Table 1 Minimal conserved anaerobic transcriptional response shared by D. dadantii 3937 and P. atrosepticum SCRI1043 and its comparison to E. coli.

ABF-0016541

ABL-0060576

ABE-0009869

exbB

membrane spanning protein in TonB-ExbB-ExbD complex

-6.6

-3.5

-3.3

ABF-0020799

ABL-0061445

ABE-0007383

nrdA

ribonucleotide reductase of class Ia (aerobic), alpha subunit

-4.3

-4.7

-2.2*

ABF-0020798

ABL-0061444

ABE-0007386

nrdB

ribonucleotide reductase of class Ia (aerobic), beta subunit

-3.7

-3.9

-2.0*

ABF-0017172

ABL-0063446

ABE-0009169

sdaC

serine transporter

-3.1

-3.2

1.3*

ABF-0020233

ABL-0063426

sfuA

iron-binding periplasmic protein

-9.1

-26.9

ABF-0019943

ABL-0062041

ABE-0003583

yceI

secreted protein

-3.1

-5.0

-6.0

ABF-0019942

ABL-0062042

ABE-0003585

yceJ

predicted cytochrome b561

-4.4

-4.3

-8.6

ABF-0020068

ABL-0062100

ABE-0005694

ydiU

hypothetical protein

-3.4

-4.2

-2.2*

ABF-0015019

ABL-0064500

ABE-0012474

yigI

conserved protein

-2.9

-7.4

-3.1

ABF-0019535

ABL-0061414

ABE-0001021

ykgM

predicted ribosomal protein

-97.0

-165.4

-1.4*

ABF-0019536

ABL-0061413

ABE-0285027

ykgO

predicted ribosomal protein

-66.7

-153.3

ABF-0017084

ABL-0062748

ABE-0006191

znuA

zinc ABC transporter, periplasmic-binding protein ZnuA

-4.3

-17.5

-1.2*

ABF-0017082

ABL-0062750

ABE-0006201

znuB

high-affinity zinc transport system membrane protein

-3.3

-2.9

1.4*

ABF-0017083

ABL-0062749

ABE-0006198

znuC

high-affinity zinc transport system ATP-binding protein

-3.1

-2.8

-1.1*

ABF-0018178

ABL-0063535

Iron dicitrate-binding protein

-10.6

-8.4

ABF-0018571

ABL-0064593

putative iron ABC transporter permease protein

-5.9

-23.3

ABF-0018572

ABL-0064592

putative iron ABC transporter, periplasmic-binding protein

-7.9

-117.8

ABF-0018573

ABL-0064591

putative iron ABC transporter ATP-binding protein

-7.3

-104.7

ABF-0018864

ABL-0063083

TonB-dependent ferric achromobactin receptor

-31.6

-4.9

ABF-0019222

ABL-0064073

putative ABC transporter substrate-binding protein

-16.8

-106.2

ABF-0019223

ABL-0064074

putative ABC transporter substrate-binding protein

-22.8

-47.8

ABF-0019568

ABL-0061801

putative transport system permease protein

-10.1

-32.4

ABF-0019569

ABL-0061802

putative ABC transporter substrate-binding protein

-23.1

-31.3

ABF-0019570

ABL-0061804

putative ABC transporter substrate-binding protein

-16.7

-20.8

ABF-0019572

ABL-0061805

putative ABC transporter substrate-binding protein

-17.0

-13.9

ABF-0020094

ABL-0060663

ABC-type transporter, periplasmic component

-4.5

-6.3

ABF-0020095

ABL-0060662

ABC transporter, permease protein

-5.9

-4.3

ABF-0020096

ABL-0060661

ABC transporter, permease protein

-3.0

-4.4

ABF-0020097

ABL-0060660

ABC transporter ATP-binding protein

-3.4

-3.2

ABF-0046525

ABL-0064075

ABC transporter substrate-binding protein

-81.6

-37.0

B. Orthologs up-regulated ≥ 3-fold in both D. dadantii and P. atrosepticum

ABF-0020642

ABL-0062590

ABE-0004164

adhE

iron-dependent alcohol dehydrogenase

16.8

3.6

3.9

ABF-0018570

ABL-0064258

ABE-0002090

ahpC

alkyl hydroperoxide reductase, C22 subunit

2.8

6.1

-2.2*

ABF-0019339

ABL-0060528

budC

2,3-butanediol dehydrogenase

36.8

4.1

ABF-0018628

ABL-0061786

ABE-0013503

dcuB

C4-dicarboxylate transporter DcuB

16.4

66.3

8.5

ABF-0018914

ABL-0063040

ABE-0002776

dps

Fe-binding and storage protein

3.2

2.9

-2.5*

ABF-0019603

ABL-0062860

ABE-0003073

focA

formate transporter

8.1

4.8

3.1

ABF-0017842

ABL-0064288

ABE-0013604

frdA

fumarate reductase (anaerobic) NAD/flavoprotein subunit

7.5

11.2

3.5

ABF-0017841

ABL-0064289

ABE-0013602

frdB

fumarate reductase (anaerobic), Fe-S subunit

8.8

8.6

5.3

ABF-0017839

ABL-0064290

ABE-0013598

fr d C

fumarate reductase (anaerobic), membrane anchor subunit

7.9

9.6

3.7

ABF-0017837

ABL-0064291

ABE-0013595

frdD

