-5.0

22

1.2

n.s.

Amino acid biosynthesis

PP0671

GlyA-2

-3.6

20

-1.3

n.s.

Cell envelope

       

Outer membrane protein H1

PP1185

OprH

only in N

8

6.6

0.01

Cellular processes

       

Small multidrug resistance

PP4930

  

4.9

216

1.1

n.s.

superoxide dismutase

PP0915

SodB

-20.0

4

-1.3

n.s.

DNA interactions

       

Transcriptional regulator, LysR

PP5375

  

-12.5

5

-1.5

n.s.

C4-type zinc finger protein

PP4693

  

-11.1

5

1.4

n.s.

Protein fate

       

ATP-dependent Clp protease

PP2300

  

only in N

7

1.2

n.s.

Protein synthesis

       

Elongation factor-G

PP0451

FusA-1

20.0

26

1

n.s.

Hypotetical protein

PP2050

  

9.4

10

28.4

0

Purine ribonucleotide biosynthesis

PP0722

PrsA

6.6

24

2.0

n.s.

Cell division

PP1342

FtsZ

-7.1

5

1.0

n.s.

Nucleoside interconversions

PP0849

NDK

-3.3

6

1.2

n.s.

Biosynthesis of co-factors

PP0842

IscS-1

-2.9

18

1.3

n.s.

Chemotaxis and motility

PP4366

FliL

-2.3

7

1.3

n.s.

  1. ¥ Bold font indicates matching between protein and transcript changes
  2. aAmount of peptides utilized for protein identification
  3. ND, Not determined
  4. n.s., P-value not significant (> 0.05)
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Microbial Cell Factories

ISSN: 1475-2859

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