Gene expression analysis and classification of mode of toxicity of polycyclic aromatic hydrocarbons (PAHs) in Escherichia coli

The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis

Pyrene is a pollutant in the environment and affects the health of living organisms. It is important to understand microbial-mediated pyrene resistance and the related molecular mechanisms due to its toxicity and biodegradability. Due to the unclear response mechanisms of bacteria to PAHs, this study detected the transcriptional changes in Escherichia coli under different pyrene concentrations using transcriptome sequencing technology. Global transcriptome analysis showed that the number of differentially expressed genes (DEGs) in multiple metabolic pathways increased with increasing concentrations of pyrene. In addition, the effects and toxicity of pyrene on Escherichia coli mainly included the up-regulation and inhibition of genes related to carbohydrate metabolism, membrane transport, sulfate reduction, various oxidoreductases, and multidrug efflux pumps. Moreover, we also constructed an association network between significantly differentially expressed sRNAs and key genes and determined the regulatory relationship and key genes of Escherichia coli under pyrene stress. Our study utilized pyrene as an exogenous stress substance to investigate the possible pathways of the bacterial stress response. In addition, this study provides a reference for other related research and serves as a foundation for future research.

Novel spiro[chromanone-2,4'-piperidine]-4-one derivatives as potential inhibitors of fatty acid synthesis in pathogens: Design, synthesis, and biological evaluation

Bacterial survival depends on membrane lipid homeostasis that enables to regulate lipid composition to adapt and optimize their growth in diverse environments. Therefore, the development of inhibitors that interfere with the bacterial fatty acid synthesis process is considered to be a promising tactic. In this study, 58 novel spirochromanone derivatives were prepared and their structure-activity relationship (SAR) was investigated. The bioassay results showed that all most of the compounds showed excellent biological activities, exampled by compounds B₁₄, C₁, B₁₅, and B₁₃, which had outstanding inhibitory activities toward various pathogenic bacteria with EC₅₀ values of 0.78 μg/mL ∼3.48 μg/mL. Preliminary antibacterial behavior was studied by a series of biochemical assays including, but not limited to, fluorescence imaging patterns, GC-MS analysis, TEM images, and fluorescence titration experiments. Notably, compound B₁₄ decreased the lipid content of the cell membrane, and increased cell membrane permeability, thereby destroying the integrity of the bacterial cell membrane. Further qRT-PCR results indicated that compound B₁₄ interfered with the mRNA expression levels of fatty acid synthesis process-related genes including ACC, ACP, and Fab family genes. Herein, we highlight the promising bactericidal skeleton based on the spiro[chromanone-2,4'-piperidine]-4-one as a potential inhibitor of fatty acid synthesis.

Genomic and physiological traits provide insights into ecological niche adaptations of mangrove endophytic Streptomyces parvulus VCCM 22513

Purpose

Endophytic Streptomyces parvulus VCCM 22513 isolated from Bruguiera gymnorrhiza in Quang Ninh mangrove forest, northern Vietnam showed abiotic stress tolerance consisting of antioxidant, salt-tolerant, and aromatic-compound degrading activities. The goal of this study was to shed light on genomic bases rendering mangrove endophytic S. parvulus more resilient to environmental stressors.

Methods

Phenotypic analysis including antioxidant activities, hydrogen peroxide and sodium chloride resistance, and aromatic compound utilization were evaluated. The genome of strain VCCM 22513 was sequenced using Illumina Miseq sequencing platform and assembled using SPAdes.

Results

Out of 15 endophytic actinomycetes associated with B. gymnorrhiza in Quang Ninh mangrove, northern Vietnam, VCCM 22513 extract showed remarkable antioxidant activities through (1,1-diphenyl-2-picrylhydrazyl) DPPH and superoxide radical scavenging assays of 72.1 ± 0.04% and 38.3 ± 0.16% at 1.6 mg/ml, respectively. The genome consists of a 7,688,855 bp linear chromosome, 6782 protein-coding sequences, and 68 tRNAs. Genomic analysis identified strain VCCM 22513 as Streptomyces parvulus and confirmed a highly conserved core genome and stability of S. parvulus under natural selection. Genome mining revealed the presence of genetic determinants involved in mycothiol and ergothioneine biosynthesis (26 genes), oxidative stress resistance (43 genes), osmoadaptation (87 genes), heat and cold stress (34 genes), aromatic compound degradation (55 genes). Further genome-wide comparison between S. parvulus VCCM 22513 and 11 Streptomyces genomes showed that VCCM 22513 possesses significantly higher copies of genes involved in mycothiol and ergothioneine biosynthesis. In support of this finding, the strain exhibited much resistance to 0.6–1.0 M H2O2 and 6% (w/v) NaCl as compared to Streptomyces cavourensis YBQ59 isolated from Cinnamomum cassia Prels. In addition, the complete pathways for degradation of aromatic compounds including protocatechuate, gentisate, 4-hydroxyphenylpyruvate, cinnamate, 3-phenylpropionate, and styrene were only identified in the genome of VCCM 22513.

