Dissecting the Arabidopsis/downy mildew interaction by haustoriated cell-specific RNA profiling

The downy mildew oomycete Hyaloperonospora arabidopsidis, an obligate filamentous pathogen, infect Arabidopsis by forming feeding structures called haustoria inside the host cell. Previous transcriptome analysis revealed host genes specifically induced during infection. However, whole infected tissue-derived RNA profiling may fail to capture the key transcriptional events that may occur exclusively in haustoriated host cells where the pathogen injects virulence effectors to modulate host immunity for successful accommodation. To understand the interaction between Arabidopsis and H. arabidopsidis at the cellular level, we established a new translating ribosome affinity purification (TRAP) system applicable to pathogen-responsive promoters, 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 new insights into the Arabidopsis/downy mildew interaction. We also expect that our new TRAP system could be applicable to several stimulus-specific contexts as well as other plant–pathogen interactions. Three-week-old plants were spray-inoculated to saturation with a spore suspension of 1 x 104 conidiospores/ml. Plants were covered with a transparent lid to maintain high humidity (90-100%) conditions in a growth cabinet at 16°C under a 10-h photoperiod for 5 days. RNA sequencing was performed by deep sequencing on Illumina NextSeq 500 using EXPRSS tag-seq protocol (BMC Genomics 2014, 15:341). Each biological replicate set of samples were sequenced as one batch (biorep1, biorep2 and biorep3 in filenames).