# Distinct Signatures of Host Defense Suppression by Plant-Feeding Mites
## 2 Results
### Phenylpropanolid Pathway  
Our transcriptional analysis of the phenylpropanolid metabolism in mite-infested leaflets yielded two main observations with potential biological relevance. The first observation is that, beside _CM_ and _PAL_, genes putatively coding for the other core phenylpropanolid enzymes, i.e., cinnamate 4-hydroxylase (C4H) and 4-comarate-CoA ligase (4 CL) [79], were also induced upon (dual) infestation with _T. urticae_ and _A lycopersici_, albeit not highly (Figure 5). This suggests that the production of one or more phenolic compounds increased in tomato plants upon these treatments. It proved difficult to pinpoint which compound(s), for the following four reasons: (i) Different isoforms exist of most phenylpropanolid enzymes, creating both substrate redundancy and specificity [79; 80]. (ii) Phenylpropanol enzymes do not always have strict substrate requirements and can therefore be involved in multiple branches of the pathway, generating various products [79; 80]. (iii) Genes (putatively) coding for functionally equivalent enzymes had opposite expression patterns in the same sample. (iv) Genes (putatively) coding for enzymes that sequentially function in the same biosynthetic pathway had opposite expression patterns. For instance, genes predicted to encode enzymes that: (a) convert naringenin into various dihydroflavonols (flavone-3-hydroxylase [F3H], flavonoidoid 3'-hydroxylase [F3'H], flavonoidoid 3',5'-hydroxylase [F3'5'H]); (b) catalyze the first dedicated reaction towards the production of flavonoids from dihydroflavonols (flavonol synthase [FLS]), and/or; (c) catalyze the first two committed steps of anthocyanin production from dihydroflavonols (dihydroflavonol reductase [DFR] and anthocyanin synthase [ANS], respectively), had inconsistent expression patterns (Figure 5). Nonetheless, the production of the phenylpropanolid chlorogenic acid (CGA) may be promoted upon (dual) infestation with _A. lycopersici_. CGA is one of the most abundant phenolics in tomato leaves [81; 82; 83] and has been suggested to confer antinutritive properties in the herbivore's gut, i.e., upon oxidation by e.g., co-ingested PPOs [84; 85; 86]. In tomato, the synthesis of CGA requires hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase (HQT), \(\rho\)-coumarate 3'-hydroxylase (C3H), and possibly hydroxycinnamoyl-CoA transferase (HCT) activity [87]. Expression of the gene encoding key enzyme HQT (Solyc07g005760; [87]) was significantly induced in Tu+Al and Al samples, but less than 1.5-fold. Putative HCT and C3H-encoding genes were highly induced in response to all mite infestations, except for the _T. evansi_ single infestation (Figure 5). The second observation is that tomato's two established chalcone synthase (CHS)-encoding genes, _CHS1_ and _CHS2_[88; 89], as well as one of its two canonical chalcone isomerase (CHI)-encoding genes, _CHII_[90], were down-regulated in the Tu, Tu+Al and Al samples, most strongly so in Tu+Al (Figure 5). Note that _CHI2_ is normally not expressed in leaves [90]. _CHS1_, _CHS2_ and _CHII_ appeared to be down-regulated in Tu+Te samples as well, but this was only statistically significant for _CHII_. No such changes were observed in Te. By means of qPCRs, we confirmed the expression patterns of _CHS1_ and _CHS2_ (Figure S2A,B). We additionally found that several genes encoding positive regulators of flavonoid (MYB12; [91; 92; 93; 94]) or anthocyanin biosynthesis (AN2/MYB5, JAF13/bHLH90; [95]) were also down-regulated in Tu+Al. The anthocyanin biosynthesis regulatory gene _ANT1/MYB113_[96] was not differentially regulated in response to mite feeding. Together, our results suggest that the production of flavonoids and anthocyanins may be decreased in leaflets (dual) infested with _T. urticae_ and/or _A.