Table 1

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

ASAP Feature ID

Gene Name

Product

Fold change

D. dadantii

P. atrosepticum

E. coli

D. dadantii

P. atrosepticum

E. coli

    A. Orthologs down-regulated
    3-fold in both
    D. dadantii and P. atrosepticum


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

frdC

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*


This list of orthologous phytopathogen genes which have a 1-1 relationship according to OrthoMCL are differentially expressed with a 3- fold or more change in gene expression for both orthologs. Where there is a single E. coli ortholog in the group, the fold change is included, and, statistically insignificant values are marked with an asterisk. Several groups have multiple orthologs in E. coli, (indicated by MO) and their expression values are not included. Orthologs showing congruent expression pattern with fold changes > 3 across all three organisms have gene names in bold. The gene names and products were selected from among the three organisms to favor the most correct or most potentially informative and edited slightly to unify the format.

Babujee et al. BMC Genomics 2012 13:110   doi:10.1186/1471-2164-13-110

Open Data