Conclusions

The present study revealed for the first time adaptive responses of mangrove endophytic S. parvulus VCCM 22513 to survive in hostile environment. The information shown here provided better understanding of underlying mechanisms related to adaptation and partially plant-microbe interaction of Streptomyces associated with mangrove plants.

Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters

Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-Ålesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.

The influence of different light quality and benzene on gene expression and benzene degradation of Chlorophytum comosum

Benzene, a carcinogenic compound, has been reported as a major indoor air pollutant. Chlorophytum comosum (C. comosum) was reported to be the highest efficient benzene removal plant among other screened plants. Our previous studies found that plants under light conditions could remove gaseous benzene higher than under dark conditions. Therefore, C. comosum exposure to airborne benzene was studied under different light quality at the same light intensity. C. comosum could remove 500 ppm gaseous benzene with the highest efficiency of 68.77% under Blue:Red = 1:1 LED treatments and the lowest one appeared 57.41% under white fluorescent treatment within 8 days. After benzene was uptaken by C. comosum, benzene was oxidized to be phenol in the plant cells by cytochrome P450 monooxygenase system. Then, phenol was catalyzed to be catechol that was confirmed by the up-regulation of phenol 2-monooxygenase (PMO) gene expression. After that, catechol was changed to cic, cis-muconic acid. Interestingly, cis,cis-muconic acid production was found in the plant tissues higher than phenol and catechol. The result confirmed that NADPH-cytochrome P450 reductase (CPR), cytochrome b5 (cyt b5), phenol 2-monooxygenase (PMO) and cytochrome P450 90B1 (CYP90B1) in plant cells were involved in benzene degradation or detoxification. In addition, phenol, catechol, and cis,cis-muconic acid production were found under the Blue-Red LED light conditions higher than under white fluorescent light conditions due to under LED light conditions gave higher NADPH contents. Hence, C. comosum under the Blue-Red LED light conditions had a high potential to remove benzene in a contaminated site.

Effect of rhamnolipid biosurfactant on solubilization of polycyclic aromatic hydrocarbons

Rhamnolipid biosurfactant-producing bacteria, Bacillus Lz-2, was isolated from oil polluted water collected from Dongying Shengli oilfield, China. The factors that influence PAH solubilization such as biosurfactant concentration, pH, ionic strength and temperature were discussed. The results showed that the solubilities of naphthalene, phenanthrene and pyrene increased linearly with the rise of rhamnolipid biosurfactant dose above the biosurfactant critical micelle concentration (CMC). Furthermore, the molar solubilization ratio (MSR) values decreased in the following order: naphthalene>phenanthrene>pyrene. However, the solubility percentage increased and followed the opposite order: pyrene>phenanthrene>naphthalene. The solubilities of PAHs in rhamnolipid biosurfactant solution increased with the rise of pH and ionic strength, and reached the maximum values under the conditions of pH11 and NaCl concentration 8 g · L(-1). The solubility of phenanthrene and pyrene increased with the rise of temperature.

PAHs reduce DNA synthesis and delay cell division in the widespread primary producer Prochlorococcus

The cyanobacteria Prochlorococcus is the most abundant primary producer in the ocean. In a global study across the Atlantic, Indian and Pacific Oceans, we tested the effect of organic pollutants on the growth and cell division of natural Prochlorococcus populations. Sub-lethal concentrations of Polycyclic Aromatic Hydrocarbons (PAHs) altered Prochlorococcus cell division by reducing DNA synthesis and decreasing the percentage of cells entering mitosis. Cell division time increased with PAHs dosage by 1.2 h per μg L(-1) of mixture added. At PAHs dosages >1 μg L(-1), Prochlorococcus cell division tended to arrest at S-phase (DNA synthesis). As a consequence, population growth was significantly reduced in the presence of PAHs. The presence of PAHs resulted in a predictable alteration of the cell cycle of the widespread cyanobacteria.The dosages tested are above concentrations in the open ocean, but found in the coastal ocean, where Prochlorococcus growth must be inhibited.

