LAUSR

Plants have evolved well-tuned surveillance systems, including perplexed defense mechanisms, to restrain pathogens. Transcription factors (TFs) are master regulators of host molecular responses against plant pathogens. While pepino mosaic virus (PepMV) constitutes a major threat to the global tomato production, there is still lack of knowledge about the key TFs that regulate host responses against the virus. A combinatorial research approach was applied relying on tomato transcriptome analysis, reverse-transcription quantitative-PCR validation, phylogenetic classification, comparative analysis of structural features, cis-regulatory element mining and in silico co-expression analysis to identify a set of 11 highly responsive TFs involved in the regulation of host responses against PepMV. An endemic PepMV isolate, generating typical mosaic symptoms, modified the expression of approximately 3.3% tomato genes resulting in 1,120 Differentially Expressed Genes (DEGs). Functional classification of 502 upregulated DEGs revealed that photosynthesis, carbon fixation and gene silencing were widely affected, whereas 618 downregulated genes had an impact on mainly plant defense and carotenoid biosynthesis. Strikingly all 11 highly responsive TFs carried abiotic stress response cis-regulatory elements, whereas 5 of them were better aligned with rice than Arabidopsis gene homologs, suggesting that plant response against viruses may predate the divergence to monocots and dicots. Interestingly, tomato C2H2 family TFs, ZAT1-like and ZF2, may have distinct roles in plant defense due to the opposite response pattern, similarly to their Arabidopsis ZAT10 and ZAT12 homologs. These highly responsive TFs set the basis to study in deep the molecular responses of tomato-PepMV pathosystem, opening a perspective to better comprehend viral infections.