Microbial Communication, Cooperation and Cheating: Quorum Sensing Drives the Evolution of Cooperation in Bacteria

An increasing body of empirical evidence suggests that cooperation among clone-mates is common in bacteria. Bacterial cooperation may take the form of the excretion of “public goods”: exoproducts such as virulence factors, exoenzymes or components of the matrix in biofilms, to yield significant benefit for individuals joining in the common effort of producing them. Supposedly in order to spare unnecessary costs when the population is too sparse to supply the sufficient exoproduct level, many bacteria have evolved a simple chemical communication system called quorum sensing (QS), to “measure” the population density of clone-mates in their close neighborhood. Cooperation genes are expressed only above a threshold rate of QS signal molecule re-capture, i.e., above the local quorum of cooperators. The cooperative population is exposed to exploitation by cheaters, i.e., mutants who contribute less or nil to the effort but fully enjoy the benefits of cooperation. The communication system is also vulnerable to a different type of cheaters (“Liars”) who may produce the QS signal but not the exoproduct, thus ruining the reliability of the signal. Since there is no reason to assume that such cheaters cannot evolve and invade the populations of honestly signaling cooperators, the empirical fact of the existence of both bacterial cooperation and the associated QS communication system seems puzzling. Using a stochastic cellular automaton approach and allowing mutations in an initially non-cooperating, non-communicating strain we show that both cooperation and the associated communication system can evolve, spread and remain persistent. The QS genes help cooperative behavior to invade the population, and vice versa; cooperation and communication might have evolved synergistically in bacteria. Moreover, in good agreement with the empirical data recently available, this synergism opens up a remarkably rich repertoire of social interactions in which cheating and exploitation are commonplace

Nutrient Availability as a Mechanism for Selection of Antibiotic Tolerant Pseudomonas aeruginosa within the CF Airway

Microbes are subjected to selective pressures during chronic infections of host tissues. Pseudomonas aeruginosa isolates with inactivating mutations in the transcriptional regulator LasR are frequently selected within the airways of people with cystic fibrosis (CF), and infection with these isolates has been associated with poorer lung function outcomes. The mechanisms underlying selection for lasR mutation are unknown but have been postulated to involve the abundance of specific nutrients within CF airway secretions. We characterized lasR mutant P. aeruginosa strains and isolates to identify conditions found in CF airways that select for growth of lasR mutants. Relative to wild-type P. aeruginosa, lasR mutants exhibited a dramatic metabolic shift, including decreased oxygen consumption and increased nitrate utilization, that is predicted to confer increased fitness within the nutrient conditions known to occur in CF airways. This metabolic shift exhibited by lasR mutants conferred resistance to two antibiotics used frequently in CF care, tobramycin and ciprofloxacin, even under oxygen-dependent growth conditions, yet selection for these mutants in vitro did not require preceding antibiotic exposure. The selection for loss of LasR function in vivo, and the associated adverse clinical impact, could be due to increased bacterial growth in the oxygen-poor and nitrate-rich CF airway, and from the resulting resistance to therapeutic antibiotics. The metabolic similarities among diverse chronic infection-adapted bacteria suggest a common mode of adaptation and antibiotic resistance during chronic infection that is primarily driven by bacterial metabolic shifts in response to nutrient availability within host tissues

Fitness of Isogenic Colony Morphology Variants of Pseudomonas aeruginosa in Murine Airway Infection

Chronic lung infections with Pseudomonas aeruginosa are associated with the diversification of the persisting clone into niche specialists and morphotypes, a phenomenon called ‘dissociative behaviour’. To explore the potential of P. aeruginosa to change its morphotype by single step loss-of–function mutagenesis, a signature-tagged mini-Tn5 plasposon library of the cystic fibrosis airway isolate TBCF10839 was screened for colony morphology variants under nine different conditions in vitro. Transposon insertion into 1% of the genome changed colony morphology into eight discernable morphotypes. Half of the 55 targets encode features of primary or secondary metabolism whereby quinolone production was frequently affected. In the other half the transposon had inserted into genes of the functional categories transport, regulation or motility/chemotaxis. To mimic dissociative behaviour of isogenic strains in lungs, pools of 25 colony morphology variants were tested for competitive fitness in an acute murine airway infection model. Six of the 55 mutants either grew better or worse in vivo than in vitro, respectively. Metabolic proficiency of the colony morphology variant was a key determinant for survival in murine airways. The most common morphotype of self-destructive autolysis did unexpectedly not impair fitness. Transposon insertions into homologous genes of strain PAO1 did not reproduce the TBCF10839 mutant morphotypes for 16 of 19 examined loci pointing to an important role of the genetic background on colony morphology. Depending on the chosen P. aeruginosa strain, functional genome scans will explore other areas of the evolutionary landscape. Based on our discordant findings of mutant phenotypes in P. aeruginosa strains PAO1, PA14 and TBCF10839, we conclude that the current focus on few reference strains may miss modes of niche adaptation and dissociative behaviour that are relevant for the microevolution of complex traits in the wild

