Dr Dany Beste


Senior Lecturer in Microbial Metabolism
Bsc (Hons) FIBMS MSc PhD
+44 (0)1483 686785
02 AX 01

About

University roles and responsibilities

  • Programme Leader for MSc Medical Microbiology

    Affiliations and memberships

    Acid Fast Club
    Committee Member
    Society of Microbiology
    Chair Elect of the Prokaryotic Division

    Research

    Research interests

    Indicators of esteem

    • BBSRC Pool of Experts  (Panel B, D and sLOLA)

    • Senior Editor of Microbiology

    • Member of UKRI Talent Peer Review College (PRC)

    Supervision

    Postgraduate research supervision

    Postgraduate research supervision

    Teaching

    Publications

    Highlights

    Khushboo Borah, Tom A Mendum, Nathaniel D Hawkins, Jane L Ward, Michael H Beale, Gerald Larrouy‐Maumus, Apoorva Bhatt, Martine Moulin, Michael Haertlein, Gernot Strohmeier, Harald Pichler, V Trevor Forsyth, Stephan Noack, Celia W Goulding, Johnjoe McFadden, DANY BESTE, Dany J V Beste (2021) Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis, In: Molecular systems biology17(5)e10280 Wiley Open Access

    DOI: 10.15252/msb.202110280

    View abstract

    Khushboo Borah Slater, Martin Beyß, Ye Xu, Jim Barber, Catia Costa, Jane Newcombe, Melanie J Bailey, Axel Theorell, Johnjoe McFadden, Dany Beste, Dany J V Beste, Katharina Nöh (2023)One-shot 13C15N-metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux, In: Molecular Systems Biologye11099 EMBO Press

    Metabolic flux is the final output of cellular regulation and has been extensively studied for carbon but much less is known about nitrogen, which is another important building block for living organisms. For the tuberculosis pathogen, this is particularly important in informing the development of effective drugs targeting the pathogen's metabolism. Here we performed 13C15N dual isotopic labeling of Mycobacterium bovis BCG steady state cultures, quantified intracellular carbon and nitrogen fluxes and inferred reaction bidirectionalities. This was achieved by model scope extension and refinement, implemented in a multi-atom transition model, within the statistical framework of Bayesian model averaging (BMA). Using BMA-based 13C15N-metabolic flux analysis, we jointly resolve carbon and nitrogen fluxes quantitatively. We provide the first nitrogen flux distributions for amino acid and nucleotide biosynthesis in mycobacteria and establish glutamate as the central node for nitrogen metabolism. We improved resolution of the notoriously elusive anaplerotic node in central carbon metabolism and revealed possible operation modes. Our study provides a powerful and statistically rigorous platform to simultaneously infer carbon and nitrogen metabolism in any biological system.

    Kalistyn H Burley, Bonnie J Cuthbert, Piyali Basu, Jane Newcombe, Ervin M Irimpan, Robert Quechol, Ilona P Foik, David L Mobley, Dany JV Beste, Celia W Goulding (2020)Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target, In: ACS Infectious Diseases7(1)pp. 174-188 American Chemical Society

    Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ contributes to lipid biosynthesis by providing reductants in the form of NAD(P)H. Here, we present the X-ray crystal structure of MEZ to 3.6 Å. We use biochemical assays to demonstrate MEZ is dimeric in solution and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn2+ and NAD(P)+, we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually flexible, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that dimeric MEZ subunits alternate between open and closed states, and that MEZ can stably bind its NAD(P)+ cofactor in multiple conformations, including an inactive, compact NAD+ form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb and not human malic enzyme homologues.

    Khushboo Borah, Tom A Mendum, Nathaniel D Hawkins, Jane L Ward, Michael H Beale, Gerald Larrouy‐Maumus, Apoorva Bhatt, Martine Moulin, Michael Haertlein, Gernot Strohmeier, Harald Pichler, V Trevor Forsyth, Stephan Noack, Celia W Goulding, Johnjoe McFadden, DANY BESTE, Dany J V Beste (2021)Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis, In: Molecular systems biology17(5)e10280 Wiley Open Access

