RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root
infection. The
infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading
enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded
proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as
infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding
cellulases, hemicellulases, β-1,3-glucanases and
glycoproteins. The most highly expressed P. parasitica
carbohydrate active
enzyme gene contains two CBM1
cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a
pectin deacetylase and a
pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex
carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic
homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic
rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on
cellulose microfibrils by non-catalytic
cellulose-
binding proteins and
enzymes with auxiliary activities may facilitate subsequent attack by glycosyl
hydrolases and
enzymes containing CBM1
cellulose-binding modules; (iv) terminal
hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the
carbohydrate chains on
glycoproteins are degraded late in
infection. A notable feature of the P. parasitica
infection transcriptome is the high level of transcription of genes encoding
enzymes that degrade β-1,3-glucanases during middle and late stages of
infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade
callose as it is produced by the plant during the defence response.