Thuricin CD: a potential therapeutic targeted against Clostridium difficile-associated diarrhea (CDAD)

Clostridium difficile is mainly a nosocomial pathogen and is a significant cause of antibioticassociated diarrhea. It is also implicated in the majority of cases of pseudomembranous colitis. The main etiological agent of C. difficile-associated diarrhea (CDAD) is perturbations to the gut microbiota by broad-spectrum antibiotics. Recently, thuricin CD, a two-peptide narrow spectrum sactibiotic bacteriocin with potent activity against C. difficile has been discovered. It is produced by Bacillus thuringiensis DPC6431. The efficacy of thuricin CD against a range of C. difficile clinical isolates has been determined in the form of minimum inhibitory concentration (MIC) values and compared to metronidazole, vancomycin, ramoplanin and actagardine in this thesis. Furthermore, by assessing paired combinations of the above-mentioned antimicrobials, it was determined that ramoplanin and actagardine function in a synergistic manner against the majority of C. difficile isolates. The functions of the genes in the thuricin CD gene cluster have also been elucidated by cloning the cluster and expressing thuricin CD in a heterologous Bacillus subtilis host and are described herein. In addition, the immunity mechanisms employed by the B. thuringiensis DPC6431 producer to protect itself from the antimicrobial actions of thuricin CD have also been elucidated. It has been shown that a small immunity peptide, TrnI, is involved in thuricin CD immunity, most likely by intercepting the thuricin CD peptides and/or blocking their access to the thuricin CD receptor. This immunity peptide and also the ABC-transporter system TrnFG serve to protect the B. thuringiensis host against thuricin CD.

Evaluation of rhizobacterial colonisation and the ability to induce Globodera pallida hatch

Three bacterial isolates, SB13 (Acinetobacter sp.), SB14 (Arthrobacter sp.) and SB15 (Bacillus sp.), were previously isolated from the rhizosphere of sugar beet (Beta vulgaris ssp. vulgaris) plants and shown to increase hatch of potato cyst nematodes in vitro. In this study, the three isolates were assayed for rhizosphere competence. Each isolate was applied to seeds at each of four concentrations (105-108 CFU ml−1) and the inoculated seeds were planted in plastic microcosms containing coarse sand. All three isolates were shown to colonise the rhizosphere, although to differing degrees, with the higher inoculation densities providing significantly better colonisation. The isolates increased sugar beet root and shoot dry weight. Isolates SB14 and SB15 were analysed for their ability to induce in vivo hatch of Globodera pallida in non-sterile soil planted with sugar beet. After 4 and 6 weeks, both isolates had induced significantly greater percentage hatch compared to controls.

Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand.

Understanding the interconversion between thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of the bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was previously shown to be unfolded in the absence of its cognate RNA or other anionic ligands. P protein was used in this study as a model system to explore general features of intrinsically disordered protein (IDP) folding mechanisms. The use of trimethylamine N-oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic traces at various final TMAO concentrations exhibited multiphasic kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea during the titration to produce a urea-TMAO titration surface of P protein. Both kinetic and equilibrium studies show evidence of a previously undetected intermediate state in the P protein folding process. The intermediate state is significantly populated, and the folding rate constants are relatively slow compared to those of intrinsically folded proteins similar in size and topology. The experiments and analysis described serve as a useful example for mechanistic folding studies of other IDPs.

Co-orientation of replication and transcription preserves genome integrity.

In many bacteria, there is a genome-wide bias towards co-orientation of replication and transcription, with essential and/or highly-expressed genes further enriched co-directionally. We previously found that reversing this bias in the bacterium Bacillus subtilis slows replication elongation, and we proposed that this effect contributes to the evolutionary pressure selecting the transcription-replication co-orientation bias. This selection might have been based purely on selection for speedy replication; alternatively, the slowed replication might actually represent an average of individual replication-disruption events, each of which is counter-selected independently because genome integrity is selected. To differentiate these possibilities and define the precise forces driving this aspect of genome organization, we generated new strains with inversions either over approximately 1/4 of the chromosome or at ribosomal RNA (rRNA) operons. Applying mathematical analysis to genomic microarray snapshots, we found that replication rates vary dramatically within the inverted genome. Replication is moderately impeded throughout the inverted region, which results in a small but significant competitive disadvantage in minimal medium. Importantly, replication is strongly obstructed at inverted rRNA loci in rich medium. This obstruction results in disruption of DNA replication, activation of DNA damage responses, loss of genome integrity, and cell death. Our results strongly suggest that preservation of genome integrity drives the evolution of co-orientation of replication and transcription, a conserved feature of genome organization.