    The co-catabolism of multiple host-derived carbon substrates is required by Mycobacterium tuberculosis (Mtb) to successfully sustain a tuberculosis infection. However, the metabolic plasticity of this pathogen and the complexity of the metabolic networks present a major obstacle in identifying those nodes most amenable to therapeutic interventions. It is therefore critical that we define the metabolic phenotypes of Mtb in different conditions. We applied metabolic flux analysis using stable isotopes and lipid fingerprinting to investigate the metabolic network of Mtb growing slowly in our steady-state chemostat system. We demonstrate that Mtb efficiently co-metabolises either cholesterol or glycerol, in combination with two-carbon generating substrates without any compartmentalisation of metabolism. We discovered that partitioning of flux between the TCA cycle and the glyoxylate shunt combined with a reversible methyl citrate cycle is the critical metabolic nodes which underlie the nutritional flexibility of Mtb. These findings provide novel insights into the metabolic architecture that affords adaptability of bacteria to divergent carbon substrates and expand our fundamental knowledge about the methyl citrate cycle and the glyoxylate shunt.

    Jared S Mackenzie, Dirk A Lamprecht, Rukaya Asmal, John H Adamson, Khushboo Borah, Dany J V Beste, Bei Shi Lee, Kevin Pethe, Simon Rousseau, Inna Krieger, James C Sacchettini, Joel N Glasgow, Adrie J C Steyn (2020)Bedaquiline reprograms central metabolism to reveal glycolytic vulnerability in Mycobacterium tuberculosis, In: Nature communications11(1)pp. 6092-6092

    The approval of bedaquiline (BDQ) for the treatment of tuberculosis has generated substantial interest in inhibiting energy metabolism as a therapeutic paradigm. However, it is not known precisely how BDQ triggers cell death in Mycobacterium tuberculosis (Mtb). Using C isotopomer analysis, we show that BDQ-treated Mtb redirects central carbon metabolism to induce a metabolically vulnerable state susceptible to genetic disruption of glycolysis and gluconeogenesis. Metabolic flux profiles indicate that BDQ-treated Mtb is dependent on glycolysis for ATP production, operates a bifurcated TCA cycle by increasing flux through the glyoxylate shunt, and requires enzymes of the anaplerotic node and methylcitrate cycle. Targeting oxidative phosphorylation (OXPHOS) with BDQ and simultaneously inhibiting substrate level phosphorylation via genetic disruption of glycolysis leads to rapid sterilization. Our findings provide insight into the metabolic mechanism of BDQ-induced cell death and establish a paradigm for the development of combination therapies that target OXPHOS and glycolysis.

    Víctor A. López-Agudelo, Andres Baena, Vianey Barrera , Felipe Cabarcas, Juan F. Alzate, DANY BESTE, Rigoberto Rios-Estepa, Luis F. Barrera (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 sciences23(3)1803 MDPI

    Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), leading to pulmonary and extrapulmonary TB, whereby Mtb is disseminated to many other organs and tissues. Dissemination occurs early during the disease, and bacteria can be found first in the lymph nodes adjacent to the lungs and then later in the extrapulmonary organs, including the spleen. The early global gene expression response of human tissue macrophages and intracellular clinical isolates of Mtb has been poorly studied. Using dual RNA-seq, we have explored the mRNA profiles of two closely related clinical strains of the Latin American and Mediterranean (LAM) family of Mtb in infected human splenic macrophages (hSMs). This work shows that these pathogens mediate a distinct host response despite their genetic similarity. Using a genome-scale host–pathogen metabolic reconstruction to analyze the data further, we highlight that the infecting Mtb strain also determines the metabolic response of both the host and pathogen. Thus, macrophage ontogeny and the genetic-derived program of Mtb direct the host–pathogen interaction.

    MICHELE BROCARD, Jia Lu, BELINDA SUZETTE HALL, KHUSHBOO BORAH, CARLA SOFIA MOLLER-LEVET, Iliana Georgana, Frederic Sorgeloos, DANY BESTE, Ian G Goodfellow, NICOLAS S LOCKER (2021)Murine norovirus infection results in anti-inflammatory response downstream of amino acid depletion in macrophages, In: Journal of Virology American Society for Microbiology

