Profiling of RNA 8-oxoG marks in Escherichia coli identifies critical intrinsic characteristics that contribute to 8-oxoG accumulation in bacteria

Abstract Reactive oxygen species (ROS) are environmentally ubiquitous and known to have pervasive impacts on cellular homeostasis. RNA is vulnerable to oxidative chemical alterations from a variety of endogenous and exogenous sources. The most common chemical modification resulting from ROS exposure to RNA is 8-oxo-7,8-dihydroguanine (8-oxoG)—an oxidized form of the canonical guanine (G) nucleobase. While 8-oxoG modifications are known to impact mRNA processing, understanding the broader biological impact of 8-oxoG requires knowledge of how these modifications accumulate. In this work, we assessed the disparate enrichment of 8-oxoG modifications within RNAs in the E. coli transcriptome using an RNA Immunoprecipitation Sequencing technique with a high-affinity 8-oxoG antibody (8-oxoG-RIP-Seq). Our investigation of the RNA 8-oxoG enrichment landscape uncovered several intrinsic RNA characteristics that correlate with 8-oxoG enrichment. These findings suggest intrinsic characteristics of RNA, most notably relative abundance, CDS length, and G nucleotide composition, significantly influence RNA 8-oxoG accumulation. We harnessed these intrinsic characteristics to construct a simple multiple linear regression model that predicts RNA 8-oxoG accumulation, which we validated in E. coli . This model was subsequently applied to predict 8-oxoG enriched RNA species in four other bacterial species spanning a wide range of oxidative stress tolerances; these predictions suggest that 8-oxoG accumulation is largely species dependent, with limited overlap in RNAs and functional pathways that are more susceptible to elevated levels of 8-oxoG accumulation. Overall, these findings better inform understanding of RNA 8-oxoG patterns in bacteria and have broader impacts towards advancing knowledge of the connection between RNA oxidation and cellular homeostasis.