Table 1 Proteins of H.hepaticus identified by LC-MS/MS whose expression was modulated by at least 2-fold in 0.05% human- or 0.1% porcine bile in the growth media

Human

Porcine

Human

Porcine

Human

Porcine

Human

Porcine

Human

Porcine

Amino acid metabolism

Dihydropicolinate reductase*

0.4 ± 0.01

3.5 ± 0.03

dapB

Lysine biosynthesis

33

23

438

201

33(7)

26(12)

6.59/6.24

5.7/6.24

Dihydropicolinate reductase*

0.1 ± 0.01

NI

32

-

430

-

44(19)

-

6.50/6.24

-

Glycine hydroxymethyltransferase

0.48 ± 0.1

2.5 ± 0.01

glyA

Glycine hydroxymethyltransferase

18

17

330

278

26(6)

16(5)

6.57/6.33

6.95/6.33

Ketol-acid reductoisomerase

2.7 ± 0.3

NI

ilvN

Valine, leucine and isoleucine biosynthesis

27

-

916

49(14)

-

6.59/6.05

-

Threonyl-tRNA synthetase

NI

4.0 ± 0.01

thrS

Glycine, threonine and serine metabolism

-

8

-

214

-

12(3)

-

5.78/6.06

2-isopropylmalate synthase

NI

5.0 ± 0.01

leuA

Valine, leucine and isoleucine biosynthesis

-

9

-

148

-

26(12)

-

5.78/5.86

Phosphoglycerate dehydrogenase

NI

0.4 ± 0.02

serA

Serine family amino acid biosynthesis

-

32

-

583

-

18(9)

-

5.70/5.84

Cellular metabolism

ATP-dependent CLP protease*

NI

0.3 ± 0.01

clpA

Endopeptidase activity

-

3

-

941

-

41(19)

-

5.92/5.70

ATP-dependent CLP protease*

NI

0.2 ± 0.06

-

4

-

1167

-

38(36)

-

5.84/5.70

Carbohydrate & energy metabolism

Aconitase*

0.25 ± 0.01

0.4 ± 0.01

acnB

Citrate cycle, glyoxylate and dicarboxylate metabolism, reductive carboxylate cycle

2

2

1237

784

48(28)

10(13)

6.65/6.21

6.46/6.21

Aconitase*

0.1 ± 0.03

0.4 ± 0.01

3

1

1491

665

29(20)

29(11)

6.54/6.21

6.54/6.21

Aconitase*

0.1 ± 0.01

NI

1

-

1488

-

43(14)

-

6.76/6.21

-

Aconitase*

0.2 ± 0.01

NI

4

-

866

-

34(12)

-

6.46/6.21

-

Alkyl hydroperoxide reductase

NI

3.0 ± 0.01

tsaA

Oxidative phosphorylation

-

28

-

288

-

50(17)

-

6.3/5.95

ATP synthase subunit A

NI

4.0 ± 0.02

atpA

-

12

-

891

-

43(19)

-

5.7/5.69

ATP synthase subunit B

NI

2.5 ± 0.1

atpB

-

15

-

1509

-

53(12)

-

5.12/5.17

dDTP-glucose dehydratase

0.3 ± 0.01

NI

rfbB

Nucleotide sugar biosynthesis

23

-

549

-

31(5)

-

5.57/6.05

-

UDP-glucose 6-dehydrogenase

0.24 ± 0.06

NI

kfiD

Pentose and glucuronate interconversions; starch & sucrose metabolism, nucleotide sugars metabolism

17

-

384

-

50(17)

-

5.51/5.27

-

Ferredoxin oxidoreductase*

3.5 ± 0.02

NI

porA

Pyruvate metabolism

37

-

514

-

11(4)

-

5.92/5.91

-

Ferredoxin oxidoreductase*

2.5 ± 0.3

NI

22

-

900

-

35(20)

-

6.38/5.91

-

Fumarase

0.25 ± 0.1

0.4 ± 0.1

fumC

Citrate cycle, reductive carboxylate cycle

30

13

566

725

47(8)

23(11)

6.62/5.61

5.7/5.61

Fumarate reductase

NI

6.0 ± 0.1

frdA

Citrate cycle, oxidative phosphorylation

-

6

-

734

-

38(36)

-

5.7/7.23

Fructose-bisphosphate aldolase

2.8 ± 0.01

NI

fba

Glycolysis, gluconogenesis

19

-

975

-

50(13)

-

6.59/5.95

-

Isocitrate dehydrogenase

NI

5.5 ± 0.02

icd

Citrate cycle

-

5

-

865

-

23(7)

-

5.7/7.10

Malate dehydrogenase

NI

2.0 ± 0.01

mdh

Pyruvate metabolism

-

21

-

710

-

42(9)

-

6.89/8.11

Phosphoglycerate kinase

2.5 ± 0.01

NI

pgk

Glycolysis, glyconogenesis

13

-

699

-

44(10)

-

6.0/5.64

-

Rod shape determining protein

2.5 ± 0.2

NI

mreB

Cell shape determining protein

20

-

455

-

33(7)

-

5.27/5.16

-

Cellular oxygen metabolism & stress response

Catalase

NI

0.1 ± 0.01

kat

Superoxide metabolism

-

10

-

715

-

27(5)

-

5.7/6.75

Superoxide dismutase

0.1 ± 0.01

0.4 ± 0.3

sodF

16

27

137

411

13(2)

31(9)

6.49/6.24

5.7/6.24

Thioredoxin reductase

0.3 ± 0.01

4.7 ± 0.03

trxB1

Oxygen & ROS metabolism

31

18

470

390

27 (12)

14(5)

