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Table 1 Compendium of quantitative proteomic changes at different growth conditions

From: The metabolic potential of Escherichia coli BL21 in defined and rich medium

Group1

Hunger

Feast

Famine

Transcriptional regulation2

Mineral salt medium at exponential phase

Rich medium at exponential phase

Rich medium at stationary phase

Protein1

Function1

Relative Protein Mass (RPM)1-%

Activation

Repression

Sigma factor

Upper glycolysis

      

 FbaB

FBP → DHAP + G3P

0.03

0.00

0.08

 

Cra

RpoS

 TpiA

DHAP → G3P

0.26

0.21

0.39

 

Cra

RpoS, RpoD

Lower glycolysis

      

 GapA

G3P → 1,3-BPG

0.70

0.97

1.23

CRP-cAMP

Cra

RpoS, RpoD

 GpmA

3PG → 2PG

0.27

0.38

0.62

 

Fur

RpoS, RpoD

Pyruvate dehydrogenase

      

 AceE

Pyruvate → Acetyl-CoA + CO2

0.82

2.15

1.49

CRP-cAMP

Cra, PdhR

RpoS, RpoD

 AceF

0.34

0.82

0.58

CRP-cAMP

Cra, PdhR

RpoS, RpoD

Acetate metabolism

      

 Acs

Acetate → Acetyl-CoA

0.10

0.06

0.35

CRP-cAMP

Fis

RpoS, RpoD

 PoxB

Pyruvate → Acetate + CO2

0.02

0.02

0.08

  

RpoS, RpoD

 Pta

Acetyl-CoA → Acetyl-Phosphate

0.14

0.35

0.17

ArcA-P

  

 AckA

Acetyl-Phosphate → Acetate

0.12

0.36

0.15

ArcA-P

 

RpoH

TCA cycle

      

 GltA

Oxaloacetate + Acetyl-CoA → Citrate

1.12

0.29

1.25

CRP-cAMP

ArcA-P

RpoD

 AcnB

Citrate → Isocitrate

0.88

0.60

1.06

CRP-cAMP

ArcA-P, Fis

RpoD

 SucD

Succinyl-CoA → Succinate

0.49

0.22

0.60

CRP-cAMP

ArcA-P

RpoS, RpoD

 SdhA

Succinate → Fumarate

0.64

0.26

0.59

CRP-cAMP

ArcA-P

RpoD

 FumA

Fumarate → (S)-Malate

0.07

0.03

0.10

CRP-cAMP

ArcA-P

RpoD

Amino acid biosynthesis

      

 IlvC

Branched-chain amino acids biosynthesis

2.83

0.16

0.13

 

Leucine 3

RpoD

 MetE

Methionine biosynthesis

3.60

0.10

0.16

 

Methionine 3

 

 CysK

Cysteine biosynthesis

0.67

0.19

0.45

 

Cysteine 3

RpoD

 ThrB

Threonine biosynthesis

0.08

0.03

0.06

DksA-ppGpp

 

RpoD

 HisC

Histidine biosynthesis

0.09

0.00

0.04

DksA-ppGpp

 

RpoD

RNA polymerases

      

 RpoA

RNA polymerase, core enzyme

0.51

0.74

0.37

 

DksA-ppGpp

RpoD

Ribosomal proteins

      

 RplL

50S ribosomal subunit protein

0.70

0.95

0.53

 

DksA-ppGpp

 

 RpsA

30S ribosomal subunit protein

0.86

2.11

0.88

 

DksA-ppGpp

RpoD

Elongation factors

      

 FusA

Elongation factor G

1.49

2.18

1.39

 

DksA-ppGpp

RpoD, RpoE

 TufA

Elongation factor Tu (EF-Tu)

3.51

5.66

3.98

 

DksA-ppGpp

RpoD, RpoE

Amino acid degradation

      

 AstA

Arginine (to succinate) degradation

0.03

0.00

0.10

  

RpoS

 AstB

0.03

0.03

0.06

  

RpoS

(Metabolite) degradation

      

 GabD

4-Aminobutyrate (GABA) degradation

0.10

0.09

0.17

CRP-cAMP

 

RpoS

 GabT

0.00

0.00

0.10

CRP-cAMP

 

RpoS

 TreA

Trehalose degradation

0.06

0.03

0.05

  

RpoS

Hydroperoxide reductases and superoxide dismutase

      

 Tpx

Antioxidant under anaerobic condition

0.08

0.06

0.17

 

ArcA-P

RpoD

 SodB

Superoxide dismutase

0.14

0.12

0.91

 

CRP-cAMP

RpoD

DNA protection and repair

      

 Dps

Protection of the DNA from damage

0.03

0.05

0.65

 

Fis

RpoS

 UspA

A member of the RecA-dependent DNA protection and repair system

0.11

0.07

0.20

 

FadR

RpoD

  1. 1Functional classification is mostly according to EcoCyc database (http://ecocyc.org/) and confirmed by KEGG database (http://www.genome.jp/kegg/). Only examples from important groups are given the detailed analysis of the abundance levels of all identified proteins is found in Additional file 1: Table S1 or Additional file 2: Table S5 for the entire data set including standard deviation. The RPM (%) of up-regulated proteins in bold letters for better recognition.
  2. 2The information of transcriptional regulation is from RegulonDB Version 7.0 (http://regulondb.ccg.unam.mx). According to the differences of each protein’s Relative Protein Mass at hunger, feast and famine conditions, the most (feasible) dominating transcription and sigma factors controlling the expression of the corresponding gene are given in bold letters.
  3. 3Feed-back inhibition of amino acid biosynthesis (enzymes) by the end products of the corresponding pathways.