Defining adaptive processes in a model bacterial species by integrating proteomic and metabolomic analytical strategies

The habitats that microbes colonise are diverse. A few key bacterial species, including Pseudomonas aeruginosa, can however transcend their original “boundaries” to colonise new niches. The driving forces that enable a microbe to leave its normal habitat and colonise a new site are not currently known. In this study, we will test the hypothesis that the phenotypic plasticity for adaptive processes that enable a microbe to colonise a new site is driven by key regulators and signalling molecules. This hypothesis will be tested using data derived from cutting edge proteomic and metabolomic technologies. This project represents a collaboration between the Institute of Pharmaceutical Science, King’s College London (KCL) and industrial partners, Applied Surface Technology Ascend UK (ASTA). The student working on this project will be supervised by Ken Bruce and James Mason (both KCL) as well as Haroun Shah and Omar Belgacem (both ASTA).

KCL will carry out the majority of the microbiological and metabolomic analyses. The Institute of Pharmaceutical Science boasts recently refurbished medicinal chemistry and fully equipped microbiology and biophysical laboratories located at Waterloo and at the Guy’s Campus. The NMR metabolomics elements of the proposal will be supported by the King’s Centre for Biomolecular Spectroscopy and The Francis Crick Institute where NMR spectrometers operating at 600 MHz (HRMAS) and 700 MHz (liquid) are used routinely. In terms of esteem in "Pharmacy and Pharmacology", KCL has been ranked fourth in the world (QS World University Rankings, 2016) and the Pharmacy, Nutritional Science and Women’s Health REF submission in Subjects Allied to Medicine was ranked second nationally for power. ASTA UK is a technology-based company that develops and manufactures analytical instruments, and is focused on the development of MALDI-TOF MS (Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry). ASTA has been developing various MALDI-TOF based medical applications including cancer diagnosis and infection. A MALDI-TOF based microorganism identification system was launched by ASTA in 2016 and the company is expanding its use to multiple applications in agriculture, industry and natural environments. Training in analytical processes and data analysis/ bioinformatics will be carried out at both KCL and ASTA.

Plan for year 1- training in microbiology and metabolomics (NMR) at KCL and in MALDI-TOF MS at ASTA. Training in bioinformatics jointly at KCL and ASTA. Experimental work – collection and cultivation of P. aeruginosa strains from diverse habitats. Once a collection of over 50 strains has been established, experimental work will proceed to initial NMR and MS analysis. The student will attend at least one scientific meeting in this first year.

Plan for year 2- Further NMR and MS e.g. including lipid extract optimisation as well as bioinformatics analysis e.g. cluster analysis. The student will present a poster at a scientific meeting.

Plan for year 3- Detailed protein/ lipid analysis. Combining/ integrating data sets e.g. to form a novel proteo-lipidomic typing system. Dendrogram generation based on NMR and MS profiles. Biomarker identification for different lines. We plan that the student will present their work orally at a scientific meeting as generate manuscripts for publication.

Plan for year 4- Detailed analysis of biomarkers using MS/MS. Detailed high resolution MS to detect post-translational modification using Top-down proteomic using strains from different habitats. PhD write up. We anticipate that the student will present his/ her work orally at a scientific meeting and write up work for publications.