Defining the metabolic phenotype of intracellular Mycobacterium tuberculosis

Lead Research Organisation: University of Surrey
Department Name: Microbial & Cellular Sciences

Abstract

Tuberculosis (TB) is a disease which plagued ancient Egyptians and is still one of the most significant human diseases thousands of years later. A key to the success of Mycobacterium tuberculosis, the bacterium which causes TB is the ability to survive and grow in white blood cells, the very cells which are equipped to eliminate bacteria from the body. In order to do this M. tuberculosis must be able to acquire nutrients and energy from this isolated niche. Several studies have highlighted that targeting nutrient utilisation as a potentially productive route for drug development yet the nutrients consumed by intracellular M. tuberculosis are currently unknown. The aim of this project is to use labelled nutrient sources to directly measure the metabolism of M. tuberculosis growing in white blood cells. This research will allow us to identify the major energy (carbon) source consumed by M. tuberculosis in the host cell. We will also in parallel investigate the metabolism of M. tuberculosis in defined environmental conditions in the laboratory in order to establish the metabolic pathways used to break down different combinations of nutrients that have been identified as being consumed intracellularly. All of the data will be incorporated into mathematical models of TB in order to generate a reconstruction of the intracellular metabolism of this pathogen. This information will be vitally important for new drug and vaccine development, as well as advancing our knowledge of the pathogenesis of this globally important pathogen.

Technical Summary

Despite decades of research many aspects of the biology of Mycobacterium tuberculosis remain unclear and this is reflected in the antiquated tools available to treat and prevent tuberculosis and consequently this disease remains a serious public health problem. Important discoveries linking the ability to metabolise specific substrates intracellularly within a macrophage to virulence have identified energy metabolism as a theoretically very powerful therapeutic target for tuberculosis. However the identity of the carbon sources and major metabolic pathways used by intracellular M. tuberculosis is poorly defined. The goal of this research is to identify the key carbon substrates and pathways ustilised by M. tuberculosis during intraphagosomal growth. We will perform comprehensive 13C-isotopologue profiling analysis of wild type and mutant strains of this pathogen in order to identify the different carbon sources which are contributing to the intracellular nutrition of M. tuberculosis. In parallel we will investigate the metabolic pathways required for consumption of these carbon sources under defined conditions in vitro using 13C-metabolic flux analysis. We will also perform transcriptomic analysis of intracellular M. tuberculosis in order to indirectly monitor metabolism. All of this data will then be used to constrain genome scale metabolic networks in order to define the metabolic phenotype of intracellular M. tuberculosis.

Planned Impact

Impact summary
Who will benefit?
This research will investigate the intracellular metabolism of one of the most significant human pathogens, M. tuberculosis. Although this research is primarily a basic research project In addition to the academic beneficiaries that are discussed elsewhere this research will also lead to new insights of interest to wider group of beneficiaries:
1. Pharmaceutical industries and charities such as the Global Alliance for TB Drug Development which have an interest in the development of novel anti-tuberculosis drugs.
2. The UK trained workforce will benefit from this proposal through the training of a PDRA who will acquire new skills in systems biology, chemostat cultivation, 13C-metabolic flux analysis and molecular biology from the combined expertise of the applicants.
3. Undergraduate and postgraduate students taught by the applicants
4. As more than one third of the world are estimated to be infected with M. tuberculosis the general public in the UK and the rest of the world could ultimately benefit in terms of new drugs to treat TB

