Concerted action of miRNA targets enables defense reprogramming upon pathogen-induced RNA silencing

Abstract

RNA silencing is an antiviral defense mechanism in plants and animals. In turn, viruses produce silencing suppressors interfering with diferent steps of that defense mechanism. It has been recently found that production of silencing suppressors is a general infection strategy also employed by pathogens as diferent as bacteria, oomycetes and fungi. Those distinct pathogens use diferent vectors and host colonizing strategies interacting with diferent host cell types throughout infection. The intracellular presence of silencing suppressors does not only disrupt a host´s defense mechanism but interferes with other endogenous processes orchestrated by this universal gene regulatory system. Of especial interest is their impact on micro RNA-mediated gene regulation (miRNA, a subclass of small RNAs). Plant miRNAs tend to regulate the expression of genes with pivotal roles in plant development and stress responses. Additionally, the repertoire of miRNAs and their targets is cell-type specifc and therefore, host cell reprogramming might difer depending on the host cells targeted by diferent pathogens for RNA silencing intervention. To ascertain the role of miRNA targets in cell-type specifc defense upon silencing suppression, we frst established the specifc cell types targeted by two single stranded RNA (ssRNA) viral and a bacterial pathogen for silencing suppression in Arabidopsis thaliana leaves. Later on, we specifcally induced the expression of silencing suppressors from those pathogens in those very same cell types and assayed their transcriptional reprogramming by isolating cells under direct reprogramming coupled to RNA-seq. Finally, we focused on determining the contribution of upregulated miRNA targeted transcription factors (TFs) to the overall reprogramming by leveraging ChIP- and RNA-seq approaches. Our results show that upon pathogen-triggered RNA silencing suppression, the concerted action of miRNA targets enables a new layer of defense to cope with silencing suppressor producing pathogens. Thus, we propose that miRNAs constitute an intracellular surveillance system for the presence of pathogen threats through sensing foreign proteins that interfere with RNA silencing.