Our lab discovered that approximately 1 in 10,000 Escherichia coli cells in stationary phase remain in suspension after a high g-force centrifuge event. To establish the mechanism behind this curious phenotype, multiple mutant strains of E. coli were independently evolved such that the majority of their populations resisted migration when exposed to high centrifugal forces. Genomic DNA sequencing of the mutants' revealed unique, isolated mutations in genes involved in capsule synthesis and exopolysaccharide (EPS) production. Each mutant exhibits a novel mechanism that allows them to remain in suspension. The mutants were further characterized by determining their growth rates, strengths of resistance to various centrifugal forces, the phenotype's dependence on a carbon source, and timing of the phenotype's presentation. The results revealed: comparable mutant generation times to the wild-type strain, variable resistance to centrifugal force, phenotype dependence on carbon source, and phenotype presentation during early stationary phase. To interrogate the mechanism by which these cells stay in suspension the production of EPS was quantified, and gene knock-outs were performed. Quantification of the EPS revealed approximately a seventeen-fold increase in EPS in the mutants' compared to the wild-type strain. Gene knock-outs revealed the EPS produced can be attached to the outer-membrane or freely secreted into the media by different mechanisms. In addition, this mechanism was further confirmed to be responsible for the centrifuge resistant trait by attaching extracted EPS to polystyrene microspheres. Experimental results show that mutant extracted EPS treated beads caused increased bead retention in suspension compared to wild-type EPS treated beads. These results reveal that E. coli is using a novel mechanism to adapt to a new environmental factor introduced to remove the bacteria. With the discovery of this mechanism and the transferability to inorganic objects industrial applications are now envisioned where particle sedimentation is controllable and mixtures remain homogenized by attaching optically transparent biomolecules.

Previous research discovered the existence of sedimentation-resistant mutants of E. coli. Genomic studies revealed that these mutants resisted sedimentation due to independent modifications to genes that influenced the Rcs signal transduction pathway, causing increased secretion of an exopolysaccharide capsule comprised primarily of colanic acid. The Rcs system is responsible for detecting envelope stressors; consequently, ampicillin and osmotic stress were used to perturb the cellular envelope and study the response of the mutants compared to wild-type cells. It was found that the overproduction of colanic acid in the mutants confers some resistance to envelope stress; however, the mutants still behaved similarly to wild-type cells. The doubling times of the strains grown in sodium chloride solutions were calculated. A wavelength scan from 400 nm to 800 nm was performed on strains grown in different salt concentrations to determine if there were significant differences in light scattering between the wild-type and mutant cells. Further analysis was performed that, along with the doubling time data, suggested that wild-type cells may have turned on genes for capsule production in response to being grown in high salt concentrations. Additional research could be conducted to test this hypothesis, perhaps through the quantification of colanic acid through a methyl pentose assay for wild-type cultures grown with high salt concentrations. The idea that wild-type cells could digest colanic acid as a carbon source when lacking resources was also investigated with different preparations of colanic acid. One preparation of colanic acid showed promising results, which could indicate that bacteria are able to digest their capsule in a novel method to produce energy when starved. Again, additional investigation should be conducted to confirm these results. Other future experiments could study the metabolome of these mutants to determine if they have increased quantities of alarmones related to biofilm formation.

Au laboratoire, une famille de tyrosine kinases propres aux bactéries et ne présentant aucune ressemblance structurale avec les protéine-kinases d’origine eucaryote a été identifiée. Ces enzymes, appelées BY-kinases, sont notamment impliquées dans la biosynthèse des polysaccharides extracellulaires, mais leurs rôles précis ainsi que leurs mécanismes catalytiques sont encore peu compris.Dans la première partie de ce travail, nous avons caractérisé le rôle physiologique de la phosphorylation sur la tyrosine de la protéine Ugd, une UDP-glucose déshydrogénase, par les BY-kinases Wzc et Etk d’E. coli. Nous avons démontré que la phosphorylation d’Ugd sur un site commun à Wzc et Etk augmente son activité. Nous avons également établi que la phosphorylation d’Ugd par Wzc participe à la régulation de la quantité d’acide colanique produit, tandis que la phosphorylation d’Ugd par Etk influence la résistance de la bactérie à la polymyxine.Nous avons également effectué une analyse structure-fonction du domaine cytoplasmique de deux BY-kinases, CapA1/CapB2 de S. aureus et Wzc d’E. coli. Nous avons montré que ces deux protéines s’associent en octamère, grâce au motif EX2RX2R et qu’elle s’autophosphoryle selon un mécanisme intermoléculaire. Nous avons, de plus, identifié le mécanisme d’activation de ces protéines et révélé l’importance d’un domaine particulier dans l’autophosphorylation de Wzc et la biosynthèse de l’acide colanique.La caractérisation structurale et fonctionnelle des BY-kinases représente une approche prometteuse et originale en vue de l’élaboration de molécules inhibant spécifiquement leur activité et pouvant affecter le pouvoir virulent des bactéries pathogènes. / A new class of bacterial enzymes, named BY-kinases, has been shown to catalyze protein-tyrosine phosphorylation. These enzymes share no structural and functional similarities with their eukaryotic counterparts. Evidence of their involvement in extracellular polysaccharide biosynthesis has been provided, but their accurate functions and their catalytic mechanism remain largely unknown.First, we characterized the physiological role of tyrosine phosphorylation of Ugd, a UDP-glucose dehydrogenase, by the BY-kinases Wzc and Etk of E. coli. We demonstrated that Ugd phosphorylation by Wzc or Etk occurs on the same site and increases its activity. We also established that Wzc-mediated phosphorylation of Ugd participates in the regulation of colanic acid production whereas Ugd phosphorylation by Etk influences resistance to polymyxin.In addition, we performed a structure-function analysis of the cytoplasmic domain of two BY-kinases, namely CapA1/CapB2 from S. aureus and Wzc from E. coli. We showed that these two proteins associate in a ring-shaped octamer in which the motif EX2RX2R plays a crucial role. In addition, we showed that BY-kinases autophosphorylate using an intermolecular mechanism. We also identified the activation mechanism of BY-kinases and we revealed the role of a particular domain, found specifically in BY-kinases from proteobacteria, in Wzc autophosphorylation and colanic acid biosynthesis.Structural and functional characterization of BY-kinases represents an original and promising approach in order to develop new molecules inhibiting specifically these enzymes and to affect the virulence of bacterial pathogens.