Pascale Bauda

Antimicrobial drug discovery through bacteriophage genomics

Over evolutionary time bacteriophages have developed unique proteins that arrest critical cellular processes to commit bacterial host metabolism to phage reproduction. Here, we apply this concept of phage-mediated bacterial growth inhibition to antibiotic discovery. We sequenced 26 Staphylococcus aureus phages and identified 31 novel polypeptide families that inhibited growth upon expression in S. aureus. The cellular targets for some of these polypeptides were identified and several were shown to be essential components of the host DNA replication and transcription machineries. The interaction between a prototypic pair, ORF104 of phage 77 and DnaI, the putative helicase loader of S. aureus, was then used to screen for small molecule inhibitors. Several compounds were subsequently found to inhibit both bacterial growth and DNA synthesis. Our results suggest that mimicking the growth-inhibitory effect of phage polypeptides by a chemical compound, coupled with the plethora of phages on earth, will yield new antibiotics to combat infectious diseases.

Identification of Tn10 insertions in the rfaG, rfaP, and galU genes involved in lipopolysaccharide core biosynthesis that affect Escherichia coli adhesion.

Escherichia coli was used as a model to study initial adhesion and early biofilm development to abiotic surface. Tn10 insertion mutants of Escherichia coli K-12 W3110 were selected for altered abilities to adhere to a polystyrene surface. Seven insertion mutants that showed a decrease in adhesion harbored insertions in genes involved in lipopolysaccharide (LPS) core biosynthesis. Two insertions were located in the rfaG gene, two in the rfaP gene, and three in the galU gene. These adhesion mutants were found to exhibit a deep-rough phenotype and to be reduced, at different levels, in type 1 fimbriae production and motility. The loss of adhesion exhibited by these mutants was associated with either the affected type 1 fimbriae production and/or the dysfunctional motility. Apart from the pleiotropic effect of the mutations affecting LPS on type 1 fimbriae and flagella biosynthesis, no evidence for an involvement of the LPS itself in adhesion to polystyrene surface could be observed.

Unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of the aoxB gene in prokaryotes.

ABSTRACT In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities.

Role of electrostatic interactions in the toxicity of titanium dioxide nanoparticles toward Escherichia coli.

The increasing production and use of titanium dioxide nanoparticles (NP-TiO(2)) has led to concerns about their possible impact on the environment. Bacteria play crucial roles in ecosystem processes and may be subject to the toxicity of these nanoparticles. In this study, we showed that at low ionic strength, the cell viability of Escherichia coli was more severely affected at pH 5.5 than at pH 7.0 and pH 9.5. At pH 5.5, nanoparticles (positively charged) strongly interacted with the bacterial cells (negatively charged) and accumulated on their surfaces. This phenomenon was observed in a much lower degree at pH 7.0 (NP-TiO(2) neutrally charged and cells negatively charged) and pH 9.5 (both NP-TiO(2) and cells negatively charged). It was also shown that the addition of electrolytes (NaCl, CaCl(2), Na(2)SO(4)) resulted in a gradual reduction of the NP-TiO(2) toxicity at pH 5.5 and an increase in this toxicity at pH 9.5, which was closely related to the reduction of the NP-TiO(2) and bacterial cell electrostatic charges.

In Situ Assessment of Phytotechnologies for Multicontaminated Soil Management

Due to human activities, large volumes of soils are contaminated with organic pollutants such as polycyclic aromatic hydrocarbons, and very often by metallic pollutants as well. Multipolluted soils are therefore a key concern for remediation. This work presents a long-term evaluation of the fate and environmental impact of the organic and metallic contaminants of an industrially polluted soil under natural and plant-assisted conditions. A field trial was followed for four years according to six treatments in four replicates: unplanted, planted with alfalfa with or without mycorrhizal inoculation, planted with Noccaea caerulescens, naturally colonized by indigenous plants, and thermally treated soil planted with alfalfa. Leaching water volumes and composition, PAH concentrations in soil and solutions, soil fauna and microbial diversity, soil and solution toxicity using standardized bioassays, plant biomass, mycorrhizal colonization, were monitored. Results showed that plant cover alone did not affect total contaminant concentrations in soil. However, it was most efficient in improving the contamination impact on the environment and in increasing the biological diversity. Leaching water quality remained an issue because of its high toxicity shown by micro-algae testing. In this matter, prior treatment of the soil by thermal desorption proved to be the only effective treatment.

