Diprotonated Parabanic Acid: A Vicinal or 1,3‐Dication?

Reacting parabanic acid with the superacidic systems XF/MF5 (X = H, D; M = As, Sb) in different ratios, led to the formation of the mono‐ and diprotonated species. Salts in terms of [C3H3N2O3][AsF6], [C3H3N2O3][SbF6], [C3H4N2O3][AsF6]2, [C3H4N2O3][SbF6]2, [C3D3N2O3][AsF6] and [C3D4N2O3][AsF6]2 were obtained and characterized by low‐temperature infrared and Raman spectroscopy. Single‐crystal X‐ray structure analyses were performed for [C3H3N2O3][SbF6] and [C3H4N2O3][AsF6]2·4HF. Additionally, quantum chemical calculations were carried out on the B3LYP/aug‐cc‐pVTZ level of theory for the mono‐ and dication. Mapped Electrostatic Potentials together with Natural Population Analysis charges were calculated in order to localize the two positive charges of the diprotonated parabanic acid. The diprotonated parabanic acid can be described as an 1,2‐C,C‐dication, stabilized by electron delocalization over the five‐membered ring

Escherichia coli genome-wide promoter analysis: Identification of additional AtoC binding target elements

<p>Abstract</p> <p>Background</p> <p>Studies on bacterial signal transduction systems have revealed complex networks of functional interactions, where the response regulators play a pivotal role. The AtoSC system of <it>E. coli </it>activates the expression of <it>atoDAEB </it>operon genes, and the subsequent catabolism of short-chain fatty acids, upon acetoacetate induction. Transcriptome and phenotypic analyses suggested that <it>atoSC </it>is also involved in several other cellular activities, although we have recently reported a palindromic repeat within the <it>atoDAEB </it>promoter as the single, <it>cis</it>-regulatory binding site of the AtoC response regulator. In this work, we used a computational approach to explore the presence of yet unidentified AtoC binding sites within other parts of the <it>E. coli </it>genome.</p> <p>Results</p> <p>Through the implementation of a computational <it>de novo </it>motif detection workflow, a set of candidate motifs was generated, representing putative AtoC binding targets within the <it>E. coli </it>genome. In order to assess the biological relevance of the motifs and to select for experimental validation of those sequences related robustly with distinct cellular functions, we implemented a novel approach that applies Gene Ontology Term Analysis to the motif hits and selected those that were qualified through this procedure. The computational results were validated using Chromatin Immunoprecipitation assays to assess the <it>in vivo </it>binding of AtoC to the predicted sites. This process verified twenty-two additional AtoC binding sites, located not only within intergenic regions, but also within gene-encoding sequences.</p> <p>Conclusions</p> <p>This study, by tracing a number of putative AtoC binding sites, has indicated an AtoC-related cross-regulatory function. This highlights the significance of computational genome-wide approaches in elucidating complex patterns of bacterial cell regulation.</p