Protein Co-Expression Analysis as a Strategy to Complement a Standard Quantitative Proteomics Approach:Case of a Glioblastoma Multiforme Study

Although correlation network studies from co-expression analysis are increasingly popular, they are rarely applied to proteomics datasets. Protein co-expression analysis provides a complementary view of underlying trends, which can be overlooked by conventional data analysis. The core of the present study is based on Weighted Gene Co-expression Network Analysis applied to a glioblastoma multiforme proteomic dataset. Using this method, we have identified three main modules which are associated with three different membrane associated groups; mitochondrial, endoplasmic reticulum, and a vesicle fraction. The three networks based on protein co-expression were assessed against a publicly available database (STRING) and show a statistically significant overlap. Each of the three main modules were de-clustered into smaller networks using different strategies based on the identification of highly connected networks, hierarchical clustering and enrichment of Gene Ontology functional terms. Most of the highly connected proteins found in the endoplasmic reticulum module were associated with redox activity while a core of the unfolded protein response was identified in addition to proteins involved in oxidative stress pathways. The proteins composing the electron transfer chain were found differently affected with proteins from mitochondrial Complex I being more down-regulated than proteins from Complex III. Finally, the two pyruvate kinases isoforms show major differences in their co-expressed protein networks suggesting roles in different cellular locations

A microfluidic system for studying ageing and dynamic single-cell responses in budding yeast

Recognition of the importance of cell-to-cell variability in cellular decision-making and a growing interest in stochastic modeling of cellular processes has led to an increased demand for high density, reproducible, single-cell measurements in time-varying surroundings. We present ALCATRAS (A Long-term Culturing And TRApping System), a microfluidic device that can quantitatively monitor up to 1000 cells of budding yeast in a well-defined and controlled environment. Daughter cells are removed by fluid flow to avoid crowding allowing experiments to run for over 60 hours, and the extracellular media may be changed repeatedly and in seconds. We illustrate use of the device by measuring ageing through replicative life span curves, following the dynamics of the cell cycle, and examining history-dependent behaviour in the general stress response

Gene expression profile in newborn rat lungs after two days of recovery of mechanical ventilation

Introduction La dysplasie bronchopulmonaire (BPD) est une maladie chronique des poumons se retrouvant chez environs 30% des prématurés nés à moins de 30 semaines d'âge de gestation et se traduisant par un arrêt de la formation alvéolo-capillaire. De nombreux facteurs de risques tels que l'immaturité pulmonaire, la ventilation mécanique, l'oxygénothérapie, la chorioamnionite et le sepsis ont été mis en évidence. De nombreux modèles animaux ont été développés afin d'étudier la pathogenèse exacte de cette maladie. Toutefois aucun model rongeur présentant une immaturité pulmonaire n'a permis pour le moment d'étudier les effets au niveau génomique de ces différents facteurs de risque à long terme. Pour cela, nous avons utilisé un modèle d'intubation atraumatique décrit récemment. Méthodes Des ratons mâles ont été attribués de manière aléatoire à 4 différents groupes, à savoir les contrôles (groupe 1), les individus avec une injection de lipopolysaccharides (LPS) afin de mimer un sepsis (groupe 2), les individus avec injection de LPS et ventilation mécanique à 0.21 de Fi02 (groupe 3) et le dernier groupe intégrant plusieurs facteurs de risque, à savoir le LPS, la ventilation mécanique et une Fi02 à 0.6 (groupe 4). 24h avant la ventilation, les ratons âgés de 4 ou 5 jours des groupes 2-3-4 ont reçut une injection de LPS intrapéritonéale et ceux du groupe 1 le même volume de NaCI 0.9%. Au 5ème ou 6ème jours de vie, les ratons des groupes 3-4 ont été ventilés sous anesthésie durant 6h, puis extubés et rendus à leur mère. Parallèlement les individus des groupes 1-2 ont été séparés de leur mère durant 6h. 48h plus tard, les individus ont été sacrifiés avec prélèvement de poumons pour analyse histologique et génomique. Des Gene Arrays ont été effectués avec contrôles des résultats par qPCR et Western Blot. Résultats L'analyse des Gene Arrays a permis de mettre en évidence 271 gènes présentant des modifications significatives entre le groupe 1 et 4. Le programme Metacore nous a permis de classifier ces gènes dans six «pathways » à savoir le système immunitaire, la réponse inflammatoire, l'hématopoïèse, la vasodilatation, la régulation du stress oxydatif et le remodelage tissulaire. Discussion Le remodelage tissulaire a été mis en évidence comme un des pathways le plus modifié à long terme dans notre modèle. Il est constitué d'un réseau de protéases/antiprotéases tels que matrix-metallo-protéinases-9 (MMP9), MMP12, Tissue-lnhibitor of Metallo-Protéinases-1 (TIMP1) et MMP8. La dérégulation de ce réseau conduit à une augmentation de la destruction de la matrice extracellulaire pulmonaire ainsi que de la membrane basale comme démontrée dans différentes études portant sur l'hyperoxie et la ventilation mécanique. Pour exemple, une souris knock-out pour MMP9 subissant un test d'hyperoxie présente un meilleur taux de survie et des modifications de l'architecture pulmonaire moins importantes qu'une souris wildtype. Une augmentation de MMP8 et MMP9 comme trouvé dans notre étude, a été corrélée chez le nouveau-né avec un besoin de ventilation mécanique prolongé. Dans une autre étude, l'inhibition de MMP8 conduit à une diminution des lésions liées à la ventilation mécanique. Conclusion et perspectives La régulation des l'activité des métalloprotéases (MMP) semblent ouvrir la possibilité de nouvelles stratégies afin de protéger les poumons des effets négatifs de la ventilation et de l'hyperoxie. Dans ce cadre MMP 9 et MMP8 et leurs régulateurs semblent être des cibles intéressantes dans la prévention de la BP

