Targeted interplay between bacterial pathogens and host autophagy

Due to the critical role played by autophagy in pathogen clearance, pathogens have developed diverse strategies to subvert autophagy. Despite previous key findings of bacteria-autophagy interplay, a systems level insight into selective targeting by the host and autophagy modulation by the pathogens is lacking. We predicted potential interactions between human autophagy proteins and effector proteins from 56 pathogenic bacterial species by identifying bacterial proteins predicted to have recognition motifs for selective autophagy receptors p62/NDP52 and LC3. Conversely, using structure-based interaction prediction methods, we identified bacterial effector proteins that could putatively modify core autophagy components. Our analysis revealed that autophagy receptors in general potentially target mostly genus specific proteins, and not those present in multiple genera. We also show that the complementarity between the predicted p62 and NDP52 targets, which has been shown for Salmonella, Listeria and Shigella, could be observed across other pathogens. Using literature evidence, we hypothesize that this complementarity potentially leave the host more susceptible to chronic infections upon the mutation of one of the autophagy receptors. To check any bias caused by our pathogenic protein selection criteria, control analysis using proteins derived from entero-toxigenic and non-toxigenic Bacillus outer membrane vesicles indicated that autophagy targets pathogenic proteins rather than non-pathogenic ones. We also observed a pathogen specific pattern as to which autophagy phase could be modulated by specific genera. We found intriguing examples of bacterial proteins which could modulate autophagy, and in turn capable of being targeted by the autophagy receptors and LC3 as a host defence mechanism. To demonstrate the validity of our predictions, we confirmed experimentally with in vitro Salmonella invasion assays the bi-directional interactions underlying the interplay between a Salmonella protease, YhjJ and autophagy. Our comparative meta-analysis points out key commonalities and differences in how pathogens could affect autophagy and how autophagy potentially recognises these pathogenic effectors

Characterisation of the lipid II-teixobactin interaction by solid state NMR

Antimicrobial resistance is likely to be one of the foremost challenges facing the world this century. With the number of viable antibiotics on the decline and a dearth of new antibiotics approved for use since the 1980s, new solutions are sorely needed. Recently a new antibiotic – teixobactin – was discovered that kills bacteria effectively and without the development of resistance. The target of this drug is lipid II, a bacteria cell wall precursor. Given the attractiveness of both lipid II as a target and teixobactin as a drug, understanding this interaction is a source of promise for driving drug discovery. Presented in this study is a novel method for the synthesis of 1H13C15N lipid II that was used in high resolution NMR studies with fully labelled teixobactin for the first time. These studies were combined with novel 31P NMR experiments and TEM studies to provide restraints for the calculation of a structure for the lipid II-teixobactin complex. It was discovered that the N-terminus of teixobactin may be more involved in directly binding lipid II than previously thought. Interactions with the pentapeptide chain of lipid II are also reported here for the first time, as are dimensions of the aggregates formed by the complex. All of these findings are new insights that are not well accounted for in current models, suggesting that at the very least such models require revision. Further though, the evidence in this study suggests that the most likely conformation of the complex may not be a 1:1 antiparallel tetramer as currently suggested but in fact may favour a 2:1 parallel hexamer