In their natural environments microorganisms exist predominantly in aggregates and biofilms. The ability of bacteria to form aggregates is associated with the biosynthesis of polymers such as polysaccharides. In this study the physical mechanisms underlying bacterial aggregation by extracellular polysaccharides are investigated by utilising the bacterium Sinorhizobium meliloti. S. meliloti biosynthesises an extracellular polysaccharide called succinoglycan, which is well characterised in terms of its structure and biosynthesis. A range of previously constructed succinoglycan biosynthesis mutants were screened for altered aggregation. An S. meliloti exoS mutant (a gain of function mutation that results in a constitutively active two component regulator called ExoS) overproduces succinoglycan and has enhanced aggregation compared to the parent strain, Rm1021. The aggregates settle to the bottom of the culture vessel resulting in loss of turbidity of the cultures and phase separation. Microscopic observation showed that succinoglycan did not appear to be attached to the aggregates, which formed ordered structures of laterally aligned cells. By addition of purified succinoglycan it was found that the critical concentration of polymer required to induce aggregation and phase separation of the cultures decreased with increasing cell concentration. These observations suggest that aggregation of S. meliloti cultures in the presence of succinoglycan is driven by macromolecular crowding, otherwise known as depletion attraction. Depletion attraction can drive the ordered arrangement and aggregation of colloidal particles in the presence of polymers. Aggregation of the particles increases the volume available to the polymers, maximising their entropy and the entropy of the system. Addition of succinoglycan to stationary phase Escherichia coli cultures and polystyrene colloids also resulted in aggregation consistent with depletion attraction. Furthermore alternative polymers such as the bacterial extracellular polysaccharide xanthan produced by Xanthomonas campestris can result in aggregation of bacteria by depletion attraction. Depletion attraction may therefore be a ubiquitous force driving aggregation of crowded dispersions of bacteria and polymers. The second part of the thesis focuses on how depletion driven aggregation can lead to surface-associated biofilm formation. Imaging of the sediment formed by the exoS mutant showed that the structure formed at the base of the culture vessel leads to development of an ordered structure composed of interlinked aggregates. The role of succinoglycan in surface attachment is complex and varies with culture conditions. Depletion attraction may facilitate interaction with a surface but alternative factors may then play a role in anchoring the cells to the surface. Under certain conditions the cells may produce factors which allow binding of the cells to a surface independently of succinoglycan. This study has demonstrated for the first time that an extracellular polysaccharide produced by bacteria can result in aggregation via depletion attraction which may be an under explored mechanism by which aggregation of bacteria can occur.

L'expression des gènes peut être contrôlée à différents niveaux : transcriptionnel post-transcriptionnel, traductionnel et post­-traductionnel. A ce jour la majorité des études se sont concentrées au niveau transcriptionnel, néanmoins l'importance des mécanismes de régulation post-transcriptionnels se fait de plus en plus évidente. Chez les procaryotes cette régulation post-transcriptionnelle est assurée par les ARN régulateurs dont le mécanisme d'action passe par l'interaction directe avec les ARN messagers ou les protéines. Grâce à l'essor des analyses transcriptomiques haut-débit (RNA-seq), l'identification de ces ARN est devenue accessible, en revanche leur caractérisation fonctionnelle demeure toujours un défi. Nous avons identifié de nombreux ARN régulateurs candidats chez Agrobacterium fabrum C58 (anciennement Agrobacterium tumefaciens C58). Cette bactérie commune du sol devient phytopathogène lorsqu'elle porte le plasmide Ti (pour Tumor inducing). Elle est alors responsable de la maladie dite de la galle du collet qui se traduit par la formation de tumeurs chez les plantes. Ces travaux de thèse ont eu pour objectif de caractériser fonctionnellement des ARN régulateurs présent sur le plasmide Ti. Deux candidats ont été étudiés en combinant prédiction de cibles et analyses phénotypiques. Le premier, nommé RNA1111, a été caractérisé tant que régulateur de la virulence. Quant au deuxième, nommé QfsR, nous avons démontré qu'il régulait des gènes responsables du transfert conjugatif du plasmide Ti et de la production du signal de quorum sensing associé, mais également des gènes chromosomiques responsables de la motilité et de la production de succinoglycane. En utilisant un système rapporteur, nous avons également démontré que QfsR agissait via une interaction directe avec les ARN messagers des gènes cibles. QfsR représente le premier exemple d'ARN régulateur plasmidique régulant des cibles chromosomiques. L'existence d'un tel régulateur chez un plasmide présent transitoirement au sein des populations d'Agrobacterium illustre le dialogue entre plasmide et chromosome / Gene expression can be controlled at different levels: transcriptional, post-transcriptional, translational and post-translational. To date, the majority of studies have been concentrated on the transcriptional level, but the importance of post-transcriptional regulation mechanisms is becoming more and more evident. In prokaryotes this post-transcriptional regulation is ensured by regulatory RNAs whose mechanism of action passes through direct interaction with messenger RNAs or proteins. With development of high-throughput transcriptomic analyzes (RNA-seq), the identification of these RNAs has become accessible, but their functional characterization remains challenging. We have identified many candidate regulatory RNAs in Agrobacterium fabrum C58 (formerly Agrobacterium tumefaciens C58). This common bacterium of the soil becomes phytopathogenic when carrying the plasmid Ti (for Tumor inducing). It is then responsible for the so-called grown gall disease which results in the formation of tumors in plants. The objective of this thesis was to characterize functionally regulatory RNAs present on the Ti plasmid. Two candidates were studied by combining target prediction and phenotypic analysis. The first, named RNA1111, was characterized as a regulator of virulence. As for the second, named QfsR, we demonstrated that it regulates genes responsible for the conjugative transfer of the Ti plasmid and the production of the associated quorum sensing signal, as well as chromosomal genes responsible for the motility and succinoglycan production. Using a reporter system, we also demonstrated that QfsR was acting via direct interaction with the messenger RNAs of the target genes. QfsR represents the first example of plasmid regulatory RNA regulating chromosomal targets. The existence of such a regulator in a plasmid transiently present in the populations of Agrobacterium illustrates the dialogue between the plasmid and the chromosome