Plazomicin activity against polymyxin-resistant Enterobacteriaceae, including MCR-1-producing isolates.

Plazomicin, a novel aminoglycoside with in vitro activity against MDR Gram-negative organisms, is under development to treat patients with serious enterobacterial infections. We evaluated the activity of plazomicin and comparators against colistin-resistant enterobacterial isolates. Susceptibility to plazomicin and comparators was tested by broth microdilution for a collection of 95 colistin-resistant enterobacterial isolates collected from 29 hospitals in eight countries. Forty-two isolates (Klebsiella pneumoniae and Klebsiella oxytoca) possessed chromosomally encoded resistance mechanisms to colistin, 21 isolates (Escherichia coli and Salmonella enterica) expressed the mcr-1 gene, 8 isolates (Serratia, Proteus, Morganella and Hafnia) were intrinsically resistant to colistin and 24 isolates (K. pneumoniae, E. coli and Enterobacter spp.) had undefined, non-mcr-1 mechanisms. Susceptibility profiles were defined according to CLSI for aminoglycosides and to EUCAST for colistin and tigecycline. Plazomicin inhibited 89.5% and 93.7% of the colistin-resistant enterobacterial isolates at ≤ 2 and ≤4 mg/L, respectively. MICs of plazomicin were ≤2 mg/L for all of the mcr-1 positive isolates and ≤4 mg/L for all the intrinsic colistin-resistant Enterobacteriaceae. Non-susceptibility to currently marketed aminoglycosides was common: amikacin, 16.8%; gentamicin, 47.4%; and tobramycin, 63.2%. Plazomicin was the most potent aminoglycoside tested with an MIC90 of 4 mg/L, compared with 32, >64 and 64 mg/L for amikacin, gentamicin and tobramycin, respectively. Plazomicin displayed potent activity against colistin-resistant clinical enterobacterial isolates, including those expressing the mcr-1 gene. Plazomicin was more active than other aminoglycosides against this collection of isolates. The further development of plazomicin for the treatment of infections due to MDR Enterobacteriaceae is warranted

Protein Co-Expression Analysis as a Strategy to Complement a Standard Quantitative Proteomics Approach:Case of a Glioblastoma Multiforme Study

Although correlation network studies from co-expression analysis are increasingly popular, they are rarely applied to proteomics datasets. Protein co-expression analysis provides a complementary view of underlying trends, which can be overlooked by conventional data analysis. The core of the present study is based on Weighted Gene Co-expression Network Analysis applied to a glioblastoma multiforme proteomic dataset. Using this method, we have identified three main modules which are associated with three different membrane associated groups; mitochondrial, endoplasmic reticulum, and a vesicle fraction. The three networks based on protein co-expression were assessed against a publicly available database (STRING) and show a statistically significant overlap. Each of the three main modules were de-clustered into smaller networks using different strategies based on the identification of highly connected networks, hierarchical clustering and enrichment of Gene Ontology functional terms. Most of the highly connected proteins found in the endoplasmic reticulum module were associated with redox activity while a core of the unfolded protein response was identified in addition to proteins involved in oxidative stress pathways. The proteins composing the electron transfer chain were found differently affected with proteins from mitochondrial Complex I being more down-regulated than proteins from Complex III. Finally, the two pyruvate kinases isoforms show major differences in their co-expressed protein networks suggesting roles in different cellular locations