Étude de la voie de signalisation de l’insuline chez la drosophile par une approche phosphoprotéomique

La phosphorylation est une modification post-traductionnelle modulant l’activité, la conformation ou la localisation d’une protéine et régulant divers processus. Les kinases et phosphatases sont responsables de la dynamique de phosphorylation et agissent de manière coordonnée. L’activation anormale ou la dérégulation de kinases peuvent conduire au développement de cancers ou de désordres métaboliques. Les récepteurs tyrosine kinase (RTKs) sont souvent impliqués dans des maladies et la compréhension des mécanismes régissant leur régulation permet de déterminer les effets anticipés sur leurs substrats. Dans ce contexte, le but de cette thèse est d’identifier les évènements de phosphorylation intervenant dans la voie de l’insuline chez la drosophile impliquant un RTK : le récepteur de l’insuline (InR). La cascade de phosphorylation déclenchée suite à l’activation du récepteur est conservée chez le mammifère. Afin d’étudier le phosphoprotéome de cellules S2 de drosophile, nous avons utilisé une étape d’enrichissement de phosphopeptides sur dioxyde de titane suivie de leur séparation par chromatographie liquide (LC) et mobilité ionique (FAIMS). Les phosphopeptides sont analysés par spectrométrie de masse en tandem à haute résolution. Nous avons d’abord démontré les bénéfices de l’utilisation du FAIMS comparativement à une étude conventionnelle en rapportant une augmentation de 50 % dans le nombre de phosphopeptides identifiés avec FAIMS. Cette technique permet de séparer des phosphoisomères difficilement distinguables par LC et l’acquisition de spectres MS/MS distincts où la localisation précise du phosphate est déterminée. Nous avons appliqué cette approche pour l’étude des phosphoprotéomes de cellules S2 contrôles ou traitées à l’insuline et avons identifié 32 phosphopeptides (sur 2 660 quantifiés) pour lesquels la phosphorylation est modulée. Étonnamment, 50 % des cibles régulées possèdent un site consensus pour la kinase CK2. Une stratégie d’inhibition par RNAi a été implémentée afin d’investiguer le rôle de CK2 dans la voie de l’insuline. Nous avons identifié 6 phosphoprotéines (CG30085, su(var)205, scny, protein CDV3 homolog, D1 et mu2) positivement régulées suite à l’insuline et négativement modulées après le traitement par RNAi CK2. Par essai kinase in vitro, nous avons identifié 29 cibles directes de CK2 dont 15 corrélaient avec les résultats obtenus par RNAi. Nous avons démontré que la phosphorylation de su(var)205 (S15) était modulée par l’insuline en plus d’être une cible directe de CK2 suite à l’expérience RNAi et à l’essai kinase. L’analyse des données phosphoprotéomiques a mis en évidence des phosphopeptides isomériques dont certains étaient séparables par FAIMS. Nous avons déterminé leur fréquence lors d’études à grande échelle grâce à deux algorithmes. Le script basé sur les différences de temps de rétention entre isomères a identifié 64 phosphoisomères séparés par LC chez la souris et le rat (moins de 1 % des peptides identifiés). Chez la drosophile, 117 ont été répertoriés en combinaison avec une approche ciblée impliquant des listes d’inclusion. Le second algorithme basé sur la présence d’ions caractéristiques suite à la fragmentation de formes qui co-éluent a rapporté 23 paires isomériques. L’importance de pouvoir distinguer des phosphoisomères est capitale dans le but d’associer une fonction biologique à un site de phosphorylation précis qui doit être identifié avec confiance.

Exploring TERRA (TElomeric Repeat-containing RNA) Expression and Regulation During Cell Growth in Saccharomyces cerevisiae

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Kinetics of Bacterial Colony Growth by Laser Induced Fluorescence

The growth kinetics of an aerial bacterial colony on solid agar media was studied using laser induced fluorescence technique. Fluorescence quenching of Rhodamin B by the bacterial colony was utilized for the study. The lag phase, log phase, and stationary phase of growth curve of bacterial colony was identified by measuring peak fluorescence intensity of dye doped bacterial colony.

