Circular RNAs in Lotus japonicus Responses to Nutrient Supply and Mesorhizobium Symbiosis

Symbiotic interactions between legumes and rhizobia enable nitrogen fixation under low nutrient conditions. The establishment and function of symbiotic interactions require coordinated changes in gene expression in both the host and the microbe. Circular RNAs (circRNAs) are endogenous gene-specific molecules that can regulate transcription and translation in response to biotic and abiotic stress through various mechanisms. Our objective was to identify circRNAs specifically generated in response to nutrient supply and rhizobial symbiosis. We sequenced nodulated and non-inoculated roots from Lotus japonicus and identified a total of 11,923 putative circRNAs originating from 5,290 nuclear-encoded transcripts in Lotus roots under low or high nutrient supply and nodulated roots. Of those, 58 circRNAs were specific and present in most nodulated root samples. We identified circRNAs for more than half of the known symbiosis-associated genes, including SymRK, CCamK, and Cyclops, and showed that several of those genes also generated circRNAs in Phaseolus vulgaris nodules. We validated select circRNAs potentially involved in regulating symbiosis and predicted miRNA recognition elements (MREs) created only by the backsplice junctions of circRNAs. These putative backsplice-generated MREs could represent an additional mechanism by which circRNAs may modulate the abundance and translation of mRNAs in competing endogenous RNA-regulatory networks.