TABLE 3.
Relative protein abundances and transcript accumulations of genes not previously implicated in plant cell wall degradationa
| IDb | Functional domainsc | IPR ID | emPAId |
RPKMe |
MCC/Glc |
Asp/Glc |
LP/Glc |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Glc | MCC | Asp | LP | Glc | MCC | Asp | LP | R | P | R | P | R | P | |||
| 139466 | Aromatic-ring hydroxylase | IPR003042 | 0.00 | 0.00 | 0.36 | 0.58 | 23 | 25 | 126 | 176 | 1.1 | 0.67 | 5.5 | 0.00 | 7.7 | 0.00 |
| 167014 | Metallophosphoesterase | IPR004843 | 0.00 | 0.00 | 0.58 | 0.34 | 39 | 125 | 210 | 177 | 3.2 | 0.00 | 5.4 | 0.00 | 4.6 | 0.00 |
| 22757 | Lysophospholipase | IPR002642 | 0.00 | 0.00 | 0.45 | 0.31 | 22 | 38 | 110 | 110 | 1.8 | 0.11 | 5.1 | 0.00 | 5.1 | 0.00 |
| 139157* | FAD-linked oxidase | IPR006094 | 0.00 | 0.00 | 0.18 | 0.20 | 10 | 9 | 39 | 51 | 0.9 | 0.53 | 4.0 | 0.00 | 5.2 | 0.00 |
| 97131* | Hypothetical (cupredoxins) | IPR008972 | 0.00 | 0.00 | 0.13 | 0.15 | 66 | 291 | 1733 | 1259 | 4.4 | 0.00 | 26.3 | 0.00 | 19.1 | 0.00 |
| 138259 | Hypothetical | 0.25 | 0.49 | 0.64 | 0.91 | 22 | 49 | 106 | 112 | 2.2 | 0.04 | 4.8 | 0.00 | 5.1 | 0.00 | |
Limited to genes with regulated transcript levels (>4-fold; P < 0.01), with predicted secretion signals and with at least two unique peptides detected by mass spectrometry. Genes exhibiting relatively low transcript levels in all four substrates (RPKM values < 10) are excluded. Expression ratios (R) and moderated t test-derived probability (P) are shown. IPR, InterPro domain.
Protein model identifiers (ID) derived from the Joint Genome Institute's databases (44). Models with asterisks each have a possible transmembrane helix.
Possible functional domains and InterPro database identifier.
emPAI, exponentially modified protein abundance index (22).
RNA-seq-normalized reads per kilobase per million (RPKM).