    Murine norovirus (MNV) infection results in a late translation shut-off, that is proposed to contribute to the attenuated and delayed innate immune response observed both in vitro and in vivo. Recently, we further demonstrated the activation of the eIF2α kinase GCN2 during MNV infection, which has been previously linked to immunomodulation and resistance to inflammatory signalling during metabolic stress. While viral infection is usually associated with activation of dsRNA binding pattern recognition receptor PKR, we hypothesised that the establishment of a metabolic stress in infected cells is a proviral event, exploited by MNV to promote replication through weakening the activation of the innate immune response. In this study, we used multi-omics approaches to characterise cellular responses during MNV replication. We demonstrate the activation of pathways related to the integrated stress response, a known driver of anti-inflammatory phenotypes in macrophages. In particular, MNV infection causes an amino acid imbalance that is associated with GCN2 and ATF2 signalling. Importantly, this reprogramming lacks the features of a typical innate immune response, with the ATF/CHOP target GDF15 contributing to the lack of antiviral responses. We propose that MNV-induced metabolic stress supports the establishment of host tolerance to viral replication and propagation.

    Kalistyn H Burley, Bonnie J Cuthbert, Piyali Basu, Jane Newcombe, Ervin M Irimpan, Robert Quechol, Ilona P Foik, David L Mobley, Dany J V Beste, Celia W Goulding (2020)Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target, In: ACS Infectious Diseases7(1)pp. 174-188 American Chemical Society

    Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ contributes to lipid biosynthesis by providing reductants in the form of NAD(P)H. Here, we present the X-ray crystal structure of MEZ to 3.6 Å. We use biochemical assays to demonstrate MEZ is dimeric in solution and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn and NAD(P), we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually flexible, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that dimeric MEZ subunits alternate between open and closed states, and that MEZ can stably bind its NAD(P) cofactor in multiple conformations, including an inactive, compact NAD form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb and not human malic enzyme homologues.

    Víctor A. López-Agudelo, Tom A. Mendum, Emma Laing, Huihai Wu, Andres Baena, Luis F. Barrera, Dany J. V. Beste, Rigoberto Rios-Estepa (2020)A systematic evaluation of mycobacterium tuberculosis genome-scale metabolic networks, In: PLOS Computational Biology16(6)e1007533 Public Library of Science

    Metabolism underpins the pathogenic strategy of the causative agent of TB, Mycobacterium tuberculosis (Mtb), and therefore metabolic pathways have recently re-emerged as attractive drug targets. A powerful approach to study Mtb metabolism as a whole, rather than just individual enzymatic components, is to use a systems biology framework, such as a Genome-Scale Metabolic Network (GSMN) that allows the dynamic interactions of all the components of metabolism to be interrogated together. Several GSMNs networks have been constructed for Mtb and used to study the complex relationship between the Mtb genotype and its phenotype. However, the utility of this approach is hampered by the existence of multiple models, each with varying properties and performances. Here we systematically evaluate eight recently published metabolic models of Mtb-H37Rv to facilitate model choice. The best performing models, sMtb2018 and iEK1011, were refined and improved for use in future studies by the TB research community.

    DANY BESTE (2022)New perspectives on an ancient pathogen: thoughts for World Tuberculosis Day 2022, In: Microbiology (Society for General Microbiology)168(3) Microbiology Society
    Laura Sandra Lello, Koen Bartholomeeusen, Sainan Wang, Sandra Coppens, Rennos Fragkoudis, Luke Alphey, Kevin K. Arien, Andres Merits, Age Utt, Dany Beste (2021)nsP4 Is a Major Determinant of Alphavirus Replicase Activity and Template Selectivity, In: Journal of virology95(20)00355 Amer Soc Microbiology

