TABLE 3.
Upregulated P. chrysosporium genes potentially involved in degradation of lignin and aromatic compoundsa
| Protein ID no. | Putative function, gene | Reference(s) | Comment(s) | Microarray signal (log2) or ratio
|
LC-MS/MS score
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CLB | NLB | RB | CLB/RB | NLB/RB | HBA | HBG | HBA/HBG | RB | NLB | CLB | NMA | HBA | WBC | ||||
| 11055 | Aryl alcohol dehydrogenase aad | 40 | Q01752 | 12.3 | 13.1 | 11.6 | 1.64 | 2.79 | 11.0 | 11.1 | 0.95 | ||||||
| 11098 | CDH cdh1 | 35, 54 | Q01738 | 13.1 | 13.0 | 12.9 | 1.22 | 1.12 | 15.4 | 12.7 | 6.45 | 92 | 3490 | 2507 | |||
| 147 | Cellulose-binding iron reductase cir1 | 60 | AAU12274; CBM1 | 13.0 | 13.0 | 12.8 | 1.1 | 1.17 | 13.7 | 12.6 | 2.19 | ||||||
| 11068 | GLX glx1 | 27, 53 | AAA33747 | 13.9 | 13.0 | 12.3 | 2.93 | 1.56 | 11.5 | 11.6 | 0.95 | 742 | 400 | 534 | |||
| 2255 | Linoleate diol synthase | 11.5 | 11.5 | 11.2 | 1.2 | 1.22 | 12.9 | 11.1 | 3.43 | ||||||||
| 137435 | P450 | Bifunctional P-450 | 12.4 | 12.3 | 12.5 | 0.9 | 0.87 | 13.6 | 12.4 | 2.86 | |||||||
| 138737 | P450 | CYP67 | 11.8 | 12.8 | 11.6 | 1.12 | 2.37 | 12.3 | 12.2 | 1.10 | |||||||
| 34295 | Peroxidase | Peroxidase 2 superfamily | 11.5 | 11.3 | 11.3 | 1.2 | 1.02 | 12.0 | 10.6 | 2.68 | |||||||
| 3589 | Peroxidase mnp2 | 39, 53 | Mn peroxidase | 12.9 | 14.8 | 12.9 | 0.96 | 3.71 | 12.1 | 12.1 | 1.04 | 244 | 506 | 278 | |||
| 121822 | Peroxidase lipB | Lignin peroxidase | 13.1 | 12.5 | 12.0 | 2.16 | 1.40 | 11.6 | 11.4 | 1.12 | |||||||
| 131738 | Peroxidase lipC | 53 | Lignin peroxidase | 12.1 | 14.1 | 11.9 | 1.16 | 5.04 | 11.5 | 11.5 | 1.03 | 123 | |||||
| 6811 | Peroxidase lipD | 39, 53 | Lignin peroxidase | 14.6 | 13.3 | 12.7 | 3.69 | 1.46 | 12.5 | 12.4 | 1.04 | 84 | 378 | 1145 | 85 | ||
| 11110 | Peroxidase lipE | 53 | Lignin peroxidase | 14.8 | 14.5 | 13.7 | 2.22 | 1.76 | 13.7 | 13.6 | 1.05 | 531 | |||||
| 131709 | Peroxidase lipJ | Lignin peroxidase | 11.3 | 13.5 | 11.0 | 1.26 | 5.90 | 10.7 | 10.6 | 1.03 | 41 | ||||||
| 140708 | Peroxidase mnp1 | Mn peroxidase MnP1 | 12.3 | 12.8 | 10.6 | 3.36 | 4.51 | 9.9 | 9.8 | 1.08 | 35 | 58 | |||||
| 137275 | Pyranose 2-oxidase, pox | 10 | AY522922 | 12.5 | 10.6 | 10.9 | 3.20 | 0.82 | 12.3 | 12.1 | 1.11 | ||||||
a
Protein model numbers (v2.1), putative function, expression levels (log2 signal strength) and ratios, and LC-MS/MS Mascot scores are presented. The protein model indicated in boldface is inaccurate, and the alternative model Pchr2001 is preferred. The media are defined in Materials and Methods. The listing includes only genes with transcripts accumulating ≥2-fold in CLB versus RB, NLB versus RB, or HBA versus HGA. Additional relevant genes not upregulated ≥2-fold, including some with high signal strength and/or LC-MS/MS evidence, are listed in Table S3 in the supplemental material.