Transcriptome analysis of silver, palladium, and selenium stresses in Pantoea sp. IMH

Bioinformatics analysis of gene bhsA and its role in Ca2+ -treated Escherichia coli

One of the commonly employed methods in molecular biology is to utilize calcium chloride to treat Escherichia coli for the preparation of competent cells to facilitate foreign gene expression. However, the molecular mechanisms underlying Ca2+ mediation of competent cell formation and identification of the key genes involved in the process remain unclear. In previous studies, the combined analysis of transcriptomics and proteomics revealed bhsA as one of the crucial genes. The gene ontology functional annotation of bhsA identified it as a member of the YhcN family encoding an outer membrane protein that confers resistance to various stresses. The IPR0108542 domain found within the protein plays a significant role in stress response and biofilm formation in E. coli. Analysis of the STRING database showed that the proteins interacting with bhsA are primarily involved in biofilm formation and stress resistance. Using the RED homologous recombination method, a bhsA deletion strain was constructed to verify its role in E. coli genetic transformation. Although the mutant strain showed no significant differences in morphology or growth trend when compared to the wild-type strain, its transformation efficiency decreased by 1.14- and 1.64-fold with plasmids pUC19 and pET-32a. Furthermore, the 1-N-phenylnaphthylamine assay indicated a 1.71-fold reduction in cell membrane permeability in the mutant strain.

Catalytic degradation of methylene blue by biosynthesized Au nanoparticles on titanium dioxide (Au@TiO2)

The degradation of methylene blue is a critical procedure in its wastewater remediation and thus has inspired wide catalysis research with semiconductors such as titanium dioxide (TiO₂) and rare metals such as gold (Au). In this study, we report bacterial cells assisting biosynthesis for Au@TiO₂ as an efficient catalyst for the catalytic degradation of methylene blue. Multiple complementary characterization for bio-Au_x@TiO₂ evidenced the evenly distributed Au nanoparticles (NPs) on the bio-TiO₂ layers. Meanwhile, bio-Au₂@TiO₂ displayed the superior catalytic activity in the degradation of methylene blue with the highest kinetics constant (k_app) value of 0.195 min^-1. In addition, bio-Au₂@TiO₂ keeps stable catalytic activity for up to 10 cycles. The origin of the catalytic activity was investigated by the hydroxyl radical fluorescence quantitative analysis and optical band gap analysis. In the bio-Au₂@TiO₂ catalytic system, Au NPs decreased the band gap energy of TiO₂ and enabled the generation of abundant photogeneration hydroxyl radicals, resulting in an enhanced photocatalytic activity. Our microbial synthesized bio-TiO₂ and bio-Au_x@TiO₂ study would be useful for developing green synthesis catalyst technology.

3D imaging of single bacterial cells using surface-enhanced Raman spectroscopy with a multivariate curve resolution model

Imaging biomolecules within a single bacterial cell is crucial for understanding cellular genetic mechanisms. Herein, we exploited a surface-enhanced Raman spectroscopy (SERS) imaging strategy for single cell analysis. Cellular biosynthesized Ag nanoparticles (NPs) provided the necessary enhancement for SERS imaging. Multiple complementary techniques, including high-resolution transmission electron microscopy (HR-TEM), high-angle annular dark-field (HAADF)-scanning transmission electron microscopy (STEM), and energy-dispersive X-ray spectroscopy (EDX), were used to characterize the biogenic Ag NPs in cells. Three-dimensional SERS imaging maps displayed spectral information of biomolecules within the single cell. The multivariate curve resolution (MCR) model and principal component analysis (PCA) model were used to analyze the cellular SERS imaging maps. The MCR model, with a specific constraint of non-negativity, resulted in meaningful identification of biomolecules associated with Ag reduction. Focusing on the molecular level reveals that Pantoea sp. IMH utilizes several mechanisms to synthesize Ag NPs, including cytoplasm reduction by glucose or nicotinamide adenine dinucleotide (NADH)-dependent reductase, and extracellular reduction by an electron transfer chain containing quinone and cytochrome C. Our results shed new light on the Ag NP biosynthesis mechanism and single cell Raman analysis.

Cu Homeostasis in Bacteria: The Ins and Outs

Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.

Gill transcriptome alterations in Macrobrachium rosenbergii under copper exposure

Copper is one of common contaminants in estuaries and coastal zones, which may cause physiological dysfunction in aquatic organisms. However, molecular response triggered by Cu have remained largely unknown in freshwater prawn Macrobrachium rosenbergii. In the present study, we performed transcriptomic analysis to characterize molecular mechanisms of copper immunotoxicity in gills from M. rosenbergii. A large number of potential simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) loci in the transcriptome were identified. 19,417 and 8989 differentially expressed genes (DEGs) were obtained at 3 h and 48 h after exposure, respectively. Most of these DEGs were down-regulated implying that gene expressions were largely inhibited by Cu, which might lead to impairments of biological functions. Functional enrichment analysis of these DEGs revealed that immune, detoxification and apoptosis were the differentially regulated processes by Cu stress. 12 DGEs involved in immune response and heavy metal detoxification were discovered and validated by qRT-PCR. The results indicated that the M. rosenbergii might counteract the toxicity of Cu at the transcriptomic level by increasing expressions of immune- and heavy metal detoxification-related genes, and these selected genes could be used as molecular indicators for Cu stress. Our study firstly reported the stress response at transcriptional level in M. rosenbergii during Cu exposure. The genes and pathways identified here not only give us new insight into molecular mechanisms underlying Cu toxicity effects in prawn, but facilitate biomarker identification and stress-resistant breeding studies.