    Alphaviruses have positive-strand RNA genomes containing two open reading frames (ORFs). The first ORF encodes the nonstructural (ns) polyproteins P123 and P1234 that act as precursors for the subunits of the viral RNA replicase (nsP1 to nsP4). Processing of P1234 leads to the formation of a negative-strand replicase consisting of nsP4 (RNA polymerase) and P123 components. Subsequent processing of P123 results in a positive-strand replicase. The second ORF encoding the structural proteins is expressed via the synthesis of a subgenomic RNA. Alphavirus replicase is capable of using template RNAs that contain essential cis-active sequences. Here, we demonstrate that the replicases of nine alphaviruses, expressed in the form of separate P123 and nsP4 components, are active. Their activity depends on the abundance of nsP4. The match of nsP4 to its template strongly influences efficient subgenomic RNA synthesis. nsP4 of Barmah Forest virus (BFV) formed a functional replicase only with matching P123, while nsP4s of other alphaviruses were compatible also with several heterologous P123s. The P123 components of Venezuelan equine encephalitis virus and Sindbis virus (SINV) required matching nsP4s, while P123 of other viruses could form active replicases with different nsP4s. Chimeras of Semliki Forest virus, harboring the nsP4 of chikungunya virus, Ross River virus, BFV, or SINV were viable. In contrast, chimeras of SINV, harboring an nsP4 from different alphaviruses, exhibited a temperature-sensitive phenotype. These findings highlight the possibility for formation of new alphaviruses via recombination events and provide a novel approach for the development of attenuated chimeric viruses for vaccination strategies. IMPORTANCE A key element of every virus with an RNA genome is the RNA replicase. Understanding the principles of RNA replicase formation and functioning is therefore crucial for understanding and responding to the emergence of new viruses. Reconstruction of the replicases of nine alphaviruses from nsP4 and P123 polyproteins revealed that the nsP4 of the majority of alphaviruses, including the mosquito-specific Eilat virus, could form a functional replicase with P123 originating from a different virus, and the corresponding chimeric viruses were replication-competent. nsP4 also had an evident role in determining the template RNA preference and the efficiency of RNA synthesis. The revealed broad picture of the compatibility of the replicase components of alphaviruses is important for understanding the formation and functioning of the alphavirus RNA replicase and highlights the possibilities for recombination between different alphavirus species.

    Holly-May Lewis, Priyanka Gupta, Kyle DG Saunders, Shazneil Briones, Johanna Von Gerichten, Paul A Townsend, Eirini Velliou, Dany Beste, Olivier Cexus, Roger Paul Webb, Melanie Jane Bailey (2023)Nanocapillary sampling coupled to liquid chromatography mass spectrometry delivers single cell drug measurement and lipid fingerprints, In: Analyst148(5)pp. 1041-1049 Royal Society of Chemistry

    This work describes the development of a new approach to measure drug levels and lipid fingerprints in single living mammalian cells. Nanocapillary sampling is an approach that enables the selection and isolation of single living cells under microscope observation. Here, live single cell nanocapillary sampling is coupled to liquid chromatography for the first time. This allows molecular species to be separated prior to ionisation and improves measurement precision of drug analytes. The efficiency of transferring analytes from the sampling capillary into a vial was optimised in this work. The analysis was carried out using standard flow liquid chromatography coupled to widely available mass spectrometry instrumentation, highlighting opportunities for widespread adoption. The method was applied to 30 living cells, revealing cell-to-cell heterogeneity in the uptake of different antibiotics. Using this system, we detected 14-158 lipid features per single cell, revealing the association between bedaquiline uptake and lipid fingerprints.

    DJV Beste, J McFadden (2010)System-level strategies for studying the metabolism of Mycobacterium tuberculosis, In: Molecular Biosystems6(12)pp. 2363-2372 Royal Society of Chemistry

    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 M. tuberculosis’s metabolism and pathogenesis have renewed interest in this area of research. Previous experimental studies were limited to the analysis of individual genes or enzymes whereas recent advances in computational systems biology and high throughput experimental technologies now allow metabolism to be studied on a genome scale. Here we discuss the progress being made in applying system level approaches to studying the metabolism of this important pathogen. The information from these studies will fundamentally change our approach to tuberculosis research and lead to new targets for therapeutic drugs and vaccines.

    DJV Beste, J Peters, T Hooper, CA Avignone Rossa, ME Bushell, JJ McFadden (2005)Compiling a molecular inventory for Mycobacterium bovis BCG at two growth rates: Evidence for growth rate-mediated regulation of ribosome biosynthesis and lipid metabolism, In: Journal of Bacteriology187(5)pp. 1677-1684 American Society of Microbiology