Effect of growth time on the surface and adhesion properties of Lactobacillus rhamnosus GG

Aims: To investigate the changes in the surface properties of Lactobacillus rhamnosus GG during growth, and relate them with the ability of the Lactobacillus cells to adhere to Caco-2 cells. Methods and Results: Lactobacillus rhamnosus GG was grown in complex medium, and cell samples taken at four time points and freeze dried. Untreated and trypsin treated freeze dried samples were analysed for their composition using SDS-PAGE analysis and Fourier transform infrared spectroscopy (FTIR), hydrophobicity and zeta potential, and for their ability to adhere to Caco-2 cells. The results suggested that in the case of early exponential phase samples (4 and 8 h), the net surface properties, i.e. hydrophobicity and charge, were determined to a large extent by anionic hydrophilic components, whereas in the case of stationary phase samples (13 and 26 h), hydrophobic proteins seemed to play the biggest role. Considerable differences were also observed between the ability of the different samples to adhere to Caco-2 cells; maximum adhesion was observed for the early stationary phase sample (13 h). The results suggested that the adhesion to Caco-2 cells was influenced by both proteins and non-proteinaceous compounds present on the surface of the Lactobacillus cells. Conclusion: The surface properties of Lact. rhamnosus GG changed during growth, which in return affected the ability of the Lactobacillus cells to adhere to Caco-2 cells. Significance and Impact of the Study: The levels of adhesion of Lactobacillus cells to Caco-2 cells were influenced by the growth time and reflected changes on the bacterial surface. This study provides critical information on the physicochemical factors that influence bacterial adhesion to intestinal cells.

Excision of anabaena PCC 7120 nifD element in escherichia coli: growth kinetics and RecA regulated xisA expression and DNA rearrangement

Anabaena PCC 7120 nifHDK operon is interrupted by an 11 kb DNA element which is excised during the development of heterocysts by Excisase A, encoded by the xisA gene residing on the element. The excision is a site-specific recombination event that occurs at the I I base pair direct repeats flanking the element. Earlier work showed the excision of the I I kb element in Escherichia coli at a frequency 0.3%. We report here the excision of this element at 1.1% and 1.98% in E. coli DH5 alpha, and 1.9% and 10.9% in E. coli JM 101 when grown on Luria broth and minimal media, respectively. Excision of nifD element in isogenic recA(-) (RK1) and recA(+) (RK2) E. coli JM101 P1 transductants, showed similar results to that of E. coli JM101 and DH5 alpha, respectively. A plasmid pMX32, carrying a xisA defective 11 kb element, showed no excision in E. coli RK2 strain. In contrast to Anabaena PCC 7120, excision of nifD element did not increase in E. call DH5 alpha grown in iron-deficient conditions. A PxisA::lacZ transcriptional fusion, used to detect the expression of elusive xisA gene, showed maximal beta-galactosidase activity in the stationary phase. The results suggest that the excision event in E. coli may involve additional factors, such as RecA and that the physiological status can influence the excision of nifD element. (C) 2007 Elsevier Ltd. All rights reserved.

Synthesis and evaluation of a solid supported molecular tweezer type receptor for cholesterol

A new macroporous stationary phase bearing 'tweezer' receptors that exhibit specificity for cholesterol has been constructed from rigid multifunctional vinylic monomers derived from 3,5-dibromobenzoic acid, propargyl alcohol and cholesterol. The synthesis of the novel tweezer monomer that contains two cholesterol receptor arms using palladium mediated Sonogashira methodologies and carbonate couplings is reported. The subsequent co-polymerisation of this tweezer monomer with a range of cross-linking agents via a 'pseudo' molecular imprinting approach afforded a diverse set of macroporous materials. The selectivity and efficacy of these materials for cholesterol binding was assessed using a chromatographic screening process. The optimum macroporous stationary phase material composition was subsequently used to construct monolithic solid phase extraction columns for use in the selective extraction of cholesterol from multi-component mixtures of structurally related steroids.

