Streptomyces tunisiensis sp. nov., a novel Streptomyces species with antibacterial activity.

A novel actinomycete strain designated CN-207(T) was isolated from northern Tunisian soil. This strain exhibited potent broad spectrum antibacterial activity against clinical isolates of methicillin-resistant Staphylococcus species and several other Gram-positive and Gram-negative bacteria. Strain CN-207(T) developed greyish aerial mycelium and pale grey substrate mycelium on yeast extract/malt agar. The isolate produced branching vegetative mycelia with sporangiophores bearing sporangia developing at a late stage of growth. The sporangia contained smooth, non-motile spores. Chemotaxonomic characteristics of strain CN-207(T) were typical of the Streptomyces genus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CN-207(T) belonged to the genus Streptomyces, and was most closely related to Streptomyces griseoincarnatus DSM 40274(T), Streptomyces variabilis DSM 40179(T), Streptomyces labedae DSM 41446(T) and Streptomyces erythrogriseus DSM 40116(T). Low DNA-DNA relatedness values were recorded between strain CN-207(T) and its closest phylogenetic neighbours. Strain CN-207(T) was also distinguished from the nearest phylogenetic neighbours using a combination of morphological and phenotypic characteristics. On the basis of its phenotypic and molecular properties, strain CN-207(T) is considered as a novel species of the Streptomyces genus, for which the name Streptomyces tunisiensis sp. nov. is proposed. The type strain is CN-207(T) (=JCM 17589(T) = DSM 42037(T)).

Graphical identification of cancer-associated gene subnetworks based on small proteomics data sets.

Proteomics is a rapidly emerging frontier in post-genomics medicine and biology, but the quantitative analysis and validation of proteomic data are in need of further improvements. Before selecting potential candidate proteomic biomarkers, it is important to understand the broader context of how biological processes are regulated under different conditions or in different phenotypes. The enrichment of proteomic data consists of extracting as much biological meaning as possible from curated, pathway-based, functional protein interaction networks. Currently, most of the enrichment tools are intended for microarray data and require parametric data, whereas proteomic data are often nonparametric. In this study, we aimed to select a suite of interactive tools that can enrich proteomic results with a graphical overview. This facilitated diagnosis and interpretation prior to further analysis. From a list of proteins, a network was constructed using a map of the most severely disrupted biological process, and the disease entity was then identified on the basis of clinical data. Taken together, this graphical and interactive method ranks potential proteins via functional analysis in order to improve the choice of biomarkers for validation with the following advantages: 1) It adds neighbor proteins that are not selected by mass spectrometry analysis, but could in fact be key proteins; 2) pinpoints the biological process most often involved; and 3) predicts the most likely disease on the basis of clinical data.

Proteomic study of the effects of microcystin-LR on organelle and membrane proteins in medaka fish liver.

The microcystin-leucine-arginine toxin (MC-LR) is produced by cyanobacteria that sometimes bloom in water reservoirs. It targets the liver, thus posing potential health risks to human and animals. Microcystin inhibits the protein phosphatases PP1 and PP2A, leading to diverse cellular deregulation processes. A proteomic approach was applied to the medaka fish (Oryzias latipes) to obtain an overview of the effects of MC-LR on the liver. As membrane and organelle proteins are major structural and functional components of several cell signalling pathways, we decided to investigate here the membrane and organelle-enriched fractions from the livers of control and MC-LR treated medaka fish. Seventeen proteins were identified by proteomic analysis as being modulated in response to MC-LR treatment. This is the first time for eight of them to be reported as being involved in MC-LR effects: prohibitin, fumarylacetoacetase, protein disulfide isomerase A4 and A6, glucose regulated protein 78kDa, 40S ribosomal protein SA, cytochrome b5, and ATP synthase mitochondrial d subunit. These proteins are involved in protein maturation or in the response to oxidative stress highlighting the role of organelles in protein processing and the complex cooperation associated with oxidative stress.

Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans.

Interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (IRRB) might be a part of the answer to the question as to how IRRB, particularly Deinococcus radiodurans R1 (Deira), resist ionizing radiation. Here, using the Database of Interacting Proteins (DIP) and the Protein Structural Interactome (PSI)-base server for PSI map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in Deira and other IRRB, but which are absent in IRSB. Among these, 18 domains and their interactomes have been identified in DNA checkpoint and repair; kinases pathways; energy and nucleotide metabolisms were the important biological processes that were found to be involved. This finding provides new clues to the cellular pathways that can to be important for ionizing-radiation resistance in Deira.

Global quantitative analysis of protein phosphorylation status in fish exposed to microcystin.