5.41/5.34

5.30/5.34

Putative thioredoxin reductase (HH1153)

0.2 ± 0.01

NI

trxB2

24

-

381

-

16(5)

-

5.95/6.15

-

Chaperone & stress response

Hsp-70 (DnaK cofactor)

2.3 ± 0.03

NI

grpE

Heat shock protein

26

-

308

-

11(8)

-

4.57/4.62

-

Cpn60

NI

3.0 ± 0.01

groEL

Chaperonin

-

14

-

705

-

42(11)

-

5.32/5.19

Lipid metabolism

Acetyl-CoA caroxylase alpha subunit

0.2 ± 0.01

NI

accA

Fatty acid biosynthesis

41

-

277

-

32(4)

-

5.59/5.47

-

7-Alpha-dehydroxysteroid dehydrogenase

2.5 ± 0.01

NI

fabG

46

-

629

-

23(11)

-

6.19/7.59

-

(3R)-hydroxymyristoyl ACP dehydratase

NI

4.0 ± 0.01

fabZ

-

7

-

356

-

28(6)

-

6.95/6.31

s-malonyltransferase

0.3 ± 0.01

NI

fabD

15

-

311

-

31(5)

-

5.49/5.45

-

Motility & chemotaxis

Flagellin*

2.5 ± 0.3

2.0 ± 0.01

flaB

Flagella assembly

11

11

946

961

41(16)

60(11)

4.81/6.38

4.57/6.38

Flagellin*

0.3 ± 0.02

NI

10

-

833

-

13(10)

-

4.95/6.38

-

Flagellin*

0.4 ± 0.01

NI

9

-

699

-

26(9)

-

4.89/6.38

-

Flagellin assembly protein*

0.4 ± 0.01

NI

fliH

35

-

474

-

31(5)

-

4.86/4.93

-

Flagellin assembly protein*

0.3 ± 0.01

NI

34

-

466

-

57(8)

-

4.80/4.93

-

Major flagellin subunit

2.4 ± 0.1

NI

flaA

12

-

827

-

47(13)

-

4.68/5.56

-

Two-component system response regulator

0.4 ± 0.01

NI

ompR

Two-component signal regulatory system

36

-

154

-

16(9)

-

4.84/5.63

-

Nucleotide metabolism

Adenylate kinase

0.2 ± 0.3

NI

adk

Purine metabolism

40

-

833

-

35(20)

-

5.22/5.09

-

DNA polymerase III subunit beta

3.0 ± 0.01

NI

dnaN

DNA metabolism

45

-

385

-

24(4)

-

5.62/5.33

-

Pathogenesis & virulence

Cytolethal distending toxin

0.1 ± 0.01

NI

cdtC

Virulence

44

-

444

-

20(9)

-

4.81/5.23

-

Urease subunit A

NI

0.3 ± 0.03

ureA

Urease activity, virulence

-

24

-

393

-

52(8)

-

5.32/5.93

Protein translation & modification

Translation elongation factor Ts

3.2 ± 0.01

2.0 ± 0.1

ef-ts

Protein translation

14

30

53

717

16(17)

36(12)

6.0/5.31

5.3/5.31

Translation elongation factor Tu

2.5 ± 0.01

2.0 ± 0.1

ef-tu

43

26

64

173

11(6)

15(13)

6.81/4.93

5.49/5.12

Signal transduction

GTP-binding protein*

3.5 ± 0.01

NI

yihK

Signal transduction

5

-

948

-

50(12)

-

5.38/5.26

-

GTP-binding protein*

3.0 ± 0.02

NI

6

-

706

-

42(11)

-

5.43/5.26

-

GTP-binding protein*

2.7 ± 0.01

NI

7

-

954

-

31(11)

-

5.49/5.26

-

GTP-binding protein*

3.5 ± 0.01

NI

8

-

638

-

37(9)

-

5.54/5.26

-

Putative ATP/GTP-binding protein

3.5 ± 0.02

NI

mpr

38

-

700

-

26(17)

-

6.08/5.77

-

Amino-acid ABC transporter periplasmic solute-binding protein

0.3 ± 0.1

NI

pbpB

ABC transporter protein

39

-

396

-

24(4)

-

4.97/5.17

-

Putative ABC transporter protein

0.4 ± 0.01

NI

yaeC

29

-

494

-

57(5)

-

4.81/5.16

-

Single-stranded DNA-binding protein

NI

0.3 ± 0.1

ssb

Single strand binding protein/primosomal replication

-

25

-

238

-

27(4)

-

5.38/5.91

Putative protein function

HH1212

0.1 ± 0.03

NI

hh1212

Hypothetical protein

25

-

349

-

14(5)

-

6.34/6.98

-

HH0952

0.3 ± 0.02

NI

hh0952

28

-

267

-

9(3)

-

4.27/4.52

-

HH1514

0.4 ± 0.01

NI

hh1514

42

-

286

-

17(9)

-

5.97/5.62

-

HH1023

0.2 ± 0.01

0.2 ± 0.01

hh1023

21

16

1312

410

43(21)

31(6)

5.86/6.15

5.86/6.15

HH1098

NI

4.0 ± 0.01

hh1098

-

31

-

156

-

10(2)

-

5.7/5.71

HH1376

NI

0.3 ± 0.01

hh1376

-

19

-

121

-

11(3)

-

5.89/5.62

HH1034

NI

2.5 ± 0.1

hh1034

-

20

-

410

-

53(9)

-

6.73/6.22

HH1426

NI

0.4 ± 0.1

hh1426

-

22

-

348

-

28(6)

-

6.49/6.12

HH0243

NI

2.5 ± 0.01

hh0243

-

29

-

297

-

22(4)

-

5.59/5.63