Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers

BACKGROUND: To unravel molecular targets involved in glycopeptide resistance, three isogenic strains of Staphylococcus aureus with different susceptibility levels to vancomycin or teicoplanin were subjected to whole-genome microarray-based transcription and quantitative proteomic profiling. Quantitative proteomics performed on membrane extracts showed exquisite inter-experimental reproducibility permitting the identification and relative quantification of >30% of the predicted S. aureus proteome. RESULTS: In the absence of antibiotic selection pressure, comparison of stable resistant and susceptible strains revealed 94 differentially expressed genes and 178 proteins. As expected, only partial correlation was obtained between transcriptomic and proteomic results during stationary-phase. Application of massively parallel methods identified one third of the complete proteome, a majority of which was only predicted based on genome sequencing, but never identified to date. Several over-expressed genes represent previously reported targets, while series of genes and proteins possibly involved in the glycopeptide resistance mechanism were discovered here, including regulators, global regulator attenuator, hyper-mutability factor or hypothetical proteins. Gene expression of these markers was confirmed in a collection of genetically unrelated strains showing altered susceptibility to glycopeptides. CONCLUSION: Our proteome and transcriptome analyses have been performed during stationary-phase of growth on isogenic strains showing susceptibility or intermediate level of resistance against glycopeptides. Altered susceptibility had emerged spontaneously after infection with a sensitive parental strain, thus not selected in vitro. This combined analysis allows the identification of hundreds of proteins considered, so far as hypothetical protein. In addition, this study provides not only a global picture of transcription and expression adaptations during a complex antibiotic resistance mechanism but also unravels potential drug targets or markers that are constitutively expressed by resistant strains regardless of their genetic background, amenable to be used as diagnostic targets

Proteomics, ultrastructure, and physiology of hippocampal synapses in a fragile X syndrome mouse model reveal presynaptic phenotype

Fragile X syndrome (FXS), the most common form of hereditary mental retardation, is caused by a loss-of-function mutation of the Fmr1 gene, which encodes fragile X mental retardation protein (FMRP). FMRP affects dendritic protein synthesis, thereby causing synaptic abnormalities. Here, we used a quantitative proteomics approach in an FXS mouse model to reveal changes in levels of hippocampal synapse proteins. Sixteen independent pools of Fmr1 knock-out mice and wild type mice were analyzed using two sets of 8-plex iTRAQ experiments. Of 205 proteins quantified with at least three distinct peptides in both iTRAQ series, the abundance of 23 proteins differed between Fmr1 knock-out and wild type synapses with a false discovery rate (q-value) <5%. Significant differences were confirmed by quantitative immunoblotting. A group of proteins that are known to be involved in cell differentiation and neurite outgrowth was regulated; they included Basp1 and Gap43, known PKC substrates, and Cend1. Basp1 and Gap43 are predominantly expressed in growth cones and presynaptic terminals. In line with this, ultrastructural analysis in developing hippocampal FXS synapses revealed smaller active zones with corresponding postsynaptic densities and smaller pools of clustered vesicles, indicative of immature presynaptic maturation. A second group of proteins involved in synaptic vesicle release was up-regulated in the FXS mouse model. In accordance, paired-pulse and short-term facilitation were significantly affected in these hippocampal synapses. Together, the altered regulation of presynaptically expressed proteins, immature synaptic ultrastructure, and compromised short-term plasticity points to presynaptic changes underlying glutamatergic transmission in FXS at this stage of development. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc

Metabolic fingerprinting reveals a novel candidate biomarker for prednisolone treatment in cattle

The use of glucocorticoids as growth promoters for meat-producing animals is strictly regulated within the European Union. However, in the past few years, a higher frequency of non-compliant bovine urine samples for prednisolone has been noticed, which could not be directly related to fraudulent use of prednisolone. As such, questions have risen about the origin of this compound. Unfortunately, at present, no decisive strategy has been established to discriminate between endogenous and exogenous prednisolone. In this study, an untargeted metabolomics strategy, based on Orbitrap and QqTOF mass spectrometry, was deployed to reveal urinary biomarkers, which are indicative for the exogenous administration of the synthetic glucocorticoid prednisolone. For this purpose, prednisolone was administered intramuscularly and per os to 12 bovines and a total of 2700 urine samples were collected before, during and after treatment. Multivariate statistical data analysis (i.e. OPLS-DA) revealed four differentiating metabolites that allowed discrimination between urine samples collected before and during prednisolone administration. None of these compounds were present in urine containing endogenous prednisolone, of which the formation was induced by the administration of a synthetic analogue of adrenocorticotropic hormone. Only one metabolite was retained as a highly suitable biomarker during growth-promoting and therapeutic prednisolone treatment, with 93.4 % sensitivity and 96.3 % specificity. Besides, this compound could be detected up to 4 days after a single therapeutic per os prednisolone administration. Based on accurate mass, isotope pattern, and MS/MS spectra, this compound was putatively annotated and is suggested as an actionable biomarker for exogenous prednisolone administration