On the structural alterations of phage proteins synthesized in the presence of pancreatic ribonuclease.

Journal Article

Heparin-binding hemagglutinin, from an extrapulmonary dissemination factor to a powerful diagnostic and protective antigen against tuberculosis.

Interactions of Mycobacterium tuberculosis with macrophages have long been recognized to be crucial to the pathogenesis of tuberculosis. The role of non-phagocytic cells is less well known. We have discovered a M. tuberculosis surface protein that interacts specifically with non-phagocytic cells, expresses hemagglutination activity and binds to sulfated glycoconjugates. It is therefore called heparin-binding hemagglutinin (HBHA). HBHA-deficient M. tuberculosis mutant strains are significantly impaired in their ability to disseminate from the lungs to other tissues, suggesting that the interaction with non-phagocytic cells, such as pulmonary epithelial cells, may play an important role in the extrapulmonary dissemination of the tubercle bacillus, one of the key steps that may lead to latency. Latently infected human individuals mount a strong T cell response to HBHA, whereas patients with active disease do not, suggesting that HBHA is a good marker for the immunodiagnosis of latent tuberculosis, and that HBHA-specific Th1 responses may contribute to protective immunity against active tuberculosis. Strong HBHA-mediated immuno-protection was shown in mouse challenge models. HBHA is a methylated protein and its antigenicity in latently infected subjects, as well as its protective immunogenicity strongly depends on the methylation pattern of HBHA. In both mice and man, the HBHA-specific IFN-gamma was produced by both the CD4(+) and the CD8(+) T cells. Furthermore, the HBHA-specific CD8(+) T cells expressed bactericidal and cytotoxic activities to mycobacteria-infected macrophages. This latter activity is most likely perforin mediated. Together, these observations strongly support the potential of methylated HBHA as an important component in future, acellular vaccines against tuberculosis.

Sistemas alternativos a los fungicidas químicos para el control de Penicillium digitatum (Pers.) Sacc. en limón

Argentina es el principal productor mundial de limones en el mundo y el 90 por ciento de esta producción se sitúa en la provincia de Tucumán. Las pérdidas económicas ocasionadas por las enfermedades de poscosecha representan uno de los principales problemas de la citricultura mundial, siendo el 80 por ciento atribuíbles a infecciones fúngicas. El moho verde causado por Penicillium digitatum (Pers.) Sacc. (PD), es la enfermedad de mayor incidencia y severidad durante la exportación de frutos de limón. Actualmente el control de estas enfermedades se realiza con el uso de fungicidas de síntesis química. Debido a las severas restricciones impuestas a estos productos, por regulaciones ambientales y de la salud, hay una fuerte necesidad de métodos alternativos de control. El objetivo de este trabajo de tesis fue evaluar alternativas de bajo impacto ambiental : bacterias lácticas, extractos vegetales, Serenade® (Bacillus subtilis QST 713) y bicarbonato de sodio; con actividad antifúngica directa o a través de la inducción de mecanismos de defensa, para el control de PD en condiciones in vitro e in vivo (frutos de limón). De un total de 33 cepas de bacterias lácticas evaluadas, se seleccionaron ocho con propiedades antifúngicas frente a PD. Se identificaron los metabolitos antifúngicos como ácidos orgánicos (ácido láctico, ácido acético y ácido fenil láctico) y se determinó la combinación óptima con mayor actividad inhibitoria. Los productos alternativos: extractos vegetales, Serenade® y bicarbonato de sodio, presentaron actividad antifúngica in vitro a PD con porcentajes de inhibición entre 2,1 - 16 por ciento. En los frutos de limón, los tratamientos alternativos no fueron efectivos por sí solos para controlar en forma directa la enfermedad. Estos tratamientos redujeron significativamente la severidad de la enfermedad, excepto el Serenade® cuando fue aplicado simultáneamente con el inóculo. Esta reducción fue más marcada cuando se dejaron transcurrir 18 h entre inoculación y aplicación de los tratamientos. El bicarbonato de sodio al 3 por ciento y en menor medida el Serenade® al 1 por ciento indujeron una respuesta de defensa de los frutos y controlaron la enfermedad en un 96,7 por ciento y 56,7 por ciento, respectivamente. En cromatografía de capa fina y fluorometría se detectó un aumento de la fitoalexina escoparona, sugiriendo que este efecto se produciría como resultado de la inducción de mecanismos de defensa, mientras que la umbeliferona no fue detectada. Estos resultados indican que los productos biológicos actuaron como una barrera al avance de la enfermedad, retrasando la severidad de la misma e induciendo de una respuesta de defensa en los frutos.

