Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22

Abstract

Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2′-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H]+ > [M + H − 116]+ transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2′-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work.

The Future of DNA Adductomic Analysis

“…The ultimate goal of DNA adductomics [ 29 ] is to characterize the modifications of DNA as a profile of specific adducts, rather than focusing only on a few adducts at a time. There are many applications of DNA adductomic analysis, including investigating the genotoxic effect of exposures from the environment [ 33 , 34 , 35 , 36 , 41 , 51 , 53 , 54 , 55 , 56 , 59 , 60 , 61 , 62 , 63 , 65 , 66 ], as well as endogenous adduct formation [ 38 , 64 , 67 ]. It can be used to investigate mechanisms of actions of genotoxic chemotherapeutic drugs [ 37 , 68 , 69 ], and the mutagenicity potential of pharmaceuticals or supplements in the context of cancer risk.…”

“…The field of DNA adductomics has been recently reviewed and [ 29 , 51 , 52 ] Table 2 summarizes the LC-MS based DNA adductomics analyses performed to date. Three recent studies [ 53 , 54 , 55 ] have used the conventional low resolution, nominal mass MS 2 approach for DNA adductomics, but the trend since our previous review is to use HRAM data acquisition for DNA adductomic experiments. Two studies [ 33 , 34 ] have relied on full scan HRAM data acquisition and a self-generated DNA adduct database searching for DNA adductomic analysis, whereas another recent study [ 35 ] used HRAM DIA data acquisition using the simultaneous acquisition of fragment ions resulting from high and low collision energy (MS E ).…”

Nanoscale battery cathode materials induce DNA damage in bacteria

“…30 DNA adductomics has been applied to investigate modes of genotoxicity in mice upon iron oxide NP exposure 36 and in a soil bacterium. 37 In this work, we used state-of-the-art DNA adductomic techniques based on the use of high resolution accurate mass (HRAM) mass spectrometry to detect a large variety of DNA modications, providing information on the chemical nature of the cellular responses upon nano-NMC exposure.…”

Mass Spectrometric Mapping of the DNA Adductome as a Means to Study Genotoxin Exposure, Metabolism, and Effect

“…45 Omics technology and methodology allows top-down exposome and DNA adductome mapping, enabling potential discovery of yet unknown DNA adduct biomarkers in different biological samples. Contrary to most other methods, MS analyses can reliably generate both qualitative and quantitative DNA adduct data.…”