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Table 1 Fold-changes of predicted and verified CtsR and HrcA regulon members a in the NZ3410 (Δ ctsR ), NZ3425 CM (Δ hrcA :: cat ), and NZ3423 CM (Δ ctsR Δ hrcA :: cat ) strains compared with the wild type

From: Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation

IDb

Name

Function

p-valuec

28°C

40°C

    

ΔctsR

ΔhrcA

ΔctsR ΔhrcA

ΔctsR

ΔhrcA

ΔctsR ΔhrcA

CtsR

         

lp_0786

clpP

Endopeptidase Clp, proteolytic subunit

 

2.42 d

−1.09

2.33

1.27

−1.29

1.12

lp_1269

clpE

ATP-dependent Clp protease, ATP-binding subunit ClpE

2.0·10-10

2.27

−1.02

2.12

−1.01

−1.20

−1.12

lp_1903

clpB

ATP-dependent Clp protease, ATP-binding subunit ClpB

5.0·10-10

7.01

1.00

6.92

4.24

−1.33

3.71

lp_1018

ctsR

transcription repressor of class III stress genes

 

−696

−1.15

−984

−526

−1.31

−161

lp_1019

clpC

ATP-dependent Clp protease, ATP-binding subunit ClpC

 

1.92

−1.09

1.84

1.76

−1.30

1.58

lp_0129

hsp1

Small heat shock protein

3.9·10-11

5.57

3.16

12.70

1.12

−1.38

1.21

lp_2945

lp _2945

Aromatic acid carboxylyase, subunit C (putative)

3.5·10-10

1.27

−1.08

1.57

1.21

1.20

1.46

lp_2451

lp _2451

Prophage P2a protein 6; endonuclease

4.9·10-7

1.05

1.11

1.12

1.03

1.40

1.32

lp_2926

lp _2926

Unknown

2.8·10-6

1.08

−1.08

−1.10

1.30

−1.19

1.05

lp_2426e

lp _2426

Prophage P2a protein 31; phage transcriptional regulator, ArpU family

2.8·10-6

−1.18

−1.56

−2.07

8.85

−1.87

1.31

lp_2540

lp _2540

Unknown

4.0·10-6

1.09

−1.31

4.11

−1.27

1.27

−1.14

lp_2541

lp _2541

ABC transporter, substrate binding protein

4.0·10-6

−1.15

−1.03

1.01

1.07

1.31

1.44

lp_2542

lp _2542

ABC transporter, permease protein (putative)

4.0·10-6

−1.03

−1.12

−1.06

−1.02

1.09

1.15

lp_2543

lp _2543

ABC transporter, ATP-binding protein

4.0·10-6

−1.18

1.02

1.27

−1.14

1.15

1.01

lp_3530

treP

Trehalose phosphorylase

4.0·10-6

−1.20

−1.25

−1.05

2.30

−1.32

−1.13

lp_2061

lp _2061

Unknown

4.0·10-6

1.38

1.53

1.47

−1.21

1.10

1.07

lp_2029

hrcA

Heat-inducible transcription repressor HrcA

5.8·10-6

−1.32

−241

−147

1.15

−176

−145

lp_2028

grpE

Heat shock protein GrpE

5.8·10-6

−1.04

1.48

1.23

−1.21

1.26

−1.27

lp_2027

dnaK

Chaperone, heat shock protein DnaK

5.8·10-6

−1.23

1.30

1.16

−1.28

1.09

−1.43

lp_2842

lp _2842

Transcription regulator, LysR family

6.7·10-6

1.08

1.14

−1.04

−1.17

−1.34

1.03

lp_1843

lp _1843

Aldose 1-epimerase family protein

9.8·10-6

−1.06

−1.14

1.06

1.50

1.19

1.20

lp_1845

hslU

ATP-dependent Hsl protease, ATP-binding subunit HslU

9.8·10-6

1.10

−1.02

1.23

1.65

1.08

1.44

lp_1846

hslV

ATP-dependent protease HslV

9.8·10-6

1.16

1.14

1.31

1.78

1.11

1.50

lp_1847

lp _1847

Integrase/recombinase, XerC/CodV family

9.8·10-6

1.22

1.22

1.36

1.73

1.11

1.36

HrcA

         

