MicroRNAs from pear stigma exudates—The next generation of anti-fire blight agents?

Introduction: Fire blight is a devastating disease, which threatens global fruit production in pear, apple, and other Rosaceae family members. The disease is caused by Erwinia amylovora bacteria, which colonize the stigma surface and grows rapidly prior to floral infection. Current strategies for controlling fire blight are insufficient; thus, alternative solutions must be sought.

Liquid excretions from different flower stigmas can interact with the stigma inhabitants including pollen grains and various microorganisms. Recently, our lab analyzed stigma exudates of several pear species and discovered extracellular RNAs (exRNAs) including microRNAs. Plant exRNAs modes of action are still poorly understood, yet recent studies have shown that plant extracellular small RNAs can be transmitted to cells from various kingdoms including mammalian and microorganisms and interfere with their transcriptional regulation.

Methods: The possibility that the pear stigma exudate microRNAs might have targets in the E. amylovora genome was explored via bioinformatic prediction of RNA–RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. The two target prediction tools used were "TargetRNA2" and "IntraRNA2.0". Target prediction was performed with the threshold set up to p < 0.05 against “Erwinia amylovora CFBP1430 chromosome” with all the parameters set at the default values.

Results: The bioinformatic target prediction analysis identified 370 E. amylovora genes that are potentially targeted by the pear stigma miRs. Moreover, molecular categorization analysis of these genes revealed that several of them are known bacterial virulent factors, while many others are differentially expressed in E. amylovora during several infection stages on apple trees.

Conclusions: Our results indicate the possible involvement of the pear stigmatic microRNAs in host–pathogen interactions and suppression of E. amylovora pathogenicity genes. Moreover, our findings can potentially lead to the development of novel bio-control microRNA-based strategies against fire blight.