Research Article

Metabolomics and mass spectrometry imaging reveal channeled de novo purine synthesis in cells

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Science  17 Apr 2020:
Vol. 368, Issue 6488, pp. 283-290
DOI: 10.1126/science.aaz6465

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Signs of a metabolon in action

Eukaryotic cells have a heterogeneous cytoplasm, with compartments large and small, membrane bound or not. Enzymes that catalyze the de novo synthesis of purine nucleotides, which are needed in rapidly dividing cells, are known to assemble into loosely associated, multienzyme structures called purinosomes, but the extent to which these structures are metabolically active has been less certain. Pareek et al. performed metabolomics to trace how purines are synthesized within purinosomes and used sophisticated mass spectrometry imaging to directly observe hotspots of metabolic activity within frozen HeLa cells (see the Perspective by Alexandrov). They found evidence for metabolic channeling between enzymes, which limits equilibration of intermediates formed in purinosomes with the bulk cellular metabolite pool. This process occurs specifically within purinosomes associated with mitochondria, because the input metabolites, glycine, aspartate, and formate, come from mitochondrial metabolism. Such channeling may help cells control the ratio and abundance of purine nucleotides.

Science, this issue p. 283; see also p. 241

Abstract

Metabolons, multiprotein complexes consisting of sequential enzymes of a metabolic pathway, are proposed to be biosynthetic “hotspots” within the cell. However, experimental demonstration of their presence and functions has remained challenging. We used metabolomics and in situ three-dimensional submicrometer chemical imaging of single cells by gas cluster ion beam secondary ion mass spectrometry (GCIB-SIMS) to directly visualize de novo purine biosynthesis by a multienzyme complex, the purinosome. We found that purinosomes comprise nine enzymes that act synergistically, channeling the pathway intermediates to synthesize purine nucleotides, increasing the pathway flux, and influencing the adenosine monophosphate/guanosine monophosphate ratio. Our work also highlights the application of high-resolution GCIB-SIMS for multiplexed biomolecular analysis at the level of single cells.

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