Skip to main content

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