TABLE 2.
Peptides and transcripts corresponding to genes implicated in the generation of extracellular oxidants when W. cocos or P. placenta was grown for 5 days in media containing glucose, microcrystalline cellulose, aspen, or lodgepole pine as the sole carbon source
| IDa | Putative functionb | emPAIc |
RPKMd |
MCC/Glc |
Asp/Glc |
LP/Glc |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Glc | MCC | Asp | LP | Glc | MCC | Asp | LP | R | P | R | P | R | P | ||
| 27193 | Benzoquinone reductase | 1.44 | 3.27 | 1.93 | 0.99 | 167 | 197 | 160 | 169 | 1.2 | 0.62 | 1.0 | 0.93 | 1.0 | 0.96 |
| 24953 | Methanol oxidase | 0.10 | 0.00 | 0.07 | 0.00 | 150 | 128 | 64 | 281 | 0.9 | 0.69 | 0.4 | 0.04 | 1.9 | 0.21 |
| 80969 | Copper radical oxidase 1 | 2 | 2 | 1 | 2 | 0.8 | 0.54 | 0.5 | 0.08 | 0.7 | 0.64 | ||||
| 106250 | Copper radical oxidase 5 | 0.00 | 0.00 | 0.52 | 0.69 | 5 | 32 | 372 | 343 | 7.1 | 0.00 | 81.0 | 0.00 | 74.7 | 0.00 |
| 83651 | Copper radical oxidase 2 | 1.41 | 2.96 | 0.99 | 1.29 | 111 | 111 | 214 | 211 | 1.0 | 0.99 | 1.9 | 0.01 | 1.9 | 0.01 |
| 87683 | Copper radical oxidase 6 | 1 | 1 | 1 | 1 | 0.5 | 0.02 | 1.0 | 0.70 | 0.7 | 0.03 | ||||
| 109665 | Ferric reductase transmembrane | 9 | 122 | 446 | 175 | 13.2 | 0.03 | 48.5 | 0.00 | 19.0 | 0.01 | ||||
| 123970 | Ferroxidase | 18 | 19 | 68 | 65 | 1.1 | 0.93 | 3.7 | 0.00 | 3.5 | 0.01 | ||||
| 76446 | Glycopeptide iron reductase | 1 | 2 | 13 | 138 | 2.0 | 0.30 | 11.8 | 0.02 | 130.1 | 0.00 | ||||
| 26263 | Glycopeptide iron reductase | 0.00 | 0.00 | 0.27 | 0.00 | 109 | 141 | 339 | 358 | 1.3 | 0.18 | 3.1 | 0.00 | 3.3 | 0.00 |
| 156960 | Glycopeptide iron reductase | 0 | 0 | 1 | 1 | 1.5 | 0.38 | 3.0 | 0.02 | 6.9 | 0.15 | ||||
| 40810 | Glycopeptide iron reductase | 611 | 617 | 923 | 790 | 1.0 | 0.96 | 1.5 | 0.03 | 1.3 | 0.17 | ||||
| 156965 | Glycopeptide iron reductase | 2 | 1 | 3 | 4 | 0.6 | 0.23 | 1.1 | 0.66 | 1.5 | 0.18 | ||||
| 105249 | Glycopeptide iron reductase | 7 | 7 | 6 | 4 | 0.9 | 0.67 | 0.8 | 0.41 | 0.6 | 0.04 | ||||
| 105247 | Glycopeptide iron reductase | 1 | 1 | 1 | 1 | 0.9 | 0.72 | 0.6 | 0.42 | 0.9 | 0.72 | ||||
| 76567 | Glycopeptide iron reductase | 1 | 0 | 0 | 0 | 0.4 | 0.33 | 0.5 | 0.18 | 0.6 | 0.40 | ||||
| 164149 | Glycopeptide iron reductase | 6 | 2 | 2 | 1 | 0.4 | 0.06 | 0.3 | 0.00 | 0.2 | 0.04 | ||||
| 139155 | Iron permease (FTR1) | 13 | 13 | 72 | 60 | 1.0 | 1.00 | 5.4 | 0.00 | 4.5 | 0.00 | ||||
| 157228 | Laccase | 2 | 2 | 41 | 79 | 0.9 | 0.56 | 18.7 | 0.00 | 36.2 | 0.00 | ||||
| 165246 | Laccase | 0.00 | 0.00 | 0.44 | 1.05 | 47 | 20 | 240 | 200 | 0.4 | 0.29 | 5.2 | 0.01 | 4.3 | 0.02 |
| 139080 | Laccase | 0.00 | 0.00 | 0.00 | 0.47 | 43 | 38 | 44 | 78 | 0.9 | 0.48 | 1.0 | 0.83 | 1.8 | 0.16 |
| 163340 | Oxalate decarboxylase | 0.00 | 0.00 | 0.00 | 0.35 | 7 | 7 | 52 | 118 | 1.0 | 0.86 | 7.5 | 0.02 | 17.0 | 0.00 |
| 106770 | Oxalate decarboxylase | 0.58 | 0.39 | 0.00 | 0.00 | 3 | 3 | 2 | 2 | 0.8 | 0.22 | 0.6 | 0.02 | 0.7 | 0.06 |
| 139266 | Tyrosinase | 9 | 20 | 74 | 270 | 2.2 | 0.09 | 8.0 | 0.03 | 29.4 | 0.01 | ||||
| 140963 | Tyrosinase | 3 | 46 | 38 | 114 | 14.6 | 0.00 | 12.0 | 0.04 | 36.1 | 0.03 | ||||
| 166774 | Siderophore iron transporter | 6 | 5 | 71 | 56 | 0.8 | 0.29 | 14.9 | 0.00 | 11.8 | 0.00 | ||||
a
Protein model identifiers (ID) derived from the Joint Genome Institute's databases (44). Expression ratios (R) and moderated t test-derived probability (P) were computed against the Glc reference.
b
Putative function based on best hit scores and percent amino acid similarity over aligned regions of known proteins.
c
emPAI, exponentially modified protein abundance index (22).
d
RNA-seq-normalized reads per kilobase per million (RPKM).