Metabolomic profiling reveals novel pathway in M. tuberculosis

26 June 2013

Using metabolomic profiling, NIMR scientists have discovered an enzymatic reaction and a glycerophospholipid catabolic pathway in Mycobacterium tuberculosis. The research is published in Proceedings of the National Academy of Sciences, USA.

Although the determinants of enzyme specificity have been studied for many decades it is still very challenging to assign function de novo to a protein. Therefore the function of most of the enzymes found in nature remains unknown and consequently their role in cell physiology is not clear. Genomics and bioinformatics have had a great impact in cataloguing and analysing enzyme families and motifs but a single amino acid change can drastically alter substrate specificity and thus enzyme function.

Using an unbiased activity-based metabolomic profiling method Luiz Pedro de Carvalho (pictured), in NIMR’s Division of Mycobacterial Research, has shown that Rv1692, a putative nucleotide phosphatase, is in fact a glycerol phosphate phosphatase. Thus, instead of being involved in the salvage of nucleic acids this enzyme is responsible for the generation of free glycerol from glycerol 3-phosphate. Experiments employing a strain of M. tuberculosis lacking Rv1692 corroborate this finding. Unexpectedly, these experiments also uncovered the accumulation of glycerol phosphate-containing lipid polar heads, indicating that Rv1692 is involved at the last step of lipid polar head degradation. Despite decades of study of M. tuberculosis and more than 10 years of the availability of its genome this pathway has not previously been identified. Furthermore, the link between glycerol production and glycerophospholipid catabolism has never been described in any organism. Future experiments will identify when and where this pathway is essential in M. tuberculosis, what role it plays in human tuberculosis, and its potential as a target for novel antibiotics.

Our results show that Rv1692 is involved at the last step of glycerophospholipid polar head catabolism. This catabolic pathway was not predicted or observed before, strengthening the value of unbiased experimental approaches to enzyme function. Notably, glycerol production from glycerophospholipids instead of glycolysis is counterintuitive and will likely help to reveal some interesting aspects of bacterial physiology, and perhaps lead to applications in the fight against human tuberculosis.

Luiz Pedro de Carvalho

Click image to view at full-size

(A) Phylogenetic tree depicting the narrow distribution of Rv1692 homologs and the restriction of mycobacterial species to the bottom part of the tree. Sequences belonging to opportunistic and pathogenic mycobacteria are further clustered in the red group. M. tuberculosis sequence marked by the red arrow.
(B) Ribbon representation of the structure of the monomer of Rv1692, with residues making up the active site shown. Green coloured segment is unique to the homologues of Rv1692, and encodes a fused-domain with structural homology to GNAT proteins.

Original article

    Gérald Larrouy-Maumus, Tapan Biswas, Debbie M. Hunt, Geoff Kelly, Oleg V. Tsodikov and Luiz Pedro Sório de Carvalho (2013)

    Discovery of a glycerol 3-phosphate phosphatase reveals glycerophospholipid polar head recycling in Mycobacterium tuberculosis

    Proceedings of the National Academy of Sciences, USA. Epub ahead of print. Publisher abstract

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