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Table 1 Expression analysis of polysaccharide processing genes during growth on barley β-glucan, starch and maltose

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

Familya

LTb

Protein product

Namec

SPd

Fold changee

Linear RPKM Valuesf

B/YE

C/YE

G/YE

S/YE

M/YE

B

C

G

S

M

YE

Barley β-glucan utilization

 GH16

0951

laminarinase

Bgl16A 1

Yes

80.3

0.2

0.2

0.4

0.1

170.2

0.4

0.5

0.8

0.3

2.1

 GH16

0952

endo-β-1,3-1,4 glucanase

Bgl16A 2

Yes

24.5

0.2

0.2

0.3

0.1

124.1

1.1

0.8

1.5

0.6

5.1

 GH16

0824

laminarinase

Bgl16A 3

Yes

0.4

0.5

0.6

0.6

0.6

1.7

2.2

2.7

2.4

2.4

4.1

 GH3g

0317

glycoside hydrolase

 

No

2.7

2.7

0.5

NS

2.4

379.0

376.6

70.7

156.1

338.1

141.5

Barley β-glucan induced xylanases

 GH67

1323

α-glucuronidase

Agu67A

No

20.6

0.8

0.4

0.6

0.4

120.2

4.4

2.1

3.5

2.5

5.8

 GH8

1182

exooligoxylanase

Xyn8

No

39.3

0.4

0.4

0.7

0.5

297.2

3.3

3.1

5.1

3.5

7.6

 GH11

4664

endoxylanase

Xyn11

Yes

3.7

0.4*

0.2

0.3*

0.2

7.5

0.8

0.4

0.5

0.4

2.1

 GH10

0221

endoxylanase

Xyn10A 1

Yes

8.8

0.2

0.1

0.3

0.1

52.0

1.2

0.8

1.6

0.6

5.9

 GH10

1324

endoxylanase

Xyn10A 2

No

24.0

0.8*

0.5

0.6*

0.6

185.3

6.2

3.5

4.7

4.4

7.7

 GH43

1325

xylosidase

Xyn43B1

No

19.6

0.9*

0.5

0.7*

0.8*

222.1

9.9

5.9

7.6

8.6

11.3

 GH43

0750

xylosidase

Xyn43B2

No

3.2

176.6

NS

NS

NS

5.0

276.7

2.7

2.6

1.8

1.6

 GH43

1907

xylosidase

Xyn43B3

No

111.5

2.3

NS

NS

0.6

1410.9

29.6

12.2

13.5

7.6

12.7

Starch utilization

 GH13

0774

α-amylase

Amy13A1

Yes

0.2

0.2

0.1

114.1

69.7

2.0

1.8

1.3

1127.3

688.4

9.9

 GH13

5200

α-amylase

Amy13A2

Yes

0.2

0.2

0.2

56.8

4.2

1.5

1.5

1.2

395.7

29.3

7.0

 GH13

0783

α-amylase

Amy13A3

No

1.5

NS

NS

112.2

95.6

7.8

5.7

6.5

584.3

497.9

5.2

 GH13

1045

α-amylase

Amy13A4

No

NS

2.7

3.8

NS

NS

2.6

4.7

6.6

1.5

1.4

1.7

 GTg

1149

α-glucan phosphorylase

MalP

No

0.3

0.1

0.5

NS

0.2

2.4

0.9

0.7

6.6

1.5

8.9

Maltose utilization

 ND

5587

oxidoreductase

ThuB

No

NS

NS

NS

NS

8.8

7.4

7.0

7.3

9.0

73.8

8.4

 GATase1

5588

hypothetical protein

ThuA

No

0.7

0.7

NS

NS

8.1

7.1

2.6

2.5

2.5

30.3

3.8

  1. aGH, glycoside hydrolase; GT, glycosyltransferase; ND, not determined; GATase1, type 1 glutamine amidotransferase (GATase1)-like domain
  2. b LT, locus tag annotated as Pjdr2_#### abbreviated to only consist of the numeric portion, ####
  3. cThe name assigned to gene candidates with enzymes characterized in our laboratory in bold
  4. dSP, sequence encodes a predicted signal peptide for secretion
  5. eTranscript 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 growth 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)
  6. fRPKM values are defined as Reads Per Kilobase per Million reads sequenced
  7. gGene 0317 and gene 1149 are included in this table as genes of interest in barley β-glucan and starch utilization pathways, respectively. Gene 0317 is increased 5.4-fold on barley β-glucan (p-value < 0.0002) and gene 1149 is increased 9.4-fold on starch (p-value < 0.037) relative to growth on glucose
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BMC Genomics

ISSN: 1471-2164

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