The fate of RNA in soils has broad implications for diverse fields including microbial ecology, ecological risk assessment of emerging RNA-based biopesticides, and biogeochemical cycling of phosphorous. Like DNA, both single-stranded (ss) and double-stranded (ds)RNA molecules are expected to be degraded by phosphodiester bond hydrolysis by nucleases in soils. However, while DNA adsorbed to soil particles is widely reported to be protected from enzymatic hydrolysis and thus persist for extended time periods, RNA adsorbed to soil particles has been found to degrade in soils. To explain this difference, we hypothesized adsorption of RNA to metal (hydr)oxide minerals present in soils may catalyze phosphodiester bond hydrolysis. We determined that RNA specifically adsorbed to the mineral goethite underwent abiotic hydrolysis (as opposed to nuclease degradation or degradation in the supernatant of the goethite suspension). In additional experiments, we found the reaction rate was altered by RNA structure, with a shorter half-live for ssRNA (~6 h) than dsRNA (~12 h). Solution constituents, like organic matter and orthophosphate, could also impede the degradation by competing adsorption sites with RNA. We determined phosphodiester bond hydrolysis was the dominant degradation mechanism by identifying monophosphate nucleotides as the primary reaction products. With these results, we proposed the mechanism of goethite-mediated RNA hydrolysis, which involves nucleophilic attack on phosphorus atoms facilitated by iron coordination. Other metal (hydr)oxides (e.g., aluminum oxide) could also catalyze RNA hydrolysis after hours of adsorption, indicating the reaction might be common in soils. As a comparison, we also validated the catalyzed hydrolysis was unique to RNA and didn’t occur to DNA (e.g., by goethite). Our results suggest mineral-mediated RNA hydrolysis, a novel pathway, may explain why adsorbed RNA in soils does not persist like DNA. Moreover, our study also indicates employing metal (hydr)oxides as model absorbents in RNA studies may cause unintended RNA degradation.

RNA hydrolysis at mineral-water interfaces

ACS Fall 2021

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