    An experimental system of Mycobacterium tuberculosis growth in a carbon-limited chemostat has been established by the use of Mycobacterium bovis BCG as a model organism. For this model, carbon-limited chemostats with low concentrations of glycerol were used to simulate possible growth rates during different stages of tuberculosis. A doubling time of 23 h (D 0.03 h 1) was adopted to represent cells during the acute phase of infection, whereas a lower dilution rate equivalent to a doubling time of 69 h (D 0.01 h 1) was used to model mycobacterial persistence. This chemostat model allowed the specific response of the mycobacterial cell to carbon limitation at different growth rates to be elucidated. The macromolecular (RNA, DNA, carbohydrate, and lipid) and elemental (C, H, and N) compositions of the biomass were determined for steady-state cultures, revealing that carbohydrates and lipids comprised more than half of the dry mass of the BCG cell, with only a quarter of the dry weight consisting of protein and RNA. Consistent with studies of other bacteria, the specific growth rate impacts on the macromolecular content of BCG and the proportions of lipid, RNA, and protein increased significantly with the growth rate. The correlation of RNA content with the growth rate indicates that ribosome production in carbon-limited M. bovis BCG cells is subject to growth rate-dependent control. The results also clearly show that the proportion of lipids in the mycobacterial cell is very sensitive to changes in the growth rate, probably reflecting changes in the amounts of storage lipids. Finally, this study demonstrates the utility of the chemostat model of mycobacterial growth for functional genomic, physiology, and systems biology studies.

    DJV Beste, E Laing, B Bonde, C Avignone-Rossa, ME Bushell, JJ McFadden (2007)Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage, In: J BACTERIOL189(11)pp. 3969-3976 AMER SOC MICROBIOLOGY
    N Fotopoulou, PT Tassios, DV Beste, S Ioannidou, A Efstratiou, ER Lawrence, J Papaparaskevas, RC George, NJ Legakis (2003)A common clone of erythromycin-resistant Streptococcus pneumoniae in Greece and the UK, In: CLINICAL MICROBIOLOGY AND INFECTION9(9)pp. 924-929
    C Bakatselou, D Beste, AO Kadri, S Somanath, CG Clark (2003)Analysis of genes of mitochondrial origin in the genus Entamoeba, In: JOURNAL OF EUKARYOTIC MICROBIOLOGY50(3)pp. 210-214 SOC PROTOZOOLOGISTS
    BK Bonde, DJV Beste, E Laing, AM Kierzek, J McFadden (2011)Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis, In: PLOS COMPUTATIONAL BIOLOGY7(6)ARTN epp. ?-? PUBLIC LIBRARY SCIENCE
    DJV Beste, J McFadden (2010)Systems biology of the metabolism of Mycobacterium tuberculosis, In: Biochemical Society Transactions38(5)pp. 1286-1289 PORTLAND PRESS LTD

    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 metabolism of M. tuberculosis and pathogenesis has renewed interest in this area of research. Previous experimental studies were limited to the analysis of individual genes or enzymes, whereas recent advances in computational systems biology and high-throughput experimental technologies now allows metabolism to be studied on a genome scale. In the present article, we discuss the progress being made in applying system-level approaches to study the metabolism of this important pathogen.

    DJ Beste, M Espasa, B Bonde, AM Kierzek, GR Stewart, J McFadden (2009)The genetic requirements for fast and slow growth in mycobacteria., In: PLoS One4(4)e5349 PLoS

    Mycobacterium tuberculosis infects a third of the world's population. Primary tuberculosis involving active fast bacterial replication is often followed by asymptomatic latent tuberculosis, which is characterised by slow or non-replicating bacteria. Reactivation of the latent infection involving a switch back to active bacterial replication can lead to post-primary transmissible tuberculosis. Mycobacterial mechanisms involved in slow growth or switching growth rate provide rational targets for the development of new drugs against persistent mycobacterial infection. Using chemostat culture to control growth rate, we screened a transposon mutant library by Transposon site hybridization (TraSH) selection to define the genetic requirements for slow and fast growth of Mycobacterium bovis (BCG) and for the requirements of switching growth rate. We identified 84 genes that are exclusively required for slow growth (69 hours doubling time) and 256 genes required for switching from slow to fast growth. To validate these findings we performed experiments using individual M. tuberculosis and M. bovis BCG knock out mutants. We have demonstrated that growth rate control is a carefully orchestrated process which requires a distinct set of genes encoding several virulence determinants, gene regulators, and metabolic enzymes. The mce1 locus appears to be a component of the switch to slow growth rate, which is consistent with the proposed role in virulence of M. tuberculosis. These results suggest novel perspectives for unravelling the mechanisms involved in the switch between acute and persistent TB infections and provide a means to study aspects of this important phenomenon in vitro.

