MRC National Institute for Medical Research, London
Science for Health
Luiz Pedro de Carvalho group project:
Metabolomics-level physiology studies
Metabolomic studies allow the discovery and simultaneous visualization of entire biochemical pathways. The information gathered by combination of metabolomics and stable isotope tracing is not accessible by genomic, transcriptomic or proteomic means and is, by definition, the representation of all regulatory cascades, and therefore the closest possible readout of phenotype. Using these methodologies we intend to evaluate regulatory, kinetic and topological aspects of M. tuberculosis metabolic networks on a systems biology level.
We are interested in combining stable isotope tracing with metabolomics profiling to probe the changes in metabolic pathways that accompany the life cycle of Mtb. We are particularly interested in finding points of greater fragility, which would represent better targets for drug discovery. This information will be derived from both pool size analysis as well as flux through metabolites and entire metabolic pathways.
Recent application of such techniques has demonstrated that Mtb can simultaneously utilize multiple carbon sources, from fatty acids to sugars, without diauxic growth kinetics (see below), a rare trait in bacteria.
Carbon source-specific variations in Mycobacterium tuberculosis growth, without diauxic behavior
Mtb growth in liquid media containing no carbon source (open circles), 0.2% (g/100 ml) dextrose (green circles), 0.2% acetate (blue circles), 0.2% glycerol (pink circles), 0.1% dextrose + 0.1% acetate (green- and blue-filled squares), 0.1% dextrose + 0.1% glycerol (green- and pink-filled squares), or 0.1% acetate + 0.1% glycerol (blue- and pink-filled squares). Cells were pre-grown on each carbon source or carbon source-mixture for 1 full growth cycle (240 h) or carbon-deprived for the same time and then re-inoculated into fresh media of identical chemical composition at 0.02 OD. Error bars denote the standard deviation of 3 biological replicates from a single experiment.
In addition, Mtb’s metabolism appears to be compartmentalized, e.g. different carbon sources have a pre-defined favorite route (see below), which lead to faster growth and higher biomass.
Metabolic preferences observed in Mycobacterium tuberculosis co-catabolism of multiple carbon sources
Click image to view at full-size
Pathway schematic of glycolysis/gluceoneogenesis, pentose phosphate shunt, and TCA cycle indicating distinct metabolic fates of dextrose (green), acetate (blue) and glycerol (pink) during growth on carbon substrate mixtures of: (left) dextrose and acetate, (middle) dextrose and glycerol, and (right) acetate and glycerol. The color and thickness of the arrows connecting metabolites indicates the predominant pattern of distribution of the corresponding carbon source.
These differences are thought to represent an evolutionary adaptation of an organism that has resided inside human macrophages for thousands of years, and therefore has an ultra-narrow niche to survive at. The phagolysosome from human macrophages is thought to be poor in carbon sources, hypoxic, acidic, flooded by reactive oxygen and nitrogen intermediates and, devoid of other bacteria, which could be competing for nutrients. These differences could be potentially explored for antibiotic discovery, but also can inform directly on how Mtb succeeds in surviving for periods as long as decades inside humans.
de Carvalho group
Recent publications
Research projects
- Functional genomics of mycobacterial enzymes
- Rational antibiotic discovery and systems pharmacology
- Metabolomics-level physiology studies
de Carvalho biography
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