Comparative analysis of the toxicogenomic effects of Ortho-Benzyl-Para-ChloroPhenol (OBPCP) and Para-Tertiary AmylPhenol (PTAP) on Staphylococcus aureus
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Project description:Global gene expression analysis of Staphylococcus aureus following Para-Tertiary Amyl Phenol (PTAP) treatment using Affymetrix GeneChip arrays. Results from this study provide insight into the molecular mechanisms underlying the cellular response of Staphylococcus aureus to PTAP. We conducted four independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Para-Tertiary Amyl Phenol (PTAP). Fold change was calculated as a ration between the signal averages of five untreated (control) and five PTAP-treated (experimental) cultures after 0, 10 and 60 min exposure time.
Project description:Global gene expression analysis of Staphylococcus aureus following Ortho-Benzyl-Para-Chloro Phenol (OBPCP) treatment using Affymetrix GeneChip arrays. Results from this study provide insight into the molecular mechanisms underlying the cellular response of Staphylococcus aureus to OBPCP. We conducted five independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Ortho-Benzyl-Para-Chloro Phenol(OBPCP). Fold change was calculated as a ration between the signal averages of five untreated (control) and five OBPCP-treated (experimental) cultures after 0, 10 and 60 min exposure time.
Project description:Staphylococcus aureus is one of the most important pathogens in humans and animals, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. Rhein, a natural plant product, has potential antimicrobial activity against Staphylococcus aureus. We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with rhein. Results provided insight into mechanisms involved in rhein - Staphylococcus aureus interactions. Keywords: rhein response Staphylococcus aureus cells were exposed for 45 minutes to rhein at concentration of 8 µg/ml (1/2à MIC), 6 samples including 3 control samples are analyzed.
Project description:Representatives of two families of bacterial Par proteins, ParA and ParB, are encoded by the majority of bacterial chromosomes in the close vicinity of oriC. ParA(Soj) and ParB(Spo0J) proteins of Pseudomonas aeruginosa are both important for optimal growth, nucleoids segregation, cell division and different types of motility. Comparative transcriptome analysis of parAnull, parBnull mutants versus parental PAO1161 strain of P. aeruginosa demonstrated global changes in genes expression pattern in logarithmic phase of planktonic cultures grown on rich medium. The set of genes that were similarly regulated in both mutant strains as compared to the wild-type strain as well as two sets of genes uniquely affected in the particular mutant were defined suggesting that ParA and ParB may act in common and independently. In general, many genes involved in cell division, DNA and RNA processing and metabolic processes were down-regulated in mutant cells, in contrast genes which products play a role in adaptation, protection, motility, cell-to-cell signaling as well as signal transduction increased their expression in par mutant cells. Besides their role in chromosome segregation, ParA and ParB seem to have the potential to regulate genes transcription. The altered expression of a large number of genes encoding known or predicted transcriptional regulators and genes coding for products involved in c-di-GMP signalling, suggests that the part of observed global changes in genes expression pattern in parAnull and parBnull mutants might be the effect of indirect regulation mediated by regulatory genes under ParA and ParB control. The extended regulatory network provides the mechanism to modulate genes expression in response to the stage of the chromosome segregation process and cell cycle. Pseudomonas aeruginosa PAO1161 (leu, r-, RifR), derivative of PAO1, as a control (reference) strain, Pseudomonas aeruginosa PAO1161 parA1-40::smh (parAnull) and Pseudomonas aeruginosa PAO1161 parB1-18::TcR (parBnull) disruption mutant strains were used in the experiments. Three independent biological replicates of total RNA were isolated for each strain from logarithmic (Log) phase of planktonic culture grown on rich medium (L broth) at 37oC. In total, nine samples of RNA were prepared.
Project description:Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated techniques depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de novo algorithm that takes advantage of experimental evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. Ribo-seq next generation sequencing technique that provides a genome-wide snapshot of the position translating ribosome along an mRNA at the time of the experiment. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds to screen for spurious ORFs based on a growth curve model. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel ORFs including variants of previously annotated and novel small ORFs (<71 codons). Our predictions were supported by matching mass spectrometry (MS) proteomics data and sequence conservation analysis. REPARATION is unique in that it makes use of experimental Ribo-seq data to perform de novo ORF delineation in bacterial genomes, and thus can identify putative coding ORFs irrespective of the sequence context of the reading frame.
