Table 1.
Expression analysis of polysaccharide processing genes during growth on barley β-glucan, starch and maltose
| 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 |
aGH, glycoside hydrolase; GT, glycosyltransferase; ND, not determined; GATase1, type 1 glutamine amidotransferase (GATase1)-like domain
b LT, locus tag annotated as Pjdr2_#### abbreviated to only consist of the numeric portion, ####
cThe name assigned to gene candidates with enzymes characterized in our laboratory in bold
dSP, sequence encodes a predicted signal peptide for secretion
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)
fRPKM values are defined as Reads Per Kilobase per Million reads sequenced
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