Editor's ChoiceMetabolism and Diagnostics

Metabolic Barcode: With or Without You, Genome

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Science Translational Medicine  14 Oct 2009:
Vol. 1, Issue 2, pp. 2ec7
DOI: 10.1126/scitranslmed.3000467

Usually, functional reconstruction of an organism’s metabolic pathways requires its genome sequence. This approach often yields paradoxical results as many database genes have yet to be annotated, or have annotations that remain equivocal, and problems with metabolite identification and quantification still exist. Now, Beloqui et al. demonstrate the broad utility of a new array-based method that can simultaneously generate a metabolic phenotype and an annotation of the relevant proteins from organisms with no sequence data. This method—dubbed a reactome array—has three main components: an inactive fluorescent dye that is conjugated to a substrate-metabolite and bound to a linker that immobilizes the trio on a glass slide. Upon treatment with cell extract, a cellular enzyme binds to the substrate, releasing the dye which then fluoresces, and the linker captures the bound enzyme on the array spot. This was performed with a total of 2483 immobilized metabolites from all metabolic pathways in KEGG, PubMed, and UM-BBD databases. The utility of the resulting reactome was first validated with two different strains of cultured bacteria, whose genomes have already been sequenced and nearly 35% of their reactions annotated in the KEGG database. These specific annotated reactions varied between strains, but the reactome profiles could distinguish compounds that are metabolized by both organisms from those that are not. Further examination of one bacterial strain with this technology revealed new functional assignments for 16% of the captured enzymes that had been previously predicted from genome sequence analysis but not characterized as proteins. This prompted the researchers to evaluate and characterize the metabolic profiles of microorganisms for which there is no sequence information available, from three highly diverse environmental habitats. Remarkably, compared to a control strain, the profiles revealed that, in addition to unique substrates, substrates that were metabolized by all three microorganisms exhibited quantitative differences, reflecting highly sensitive, ecological niche–specific differences. This suggests that application of the rapid, high-throughput reactome array to reconstruct metabolic networks in cells without any prior genomic information is possible, and hints at the promise for utility in cell populations or tissues for diagnostic purposes.

A. Beloqui et al., Reactome array: Forging a link between metabolome and genome. Science326, 252–256 (2009). http://www.sciencemag.org/cgi/content/abstract/326/5950/252

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