    DJV Beste, T Hooper, G Stewart, B Bonde, C Avignone-Rossa, M Bushell, P Wheeler, S Klamt, AM Kierzek, J McFadden (2007)GSMN-TB: a web-based genome scale network model of Mycobacterium tuberculosis metabolism, In: GENOME BIOLOGY8(5)ARTN rpp. ?-? BIOMED CENTRAL LTD
    DJ Beste, K Nöh, S Niedenführ, TA Mendum, ND Hawkins, JL Ward, MH Beale, W Wiechert, J McFadden (2013)(13)C-Flux Spectral Analysis of Host-Pathogen Metabolism Reveals a Mixed Diet for Intracellular Mycobacterium tuberculosis., In: Chem Biol20(8)pp. 1012-1021 Elsevier

    Whereas intracellular carbon metabolism has emerged as an attractive drug target, the carbon sources of intracellularly replicating pathogens, such as the tuberculosis bacillus Mycobacterium tuberculosis, which causes long-term infections in one-third of the world's population, remain mostly unknown. We used a systems-based approach-(13)C-flux spectral analysis (FSA) complemented with manual analysis-to measure the metabolic interaction between M. tuberculosis and its macrophage host cell. (13)C-FSA analysis of experimental data showed that M. tuberculosis obtains a mixture of amino acids, C1 and C2 substrates from its host cell. We experimentally confirmed that the C1 substrate was derived from CO2. (13)C labeling experiments performed on a phosphoenolpyruvate carboxykinase mutant revealed that intracellular M. tuberculosis has access to glycolytic C3 substrates. These findings provide constraints for developing novel chemotherapeutics.

    Khushboo Borah, Martin Beyß, Axel Theorell, Huihai Wu, Piyali Basu, Tom A. Mendum, Katharina Nӧh, Dany J.V. Beste, Johnjoe McFadden (2019)Intracellular Mycobacterium tuberculosis Exploits Multiple Host Nitrogen Sources during Growth in Human Macrophages, In: Cell Reports29(11)pp. 3580-3591.e4 Elsevier

    Nitrogen metabolism of Mycobacterium tuberculosis(Mtb) is crucial for the survival of this important pathogen in its primary human host cell, the macrophage, but little is known about the source(s) and their assimilation within this intracellular niche. Here, we have developed 15N-flux spectral ratio analysis(15N-FSRA) to explore Mtb’s nitrogen metabolism; we demonstrate that intracellular Mtb has access to multiple amino acids in the macrophage, including glutamate, glutamine, aspartate, alanine, glycine,and valine; and we identify glutamine as the pre-dominant nitrogen donor. Each nitrogen source is uniquely assimilated into specific amino acid pools,indicating compartmentalized metabolism during intracellular growth. We have discovered that serine is not available to intracellular Mtb, and we show that a serine auxotroph is attenuated in macrophages. This work provides a systems-based tool for exploring the nitrogen metabolism of intracellular pathogens and highlights the enzyme phosphoserine transaminase as an attractive target for the development of novel anti-tuberculosis therapies.

    EK Lofthouse, PR Wheeler, DJV Beste, BL Khatri, H Wu, TA Mendum, AM Kierzek, J McFadden (2013)Systems-Based Approaches to Probing Metabolic Variation within the Mycobacterium tuberculosis Complex, In: PLOS ONE8(9)ARTN e7591 PUBLIC LIBRARY SCIENCE
    DJ Beste, B Bonde, N Hawkins, JL Ward, MH Beale, S Noack, K Nöh, NJ Kruger, RG Ratcliffe, J McFadden (2011)¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation., In: PLoS Pathog7(7)pp. e1002091-? PLoS