Influence of environmental stress on distributions of times to first division in Escherichia coli populations, as determined by digital-image analysis of individual cells

The distributions of times to first cell division were determined for populations of Escherichia coli stationary-phase cells inoculated onto agar media. This was accomplished by using automated analysis of digital images of individual cells growing on agar and calculation of the "box area ratio." Using approximately 300 cells per experiment, the mean time to first division and standard deviation for cells grown in liquid medium at 37 degrees C and inoculated on agar and incubated at 20 degrees C were determined as 3.0 h and 0.7 h, respectively. Distributions were observed to tail toward the higher values, but no definitive model distribution was identified. Both preinoculation stress by heating cultures at 50 degrees C and postinoculation stress by growth in the presence of higher concentrations of NaCl increased mean times to first division. Both stresses also resulted in an increase in the spread of the distributions that was proportional to the mean division time, the coefficient of variation being constant at approximately 0.2 in all cases. The "relative division time," which is the time to first division for individual cells expressed in terms of the cell size doubling time, was used as measure of the "work to be done" to prepare for cell division. Relative division times were greater for heat-stressed cells than for those growing under osmotic stress.

Ribosome modulation factor protects Escherichia coli during heat stress, but this may not be dependent on ribosome dimerisation

The role of ribosome modulation factor (RMF) in protecting heat-stressed Escherichia coli cells was identified by the observation that cultures of a mutant strain lacking functional RMF (HMY15) were highly heat sensitive in stationary phase compared to those of the parent strain (W3110). No difference in heat sensitivity was observed between these strains in exponential phase, during which RMF is not synthesised. Studies by differential scanning calorimetry demonstrated that the ribosomes of stationary-phase cultures of the mutant strain had lower thermal stability than those of the parent strain in stationary phase, or exponential-phase ribosomes. More rapid breakdown of ribosomes in the mutant strain during heating was confirmed by rRNA analysis and sucrose density gradient centrifugation. Analyses of ribosome composition showed that the 100S dimers dissociated more rapidly during heating than 70S particles. While ribosome dimerisation is a consequence of the conformational changes caused by RMF binding, it may not therefore be essential for RMF-mediated ribosome stabilisation.

Factors affecting the pressure resistance of some Campylobacter species

Aims: To compare pressure resistance between strains of Campylobacter jejuni, Campylobacter coli, Campylobacter lari and Campylobacter fetus, and to investigate the effect of suspending medium on pressure resistance of sensitive and more resistant strains. Methods and Results: Six strains of C. jejuni and four each of C. coli, C. lari and C. fetus were pressure treated for 10 min at 200 and 300 MPa. Individual strains varied widely in pressure resistance but there were no significant differences between the species C. jejuni, C. coli and C. lari. Campylobacter fetus was significantly more pressure sensitive than the other three species. The pressure resistance of C. jejuni cultures reached a maximum at 16-18 h on entry into stationary phase then declined to a minimum at 75 h before increasing once more. Milk was more baroprotective than water, broth or chicken slurry but did not prevent inactivation even of a resistant strain at 400 MPa. Conclusions: Pressure resistance varies considerably between species of Campylobacter and among strains within a species, and survival after a pressure challenge will be markedly influenced by culture age and food matrix. Significance and Impact of the Study: Despite the strain variation in pressure resistance and protective effects of food, Campylobacter sp. do not present a particular problem for pressure processing.

The activity of ribosome modulation factor during growth of Escherichia coli under acidic conditions

Expression of the gene encoding ribosome modulation factor (RMF), as measured using an rmf-lacZ gene fusion, increased with decreasing pH in exponential phase cultures of Escherichia coli. Expression was inversely proportional to the growth rate and independent of the acidifying agent used and it was concluded that expression of rmf was growth rate controlled in exponential phase under acid conditions. Increased rmf expression during exponential phase was not accompanied by the formation of ribosome dimers as occurs during stationary phase. Nor did it appear to have a significant effect on cell survival under acid stress since the vulnerability of an RMF-deficient mutant strain was similar to that of the parent strain. Ribosome degradation was increased in the mutant strain compared to the parent strain at pH 3.75. Also, the peptide elongation rate was reduced in the mutant strain but not the parent during growth under acid conditions. It is speculated that the function of RMF during stress-induced reduction in growth rate is two-fold: firstly to prevent reduced elongation efficiency by inactivating surplus ribosomes and thus limiting competition for available protein synthesis factors, and secondly to protect inactivated ribosomes from degradation.

