Exocyclic Carbons Adjacent to the N6 of Adenine are Targets for Oxidation by the Escherichia coli Adaptive Response Protein AlkB

The DNA and RNA repair protein AlkB removes alkyl groups from nucleic acids by a unique iron- and α-ketoglutarate-dependent oxidation strategy. When alkylated adenines are used as AlkB targets, earlier work suggests that the initial target of oxidation can be the alkyl carbon adjacent to N1. Such may be the case with ethano-adenine (EA), a DNA adduct formed by an important anticancer drug, BCNU, whereby an initial oxidation would occur at the carbon adjacent to N1. In a previous study, several intermediates were observed suggesting a pathway involving adduct restructuring to a form that would not hinder replication, which would match biological data showing that AlkB almost completely reverses EA toxicity in vivo. The present study uses more sensitive spectroscopic methodology to reveal the complete conversion of EA to adenine; the nature of observed additional putative intermediates indicates that AlkB conducts a second oxidation event in order to release the two-carbon unit completely. The second oxidation event occurs at the exocyclic carbon adjacent to the N[superscript 6] atom of adenine. The observation of oxidation of a carbon at N[superscript 6] in EA prompted us to evaluate N[superscript 6]-methyladenine (m6A), an important epigenetic signal for DNA replication and many other cellular processes, as an AlkB substrate in DNA. Here we show that m6A is indeed a substrate for AlkB and that it is converted to adenine via its 6-hydroxymethyl derivative. The observation that AlkB can demethylate m6A in vitro suggests a role for AlkB in regulation of important cellular functions in vivo.National Institutes of Health (U.S.) (Grant number CA080024)National Institutes of Health (U.S.) (Grant number CA26731)National Institutes of Health (U.S.) (Grant number ES02109

Heightened hurricane surge risk in northwest Florida revealed from climatological-hydrodynamic modeling and paleorecord reconstruction

Historical tropical cyclone (TC) and storm surge records are often too limited to quantify the risk to local populations. Paleohurricane sediment records uncover long-term TC activity, but interpreting these records can be difficult and can introduce significant uncertainties. Here we compare and combine climatological-hydrodynamic modeling (including a method to account for storm size uncertainty), historical observations, and paleohurricane records to investigate local surge risk, using Apalachee Bay in northwest Florida as an example. The modeling reveals relatively high risk, with 100 year, 500 year, and “worst case” surges estimated to be about 6.3 m, 8.3 m, and 11.3 m, respectively, at Bald Point (a paleorecord site) and about 7.4 m, 9.7 m, and 13.3 m, respectively, at St. Marks (the head of the Bay), supporting the inference from paleorecords that Apalachee Bay has frequently suffered severe inundation for thousands of years. Both the synthetic database and paleorecords contain a much higher frequency of extreme events than the historical record; the mean return period of surges greater than 5 m is about 40 years based on synthetic modeling and paleoreconstruction, whereas it is about 400 years based on historical storm analysis. Apalachee Bay surge risk is determined by storms of broad characteristics, varies spatially over the area, and is affected by coastally trapped Kelvin waves, all of which are important features to consider when accessing the risk and interpreting paleohurricane records. In particular, neglecting size uncertainty may induce great underestimation in surge risk, as the size distribution is positively skewed. While the most extreme surges were generated by the uppermost storm intensities, medium intensity storms (categories 1–3) can produce large to extreme surges, due to their larger inner core sizes. For Apalachee Bay, the storms that induced localized barrier breaching and limited sediment transport (overwash regime; surge between 3 and 5 m) are most likely to be category 2 or 3 storms, and the storms that inundated the entire barrier and deposited significantly more coarse materials (inundation regime; surge > 5 m) are most likely to be category 3 or 4 storms.United States. National Oceanic and Atmospheric Administration (Grant NA11OAR4310101)National Science Foundation (U.S.) (Grant OCE-0903020)National Science Foundation (U.S.) (Grant OCE-1250506

Recognition and processing of a new repertoire of DNA substrates by human 3-methyladenine DNA glycosylase (AAG)

The human 3-methyladenine DNA glycosylase (AAG) recognizes and excises a broad range of purines damaged by alkylation and oxidative damage, including 3-methyladenine, 7-methylguanine, hypoxanthine (Hx), and 1,N[superscript 6]-ethenoadenine (εA). The crystal structures of AAG bound to εA have provided insights into the structural basis for substrate recognition, base excision, and exclusion of normal purines and pyrimidines from its substrate recognition pocket. In this study, we explore the substrate specificity of full-length and truncated Δ80AAG on a library of oligonucleotides containing structurally diverse base modifications. Substrate binding and base excision kinetics of AAG with 13 damaged oligonucleotides were examined. We found that AAG bound to a wide variety of purine and pyrimidine lesions but excised only a few of them. Single-turnover excision kinetics showed that in addition to the well-known εA and Hx substrates, 1-methylguanine (m1G) was also excised efficiently by AAG. Thus, along with εA and ethanoadenine (EA), m1G is another substrate that is shared between AAG and the direct repair protein AlkB. In addition, we found that both the full-length and truncated AAG excised 1,N[superscript 2]-ethenoguanine (1,N[superscript 2]-εG), albeit weakly, from duplex DNA. Uracil was excised from both single- and double-stranded DNA, but only by full-length AAG, indicating that the N-terminus of AAG may influence glycosylase activity for some substrates. Although AAG has been primarily shown to act on double-stranded DNA, AAG excised both εA and Hx from single-stranded DNA, suggesting the possible significance of repair of these frequent lesions in single-stranded DNA transiently generated during replication and transcription.United States. National Institutes of Health (grant ES05355)United States. National Institutes of Health (grant CA75576)United States. National Institutes of Health (grant CA55042)United States. National Institutes of Health (grant ES02109)United States. National Institutes of Health (grant T32-ES007020)United States. National Institutes of Health (grant CA80024)United States. National Institutes of Health (grant CA26731