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Table 3 Expression analysis of genes encoding ABC transporters during growth on barley β-glucan, starch, cellobiose and maltose

From: Genomic and transcriptomic analysis of carbohydrate utilization by Paenibacillus sp. JDR-2: systems for bioprocessing plant polysaccharides

LTa

Protein productb

Fold changec

Linear RPKM Valuesd

B/YE

C/YE

G/YE

S/YE

M/YE

B

C

G

S

M

YE

0472

BPD transport system IMP

NS

23.1

18.3

NS

2.7*

1.7

27.7

22

1.1

3.3

1.2

0473

BPD transport system IMP

NS

20.8

18.9

NS

3

1.8

31

28.2

1.9

4.4

1.5

0474

extracellular SBP

0.7

7.4

9.6

NS

NS

6.5

71.7

92.8

8.6

13.4

9.7

0728

extracellular SBP

0.3

7.2

0.2

NS

0.2

7.1

173.8

4

19

6

24

0729

BPD transport system IMP

0.4

8.6

0.5

NS

0.4

6.2

119.1

6.5

12.8

5.1

13.9

0730

BPD transport system IMP

0.5

8.8

0.5

NS

0.5

7.3

134.5

8.2

16.4

7.7

15.2

0771

extracellular SBP

0.1

0

0

86.4

24.1

3.9

2.4

2.6

5524

1543.1

64

0772

BPD transport system IMP

0.1

0.1

0.1

94.3

34.7

1.1

0.8

0.9

1174

432.6

12.5

0773

BPD transport system IMP

0.1

0.1

0.1

134.8

58.3

1.3

0.8

0.8

1390

600.5

10.3

0949

BPD transport system IMP

1451.2

NS

NS

NS

NS

3602

2.1

2

2.2

3.1

2.5

0950

BPD transport system IMP

1498.5

1.7

NS

NS

NS

5522

6.4

3.5

4.8

4.9

3.7

0953

extracellular SBP

1220.8

2

NS

NS

0.6

5381

8.8

3.5

5

2.6

4.4

1320

extracellular SBP

0.2*

0.6

0.1

0.4*

0.1

4.2

11.5

1.4

6.9

1.8

18.6

1321

BPD transport system IMP

0.1

NS

0.1

0.6*

0.1

0.7

4.8

0.5

3

0.5

5

1322

BPD transport system IMP

15.1

NS

0.3

0.6

0.4

111.3

8.1

2.6

4.6

3.2

7.4

3245

periplasmic binding protein

3.5

2.6

2.3

2.3

10.9

158.4

119.1

103.9

107

500.4

45.7

3597

extracellular SBP

15

0.5

0.6*

2.4*

NS

19.9

0.7

0.8

3.2

1.1

1.3

5314

BPD transport system IMP

39.9

0.4

0.2

0.5

0.3

426.6

4.4

2.1

5.8

2.7

10.7

5315

BPD transport system IMP

42.1

0.4

0.2

0.4*

0.2

379.7

3.2

1.4

3.7

1.4

9

5316

extracellular SBP

31.1

0.2

0.1

0.3

0.1

797.5

5.4

1.9

7.5

1.6

25.7

5589

extracellular SBP

0.5

0.5

0.5*

NS

9.8

2.2

2.1

2.3

3.3

42.9

4.4

5590

BPD transport system IMP

NS

NS

NS

NS

10.9

1.1

1.2

1.8

1.4

15.3

1.4

5591

BPD transport system IMP

0.5

NS

NS

NS

14.9

0.4

0.6

0.9

1.1

13.7

0.9

5596

BPD transport system IMP

3.1

44.8

0.6

0.6

0.4

19.7

281.7

3.5

3.5

2.4

6.3

5597

BPD transport system IMP

3.3

52.2

0.5*

NS

0.2

14.1

219.5

2.1

2.2

1

4.2

5598

extracellular SBP

4.4

54.5

0.1

0.2*

0.1

40.3

494.9

1.1

2.3

0.9

9.1

5960

BPD transport system IMP

15.3

154.6

15.2

NS

0.5

269.7

2721

267.6

22.6

8.8

17.6

5961

BPD transport system IMP

16

145.5

12.7

NS

0.5

227.1

2062

179.8

22.6

7.8

14.2

5962

extracellular SBP

18.1

118.5

12.2

NS

0.3

620.6

4070

419.6

33.1

9.4

34.3

  1. aLT, locus tag annotated as Pjdr2_#### abbreviated to consist only of the numeric portion, ####
  2. bSBP, solute binding protein; IMP, inner membrane protein; BPD, binding protein dependent
  3. cTranscript levels of candidate genes that were expressed 2-fold greater (underlined) and those that were expressed 4-fold greater (bold) than the yeast extract without carbohydrate are indicated. The growth substrates are shown as follows: B, barley β-glucan; C, cellobiose; G, glucose; S, starch; M, maltose; YE, yeast extract. Significance of fold change data is judged by having a p-value no more than 0.01. Data with p-values between 0.01 and 0.05 are denoted with an asterisk, and those with p-values greater than 0.05 are designated as not significant (NS)
  4. dRPKM values are defined as Reads Per Kilobase per Million reads sequenced
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BMC Genomics

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