High hydrostatic pressure resistance of Campylobacter jejuni after different sublethal stresses

Aims: To study the development of resistance responses in Campylobacter jejuni to High Hydrostatic Pressure (HHP) treatments after the exposure to different stressful conditions that may be encountered in food processing environments, such as acid pH, elevated temperatures and cold storage. Methods and Results: C. jejuni cells in exponential and stationary growth phase were exposed to different sublethal stresses (acid, heat and cold shocks) prior to evaluate the development of resistance responses to HHP. For exponential-phase cells, neither of the conditions tested increased nor decreased HHP resistance of C. jejuni. For stationary-phase cells, acid and heat adaptation sensitized C. jejuni cells to the subsequent pressure treatment. On the contrary, cold-adapted stationary-phase cells developed resistance to HHP. Conclusions: Whereas C. jejuni can be classified as a stress sensitive microorganism, our findings have demonstrated that it can develop resistance responses under different stressing conditions. The resistance of stationary phase C. jejuni to HHP was increased after cells were exposed to cold temperatures. Significance and Impact of the Study: The results of this study contribute to a better knowledge of the physiology of C. jejuni and its survival to food preservation agents. Results here presented may help in the design of combined processes for food preservation based on HHP technology.

The inhibitory effect of natural microflora of food on growth of Listeria monocytogenes in enrichment broths

The aims of this study were to (i) compare the inhibitory effects of the natural microflora of different foods on the growth of Listeria monocytogenes during enrichment in selective and non-selective broths; (ii) to isolate and identify components of the microflora of the most inhibitory food; and (iii) to determine which of these components was most inhibitory to growth of L. monocytogenes in co-culture studies. Growth of an antibioticresistant marker strain of L. monocytogenes was examined during enrichment of a range of different foods in Tryptone Soya Broth (TSB), Half Fraser Broth (HFB) and Oxoid Novel Enrichment (ONE) Broth. Inhibition of L. monocytogenes was greatest in the presence of minced beef, salami and soft cheese and least with prepared fresh salad and chicken pâté. For any particular food the numbers of L. monocytogenes present after 24 h enrichment in different broths increased in the order: TSB, HFB and ONE Broth. Numbers of L. monocytogenes recovered after enrichment in TSB were inversely related to the initial aerobic plate count (APC) in the food but with only a moderate coefficient of determination (R2) of 0.51 implying that microbial numbers and the composition of the microflora both influenced the degree of inhibition of L. monocytogenes. In HFB and ONE Broth the relationship between APC and final L. monocytogenes counts was weaker. The microflora of TSB after 24 h enrichment of minced beef consisted of lactic acid bacteria, Brochothrix thermosphacta, Pseudomonas spp., Enterobacteriaceae, and enterococci. In co-culture studies of L. monocytogenes with different components of the microflora in TSB, the lactic acid bacteria were the most inhibitory followed by the Enterobacteriaceae. The least inhibitory organisms were Pseudomonas sp., enterococci and B. thermosphacta. In HFB and ONE Broth the growth of Gram-negative organisms was inhibited but lactic acid bacteria still reached high numbers after 24 h. A more detailed study of the growth of low numbers of L. monocytogenes during enrichment of minced beef in TSB revealed that growth of L. monocytogenes ceased at a cell concentration of about 102 cfu/ml when lactic acid bacteria entered stationary phase. However in ONE Broth growth of lactic acid bacteria was slower than in TSB with a longer lag time allowing L. monocytogenes to achieve much higher numbers before lactic acid bacteria reached stationary phase. This work has identified the relative inhibitory effects of different components of a natural food microflora and shown that the ability of low numbers of L. monocytogenes to achieve high cell concentrations is highly dependent on the extent to which enrichment media are able to inhibit or delay growth of the more effective competitors.

