No description available.

No description available.

No description available.

No description available.

No description available.

No description available.

Bacteria communicate with their hosts in part via surface, secreted and transmembrane proteins (collectively the secretome) resulting in probiotic (beneficial) or pathogenic (harmful) outcomes to the host. Therapeutic benefits of probiotic bacteria have been shown previously, but the molecular mechanisms and the health-promoting effector components involved are still being elucidated. Some evidence suggests that probiotic bacteria can competitively adhere to intestinal mucus and displace pathogens. The adherence of probiotic bacteria to human intestinal mucus and cells appears to be mediated, at least in part, by secretome proteins. Secretome proteins-encoding open reading frames can be identified in bacterial genome sequences using bioinformatics. However, functional analysis of the translated secretome is possible only if many secretome proteins are expressed and purified individually. Phage display technology offers a very efficient way to purify and functionally characterise proteins by displaying them on the surface of the bacteriophage. While a phage display system for cloning secretome proteins has been previously reported it is not efficient for enrichment and display of Gram-positive secretome proteins. In this study a new phage display system has been developed and applied in direct selection, identification, expression and purification of Gram-positive Lactobacillus rhamnosus strain HN001 secretome proteins. The new phage display system is based on the requirement of a signal sequence for assembly of sarcosyl-resistant filamentous phage virions. Using this system 89 secretome open reading frames were identified from a library of only 106 clones, performing at least 20-fold more efficiently than the previously reported enrichment method. Seven of the identified secretome proteins are unique for L. rhamnosus HN001. A L. rhamnosus HN001 shot-gun phage display library was also constructed to capture proteins that mediate adhesion or aggregation, initial steps in establishing host-microbe contact or forming multicellular aggregates, both of which may lead to beneficial effects – colonisation of the gastro-intestinal tract and exclusion of pathogens. In search for proteins involved in adhesion, a L. rhamnosus HN001 shot-gun phage display library was screened against the human extracellular matrix component fibronectin commonly used as binding target by bacteria that colonise diverse tissues. This screen selected, instead of a fibronectin-binding protein, a protein that binds to avidin, used to immobilise biotinylated fibronectin. Affinity screening of the shot-gun library for binding to L. rhamnosus HN001 cells identified a secretome protein, Lrh33, as an HN001-cell surface binding protein. This protein contains two bacterial immunoglobulin-like domains type 3. Analysis of phage-displayed nested deletions of Lrh33 determined that the proximal (N-terminal) immunoglobulin-like domain is not sufficient for binding; only the constructs displaying both domains demonstrated binding to HN001. Lrh33 does not have any similarity to previously identified Lactobacillus-binding proteins and no match in the NCBI database (at a cutoff value of > e-13), hence it represents potentially a new type of bacterial auto-aggregation protein.

Pseudomonas fluorescens SBW25 is a gram-negative soil bacterium capable of growing on histidine as the sole source of carbon and nitrogen. Expression of histidine utilization (hut) genes is controlled by the HutC repressor with urocanate, the first intermediate of the histidine degradation pathway, as the direct inducer. Recent genome sequencing of P. fluorescens SBW25 revealed the presence of hutD in the hut locus, which encodes a highly conserved hypothetical protein. Previous genetic analysis showed that hutD is involved in hut regulation, in such a way that it prevents overproduction of the hut enzymes. Deletion of hutD resulted in a slow growth phenotype in minimal medium with histidine as the sole carbon and nitrogen source. While the genetic evidence supporting a role of hutD in hut regulation is strong, nothing is known of the mechanism of HutD action. Here I have cloned and expressed the P. fluorescens SBW25 hutD in E. coli. Purified HutD was subjected to chemical and structural analysis. Analytic size-exclusion chromatography indicated that HutD forms a dimer in the elution buffer. The crystal structure of HutD was solved at 1.80 Å (R = 19.3% and Rfree = 22.3%) by using molecular replacement based on HutD from P. aeruginosa PAO1. P. fluorescens SBW25 HutD has two molecules in an asymmetric unit and each monomer consists of one subdomain and two ß-barrel domains. Comparative structural analysis revealed a conserved binding pocket. The interaction of formate with a highly conserved residue Arg61 via salt-bridges in the pocket suggests HutD binds to small molecules with carboxylic group(s) such as histidine, urocanate or formyl-glutamate. The hypothesis that HutD functions via binding to urocanate, the hut inducer, was tested. Experiments using a thermal shift assay and isothermal titration calorimetry (ITC) analysis suggested that HutD binds to urocanate but not to histidine. However, the signal of HutD-urocanate binding was very weak and detected only at high urocanate concentration (53.23 mM), which is not physiologically relevant. The current data thus does not support the hypothesis of HutD-urocanate binding in vivo. Although the HutD-urocanate binding was not confirmed, this work has laid a solid foundation for further testing of the many alternative hypotheses regarding HutD function.

This thesis attempts to broaden what is known about bacterial symbionts within amoebae by the use of a number of different molecular methods. Initially a number of different amoeba strains were screened for bacterial symbionts by 16S rRNA gene PCR, then the symbionts were identified by comparative sequence analysis and phylogenetic analysis. The amoeba strains containing bacterial symbionts were characterised by cell morphology, 18S rRNA gene sequencing, internal transcribed spacer sequencing and allozyme electrophoresis. Amoebae belonging to the genera Acanthamoeba, Naegleria, Ripidomyxa and Saccamoeba were identified as containing symbionts that belonged to a wide range of different bacterial genera. Relationships between bacterial symbionts and their host amoebae were analysed by the use of transmission electron microscopy and fluorescent in situ hybridisation using symbiont specific probes. Also described are attempts that were made to isolate and grow the bacterial symbionts outside of their host amoebae as well as experiments to try to transfer bacterial symbionts from one amoeba strain to another. Lastly the results from this study are discussed as a whole to put into perspective how they contribute to the body of knowledge of symbionts within protozoa.