    Mycobacterium tuberculosis requires the enzyme isocitrate lyase (ICL) for growth and virulence in vivo. The demonstration that M. tuberculosis also requires ICL for survival during nutrient starvation and has a role during steady state growth in a glycerol limited chemostat indicates a function for this enzyme which extends beyond fat metabolism. As isocitrate lyase is a potential drug target elucidating the role of this enzyme is of importance; however, the role of isocitrate lyase has never been investigated at the level of in vivo fluxes. Here we show that deletion of one of the two icl genes impairs the replication of Mycobacterium bovis BCG at slow growth rate in a carbon limited chemostat. In order to further understand the role of isocitrate lyase in the central metabolism of mycobacteria the effect of growth rate on the in vivo fluxes was studied for the first time using ¹³C-metabolic flux analysis (MFA). Tracer experiments were performed with steady state chemostat cultures of BCG or M. tuberculosis supplied with ¹³C labeled glycerol or sodium bicarbonate. Through measurements of the ¹³C isotopomer labeling patterns in protein-derived amino acids and enzymatic activity assays we have identified the activity of a novel pathway for pyruvate dissimilation. We named this the GAS pathway because it utilizes the Glyoxylate shunt and Anapleurotic reactions for oxidation of pyruvate, and Succinyl CoA synthetase for the generation of succinyl CoA combined with a very low flux through the succinate--oxaloacetate segment of the tricarboxylic acid cycle. We confirm that M. tuberculosis can fix carbon from CO₂ into biomass. As the human host is abundant in CO₂ this finding requires further investigation in vivo as CO₂ fixation may provide a point of vulnerability that could be targeted with novel drugs. This study also provides a platform for further studies into the metabolism of M. tuberculosis using ¹³C-MFA.

    Piyali Basu, Noor Sandhu, Apoorva Bhatt, Albel Singh, Ricardo Balhana, Irene Gobe, Nicola A Crowhurst, Thomas Mendum, Liang Gao, Jane L Ward, Michael H Beale, Johnjoe McFadden, Dany Beste (2018)The anaplerotic node is essential for the intracellular survival of Mycobacterium tuberculosis, In: Journal of Biological Chemistry293(15)pp. 5695-5704 American Society for Biochemistry and Molecular Biology

    Enzymes at the phosphoenolpyruvate (PEP)–pyruvate–oxaloacetate or anaplerotic (ANA) node control the metabolic flux to glycolysis, gluconeogenesis, and anaplerosis. Here we used genetic, biochemical, and 13C isotopomer analysis to characterize the role of the enzymes at the ANA node in intracellular survival of the world's most successful bacterial pathogen, Mycobacterium tuberculosis (Mtb). We show that each of the four ANA enzymes, pyruvate carboxylase (PCA), PEP carboxykinase (PCK), malic enzyme (MEZ), and pyruvate phosphate dikinase (PPDK), performs a unique and essential metabolic function during the intracellular survival of Mtb. We show that in addition to PCK, intracellular Mtb requires PPDK as an alternative gateway into gluconeogenesis. Propionate and cholesterol detoxification was also identified as an essential function of PPDK revealing an unexpected role for the ANA node in the metabolism of these physiologically important intracellular substrates and highlighting this enzyme as a tuberculosis (TB)-specific drug target. We show that anaplerotic fixation of CO2 through the ANA node is essential for intracellular survival of Mtb and that Mtb possesses three enzymes (PCA, PCK, and MEZ) capable of fulfilling this function. In addition to providing a back-up role in anaplerosis we show that MEZ also has a role in lipid biosynthesis. MEZ knockout strains have an altered cell wall and were deficient in the initial entry into macrophages. This work reveals that the ANA node is a focal point for controlling the intracellular replication of Mtb, which goes beyond canonical gluconeogenesis and represents a promising target for designing novel anti-TB drugs.

    Khushboo Borah, Karina do Carmo de Vasconcelos Girardi, Thomas A. Mendum, Leticia Miranda Santos Lery, Dany J.V. Beste, Flavio Alves Lara, Maria Cristina Vidal Pessolani, Johnjoe McFadden, Jon P. Boyle (2019)Intracellular Mycobacterium leprae Utilizes Host Glucose as a Carbon Source in Schwann Cells, In: Jon P. Boyle (eds.), mBio10(6) American Society for Microbiology

    New approaches are needed to control leprosy, but understanding of the biology of the causative agent Mycobacterium leprae remains rudimentary, principally because the pathogen cannot be grown in axenic culture. Here, we applied 13C isotopomer analysis to measure carbon metabolism of M. leprae in its primary host cell, the Schwann cell. We compared the results of this analysis with those of a related pathogen, Mycobacterium tuberculosis, growing in its primary host cell, the macrophage. Using 13C isotopomer analysis with glucose as the tracer, we show that whereas M. tuberculosis imports most of its amino acids directly from the host macrophage, M. leprae utilizes host glucose pools as the carbon source to biosynthesize the majority of its amino acids. Our analysis highlights the anaplerotic enzyme phosphoenolpyruvate carboxylase required for this intracellular diet of M. leprae, identifying this enzyme as a potential antileprosy drug target.

