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Measuring tuberculosis metabolism noninvasively to understand antibiotic action


Project Description

Background
Tuberculosis is a devastating disease caused by Mycobacterium tuberculosis and is one of the top 10 causes of death worldwide (World Health Organisation; 2016). Current treatments require administering a cocktail of antibiotics over an extended period with unpleasant side-effects; drug resistance threatens to render even these treatments ineffective. The first new drug for several decades is bedaquiline. Remarkably, bedaquiline targets the ATP synthase of tuberculosis, a mechanism of action that has never before been used to inhibit the growth of pathogens. ATP synthase provides the energy currency of the cell, ATP, by phosphorylating ADP. Diverse biochemical reactions are powered by the hydrolysis of ATP, so disrupting the organism’s ability to produce this essential molecule will have a large number of potentially lethal effects.
As bedaquiline has a radically new target we need new methods to measure its effects on the bacterium. This project will use advanced biophysical methods, never applied before to mycobacteria, to measure phosphorylated metabolites and the status of the electron transport chain as they exist in living bacteria without the need to break or disturb the cells. These methods will then be used to measure the response of the mycobacteria when they are challenged by bedaquiline. By understanding the detailed effects bedaquiline has on the cells, we will be able to clarify its mechanism of action in vivo and help develop better drugs in the future.

Objectives
-Culture Mycobacterium smegmatis, a harmless and fast-growing model organism of tuberculosis, and also the biosafe BCG strains of M. tuberculosis in defined growth media and oxygen concentrations to induce specific growth modes that are relevant to pathophysiological scenarios.
-Develop and apply 31P-NMR and in-cell spectroscopy to noninvasively measure key metabolites such as ATP and the energetic status (occupancy) of the electron-transport-chain.
-Measure the response of the mycobacteria to challenge by bedaquiline and other antibiotics to see how energy metabolism is affected by this drug and differentiate between different modes of action: direct inhibition or making the ATP synthase leaky to protons.

Experimental approach
By growing bacteria in a wide-bore NMR machine, it will be possible to use saturation based 31P-NMR to measure phosphorylated metabolites such as ATP and underlying pH. We’ll combine these measurements with in-cell visible-wavelength spectroscopy, which measures the electron-occupancy of the electron transport chain (which powers ATP synthase), to get a view into the metabolism of the mycobacteria that is not clouded by having to disrupt the cells.

Novelty
These biophysical methods are yet to be applied to mycobacteria. Before now, energy metabolism in mycobacteria has been neglected. The approval of bedaquiline, and development of several more drug-candidates targeting energy metabolism, has demonstrated that these processes are important and demand further investigation. This work will address this unmet need for basic knowledge.

Training
The student will be introduced to antibiotics and antimicrobial resistance, which are incredibly important topics for the sustained health of humanity. They will learn about the application of advanced X-nuclei NMR and visible-wavelength in-cell spectroscopic techniques to biological problems. They will be introduced to bacteriological techniques and bacterial physiology. Additional programming training will be provided allowing the student to focus on the signal processing of complex spectra (time and frequency based) from the multimodal spectroscopic techniques used within this project and for kinetic modelling. Increasingly, the interdisciplinary areas of science, for instance between physics and biology, are the most productive and the student will obtain experience in this key area.

All Chemistry research students have access to our innovative Doctoral Training in Chemistry (iDTC): cohort-based training to support the development of scientific, transferable and employability skills: https://www.york.ac.uk/chemistry/postgraduate/idtc/

The Department of Chemistry holds an Athena SWAN Gold Award and is committed to supporting equality and diversity for all staff and students. The Department strives to provide a working environment which allows all staff and students to contribute fully, to flourish, and to excel: https://www.york.ac.uk/chemistry/ed/. This PhD project is available to study full-time or part-time (50%).

This PhD will formally start on 1 October 2020. Induction activities will start on 28 September.

Funding Notes

This studentship is fully funded for 3 years and covers: (i) a tax-free annual stipend at the standard Research Council rate (£15,009 estimated for 2020 entry), (ii) research costs, and (iii) tuition fees at the UK/EU rate. Teaching studentships are available to any student who is eligible to pay tuition fees at the home rate: View Website
Other funding is available to those who are eligible for research council studentships: View Website
Funding may be provided by a Chemistry Teaching Studentship for which you should submit a separate application: View Website

References

Candidate selection process:
• Applicants should submit a PhD application to the University of York by 8 January 2020
• Applicants should submit a Teaching Studentship Application by 8 January 2020: https://www.york.ac.uk/chemistry/postgraduate/research/teachingphd/
• Supervisors may contact candidates either by email, telephone, web-chat or in person
• Supervisors can nominate up to 2 candidates to be interviewed for the project
• The interview panel will shortlist candidates for interview from all those nominated
• Shortlisted candidates will be invited to a panel interview at the University of York in the week commencing 10 February 2020
• The awarding committee will award studentships following the panel interviews
• Candidates will be notified of the outcome of the panel’s decision by email

Related Subjects

How good is research at University of York in Chemistry?

FTE Category A staff submitted: 47.06

Research output data provided by the Research Excellence Framework (REF)

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