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. 2016 Jun 13;82(13):3979–3987. doi: 10.1128/AEM.00639-16

TABLE 1.

Glycoside hydrolases and carbohydrate esterases with transcripts accumulating ≥4 fold (P < 0.01) on media containing microcrystalline cellulose, aspen, or lodgepole pine relative to glucose (Glc)a

IDb Putative functionc emPAId
 RPKMe
 MCC/Glc
 Asp/Glc
 LP/Glc
 LP/Asp
Glc MCC Asp LP Glc MCC Asp LP R P R P R P R P
164484 GH10 endoxylanase 0.51 0.98 3.45 2.08 32 612 857 853 19.1 0.02 26.8 0.00 26.7 0.00 1.0 1.00
139561 GH5_22 β-glycanase 0.00 0.00 0.77 0.60 5 40 125 266 8.4 0.01 26.4 0.00 56.0 0.00 2.1 0.14
128405* GH28 exopolygalacturonase 0.00 0.00 0.30 0.45 3 9 64 130 3.5 0.00 25.3 0.00 51.1 0.00 2.0 0.40
146767 GH18/CBM5 chitinase 0.00 0.64 7.06 4.80 119 1206 2667 2044 10.2 0.00 22.5 0.00 17.2 0.00 0.8 0.22
26703 GH115 α-glucuronidase 0.00 0.00 1.03 1.29 29 88 275 397 3.1 0.00 9.6 0.00 13.8 0.00 1.4 0.45
106510 GH5_22 β-glycanase 1 5 9 17 4.4 0.17 7.3 0.01 13.9 0.00 1.9 0.42
21871 GH16 1,3(4)-β-glucanase 0.33 0.93 0.35 0.40 84 468 613 721 5.6 0.00 7.3 0.00 8.6 0.00 1.2 0.66
137577 GH3 β-glucosidase 0.00 0.00 0.22 0.38 4 15 31 68 3.3 0.07 6.9 0.00 15.1 0.00 2.2 0.10
24959 GH79 glycoside hydrolase 0.42 0.77 0.38 0.67 44 132 238 333 3.0 0.00 5.4 0.00 7.6 0.00 1.4 0.19
76203 GH18 possible chitinase 4.78 8.09 5.40 3.68 1103 2784 5855 4934 2.5 0.01 5.3 0.00 4.5 0.00 0.8 0.62
89691 GH18/CBM5 chitinase 118 424 575 488 3.6 0.01 4.9 0.00 4.1 0.00 0.8 0.48
26848 GH5_15 β-1,6-glucanase 0.38 0.45 1.61 2.19 76 135 368 373 1.8 0.05 4.8 0.00 4.9 0.01 1.0 1.00
103638 GH10 endoxylanase 0.00 0.00 1.11 1.64 25 56 119 129 2.3 0.42 4.8 0.00 5.2 0.01 1.1 0.96
138209 GH115 α-glucuronidase 0.00 0.00 0.12 0.11 2 3 8 17 1.7 0.13 4.3 0.00 9.8 0.00 2.3 0.13
78411 GH1 β-glucosidase 3 10 15 16 3.0 0.09 4.2 0.00 4.7 0.00 1.1 0.81
19345 GH51 α-arabinofuranosidase 0.35 0.53 0.20 0.23 22 100 88 85 4.6 0.00 4.0 0.01 3.9 0.05 1.0 0.99
24785 GH2 β mannosidase 0.00 0.00 0.00 0.12 30 62 117 163 2.1 0.03 3.9 0.00 5.5 0.00 1.4 0.05
137392 GH125 α-mannosidase 0.60 1.21 0.45 0.59 79 152 248 317 1.9 0.05 3.1 0.00 4.0 0.00 1.3 0.34
102857 GH78 possible α-rhamnosidase 6 7 17 31 1.3 0.68 2.8 0.00 5.3 0.00 1.9 0.05
125762 GH28 exopolygalacturonase 3 3 7 29 0.9 0.82 2.7 0.00 10.4 0.01 3.8 0.12
149294 GH31 α-xylosidase 19 34 49 122 1.8 0.27 2.5 0.00 6.3 0.00 2.5 0.00
147868 GH5_7 endo-β-1,4-mannanase 0.14 0.21 0.16 0.18 24 42 59 105 1.7 0.33 2.5 0.00 4.3 0.00 1.8 0.02
23559 GH3 β-glucosidase 0.00 0.00 0.06 0.00 23 33 56 99 1.4 0.53 2.4 0.00 4.3 0.00 1.8 0.02
79505* GH28 exopolygalaturonase 0.00 0.00 0.00 0.16 4 6 7 17 1.6 0.02 1.8 0.02 4.1 0.01 2.3 0.17
31035* CE4 chitin deacetylase 3 18 146 161 5.1 0.00 42.5 0.00 46.8 0.00 1.1 0.75
165643 CE8 possible pectinesterase 0.00 0.00 0.20 0.31 1 3 15 40 3.7 0.00 16.9 0.00 46.1 0.00 2.7 0.08
86713 CE4 possible chitin deacetylase 38 98 173 158 2.6 0.01 4.6 0.00 4.2 0.00 0.9 0.75
a

Genes exhibiting relatively low expression levels in all four substrates (RPKM values < 10) are excluded. Expression ratios (R) and moderated t test-derived probability (P) are shown. Proteins are ranked by transcript ratios on Asp relative to Glc.

b

Protein model identifiers (ID) derived from the Joint Genome Institute's databases (44). Models with asterisks need editing.

c

Putative function based on CAZy classification (http://www.cazy.org) and, in the case of GH5 family members, the analysis of Aspeborg et al. (45). Excluding “possible” designations, SwissProt BLASTP score swere >500. CE, carbohydrate esterase.

d

emPAI, exponentially modified protein abundance index (22).

e

RNA-seq-normalized reads per kilobase per million (RPKM). For perspective, 11,190 and 11,205 genes had at least one transcript detected in Asp and LP samples, respectively. Moreover, genes with Asp/Glc and LP/Glc ratios of >7.1 and >9.2, respectively, were within the top 1%.