Presencia de una microflora patógena en lotes comerciales de Syngonium podophyllum

p.145-148

Sistemas alternativos a los fungicidas químicos para el control de Penicillium digitatum (Pers.)Sacc. en limón

Argentina es el principal productor mundial de limones en el mundo y el 90 por ciento de esta producción se sitúa en la provincia de Tucumán. Las pérdidas económicas ocasionadas por las enfermedades de poscosecha representan uno de los principales problemas de la citricultura mundial, siendo el 80 por ciento atribuíbles a infecciones fúngicas. El moho verde causado por Penicillium digitatum (Pers.)Sacc. (PD), es la enfermedad de mayor incidencia y severidad durante la exportación de frutos de limón. Actualmente el control de estas enfermedades se realiza con el uso de fungicidas de síntesis química. Debido a las severas restricciones impuestas a estos productos, por regulaciones ambientales y de la salud, hay una fuerte necesidad de métodos alternativos de control. El objetivo de este trabajo de tesis fue evaluar alternativas de bajo impacto ambiental : bacterias lácticas, extractos vegetales, Serenade® (Bacillus subtilis QST 713)y bicarbonato de sodio; con actividad antifúngica directa o a través de la inducción de mecanismos de defensa, para el control de PD en condiciones in vitro e in vivo (frutos de limón). De un total de 33 cepas de bacterias lácticas evaluadas, se seleccionaron ocho con propiedades antifúngicas frente a PD. Se identificaron los metabolitos antifúngicos como ácidos orgánicos (ácido láctico, ácido acético y ácido fenil láctico)y se determinó la combinación óptima con mayor actividad inhibitoria. Los productos alternativos: extractos vegetales, Serenade® y bicarbonato de sodio, presentaron actividad antifúngica in vitro a PD con porcentajes de inhibición entre 2,1 - 16 por ciento. En los frutos de limón, los tratamientos alternativos no fueron efectivos por sí solos para controlar en forma directa la enfermedad. Estos tratamientos redujeron significativamente la severidad de la enfermedad, excepto el Serenade® cuando fue aplicado simultáneamente con el inóculo. Esta reducción fue más marcada cuando se dejaron transcurrir 18 h entre inoculación y aplicación de los tratamientos. El bicarbonato de sodio al 3 por ciento y en menor medida el Serenade® al 1 por ciento indujeron una respuesta de defensa de los frutos y controlaron la enfermedad en un 96,7 por ciento y 56,7 por ciento, respectivamente. En cromatografía de capa fina y fluorometría se detectó un aumento de la fitoalexina escoparona, sugiriendo que este efecto se produciría como resultado de la inducción de mecanismos de defensa, mientras que la umbeliferona no fue detectada. Estos resultados indican que los productos biológicos actuaron como una barrera al avance de la enfermedad, retrasando la severidad de la misma e induciendo de una respuesta de defensa en los frutos.

Interference with the germination and growth ofUlvazoospores by quorum-sensing molecules fromUlva-associated epiphytic bacteria

Ulva zoospores preferentially settle on N-acylhomoserine lactone (AHL) producing marine bacterial biofilms. To investigate whether AHL signal molecules also affect the success and rate of zoospore germination in addition to zoospore attraction, the epiphytic bacteria associated with mature Ulva linza were characterized and bacterial isolates representative of this community tested for the ability to produce AHLs. Two of these AHL-producing isolates, Sulfitobacter spp. 376 and Shewanella spp. 79, were transformed with plasmids expressing the Bacillus spp. AHL lactonase gene aiiA to generate AHL-deficient variants. The germination and growth of U. linza zoospores was studied in the presence of these AHL-deficient strains and their AHL-producing counterparts. This revealed that the AHLs produced by Sulfitobacter spp. and Shewanella spp. or the bacterial products they regulate have a negative impact on both zoospore germination and the early growth of the Ulva germling. Further experiments with Escherichia coli biofilms expressing recombinant AHL synthases and synthetic AHLs provide data to demonstrate that zoospores germinated and grown in the absence of AHLs were significantly longer than those germinated in the presence of AHLs. These results reveal an additional role for AHLs per se in the interactive relationships between marine bacteria and Ulva zoospores.

