Table 5

Summary of genes up-regulated by σB

Locus

EGD-e locus

Description

Avg. fold change (WT/ΔsigB)a

10403S Average GEIb

ΔsigB Average GEIc

σB-dependent genes found by RNA-Seq and not previously identified by microarray analyses of stationary phase cells


LMRG_02371

lmo0122

similar to phage proteins

3.9

2.37

0.6

LMRG_02611

lmo0265

similar to succinyldiaminopimelate desuccinylase

204.5

17.95

0

LMRG_02602

lmo0274

unknown

3.17

2.89

0.91

LMRG_00064

lmo0372

similar to beta-glucosidase

4.26

2.4

0.66

LMRG_00126d

lmo0433 (inlA)

Internalin A

5.86

6.19

1.06

LMRG_00127d

lmo0434 (inlB)

Internalin B

6

2.71

0.47

LMRG_02244

lmo0819

unknown

3.01

18.35

6.09

LMRG_00873d

lmo1421

similar to glycine betaine/carnitine/choline ABC transporter (ATP-binding protein)

28.44

5.27

0.67

LMRG_00877d

lmo1425 (opuCD)

similar to betaine/carnitine/choline ABC transporter (membrane p)

3.56

22.59

6.51

LMRG_00878d

lmo1426 (opuCC)

similar to glycine betaine/carnitine/choline ABC transporter (osmoprotectant-binding protein)

3.77

19.78

5.41

LMRG_01013

lmo1866

similar to conserved hypothetical proteins

2.63

4.87

1.79

LMRG_01151

lmo2003

similar to transcription regulator GntR family

14.67

3.15

0.32

LMRG_01963

lmo2733

similar to PTS system, fructose-specific IIABC component

7.95

1.35

0.32

Noncoding

ND

putative ncRNA, sbrE

186.09

2359.89

20.95

σB-dependent genes with Average GEI ≥ 25 in 10403S

Noncoding

ND

rliA (sbrE)

186.09

2359.89

20.95

LMRG_01674

lmo2158

similar to B. subtilis YwmG protein

479.39

509.23

22.8

LMRG_01365

lmo1602

similar to unknown proteins

5.47

157.02

30.08

LMRG_00221

lmo0539

similar to tagatose-1,6-diphosphate aldolase

14.54

132.74

9.3

LMRG_01602

lmo2230

similar to arsenate reductase

411

96.43

0

LMRG_02052

lmo0953

unknown

167

73.18

0.48

LMRG_00357

lmo0669

similar to oxidoreductase

75.93

64.6

0.89

LMRG_00358

lmo0670

unknown

105.5

59.6

0.58

LMRG_00341

lmo0654

unknown

7.1

56.61

7.94

LMRG_02219

lmo2674

similar to ribose 5-phosphate epimerase

5.42

52.93

9.94

LMRG_01794

lmo2454

unknown

84.5

50.24

0.76

LMRG_01850

lmo2398 (ltrC)

low temperature requirement C protein, also similar to B. subtilis YutG protein

2.8

50.03

18.94

LMRG_00745

lmo1295(hfq)

similar to host factor-1 protein

4.83

49.77

11.19

LMRG_01948

lmo2748

similar to B. subtilis stress protein YdaG

207.5

49.37

0

LMRG_00583

lmo1140

unknown

11.93

47.84

4.28

LMRG_02036

lmo0937

unknown

54.38

44.68

0.91

LMRG_00484

lmo0796

conserved hypothetical protein

4.21

43.88

10.61

LMRG_02772

lmo1698

similar to ribosomal-protein-alanine N-acetyltransferase

4.1

42.94

10.92

LMRG_02736

lmo2391

conserved hypothetical protein similar to B. subtilis YhfK protein

11.76

39.48

4.54

LMRG_02011

lmo0911

unknown

4.04

33.9

8.58

LMRG_01763

lmo2485

similar to B. subtilis yvlC protein

3.93

32.87

8.47

LMRG_00482

lmo0794

similar to B. subtilis YwnB protein

67.02

32.5

0.72

LMRG_00278

lmo0596

similar to unknown proteins

170.5

32.33

0.09

LMRG_02218

lmo2673

conserved hypothetical protein

150.5

31.92

0.11

LMRG_02013

lmo0913

similar to succinate semialdehyde dehydrogenase

330.38

30.05

0.11

LMRG_00469

lmo0781

similar to mannose-specific phosphotransferase system (PTS) component IID

59.58

29.59

0.65

LMRG_00470

lmo0782

similar to mannose-specific phosphotransferase system (PTS) component IIC

18.99

29.59

1.58

LMRG_01360

lmo1606

similar to DNA translocase

7.88

29.5

3.97

LMRG_02696

lmo2572

similar to Chain A, Dihydrofolate Reductase

8.05

29.05

3.59

LMRG_02768

lmo1694

similar to CDP-abequose synthase

155.31

27.51

0.2

LMRG_02216

lmo2671

unknown

3.13

27.29

8.82

LMRG_02695

lmo2573

similar to zinc-binding dehydrogenase

7.52

25.91

3.83

LMRG_00472

lmo0784

similar to mannose-specific phosphotransferase system (PTS) component IIA

88.5

25.25

0.21

LMRG_02215

lmo2670

conserved hypothetical protein

3

25.23

8.58

LMRG_02697

lmo2571

similar to nicotinamidase

9.84

25.15

2.99


aAverage fold changes from the 10403S and ΔsigB. Genes with no matching reads in ΔsigB had their GEI set to 1 to allow for calculation of the fold change;

bAverage normalized number of reads matching each of the σB-dependent genes in the two 10403S datasets relative to the length of the genes times 100 bp;

cAverage normalized number of reads matching each of the σB-dependent genes in the two ΔsigB datasets relative to the length of the genes times 100 bp;

dGenes previously identified as σB-dependent under salt stress in L. monocytogenes10403S by Raengpradub et al., 2008.

Oliver et al. BMC Genomics 2009 10:641   doi:10.1186/1471-2164-10-641

Open Data