Cell-specific RNA profiling reveals host genes expressed in Arabidopsis cells haustoriated by downy mildew

A translating ribosome affinity purification system is used to analyze gene expression in pathogen-infected host cells and identify host genes whose expression is induced in infected cells. The downy mildew oomycete Hyaloperonospora arabidopsidis, an obligate filamentous pathogen, infects Arabidopsis (Arabidopsis thaliana) by forming structures called haustoria inside host cells. Previous transcriptome analyses have revealed that host genes are specifically induced during infection; however, RNA profiling from whole-infected tissues may fail to capture key transcriptional events occurring exclusively in haustoriated host cells, where the pathogen injects virulence effectors to modulate host immunity. To determine interactions between Arabidopsis and H. arabidopsidis at the cellular level, we devised a translating ribosome affinity purification system using 2 high-affinity binding proteins, colicin E9 and Im9 (immunity protein of colicin E9), applicable to pathogen-responsive promoters, thus enabling haustoriated cell-specific RNA profiling. Among the host genes specifically expressed in H. arabidopsidis-haustoriated cells, we found genes that promote either susceptibility or resistance to the pathogen, providing insights into the Arabidopsis-downy mildew interaction. We propose that our protocol for profiling cell-specific transcripts will apply to several stimulus-specific contexts and other plant-pathogen interactions.

Automated summary

A translating ribosome affinity purification system is used to analyze gene expression in pathogen-infected host cells and identify host genes whose expression is induced in infected cells. The study found that host genes are specifically induced during infection by the pathogen. This method can help us better understand the interaction between plants and pathogens.