Interference with the germination and growth of Ulvazoospores by quorum-sensing molecules from Ulva-associated epiphytic bacteria

Ulva zoospores preferentially settle on N-acylhomoserine lactone (AHL) producing marine bacterial biofilms. To investigate whether AHL signal molecules also affect the success and rate of zoospore germination in addition to zoospore attraction, the epiphytic bacteria associated with mature Ulva linza were characterized and bacterial isolates representative of this community tested for the ability to produce AHLs. Two of these AHL-producing isolates, Sulfitobacter spp. 376 and Shewanella spp. 79, were transformed with plasmids expressing the Bacillus spp. AHL lactonase gene aiiA to generate AHL-deficient variants. The germination and growth of U. linza zoospores was studied in the presence of these AHL-deficient strains and their AHL-producing counterparts. This revealed that the AHLs produced by Sulfitobacter spp. and Shewanella spp. or the bacterial products they regulate have a negative impact on both zoospore germination and the early growth of the Ulva germling. Further experiments with Escherichia coli biofilms expressing recombinant AHL synthases and synthetic AHLs provide data to demonstrate that zoospores germinated and grown in the absence of AHLs were significantly longer than those germinated in the presence of AHLs. These results reveal an additional role for AHLs per se in the interactive relationships between marine bacteria and Ulva zoospores.

Structure of the adenylation domain of an NAD+-dependent DNA ligase

Background: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target.

Results: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 Å resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site.

Conclusions: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.

Quantitative surface-enhanced Raman spectroscopy of dipicolinic acid - towards rapid anthrax endospore detection

Dipicolinic acid (DPA) is an excellent marker compound for bacterial spores, including those of Bacillus anthracis ( anthrax). Surface-enhanced Raman spectroscopy (SERS) potentially has the sensitivity and discrimination needed for trace DPA analysis, but mixing DPA solutions with citrate-reduced silver colloid only yielded measurable SERS spectra at much higher (> 80 ppm) concentrations than would be desirable for anthrax detection. Aggregation of the colloid with halide salts eliminated even these small DPA bands but aggregation with Na2SO4(aq) resulted in a remarkable increase in the DPA signals. With sulfate aggregation even 1 ppm solutions gave detectable signals with 10 s accumulation times, which is in the sensitivity range required. Addition of CNS- as an internal standard allowed quantitative DPA analysis, plotting the intensity of the strong DPA 1010 cm(-1) band (normalised to the ca. 2120 cm(-1) CNS- band) against DPA concentration gave a linear calibration (R-2 = 0.986) over the range 0 - 50 ppm DPA. The inclusion of thiocyanate also allows false negatives due to accidental deactivation of the enhancing medium to be detected.

Biodegradation and biosorption of acid anthraquinone dye

The acid anthraquinone dye Tectilon Blue (TB4R) is a major coloured component from the aqueous effluent of a carpet printing plant in Northern Ireland. The aerobic biodegradation of TB4R has been investigated experimentally in batch systems, using three strains of bacteria, namely, Bacillus gordonae (NCIMB 12553), Bacillus benzeovorans (NCIMB 12555) and Pseudomonas putida (NCIMB 9776). All three strains successfully decolourised the dye, and results were correlated using Michaelis-Menten kinetic theory. A recalculation of the reaction rate constants, to account for biosorption, gave an accurate simulation of the colour removal over a 24-h period. Up to 19% of the decolorisation was found to be caused by biosorption of the dye onto the biomass, with the majority of the decolorisation caused by utilisation of the dye by the bacteria. The reaction rate was found to be intermediate between zero and first order at dye concentrations of 200-1000 mg/l. (C) 2000 Elsevier Science Ltd. All rights reserved.

Natural Exposure to Cutaneous Anthrax Gives Long-Lasting T Cell Immunity Encompassing Infection-Specific Epitopes

There has been a long history of defining T cell epitopes to track viral immunity and to design rational vaccines, yet few data of this type exist for bacterial infections. Bacillus anthracis, the causative agent of anthrax, is both an endemic pathogen in many regions and a potential biological warfare threat. T cell immunity in naturally infected anthrax patients has not previously been characterized, which is surprising given concern about the ability of anthrax toxins to subvert or ablate adaptive immunity. We investigated CD4 T cell responses in patients from the Kayseri region of Turkey who were previously infected with cutaneous anthrax. Responses to B. anthracis protective Ag and lethal factor (LF) were investigated at the protein, domain, and epitope level. Several years after antibiotic-treated anthrax infection, strong T cell memory was detectable, with no evidence of the expected impairment in specific immunity. Although serological responses to existing anthrax vaccines focus primarily on protective Ag, the major target of T cell immunity in infected individuals and anthrax-vaccinated donors was LF, notably domain IV. Some of these anthrax epitopes showed broad binding to several HLA class alleles, but others were more constrained in their HLA binding patterns. Of specific CD4 T cell epitopes targeted within LF domain IV, one is preferentially seen in the context of bacterial infection, as opposed to vaccination, suggesting that studies of this type will be important in understanding how the human immune system confronts serious bacterial infection.