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The interaction between natural amino acids and hydrogen peroxide is of paramount importance due to the widespread use of hydrogen peroxide in biological and environmentally significant processes. Given that both amino acids and hydrogen peroxide occur in nature in two enantiomeric forms, it is crucial to investigate the formation of complexes between them, considering the role of molecular chirality. In this work, we report a theoretical study on the hydrogen peroxide enantiomers and their interactions with L- and S-serine and their clusters. We aimed to evaluate the non-covalent interactions between each hydrogen peroxide enantiomer and the L- and D-enantiomers of the non-essential amino acid serine and their clusters. First, the potential energy surfaces (PES) of transitions between enantiomers of the simplest chiral molecule, hydrogen peroxide, in the gas phase and in aqueous solution were studied using the Møller–Plesset theory method MP2/aug-cc-pVDZ. The activation energies of such transitions were calculated. The interactions of both hydrogen peroxide enantiomers (P and M) with L- and D-serine enantiomers were analyzed by density functional theory (DFT) with ωb97xd/6-311+G**, B3Lyp/6-311+G**, B3P86/6-311+G**, and M06/6-311+G** functionals. We found that both enantiomers of hydrogen peroxide bind more strongly to L-serine and its clusters than to D-serine, especially highlighting that the L form is the predominant natural form of this and other chiral amino acids. The optimized geometric parameters, interaction energies, and HOMO-LUMO energies for various complexes were estimated. Furthermore, circular dichroism (CD) spectra, which are optical chirality characteristics, were simulated for all the complexes under study. [ABSTRACT FROM AUTHOR]

Enantiomeric-enriched ferrocene-modified pyrazoles were synthesized via the reaction of the ferrocene alcohol, (S)-FcCH(OH)CH3 (Fc = ferrocenyl), with various pyrazoles in acidic conditions at room temperature within several minutes. X-ray structural data for racemic (R,S)-1N-(3,5-dimethyl pyrazolyl)ethyl ferrocene (1) and its (S)-enantiomer (S)-1 were determined. A series of racemic pyrazolylalkyl ferrocenes was separated into enantiomers by analytical HPLC on β- and γ-cyclodextrins (CD) chiral stationary phases. The quantum chemical calculations of interaction energies of β-CD were carried out for both (R)- and (S)-enantiomers. A high correlation between experimental HPLC data and calculated interaction energies values was obtained. [ABSTRACT FROM AUTHOR]

Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these "exotic" regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased "non-optimal" codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for "alien" regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions.en [ABSTRACT FROM AUTHOR]

Recently, it has been found that bacteria secrete short RNAs able to affect gene expression in eukaryotic cells, while certain mammalian microRNAs shape the gut microbiome altering bacterial transcriptome. The involvement of bacterial RNAs in communication with other bacteria is also expected, but has not been documented yet. Here, we compared the fractions of extremely short (12–22 nucleotides) RNAs secreted by Escherichia coli grown in a pure culture and jointly with bacteria of the Paenibacillus genus. Besides fragments of rRNAs and tRNAs, abundant in all samples, secreted oligonucleotides (exoRNAs) predominantly contained GC-rich fragments of messenger and antisense RNAs processed from regions with stable secondary structures. They differed in composition from oligonucleotides of intracellular fraction, where fragments of small regulatory RNAs were prevalent. Both fractions contained RNAs capable of forming complementary duplexes, while for exoRNA samples a higher percentage of 3΄-end modified RNAs and different endonuclease cleavage were detected. The presence of a cohabiting bacterium altered the spectrum of E. coli exoRNAs, indicating a population-dependent control over their composition. Possible mechanisms of this effect are discussed. [ABSTRACT FROM AUTHOR]