Inhibition of Free DNA Degradation by the Deformation of DNA Exposed to Trace Polycyclic Aromatic Hydrocarbon Contaminants

A rapid inhibitory effect of polycyclic aromatic hydrocarbons (PAHs) on DNA degradation was examined by conventional spectral analysis and microtitration. The purpose was to determine whether PAHs inhibited free DNA degradation by the enzyme DNase I. The results showed that model PAHs phenanthrene and pyrene combined with free DNA to decelerate DNA degradation by DNase I. Phenanthrene-induced inhibition was stronger than that of pyrene. Trace level of PAHs did not induce DNase I deactivation. The DNase I enzyme exhibited only slight shifts in IR absorption bands related to amide II and III upon PAH exposure, and no change was observed with other bands. The decelerating degradation of DNA is attributed to the changes in structure, backbone composition, and guanine constituents of DNA induced by PAHs inserted into double strands, and to the imidazole-like derivates from the combination of imidazole rings with pyrene

Microbial Extracellular Polymeric Substances Reduce Ag⁺ to Silver Nanoparticles and Antagonize Bactericidal Activity

Whereas the antimicrobial mechanisms of silver have been extensively studied and exploited for numerous applications, little is known about the associated bacterial adaptation and defense mechanisms that could hinder disinfection efficacy or mitigate unintended impacts to microbial ecosystem services associated with silver release to the environment. Here, we demonstrate that extracellular polymeric substances (EPS) produced by bacteria constitute a permeability barrier with reducing constituents that mitigate the antibacterial activity of silver ions (Ag⁺). Specifically, manipulation of EPS in Escherichia coli suspensions (e.g., removal of EPS attached to cells by sonication/centrifugation or addition of EPS at 200 mg L^–1) demonstrated its critical role in hindering intracellular silver penetration and enhancing cell growth in the presence of Ag⁺ (up to 0.19 mg L^–1). High-resolution transmission electron microscopy (HRTEM) combined with X-ray photoelectron spectroscopy (XPS) and energy-dispersive spectrometry (EDS) analyses showed that Ag⁺ was reduced to silver nanoparticles (AgNPs; 10–30 nm in diameter) that were immobilized within the EPS matrix. Fourier transform infrared (FTIR) and ¹³C nuclear magnetic resonance (NMR) spectra suggest that Ag⁺ reduction to AgNPs by the hemiacetal groups of sugars in EPS contributed to immobilization. Accordingly, the amount and composition of EPS produced have important implications on the bactericidal efficacy and potential environmental impacts of Ag⁺

Noncovalent Binding of Polycyclic Aromatic Hydrocarbons with Genetic Bases Reducing the <i>in Vitro</i> Lateral Transfer of Antibiotic Resistant Genes

In current studies of noncovalent interactions of polycyclic aromatic hydrocarbons (PAHs) with genetic units, the impact of such interactions on gene transfer has not been explored. In this study, we examined the association of some widely occurring PAHs (phenanthrene, pyrene, benzo­[g,h,i]­perylene, and other congeners) with antibiotic resistant plasmids (pUC19). Small molecular PAHs (e.g., phenanthrene) bind effectively with plasmids to form a loosely clew-like plasmid–PAH complex (16.5–49.5 nm), resulting in reduced transformation of ampicillin resistance gene (Ampr). The <i>in vitro</i> transcription analysis demonstrated that reduced transformation of Ampr in plasmids results from the PAH-inhibited Ampr transcription to RNA. Fluorescence microtitration coupled with Fourier transform infrared spectroscopy (FTIR) and theoretical interaction models showed that adenine in plasmid has a stronger capacity to sequester small Phen and Pyre molecules via a π–π attraction. Changes in Gibbs free energy (Δ<i>G</i>) suggest that the CT–PAH model reliably depicts the plasmid–PAH interaction through a noncovalently physical sorption mechanism. Considering the wide occurrence of PAHs and antibiotic resistant genes (ARGs) in the environment, our findings suggest that small-sized PAHs can well affect the behavior of ARGs via above-described noncovalent interactions

Chromatogram of the four bases of DNA, DNA–phenanthrene, DNA–phenanthrene-Ca²⁺, DNA–pyrene, and DNA–pyrene-Ca²⁺.

<p>C: cytosine, G: guanine, A: adenine, T: thymine. The HPLC-MS spectra showed an absence of PAH–DNA adducts.</p

Extracellular Saccharide-Mediated Reduction of Au³⁺ to Gold Nanoparticles: New Insights for Heavy Metals Biomineralization on Microbial Surfaces

Biomineralization is a critical process controlling the biogeochemical cycling, fate, and potential environmental impacts of heavy metals. Despite the indispensability of extracellular polymeric substances (EPS) to microbial life and their ubiquity in soil and aquatic environments, the role played by EPS in the transformation and biomineralization of heavy metals is not well understood. Here, we used gold ion (Au³⁺) as a model heavy metal ion to quantitatively assess the role of EPS in biomineralization and discern the responsible functional groups. Integrated spectroscopic analyses showed that Au³⁺was readily reduced to zerovalent gold nanoparticles (AuNPs, 2–15 nm in size) in aqueous suspension of <i>Escherichia coli</i> or dissolved EPS extracted from microbes. The majority of AuNPs (95.2%) was formed outside <i>Escherichia coli</i> cells, and the removal of EPS attached to cells pronouncedly suppressed Au³⁺ reduction, reflecting the predominance of the extracellular matrix in Au³⁺ reduction. XPS, UV–vis, and FTIR analyses corroborated that Au³⁺ reduction was mediated by the hemiacetal groups (aldehyde equivalents) of reducing saccharides of EPS. Consistently, the kinetics of AuNP formation obeyed pseudo-second-order reaction kinetics with respect to the concentrations of Au³⁺ and the hemiacetal groups in EPS, with minimal dependency on the source of microbial EPS. Our findings indicate a previously overlooked, universally significant contribution of EPS to the reduction, mineralization, and potential detoxification of metal species with high oxidation state

The transformation efficiency of plasmid DNA as a function of phenanthrene/pyrene concentrations.

<p>The transformation efficiency was calculated according to Equation I. Error bars represent 1 standard deviation (n = 3).</p

Molecular model combining the –POO^–– group of DNA with Ca²⁺ linked by an electrovalent bond.

<p>R₁, R₂, R₃, and R₄ represent the different bases in DNA, and the blue dashed line represents the electrovalent bond between Ca²⁺ and the –POO^–– group.</p

The absorption bands of DNA from FTIR spectra and their corresponding functional groups.

<p>The absorption bands of DNA from FTIR spectra and their corresponding functional groups.</p

Diagram of the mechanism of Ca²⁺-inhibited PAH adsorption via blocking of the binding site in plasmid DNA.

<p>A hydrophobic interaction between pyrene and DNA bases occurred via a phosphate backbone structure (A). Ca²⁺-inhibition of the interaction between pyrene and DNA occurred via the capture of PAHs by DNA, thereby blocking the phosphate backbone structure of the DNA periphery (B).</p

XPS analysis of oxygen in DNA, DNA–pyrene, and DNA–Ca.

<p>XPS analysis of oxygen in DNA, DNA–pyrene, and DNA–Ca.</p