Identification of persulfate oxidation products of polycyclic aromatic hydrocarbon during remediation of contaminated soil

The extent of PAH transformation, the formation and transformation of reaction byproducts during persulfate oxidation of polycyclic aromatic hydrocarbons (PAHs) in coking plant soil was investigated. Pre-oxidation analyses indicated that oxygen-containing PAHs (oxy-PAHs) existed in the soil. Oxy-PAHs including 1H-phenalen-1-one, 9H-fluoren-9-one, and 1,8-naphthalic anhydride were also produced during persulfate oxidation of PAHs. Concentration of 1,8-naphthalic anhydride at 4h in thermally activated (50°C) persulfate oxidation (TAPO) treatment increased 12.7 times relative to the oxidant-free control. Additionally, the oxy-PAHs originally present and those generated during oxidation can be oxidized by unactivated or thermally activated persulfate oxidation. For example, 9H-fluoren-9-one concentration decreased 99% at 4h in TAPO treatment relative to the control. Thermally activated persulfate resulted in greater oxy-PAHs removal than unactivated persulfate. Overall, both unactivated and thermally activated persulfate oxidation of PAH-contaminated soil reduced PAH mass, and oxidized most of the reaction byproducts. Consequently, this treatment process could limit environmental risk related to the parent compound and associated reaction byproducts.

Characteristic molecular signature for the early detection and prediction of polycyclic aromatic hydrocarbons in rat liver

Predictions of toxicity are central for the assessment of chemical toxicity, and the effects of environmental toxic compounds are still a major issue for predicting potential human health risks. Among the various environmental toxicants, polycyclic aromatic hydrocarbons (PAHs) are an important class of environmental pollutant, and many PAHs are known or suspected carcinogens. In the present study, to investigate whether characteristic expression profiles of PAHs exist in rat liver and whether a characteristic molecular signature can discriminate and predict among different PAHs at an early exposure time, we analyzed the genome-wide expression profiles of rat livers exposed to PAHs [benzo[a]anthracene (BA), benzo[a]pyrene (BP), phenanthrene (PA) and naphthalene (NT)]. At early time-point PAH exposure, large-scale gene expression analysis resulted in characteristic molecular signatures for each PAH, and supervised analysis identified 1183 outlier genes as a distinct molecular signature discerning PAHs from the normal control group. We identified 158 outlier genes as early predictive and surrogate markers for predicting each tested PAH by combination of two different multi-classification algorithms with 100% accuracy through a leave-one out cross-validation method. In conclusion, the characteristic gene expression signatures from a rat model system could be used as predictable and discernible gene-based biomarkers for the detection and prediction of PAHs, and these molecular markers may provide insights into the underlying mechanisms for genotoxicity of exposure to PAHs from environmental aspect.

Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil

Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8-fold to 33-fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P-type ATPases and thioredoxin transcripts were more abundant in the phenanthrene-amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH-degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.

Towards clarification of the inhibitory mechanism of wheat bran leachate on Microcystis aeruginosa NIES-843 (Cyanobacteria): physiological responses

Wheat bran leachate (WBL) has been shown to have an inhibitory effect on Microcystis aeruginosa in this study. In order to explore the inhibitory mechanism of WBL on M. aeruginosa, physiological responses of M. aeruginosa NIES-843 under the WBL stress were studied. The expressions of six important genes related to the D1 protein of photosynthetic processes (psbA), synthesis of microcystins (mcyB), antioxidant protein peroxiredoxin (prx), synthesis of fatty acid (fabZ) and the repair of biological macromolecules (recA, grpE) were studied. Under the WBL stress, no significant change was found in expressions of both grpE and recA, but expressions of psbA, fabZ and prx were shown to be down-regulated, and slight up-regulated expression was found in mcyB. It was shown that oxygen evolution of M. aeruginosa NIES-843 was significantly depressed, and intracellular ATP contents became lower, after exposure to WBL. Similarly, maximum electron transport rates of photosynthetic activities decreased significantly, but intracellular reactive oxygen species levels boosted dramatically under the WBL stress, and cell lysis was observed. Therefore, it is suggested that photosynthetic systems and membranes were the potential targets of toxicity of WBL on M. aeruginosa, and the oxidative damage is an important mechanism explaining the inhibitory effect of WBL on M. aeruginosa.