    DJV Beste, E Laing, B Bonde, C Avignone-Rossa, ME Bushell, JJ McFadden (2007)Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage, In: JOURNAL OF BACTERIOLOGY189(11)pp. 3969-3976 AMER SOC MICROBIOLOGY
    Kyle David George Saunders, HOLLY-MAY LEWIS, Dany Beste, Olivier Cexus, Melanie Jane Bailey (2023)Spatial single cell metabolomics: Current challenges and future developments, In: Current opinion in chemical biology75102327 Elsevier Ltd

    Single cell metabolomics is a rapidly advancing field of bio-analytical chemistry which aims to observe cellular biology with the greatest detail possible. Mass spectrometry imaging and selective cell sampling (e.g. using nanocapillaries) are two common approaches within the field. Recent achievements such as observation of cell-cell interactions, lipids determining cell states and rapid phenotypic identification demonstrate the efficacy of these approaches and the momentum of the field. However, single cell metabolomics can only continue with the same impetus if the universal challenges to the field are met, such as the lack of strategies for standardisation and quantification, and lack of specificity/sensitivity. Mass spectrometry imaging and selective cell sampling come with unique advantages and challenges which, in many cases are complementary to each other. We propose here that the challenges specific to each approach could be ameliorated with collaboration between the two communities driving these approaches.

    Claire Davison, Dany Beste, Melanie Bailey, Mónica Felipe-Sotelo (2023)Expanding the boundaries of atomic spectroscopy at the single-cell level: critical review of SP-ICP-MS, LIBS and LA-ICP-MS advances for the elemental analysis of tissues and single cells, In: Analytical and bioanalytical chemistry Springer

    Metals have a fundamental role in microbiology, and accurate methods are needed for their identification and quantification. The inability to assess cellular heterogeneity is considered an impediment to the successful treatment of different diseases. Unlike bulk approaches, single-cell analysis allows elemental heterogeneity across genetically identical populations to be related to specific biological events and to the effectiveness of drugs. Single particle-inductively coupled plasma-mass spectrometry (SP-ICP-MS) can analyse single cells in suspension and measure this heterogeneity. Here we explore advances in instrumental design, compare mass analysers and discuss key parameters requiring optimisation. This review has identified that the effect of pre-treatment of cell suspensions and cell fixation approaches require further study and novel validation methods are needed as using bulk measurements is unsatisfactory. SP-ICP-MS has the advantage that a large number of cells can be analysed; however, it does not provide spatial information. Techniques based on laser ablation (LA) enable elemental mapping at the single-cell level, such as laser-induced breakdown spectroscopy (LIBS) and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). The sensitivity of commercial LIBS instruments restricts its use for sub-tissue applications; however, the capacity to analyse endogenous bulk components paired with developments in nano-LIBS technology shows great potential for cellular research. LA-ICP-MS offers high sensitivity for the direct analysis of single cells, but standardisation requires further development. The hyphenation of these trace elemental analysis techniques and their coupling with multi-omic technologies for single-cell analysis have enormous potential in answering fundamental biological questions.

    ER Lawrence, CA Arias, B Duke, D Beste, K Broughton, A Efstratiou, RC George, LMC Hall (2000)Evaluation of serotype prediction by cpsA-cpsB gene polymorphism in Streptococcus pneumoniae, In: JOURNAL OF CLINICAL MICROBIOLOGY38(4)pp. 1319-1323 AMER SOC MICROBIOLOGY
    DJV Beste, J McFadden (2012)System-level Strategies for Studying the Metabolism of Mycobacterium tuberculosis, In: BD Robertson, BW Wren (eds.), Systems Microbiology: Current Topics and Applications(7)

    Brian D. Robertson and Brendan W. Wren

    J McFadden, DJV Beste, AM Kierzek (2012)Systems Biology of Tuberculosis Springer

    The book starts with a general introduction into the relevance of systems biology for understanding tuberculosis.

    DJV Beste, J McFadden (2013)Metabolism of Mycobacterium tuberculosis, In: Systems biology of tuberculosis(4)