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.
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.
Organisations
- University of Surrey, United Kingdom (Lead Research Organisation)
- University of California, Berkeley (Collaboration)
- The Global Alliance for TB Drug Development (Collaboration)
- University of Birmingham, United Kingdom (Collaboration)
- King's College London, United Kingdom (Collaboration)
- Indian Institute of Science Bangalore, India (Collaboration)
Publications

Basu P
(2018)
The anaplerotic node is essential for the intracellular survival of Mycobacterium tuberculosis.
in The Journal of biological chemistry


Borah K
(2019)
Intracellular Mycobacterium tuberculosis Exploits Multiple Host Nitrogen Sources during Growth in Human Macrophages.
in Cell reports

Borah K
(2021)
Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis.
in Molecular systems biology

Burley KH
(2021)
Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target.
in ACS infectious diseases

López-Agudelo VA
(2022)
Dual RNA Sequencing of Mycobacterium tuberculosis-Infected Human Splenic Macrophages Reveals a Strain-Dependent Host-Pathogen Response to Infection.
in International journal of molecular sciences

López-Agudelo VA
(2020)
A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks.
in PLoS computational biology

Mackenzie JS
(2020)
Bedaquiline reprograms central metabolism to reveal glycolytic vulnerability in Mycobacterium tuberculosis.
in Nature communications
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 | 04/2020 |
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 | Article and workshop for schools on scientific careers |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Dany was recently featured in an article and activity sheet aimed at inspiring the next generation of scientists, engineers and researchers (https://futurumcareers.com/five-researchers-working-on-lifelong-health-in-very-different-ways). |
Year(s) Of Engagement Activity | 2020 |
URL | https://futurumcareers.com/five-researchers-working-on-lifelong-health-in-very-different-ways |
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 |