lp_0727

groEL

GroEL chaperonin

5.9·10-9

−1.19

2.00

1.59

−1.46

1.06

−1.50

lp_0728

groES

GroES co-chaperonin

5.9·10-9

−1.21

2.13

1.62

−1.55

1.14

−1.50

lp_2029

hrcA f

Heat-inducible transcription repressor HrcA

2.9·10-14

−1.32

−241

−147

1.15

−176

−145

lp_2028

grpE

Heat shock protein GrpE

2.9·10-14

−1.04

1.48

1.23

−1.21

1.26

−1.27

lp_2027

dnaK

Chaperone, heat shock protein DnaK

2.9·10-14

−1.23

1.30

1.16

−1.28

1.09

−1.43

lp_2026

dnaJ

Chaperone protein DnaJ

 

−1.13

1.05

1.17

−1.07

1.08

1.14

lp_0726

lp _0726

Membrane-bound protease, CAAX family

1.0·10-7

1.90

−1.07

1.56

2.26

−1.22

2.44

lp_0129

hsp1

Small heat shock protein

 

5.57

3.16

12.70

1.12

−1.38

1.21

lp_0413

plnQ

Plantaricin biosynthesis protein PlnQ

6.9·10-7

−1.03

1.23

1.51

−2.14

−1.16

1.16

lp_3578

kat

Catalase

1.0·10-6

1.02

1.02

1.03

1.28

−1.20

−1.13

lp_3617

tal3

Transaldolase

1.7·10-6

−1.19

−1.04

1.22

1.26

1.14

−1.28

lp_3618

pts37A

Sorbitol PTS, EIIA

1.7·10-6

1.03

1.02

1.33

4.51

1.33

1.26

lp_3619

pts37BC

Sorbitol PTS, EIIBC

1.7·10-6

2.15

1.31

2.50

2.68

−1.40

−1.23

lp_3620

pts37C

Sorbitol PTS, EIIC

1.7·10-6

1.00

−1.33

−1.10

1.88

1.19

1.46

lp_3621

srlM1

Sorbitol operon activator

1.7·10-6

1.39

1.17

2.13

2.22

1.08

1.40

lp_3622

srlR1

Sorbitol operon transcription antiterminator, BglG family

1.7·10-6

−1.36

−1.13

−1.05

2.17

1.01

1.30

lp_3623

srlD1

Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140)

1.7·10-6

−1.10

−1.35

−1.43

1.37

−1.16

1.88

lp_1268

lp _1268

Integrase/recombinase

3.7·10-6

−2.21

−1.10

−1.56

−3.07

1.49

−3.38

lp_0387

lp _0387

Unknown

2.4·10-6

1.18

1.04

1.25

1.06

−1.00

1.35

lp_1879

hbsU

DNA-binding protein

9.9·10-6

−1.14

1.04

−1.14

−1.23

1.04

−1.27

lp_1880

lp _1880

Unknown

9.9·10-6

−1.13

1.11

−1.14

−1.59

1.20

−1.71

  1. aAdapted from [1].
  2. bThe lp_number indicates gene number on L. plantarum WCFS1 chromosome [2].
  3. cp-value of the best match on the upstream sequence after comparing the canonical regulatory factor binding site. Values lower than 1.0·10-5 were included.
  4. dFold-changes in bold are significant (FDR adjusted p-value < 0.05).
  5. eThe cis-element is predicted to be in front of this operon that contains lp _2426 until lp _2431, which all encode proteins of prophage P2a. Fold-changes are only given for lp _2426.
  6. fThe upstream region of hrcA contains two CIRCE elements. The second has a p-value of 8.3·10-9.
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