Characterization of the ars Gene Cluster from Extremely Arsenic-Resistant Microbacterium sp. Strain A33

ABSTRACT The arsenic resistance gene cluster of Microbacterium sp. A33 contains a novel pair of genes (arsTX) encoding a thioredoxin system that are cotranscribed with an unusual arsRC2 fusion gene, ACR3, and arsC1 in an operon divergent from arsC3. The whole ars gene cluster is required to complement an Escherichia coli ars mutant. ArsRC2 negatively regulates the expression of the pentacistronic operon. ArsC1 and ArsC3 are related to thioredoxin-dependent arsenate reductases; however, ArsC3 lacks the two distal catalytic cysteine residues of this class of enzymes.

Taxonomic and functional prokaryote diversity in mildly arsenic-contaminated sediments

Arsenic-resistant prokaryote diversity is far from being exhaustively explored. In this study, the arsenic-adapted prokaryotic community present in a moderately arsenic-contaminated site near Sainte-Marie-aux-Mines (France) was characterized, using metaproteomic and 16S rRNA-encoding gene amplification. High prokaryotic diversity was observed, with a majority of Proteobacteria, Acidobacteria and Bacteroidetes, and a large archaeal community comprising Euryarchaeaota and Thaumarchaeota. Metaproteomic analysis revealed that Proteobacteria, Planctomycetes and Cyanobacteria are among the active bacteria in this ecosystem. Taken together, these results highlight the unsuspected high diversity of the arsenic-adapted prokaryotic community, with some phyla never having been described in highly arsenic-exposed sites.

Insight into the primary mode of action of TiO2 nanoparticles on Escherichia coli in the dark.

Large‐scale production and incorporation of titanium dioxide nanoparticles (NP‐TiO2) in consumer products leads to their potential release into the environment and raises the question of their toxicity. The bactericidal mechanism of NP‐TiO2 under UV light is known to involve oxidative stress due to the generation of reactive oxygen species. In the dark, several studies revealed that NP‐TiO2 can exert toxicological effects. However, the mode of action of these nanoparticles is still controversial. In the present study, we used a combination of fluorescent probes to show that NP‐TiO2 causes Escherichia coli membrane depolarization and loss of integrity, leading to higher cell permeability. Using both transcriptomic and proteomic global approaches we showed that this phenomenon translates into a cellular response to osmotic stress, metabolism of cell envelope components and uptake/metabolism of endogenous and exogenous compounds. This primary mechanism of bacterial NP‐TiO2 toxicity is supported by the observed massive cell leakage of K+/Mg2+ concomitant with the entrance of extracellular Na+, and by the depletion of intracellular ATP level.

The use of soil mites in ecotoxicology: a review

Mites, and especially soil-inhabiting ones, have been less studied than the other invertebrates used in bio-assays for the assessment of soil quality and the hazards of chemicals, although these organisms are included in the regulatory assessment scheme of pesticides. The recent advances in the development of test methods for soil mites groups have provided more information on their sensitivities towards chemicals, which needs to be presented for a more robust assessment of the current trends in soil mite ecotoxicology. Moreover, interestingly mite is the only taxa for which test methods were developed and standardized on predatory organisms. This review summarizes the different protocols for the assessment of chemicals using soil-inhabiting mites, including laboratory, semi-field and field studies. Among the data found in the literature, most of the chemicals assessed with mites were pesticides, while a few environmental samples were assessed with these organisms. Their sensitivities towards chemicals were then compared and discussed regarding other soil invertebrates. Finally, we conclude on the usefulness of soil mites in ecotoxicology, and provide future research trail in this area.

Modifications of the bacterial reverse mutation test reveals mutagenicity of TiO2 nanoparticles and byproducts from a sunscreen TiO2-based nanocomposite

The bacterial reverse mutation test, recommended by the Organization for Economic Co-operation and Development (OECD) to determine genotoxicity of chemical compounds, has been recently used by several authors to investigate nanoparticles. Surprisingly, test results have been negative, whereas in vitro mammalian cell tests often give positive genotoxic responses. In the present study, we used the fluctuation test procedure with the Salmonella typhimurium strains TA97a, TA98, TA100 and TA102 to determine the mutagenic potential of TiO(2) nanoparticles (NP-TiO(2)) and showed that, when it is used conventionally, this test is not suitable for nanoparticle genotoxicity assessment. Indeed, the medium used during exposure prevents electrostatic interactions between bacterial cells and nanoparticles, leading to false-negative responses. We showed that a simple pre-exposure of bacteria to NP-TiO(2) in a low ionic strength solution (NaCl 10mM) at a pH below the nanoparticle isoelectric points (pH 5.5) can strongly improve the accuracy of the test. Thus, based on these improvements, we have demonstrated the genotoxicity of the engineered NP-TiO(2) tested and a NP-TiO(2) byproduct from a sunscreen nanocomposite. It was also shown that strain TA102 is more sensitive than the other strains, suggesting an oxidative stress-mediated mechanism of genotoxicity.