Dr Dany Beste

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Publications

Journal articles

  • Beste DJ, Nöh K, Niedenführ S, Mendum TA, Hawkins ND, Ward JL, Beale MH, Wiechert W, McFadden J. (2013) '(13)C-Flux Spectral Analysis of Host-Pathogen Metabolism Reveals a Mixed Diet for Intracellular Mycobacterium tuberculosis.'. Elsevier Chem Biol, 20 (8), pp. 1012-1021.
  • Lofthouse EK, Wheeler PR, Beste DJV, Khatri BL, Wu H, Mendum TA, Kierzek AM, McFadden J. (2013) 'Systems-Based Approaches to Probing Metabolic Variation within the Mycobacterium tuberculosis Complex'. PUBLIC LIBRARY SCIENCE PLOS ONE, 8 (9) Article number ARTN e75913
  • Beste DJ, Bonde B, Hawkins N, Ward JL, Beale MH, Noack S, Nöh K, Kruger NJ, Ratcliffe RG, McFadden J. (2011) '¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation.'. PLoS PLoS Pathog, United States: 7 (7)

    Abstract

    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.

  • Bonde BK, Beste DJV, Laing E, Kierzek AM, McFadden J. (2011) 'Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis'. PUBLIC LIBRARY SCIENCE PLOS COMPUTATIONAL BIOLOGY, 7 (6) Article number ARTN e1002060
  • Beste DJV, McFadden J. (2010) 'Systems biology of the metabolism of Mycobacterium tuberculosis'. PORTLAND PRESS LTD BIOCHEMICAL SOCIETY TRANSACTIONS, 38, pp. 1286-1289.
  • Beste DJV, McFadden J. (2010) 'System-level strategies for studying the metabolism of Mycobacterium tuberculosis'. Royal Society of Chemistry Molecular Biosystems, 6 (12), pp. 2363-2372.

    Abstract

    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.

  • Beste DJ, Espasa M, Bonde B, Kierzek AM, Stewart GR, McFadden J. (2009) 'The genetic requirements for fast and slow growth in mycobacteria.'. PLoS PLoS One, United States: 4 (4) Article number e5349 , pp. ---.

    Abstract

    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.

  • Beste DJ, Laing E, Bonde B, Avignone-Rossa C, Bushell ME, McFadden JJ. (2007) 'Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage.'. J Bacteriol, United States: 189 (11), pp. 3969-3976.

    Abstract

    The adaptation of the tubercle bacillus to the host environment is likely to involve a complex set of gene regulatory events and physiological switches in response to environmental signals. In order to deconstruct the physiological state of Mycobacterium tuberculosis in vivo, we used a chemostat model to study a single aspect of the organism's in vivo state, slow growth. Mycobacterium bovis BCG was cultivated at high and low growth rates in a carbon-limited chemostat, and transcriptomic analysis was performed to identify the gene regulation events associated with slow growth. The results demonstrated that slow growth was associated with the induction of expression of several genes of the dormancy survival regulon. There was also a striking overlap between the transcriptomic profile of BCG in the chemostat model and the response of M. tuberculosis to growth in the macrophage, implying that a significant component of the response of the pathogen to the macrophage environment is the response to slow growth in carbon-limited conditions. This demonstrated the importance of adaptation to a low growth rate to the virulence strategy of M. tuberculosis and also the value of the chemostat model for deconstructing components of the in vivo state of this important pathogen.

  • Beste DJV, Hooper T, Stewart G, Bonde B, Avignone-Rossa C, Bushell M, Wheeler P, Klamt S, Kierzek AM, McFadden J. (2007) 'GSMN-TB: a web-based genome scale network model of Mycobacterium tuberculosis metabolism'. BIOMED CENTRAL LTD GENOME BIOLOGY, 8 (5) Article number ARTN r89
  • Beste DJV, Peters J, Hooper T, Avignone Rossa CA, Bushell ME, McFadden JJ. (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'. American Society of Microbiology Journal of Bacteriology, 187 (5), pp. 1677-1684.

    Abstract

    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.

  • Fotopoulou N, Tassios PT, Beste DV, Ioannidou S, Efstratiou A, Lawrence ER, Papaparaskevas J, George RC, Legakis NJ. (2003) 'A common clone of erythromycin-resistant Streptococcus pneumoniae in Greece and the UK.'. Clin Microbiol Infect, France: 9 (9), pp. 924-929.
  • Bakatselou C, Beste D, Kadri AO, Somanath S, Clark CG. (2003) 'Analysis of genes of mitochondrial origin in the genus Entamoeba'. SOC PROTOZOOLOGISTS JOURNAL OF EUKARYOTIC MICROBIOLOGY, 50 (3), pp. 210-214.
  • Lawrence ER, Arias CA, Duke B, Beste D, Broughton K, Efstratiou A, George RC, Hall LMC. (2000) 'Evaluation of serotype prediction by cpsA-cpsB gene polymorphism in Streptococcus pneumoniae'. AMER SOC MICROBIOLOGY JOURNAL OF CLINICAL MICROBIOLOGY, 38 (4), pp. 1319-1323.

Books

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

Book chapters

  • Beste DJV, McFadden J. (2013) 'Metabolism of Mycobacterium tuberculosis'. in (ed.) Systems biology of tuberculosis Article number 4
  • Beste DJV, McFadden J. (2012) 'System-level Strategies for Studying the Metabolism of Mycobacterium tuberculosis'. in Robertson BD, Wren BW (eds.) Systems Microbiology: Current Topics and Applications Article number 7

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