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Table 2 List of genes linked to environmental stress response

From: Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils

Product name

Gene symbol

Enzymes

COGs

1

2

3

4

5

6

7

8

9

10

11

12

13

14

SIGMA FACTORS

                 

DNA-directed RNA polymerase sigma 24

rpoE

-

COG1595

15

11

9

6

14

8

9

7

7

13

9

7

12

9

DNA-directed RNA polymerase sigma 28

fliA

-

COG1191

1

-

2

1

1

1

1

-

1

-

1

2

-

2

DNA-directed RNA polymerase, sigma 70

rpoD

-

COG0568

1

4

2

1

1

1

1

1

1

7

1

1

1

1

OXIDATIVE STRESS RESPONSE

                 

Superoxide dismutase

sodA

EC:1.15.1.1

COG0605

1

1

1

1

2

1

1

1

1

1

1

1

1

1

Cu/Zn superoxide dismutase

sodC

EC:1.15.1.1

COG2032

-

-

-

-

-

-

-

-

-

-

1

-

-

-

Mn-containing catalase

-

-

COG3546

1

-

-

-

1

-

-

-

2

-

1

1

-

-

Catalase

katE

EC:1.11.1.6

COG0753

2

2

2

1

2

3

2

1

3

2

2

2

2

1

Catalase (peroxidase I)

katG

EC:1.11.1.21

COG0376

-

-

1

1

-

1

-

-

-

-

-

-

-

-

Peroxiredoxin

bcp

EC:1.11.1.15

COG1225

2

3

3

1

3

3

2

5

4

4

3

4

4

6

Organic hydroperoxide reductase

osmC, ohr

-

COG1764

3

2

3

3

3

3

3

2

2

2

3

2

2

3

Thioredoxin

trx

EC:1.8.1.8

COG3118

4

3

5

3

6

5

5

3

7

5

4

3

5

4

Thioredoxin reductase

trxB

EC:1.8.1.9

COG0492

4

4

3

3

3

6

2

4

5

4

1

4

2

2

Thiol-disulfide isomerase and thioredoxins

trxA

-

COG0526

2

3

2

-

1

2

5

4

3

2

2

1

3

1

Redox-sensitive transcriptional activator

soxR

-

COG0789

1

-

-

-

1

-

-

-

-

2

1

-

1

-

OSMOPROTECTION

                 

Glycogen metabolism

                 

Glycogen synthase

glgA

EC:2.4.1.21

COG0438

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1,4-alpha-glucan branching enzyme

glgB

EC:2.4.1.18

COG0296

1

1

1

1

1

1

1

1

1

1

1

1

1

1

ADP-glucose pyrophosphorylase

glgC

EC:2.7.7.27

COG0448

1

1

1

1

1

1

1

2

2

1

1

2

1

1

Glucan phosphorylase

glgP

EC:2.4.1.1

COG0058

1

1

1

1

1

1

1

1

1

1

1

1

1

1

Glycogen debranching enzyme

glgX

EC:3.2.1.33

COG1523

2

2

2

3

2

1

2

2

2

2

2

2

2

2

Trehalose metabolism

                 

Trehalose-6-phosphate synthase

otsA

EC:2.4.1.15

COG0380

1

1

1

1

1

1

1

1

1

1

1

1

1

1

Trehalose-6-phosphatase

otsB

EC:3.1.3.12

COG1877

2

1

1

1

1

1

1

1

1

1

1

1

1

1

Trehalose synthase

treS

EC:3.2.1.1, EC:5.4.99.16

COG0366

2

1

2

3

2

3

1

1

1

1

1

1

1

1

Maltooligosyl trehalose synthase

treY

EC:5.4.99.15

COG3280

1

1

1

1

1

1

1

1

1

1

1

1

1

1

Malto-oligosyltrehalose trehalohydrolase

treZ

EC:3.2.1.141

COG0296

1

1

1

1

1

1

1

1

1

1

1

1

1

1

Glycine betaine/proline ABC transporter

                 

glycine betaine/proline ABC transporter - ATP binding subunit

proV

-

COG1125

2

3

1

1

3

1

1

2

3

3

2

3

3

1

glycine betaine/proline ABC transporter - membrane subunit

proW

-

COG1174

2

6

2

2

3

2

2

4

6

6

4

6

6

2

glycine betaine/proline ABC transporter - periplasmic binding protein

proX

-

COG1732

2

3

1

1

1

1

1

2

3

3

2

3

3

1

COLD SHOCK RESPONSE

                 

Cold shock' DNA binding domain

csd

-

COG1278

3

4

5

4

3

4

4

3

3

4

3

3

2

4

CspA-like cold acclimation protein

capA

-

COG1278

1

1

1

1

1

1

1

1

-

1

-

-

1

1

Transcription elongation factor

nusA

-

COG0195

1

1

1

1

1

1

1

1

1

1

1

1

1

1

Polyribonucleotide nucleotidyltransferase

pnp

EC:2.7.7.8

COG1185

1

1

1

1

1

1

1

1

1

1

1

1

1

1

Ribosome-binding factor A

rbfA

-

COG0858

1

1

1

1

1

1

1

1

2

1

1

1

1

1

Translation initiation factor 1

infA

-

COG0361

1

1

1

1

1

1

1

1

1

1

-

1

1

1

Translation initiation factor 2

infB

-

COG0532

1

1

1

1

1

1

1

1

1

1

1

1

1

1

MEMBRANE ADAPTATIONS

                 

Delta6-desaturase

desA

EC:1.14.19.3

COG3239

3

1

1

2

3

1

2

2

1

5

3

6

4

2

Carotenoid biosynthesis

                 

Isopentenyldiphosphate δ isomerase

idi

EC 5.3.3.2

COG1443

1

1

-

-

1

-

-

1

1

1

1

1

-

-

Geranylgeranyl pyrophosphate synthase

crtE

EC:2.5.1.1, EC:2.5.1.10, EC:2.5.1.29

COG0142

1

2

-

-

1

1

-

2

2

1

2

4

2

1

Phytoene synthase

crtB

-

COG1562

1

1

-

-

1

-

-

1

1

1

1

1

-

-

Phytoene desaturase

crtI

EC:1.3.99.26, EC:1.3.99.28, EC:1.3.99.29, EC:1.3.99.31

COG1233

1

2

-

-

1

1

1

3

3

3

3

2

2

2

Lycopene elongase

crtEB

-

COG0382

1

1

-

-

1

-

-

1

1

1

1

1

-

-

Lycopene epsilon cyclase domain crtYe

crtYe

-

TIGR03462

1

1

-

-

-

-

-

1

-

1

1

-

-

-

Lycopene epsilon cyclase domain crtYf

crtYf

-

TIGR03462

-

1

-

-

-

-

-

1

-

1

1

-

-

-

  1. 1, A. aurescens TC1; 2, A. castelli DSM 16402; 3, A. chlorophenolicus A6; 4, A. globiformis NBRC 12137; 5, A. nitroguajacolicus Rue61a; 6, A. phenanthrenivorans Sphe3; 7, Arthrobacter sp. FB24; 8, 35/47; 9, Br18; 10, H14; 11, H20; 12, H41; 13, H5; 14, I3.
  2. Numbers in each column represent copy numbers per genome. Locus tags for each copy number are listed in Additional file 5.