Proteomic analyses of a Listeria monocytogenes mutant lacking σB identify new components of the σB regulon and highlight a role for σB in the utilization of glycerol

In Listeria monocytogenes the alternative sigma factor σB plays important roles in both virulence and stress tolerance. In this study a proteomic approach was used to define components of the σB regulon in L. monocytogenes 10403S (serotype 1/2a). Using two-dimensional gel electrophoresis and the recently developed isobaric tags for relative and absolute quantitation technique, the protein expression profiles of the wild type and an isogenic ΔsigB deletion strain were compared. Overall, this study identified 38 proteins whose expression was σB dependent; 17 of these proteins were found to require the presence of σB for full expression, while 21 were expressed at a higher level in the ΔsigB mutant background. The data obtained with the two proteomic approaches showed limited overlap (four proteins were identified by both methods), a finding that highlights the complementarity of the two technologies. Overall, the proteomic data reaffirmed a role for σB in the general stress response and highlighted a probable role for σB in metabolism, especially in the utilization of alternative carbon sources. Proteomic and physiological data revealed the involvement of σB in glycerol metabolism. Five newly identified members of the σB regulon were shown to be under direct regulation of σB using reverse transcription-PCR (RT-PCR), while random amplification of cDNA ends-PCR was used to map four σB-dependent promoters upstream from lmo0796, lmo1830, lmo2391, and lmo2695. Using RT-PCR analysis of known and newly identified σB-dependent genes, as well as proteomic analyses, σB was shown to play a major role in the stationary phase of growth in complex media.

Effects of repeated cycles of acid challenge and growth on the phenotype and virulence of Salmonella enterica

Aims: The aim of the study was to investigate how stresses like low pH, which may be encountered in farms or food preparation premises, shape populations of Salmonella enterica by the selection of stress-resistant variants. Methods and Results: Stationary-phase cultures of S. enterica serovar Enteritidis and serovar Typhimurium (one strain of each) were exposed to pH 2Æ5 for up to 4 h, followed by growth at pH 7 for 48 h. This process was repeated 15 times in two separate experiments, which increased the acid resistance of the three out of four populations we obtained, by three- to fourfold. Sustainable variants derived from the populations showed changes in colony morphology, expression of SEF17 fimbriae, growth, increased heat resistance and reduced virulence. Conclusions: The study demonstrates that low pH environments can select for populations of S. enterica with persistent phenotypic changes such as increased acid resistance and occasionally increased SEF17 expression and lower virulence. Significance and Impact of the Study: There is a common belief that increased acid resistance coincides with increased virulence. This study demonstrates for the first time that increased acid resistance often impairs virulence and affects the general phenotype of S. enterica.

Characterization of a Listeria monocytogenes Scott A isolate with high tolerance towards high hydrostatic pressure

An isolate of L. monocytogenes Scott A that is tolerant to high hydrostatic pressure (HHP), named AK01, was isolated upon a single pressurization treatment of 400 MPa for 20 min and was further characterized. The survival of exponential- and stationary-phase cells of AK01 in ACES [N-(2-acetamido)-2-aminoethanesulfonic acid] buffer was at least 2 log units higher than that of the wild type over a broad range of pressures (150 to 500 MPa), while both strains showed higher HHP tolerance (piezotolerance) in the stationary than in the exponential phase of growth. In semiskim milk, exponential-phase cells of both strains showed lower reductions upon pressurization than in buffer, but again, AK01 was more piezotolerant than the wild type. The piezotolerance of AK01 was retained for at least 40 generations in rich medium, suggesting a stable phenotype. Interestingly, cells of AK01 lacked flagella, were elongated, and showed slightly lower maximum specific growth rates than the wild type at 8, 22, and 30°C. Moreover, the piezotolerant strain AK01 showed increased resistance to heat, acid, and H2O2 compared with the wild type. The difference in HHP tolerance between the piezotolerant strain and the wild-type strain could not be attributed to differences in membrane fluidity, since strain AK01 and the wild type had identical in situ lipid melting curves as determined by Fourier transform infrared spectroscopy. The demonstrated occurrence of a piezotolerant isolate of L. monocytogenes underscores the need to further investigate the mechanisms underlying HHP resistance of food-borne microorganisms, which in turn will contribute to the appropriate design of safe, accurate, and feasible HHP treatments.