How will they benefit?
1. The market for anti-tuberculous drugs is estimated to be USD 612-670 million annually. In the UK there are several pharmaceutical companies that that have an interest in development of TB drugs, such GSK and AstraZeneka. The metabolic analysis of intracellular pathogens in their host cell is of immense importance in drug design and therefore in the long term this research could help develop the anti-TB drug market in the UK. Within the three years of this research project we will have generated extensive data about the carbon substrates and metabolic pathways required for the intracellular growth of this globally important pathogen. This data can then be exploited by those in industry to guide drug development particularly targeting transporters. By incorporating the data generated during this research into the available genome scale model of M. tuberculosis growing within its host macrophage we will also create a very valuable tool for those working in TB drug development. This new constrained model will be able to test large numbers of multiple target inactivations, which would be otherwise impossible to do by visual examination alone.
2. By developing skills in 13C isotopologue profiling/chemostat/systems biology the PDRA will mature into a highly trained researcher able to pursue a career in academic or industrial research.
3. The knowledge obtained through this project will contribute to fundamental theories and concepts underlying the metabolism of intracellular pathogens. We will impart this knowledge to undergraduate and post graduate students via teaching and research supervision.
4. Studying the metabolism of Mtb directly within its host macrophage has never been performed before and therefore the outcomes of this research will be of interest to the media and public. In the longer term this research could lead to new drugs for treating TB and therefore impacting in the area of public health and societal issues.

Publications

10 25 50
 
Description BBSRC: The role of the anaplerotic node in redox homeostasis and pathogenesis of Mycobacterium tuberculosis and its exploitation as a therapeutic target
Amount £733,630 (GBP)
Funding ID BB/T007648/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2020 
End 05/2023
 
Description Victor
Amount £6,000 (GBP)
Organisation University of Antioquia 
Sector Academic/University
Country Colombia
Start 01/2017 
End 07/2017
 
Title Updated genome scale model of Mycobacterium tuberculosis metabolism 
Description We have systematically analysed the existing genome scale metabolic netwroks of TB and generated two updated models for the TB community 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? Yes  
Impact None as yet 
 
Description Apoova 
Organisation University of Birmingham
Country United Kingdom 
Sector Academic/University 
PI Contribution We have provided Apoova Bhatt with lipid samples from mutant strains of Mycobacterium tuberculosis
Collaborator Contribution Apoorva Bhatt is analysing the lipid differences between wild-type and mutant strains of M. tuberculosis
Impact We have identifeid key differences in the lipid profile which will be incorporatde into a manuscript
Start Year 2016
 
Description Celia Golding at the University of California 
Organisation University of California
Country United States 
Sector Academic/University 
PI Contribution We have supplied Celia with expression constructs in order to crystalise the malic enzyme of Mycobacterium tuberculosis
Collaborator Contribution Celia will be crystalising the protein
Impact Multi-disciplinary
Start Year 2016
 
Description TB Alliance 
Organisation The Global Alliance for TB Drug Development
Country Global 
Sector Private 
PI Contribution We now have a collaborative agreement to provide information about targets in the anaplerotic node and to also provide information on compounds which show anti-TB activity
Collaborator Contribution The TB Alliance are committed to expediting any promising lead compounds which come from this collaborations
Impact None yet
Start Year 2019
 
Description TB drugs 
Organisation King's College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Knowledge exchange with a medicinal chemist
Collaborator Contribution Analysis of TB drug targets
Impact None as yet
Start Year 2018
 
Description redox 
Organisation Indian Institute of Science Bangalore
Country India 
Sector Academic/University 
PI Contribution I have shared mutant strains with the institutes and they are going to test them using their reporters
Collaborator Contribution Scientific experiments
Impact No outputs yet
Start Year 2017
 
Description Newton Bhabha-funded workshop "Challenges of TB: A focus on India" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This was a workshop to potentiate collaborations between scientists and clinicicans working in India and the UK in order to develop networks and future collaborative projects.
Year(s) Of Engagement Activity 2019
 
Description Stand at Superbugs Exhibition at the Science Museum 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A stand on Antimicrobial resistance which had spin the wheel and other interactive games to engage the public in AMR
Year(s) Of Engagement Activity 2018
 
Description Work experience for a student studying for a levels to inform decision about degree selection 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact A student visited my laboratory for one week and performed experiments. She has now applied to do a BSc degree in a Biological Science discipline
Year(s) Of Engagement Activity 2018
 
Description Workshop on AMR in Bangaluru India 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact 50 participants including Dany Beste at PHE/RGICD Newton Bhabha Fund AMR Workshop in Bengaluru (Working at the chemistry/microbiology interface to develop new antibiotics for tackling anti-microbial resistance and resistant TB.)
Year(s) Of Engagement Activity 2017