fumarate reductase (anaerobic), membrane anchor subunit

7.0

7.8

4.5

ABF-0019825

ABL-0062949

ABE-0002893

grxA

glutaredoxin 1,coenzyme for ribonucleotide reductase

4.3

3.1

1.0*

ABF-0017078

ABL-0061498

hoxN

high-affinity nickel transport protein

6.7

17.6

ABF-0017349

ABL-0061473

ABE-0009830

hybB

predicted hydrogenase 2 cytochrome b type component

5.4

18.8

2.6*

ABF-0017353

ABL-0061476

ABE-0009824

hybE

hydrogenase 2-specific chaperone

5.7

15.3

2.1*

ABF-0017346

ABL-0061471

ABE-0009834

hybO

hydrogenase 2, small subunit

3.4

18.1

14.6

ABF-0015747

ABL-0061483

ABE-0008931

hycI

protease involved in processing C-terminal end of HycE

9.6

25.8

1.4*

ABF-0015752

ABL-0061495

ABE-0008919

hydN

formate dehydrogenase-H, ferredoxin subunit

55.3

183.5

1.7*

ABF-0015735

ABL-0061493

2 orthologs

hyfA

hydrogenase 4, 4Fe-4S subunit

32.2

128.0

MO

ABF-0015736

ABL-0061492

2 orthologs

hyfB

hydrogenase 4, membrane subunit

26.7

163.1

MO

ABF-0015737

ABL-0061491

2 orthologs

hyfC

hydrogenase 4, membrane subunit

10.9

123.6

MO

ABF-0015738

ABL-0061490

ABE-0008185

hyfD

hydrogenase 4, membrane subunit

26.2

173.6

-1.7*

ABF-0015739

ABL-0061489

ABE-0008188

hyfE

hydrogenase 4, membrane subunit

29.4

72.0

1.5*

ABF-0015740

ABL-0061488

ABE-0008191

hyfF

hydrogenase 4, membrane subunit

15.8

57.3

2.7*

ABF-0015741

ABL-0061487

2 orthologs

hyfG

hydrogenase 4, subunit

26.7

75.1

MO

ABF-0015742

ABL-0061486

ABE-0008942

hyfH

hydrogenase 4, Fe-S subunit

17.0

64.9

1.9*

ABF-0015744

ABL-0061485

2 orthologs

hyfI

hydrogenase 4, Fe-S subunit

17.5

62.2

MO

ABF-0015745

ABL-0061484

2 orthologs

hyfJ

predicted processing element hydrogenase 4

31.3

46.9

MO

ABF-0017358

ABL-0061480

ABE-0008960

hypB

GTP hydrolase involved in nickel liganding into hydrogenases

5.8

41.4

2.3*

ABF-0020729

ABL-0061479

ABE-0008962

hypC

[NiFe] hydrogenase metallocenter assembly protein HybG

21.1

18.4

3.8

ABF-0017360

ABL-0061478

ABE-0008965

hypD

protein required for maturation of hydrogenases

3.6

31.6

2.4*

ABF-0047122

ABL-0062652

ABE-0006058

manZ

mannose-specific enzyme IID component of PTS

3.9

4.1

-2.1*

ABF-0016556

ABL-0060593

ABE-0013865

nrdD

anaerobic ribonucleoside-triphosphate reductase

17.8

24.4

4.4

ABF-0016554

ABL-0060592

ABE-0013860

nrdG

anaerobic ribonucleotide reductase activating protein

4.9

6.2

4.5

ABF-0017768

ABL-0062712

ABE-0003800

pepT

peptidase T

31.3

19.7

3.6

ABF-0019604

ABL-0062861

2 orthologs

pflB

pyruvate formate lyase I

10.3

3.4

MO

ABF-0174126

ABL-0064936

ABE-0003227

rmf

ribosome modulation factor

8.3

3.2

1.9*

ABF-0015967

ABL-0063825

ABE-0008501

trxC

thioredoxin 2

7.0

21.3

-3.8

ABF-0016966

ABL-0061596

ABE-0002386

ybfA

predicted protein

6.7

3.9

2.2*

ABF-0019390

ABL-0062816

ABE-0003125

ycbJ

conserved protein

6.1

4.9

3.3

ABF-0018000

ABL-0062073

ABE-0003740

ycfP

conserved protein

3.1

3.2

1.7*

ABF-0020593

ABL-0063322

ABE-0007565

yfbS

predicted transporter

3.5

4.6

1.0*

ABF-0020590

ABL-0063324

ABE-0007571

yfbU

conserved protein

3.2

7.3

1.4*

ABF-0020347

ABL-0063577

ABE-0008489

yfiD

pyruvate formate lyase subunit

18.8

3.1

5.9

ABF-0018102

ABL-0060954

ABE-0010380

yhbU

predicted peptidase (collagenase-like)

8.5

25.5

5.9

ABF-0018103

ABL-0060953

ABE-0010382

yhbV

predicted protease

9.9

18.0

3.7

ABF-0015647

ABL-0060483

ABE-0010667

yhdH

predicted oxidoreductase, Zn-dependent and NAD(P)-binding

4.9

3.0

1.8*

ABF-0020757

ABL-0062521

ABE-0005319

ynfK

predicted dethiobiotin synthetase

9.6

16.3

5.3

ABF-0017163

ABL-0063441

putative membrane protein

7.8

8.8

ABF-0018208

ABL-0060635

hypothetical protein

14.1

30.7

ABF-0018787

ABL-0063809

lactoylglutathione lyase-like lyase

53.8

3.8

ABF-0019032

ABL-0061661

ABE-0004921

formate dehydrogenase, cytochrome B556 subunit

24.3

27.1

1.5*