RNA hydrolysis at mineral-water interfaces

Abstract

The adsorption of DNA at mineral-water interfaces is well-established to increase its persistence in soils and sediments; however, adsorbed RNA in similar environments degrades rapidly, in some cases outpacing solution-phase degradation occurring over hours to days. Herein, we elucidate a novel abiotic mechanism by which RNA, but not DNA, degrades upon adsorption to surfaces of iron (oxyhydr)oxides such as goethite (α-FeOOH) that are abundant in soils and sediments. Upon adsorption to goethite, both single-stranded and double-stranded RNA hydrolyzed on the timescale of hours under environmentally relevant physicochemical conditions. The reaction products were consistent with iron present in goethite acting as a Lewis acid to accelerate non-selective hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to well-established acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. We further confirmed that contact of the RNA with the mineral surface is necessary for hydrolysis to occur by demonstrating RNA degradation was inhibited by compact RNA conformation at elevated ionic strength and competitive adsorption with orthophosphate and organic matter. In addition to goethite, we observed RNA hydrolysis was also catalyzed by hematite (α-Fe2O3), but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.

Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation

“…In the binding experiments, lower molecular weight products were not detected via gel electrophoresis, ruling out unintended degradation. 17,23 Additionally, because DOM had an inhibitory effect on RNase Imediated RNA degradation, as determined in the degradation experiments detailed below, the contribution of residual RNases in DOM solutions to RNA degradation was inferred to be negligible relative to RNase I added as a reagent. RNA-DOM and RNA-Homopeptide Binding Experiments.…”

“…For example, the suppression of mineral-catalyzed hydrolysis of RNA by DOM could increase the persistence of dsRNA biopesticides in relevant soils and sediments. 17 The increased persistence of dsRNA biopesticides may increase risks posed to nontarget organisms, 15 particularly if bioactivity of dsRNA is retained upon binding by DOM. Our findings additionally suggest that the protective effect of DOM in wastewater 82,83 needs to be considered when modeling degradation rates of free genomic viral RNA 84 in the context of wastewater-based epidemiology.…”

“…While some of these processes likely parallel processes that impact DNA fate (e.g., adsorption to surfaces), 16 others (e.g., abiotic degradation or biodegradation) may diverge. 3,14,17 One important process controlling both DNA and RNA persistence is biodegradation, which can in principle be mediated by both active microbes and extracellular enzymes in environmental systems (e.g., soil). The specific role of active microbes in DNA degradation has been supported by slower DNA loss in sterilized environmental media.…”

The definition of RNA age related to RNA sequence changes

“…However, RNAs can come from other sources, including artificial RNAs, semi-conservative replication of RNAs in RNA viruses, etc. (Lohmann et al, 1999;Isaacs et al, 2006;Ossowski et al, 2008;Khalil and Collins, 2010;Simon-Loriere and Holmes, 2011;Dykstra et al, 2022); RNAs can be detected outside the cells, and the RNAs outside the cells go through diverse processes of existence than inside the cell (Karl and Bailiff, 1989;Paul et al, 1990;Sakano and Kamatani, 1992;Flores et al, 2005;Ickenstein and Garidel, 2019;Chatterjee et al, 2022;Tahtinen et al, 2022;Zhang et al, 2023). This demonstrates the application limitations of the previous definition of RNA age, which predominantly describes RNA in cells.…”

“…Like other biological molecules, RNA is destroyed when strong chemical reactions, such as combustion occur or when it encounters chemicals, including strong acids and alkalis. In the environment, non-enzymatic RNA hydrolysis is a spontaneous process that can be accelerated by the action of diverse ions, buffers, and pH levels (Tenhunen, 1989;Matsumura and Komiyama, 1997;AbouHaidar and Ivanov, 1999;Li and Breaker, 1999;Chatterjee et al, 2022;Zhang et al, 2023). Temperature is one of the major physical factors that affect RNA degradation.…”