Project description:Wall teichoic acids (WTAs) are phosphate-rich, sugar-based polymers attached to the cell walls of most Gram-positive bacteria. In Staphylococcus aureus, these anionic polymers regulate cell division, protect cells from osmotic stress, mediate host colonization, and mask enzymatically susceptible peptidoglycan bonds. Although WTAs are not required for survival in vitro, blocking the pathway at a late stage of synthesis is lethal. We recently discovered a novel antibiotic, targocil, that inhibits a late acting step in the WTA pathway. Its target is TarG, the transmembrane component of the ABC transporter (TarGH) that exports WTAs to the cell surface. Here we examine the effects of targocil on S. aureus using transmission electron microscopy (TEM) and gene expression profiling. We report that targocil treatment leads to multicellular clusters containing swollen cells displaying evidence of osmotic stress, strongly induces the cell wall stress stimulon, and reduces the expression of key virulence genes, including dltABCD and capsule genes. We conclude that WTA inhibitors that act at a late stage of the biosynthetic pathway may be useful as antibiotics, and we present evidence that they could be particularly useful in combination with beta-lactams. Growth conditions for microarray analysis-For transcriptional profiling, an overnight S. aureus SH1000 culture was diluted (2% (v/v) into 20 mL TSB medium in a 50 mL Erlenmeyer flask and grown at 37 °C with shaking at 200 rpm. For the targocil treatment experiments, S. aureus was grown to an OD600 ~0.4 and challenged with 8x MIC of targocil dissolved in DMSO) for 30 min. Simultaneously, an equal amount of DMSO (final concentration 2% (v/v)) was added to the control culture, which was incubated along with the treated cultures. After 30 min, 5 mL aliquots were collected from control and treated cultures and used for toatl RNA preparation.
Project description:Whole genome expression profile comparing MGAS315 treated with XIP pheromone versus vehicle-treated cells Interpretations are described further in the manuscript to be submitted: authors Mashburn-Warren, Morrison, and Federle. Title: The Cryptic Competence Pathway in Streptococcus pyogenes is Controlled by a Peptide Pheromone. A two chip study using total RNA recovered from three separate cultures of Streptococcus pyogenes MGAS315, each treated with either XIP pheromone or with vehicle; RNA preparation of cultures receiving same type of treatment were pooled using equivalent amounts of RNA from each culture. RNA pools were fluorescently labeled and hybridized to arrays designed to the S. pyogenes NZ131 genome.
Project description:The rapid rise of antibiotic resistance and the urgent need for new antibiotics call for the unique skeleton of compounds with different mechanisms of action. Microbial natural products dominate the preferred chemical scaffolds for antibiotic discovery. A plant-microbial antibiotic is an appealing origin yet underexplored due to a dearth of comprehensive studies of antibacterial activity and structural characteristics. In this study, phloroglucinol derived isolated from the plant-root-associated bacterium Pseudomonas fluorescens was modified for structure–activity relationship study. 2,4-diproylphloroglucinol (DPPG) displayed bactericidal activity against a wide range of Gram-positive bacteria including multidrug-resistant pathogens. Interestingly, the bactericidal mechanism study exhibits that DPPG binds to type II NADH dehydrogenases (NDH-2) in the respiratory chain and disrupts the proton-motive force of S. aureus. We validated the efficacy of DPPG in vivo through mice models associated with infection or contamination. Our finding provides a novel antibiotic to treat S. aureus- associated infections and a potential target for antibiotic design and study.
Project description:Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. Cryptotanshinone, a natural plant product, has potent antimicrobial activity against S. aureus. We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with cryptotanshinone. Keywords: gene expression array-based, count Staphylococcus aureus cells were exposed for 45 minutes to cryptotanshinone at concentration of 2 µg/ml (1/2� MIC), 6 samples including 3 control samples are analyzed.
Project description:Expression data from B. japonicum strains 110spc4 (wild type), 0202 (Dbll1028), 9688 (Dblr3038-39) grown micro-oxically unstressed or stressed with 2 mM H2O2 for 10 min and strain 9692 (Dblr3039) grown micro-oxically Comparative transcriptome analysis of B. japonicum strains 110spc4, 0202, 9688, and 9692 grown micro-oxically with or without exposure to 2 mM H2O2 for 10 min