The hepatotoxins, microcystins (MCs) are potent inhibitors of protein phosphatases PP1 and PP2A. These nonribosomal peptides are getting more and more attention because of their acute toxicity and potent tumor-promoting activity. These toxins are produced by freshwater cyanobacteria. Herein, we report a toxicological study conducted on aquatic animal models such as the medaka fish. To date, the detailed mechanisms underlying the toxicity of microcystins are unknown. MC-leucine-arginine (MC-LR) is the most toxic and the most commonly encountered variant of MCs in aquatic environment. It has been used for toxicological investigations on the liver of intoxicated medaka. We performed differential proteome analyses of MC-LR-treated and untreated medaka fish to investigate the mechanisms of establishment of early responses to the toxin. The identification of proteins involved in these early responses might constitute candidates of biomarkers of MC-LR exposure. Cytosolic proteins from livers of exposed or nonexposed medaka were resolved by 2D electrophoresis and detected using stains specific for phosphoproteins and for whole protein content. Overall, 15 spots were found to vary significantly on the proteomic 2D maps or on the phosphoproteomic 2D maps. Of these 15 proteins, only two could not be identified by mass spectrometry. Among the other proteins that were identified, phenylalanine hydroxylase and keratin 18 (type I) showed variations in phoshoryl content in agreement with inhibition of PP2A activity after exposure of the fish to MC-LR. The other identified proteins exhibited variations in their expression level. The identified proteins appear to be involved in cytoskeleton assembly, cell signalling, oxidative stress, and apoptosis. The functional implications of responses to MC-LR exposure of these proteins are discussed. The methodology described in this report should be widely used to a number of tissues and organisms, thus helping in the search for biomarkers of MC-LR contamination.

Global quantitative analysis of protein expression and phosphorylation status in the liver of the medaka fish (Oryzias latipes) exposed to microcystin-LR I. Balneation study.

Microcystins (MCs) are hepatotoxins with potent inhibitor activity of protein phosphatases PP1 and PP2A. These non-ribosomal peptides are getting more and more attention due to their acute toxicity and potent tumor-promoting activity. These toxins are produced by freshwater cyanobacteria. The most toxic and most commonly encountered variant in aquatic environment is MC-LR (MC Leucine-Arginine). It has been used for toxicological investigations on the liver of intoxicated medaka. Differential proteome as well as differential phosphoproteome analyses have been performed for providing new information on early responses to the toxin. The experiments are also aiming at selecting biomarkers of MC-LR exposure. In the 2D electrophoresis gel protein maps from cytosol of liver cells of animals exposed or non-exposed to the cyanotoxin, 15 spots showed a significant increase or decrease of their stain signal either in specific phosphoprotein stain or total protein stain. Thirteen of these proteins have been identified by mass spectrometry. Among them, phenylalanine hydroxylase (PAH) and keratin 18 type I showed variations in phosphorylation stain in possible agreement with inhibition of PP2A activity. The other identified proteins exhibited variations in their expression level. The identified proteins appear to be involved in cytoskeleton assembly, cell signalling, oxidative stress and apoptosis. Such results confirm that proteomics and phosphoproteomics approaches may become valuable tools to identify signalling pathways implied in MC-LR effects. From accumulated data, specific pools of biomarkers could possibly be selected as specific for toxin exposure.

Toxicity to medaka fish embryo development of okadaic acid and crude extracts of Prorocentrum dinoflagellates.

Chronic and subchronic toxicity following exposure to the DSP (Diarrhetic shellfish poisoning) toxin okadaic acid (OA) is receiving increasing attention as a public human health biohazard. However information on ecological impacts induced by proliferation of the OA producing dinoflagellate Prorocentrum is scarce. In order to analyse the toxicity of these substances, in vivo experiments were conducted on medaka fish (Oryzias latipes) embryos used as an experimental model. The study was focused on two strains of benthic Prorocentrum species, P. arenarium and P. emarginatum, naturally found in the Indian Ocean. Sample extracts (crude extracts, CE) were obtained from algal cultures and their toxic potential was explored. Their OA (and derivatives) content was evaluated by two methods: one based on chemical analysis using HPLC-MS, the other based on screening the inhibiting effect on protein phosphatase PP2A. P. arenarium extracts inhibit PP2A and the active toxin was confirmed as being OA by HPLC-MS. In contrast, P. emarginatum showed negative results regardless of the method used. The development of medaka fish embryos kept in medium containing pure OA or Prorocentrum CE was examined. Survival rates were reduced up to 100% depending on the concentrations used of both OA and CE of P. arenarium, while no effect was observed with CE of P. emarginatum. Anatomopathological studies of surviving embryos indicate that OA treatment resulted in significant increases in liver and digestive tract areas compared to controls. P. arenarium treated surviving embryos exhibited significant quantitative increases of global body and vitellus areas. Together, our results indicate that the toxic effects to medaka embryos development of pure OA and P. arenarium extracts containing OA are distinguishable. The differences may indicate the presence of additional toxic substance(s) (or molecules able to modulate OA impact) in the P. arenarium CE that probably are not present in P. emarginatum.