Escherichia coli as a bioreporter in ecotoxicology

Ecotoxicological assessment relies to a large extent on the information gathered with surrogate species and the extrapolation of test results across species and different levels of biological organisation. Bacteria have long been used as a bioreporter for genotoxic testing and general toxicity. Today, it is clear that bacteria have the potential for screening of other toxicological endpoints. Escherichia coli has been studied for years; in-depth knowledge of its biochemistry and genetics makes it the most proficient prokaryote for the development of new toxicological assays. Several assays have been designed with E. coli as a bioreporter, and the recent trend to develop novel, better advanced reporters makes bioreporter development one of the most dynamic in ecotoxicology. Based on in-depth knowledge of E. coli, new assays are being developed or existing ones redesigned, thanks to the availability of new reporter genes and new or improved substrates. The technological evolution towards easier and more sensitive detection of different gene products is another important aspect. Often, this requires the redesign of the bacterium to make it compatible with the novel measuring tests. Recent advances in surface chemistry and nanoelectronics open the perspective for advanced reporter based on novel measuring platforms and with an online potential. In this article, we will discuss the use of E. coli-based bioreporters in ecotoxicological applications as well as some innovative sensors awaited for the future.

Allelopathic mechanism of pyrogallol to Microcystis aeruginosa PCC7806 (Cyanobacteria): from views of gene expression and antioxidant system

Pyrogallol is a potent allelochemical on Microcystis aeruginosa, but its allelopathic mechanism is not fully known. In order to explore this mechanism, gene expressions for prx, mcyB, psbA, recA, grpE, fabZ under pyrogallol stress were studied, and activities of the main antioxidant enzymes were also measured. The results showed that expression of grpE and recA showed no significant change under pyrogallol stress, while psbA and mcyB were up-regulated at 4 mg L(-1). Both prx and fabZ were up-regulated even under exposure to 1 mg L(-1) pyrogallol concentration. The activities of superoxide dismutase (SOD) and catalase (CAT) were enhanced under pyrogallol stress. Levels of malodialdehyde (MDA) at 2 and 4 mg L(-1) pyrogallol were significantly higher than those of the controls. It was concluded that oxidant damage is an important mechanism for the allelopathic effect of pyrogallol on M. aeruginosa.

Interfacial approach to polyaromatic hydrocarbon toxicity: phosphoglyceride and cholesterol monolayer response to phenantrene, anthracene, pyrene, chrysene, and benzo[a]pyrene

Interactions of phenantrene, anthracene, pyrene, chrysene, and benzo[a]pyrene (polyaromatic hydrocarbons) with model phospholipid membranes were probed using the Langmuir technique. The lipid monolayers were prepared using 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine, 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol, 1,2-dipalmitoyl-sn-glycero-3-phosphoserine, 1,2-myristoyl-sn-glycero-3-phosphoethanolamine, 1,2-dilauroyl-sn-glycero-3-phosphocholine, and cholesterol. Surface pressure and electrical surface potential were measured on mixed phospholipid/PAH monolayers spread on a pure water subphase. The morphology of the mixed monolayers was followed with Brewster angle microscopy. Polarization-modulation infrared reflection-absorption spectroscopy spectra obtained on DPPE/benzo[a]pyrene showed that the latter interacts with the carbonyl groups of the phospholipid. On the other hand, the activity of phospholipase A2 toward DLPC used as a probe to locate benzo[a]pyrene in the monolayers indicates that the polyaromatic hydrocarbons are not accessible to the enzyme. The results obtained show that all PAHs studied affect the properties of the pure lipid, albeit in different ways. The most notable effects, namely, film fluidization and morphology changes, were observed with benzo[a]pyrene. In contrast, the complexity of mixed lipid monolayers makes the effect of PAHs difficult to detect. It can be assumed that the differences observed between PAHs in monolayers correlate with their toxicity.