Mining bacterial genomes for novel antimicrobials

Thesis

Bacteria have evolved an arsenal of antimicrobial peptides and proteins to compete with each other. Bacteriocins are diffusible toxins released into the environment and differ from contact-dependent inhibitors (CDI) or type six secretions systems (T6SS) which require cell-cell contact. Protein bacteriocins are potent narrow-spectrum toxins with a modular domain organisation, making them ideal candidates for developing future antimicrobials. Though progress is being made to exploit protein bacteriocins, current limitations in our understanding of protein bacteriocin biology limits their possible use as antimicrobials. Firstly, due to high sequence diversity and similarity to other competition systems our understanding of the diversity and prevalence of protein bacteriocins in bacteria is poor. Secondly, high levels of resistance have been reported with tested under lab conditions. Finally, how protein bacteriocins translocate into the cell is poorly understood. The aim of this study is to answer a sequence of questions relating to these central limitations in our knowledge of protein bacteriocins. A bioinformatic pipeline was developed which exploits Hidden Markov Models to unambiguously identify nuclease bacteriocins and revealed a diverse family of proteins present in >2000 strains throughout the Enterobacteriaceae family and Pseudomonas spp. A novel grouping scheme is devised for NBs based on conserved structural organisation. Investigation of non-speci1c colicin resistance mechanism revealed an O-antigen dependent resistance involving density dependent blocking of the receptor proteins in the outer membrane. This resistance mechanism was sensitive to changes in environment and could be overcome by additives. Finally, a conserved motif, the ’DPY’ motif, was identi1ed across the nuclease bacteriocin family and effectors of the T6SS. While the role of the DPY motif is still unclear, it is associated with toxins which cross the inner membrane.

Authors: Sharp, C

• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford