Extending biochemical databases by metabolomic surveys

Abstract

Metabolomics can map the large metabolic diversity in species, organs, or cell types. In addition to gains in enzyme specificity, many enzymes have retained substrate and reaction promiscuity. Enzyme promiscuity and the large number of enzymes with unknown enzyme function may explain the presence of a plethora of unidentified compounds in metabolomic studies. Cataloguing the identity and differential abundance of all detectable metabolites in metabolomic repositories may detail which compounds and pathways contribute to vital biological functions. The current status in metabolic databases is reviewed concomitant with tools to map and visualize the metabolome.

FIGURE 1.

Metabolome diversity observed by MS. Shown are the results from cold injection GC/TOF MS of human ileal effluent (70). Upper panel, total ion chromatogram for a 10-s retention time window out of a 20-min chromatogram. Lower panel, extracted ion chromatogram for the same 10-s retention time window. As each ion trace can be deconvoluted into individual peaks with resolved mass spectra, many co-eluting compounds can be separated and identified. Novel compounds of unknown structure are detected along with known “primary” metabolites. Compound 1, unknown; compound 2, unknown; compound 3, serine; compound 4, unknown; compound 5, benzoic acid; compound 6, unknown; compound 7, glycerol; compound 8, ethanolamine; compound 9, phosphate; compound 10, isoleucine.

FIGURE 2.

Enzyme evolution toward higher specificity, retaining some substrate and reaction ambiguity. Shown is a schematic diagram of the origin of metabolome diversity between species and within species (adapted from Ref. 1). Given the currently accepted model of enzyme evolution by gene duplication and subsequent specialization, a generalist progenitor enzyme may have performed catalytic reactions (a and b) on substrates (A, B, and C). The phylogenetic tree for this enzyme may have led to isoenzymes that accept only substrate B for reaction a, whereas others retained some level of substrate and reaction ambiguity, leading to higher metabolome diversity (e.g. adding reaction a to substrate C or accepting the novel substrate D for reactions a and b).

FIGURE 3.

Mapping metabolome regulation on biochemical networks. Shown is the regulation of the human ileal effluent metabolome after versus before ileostomy surgery (70), magnified for the carbohydrate cluster. Identified metabolites are mapped to the biochemical KEGG RPAIR Database and chemical similarity (green edges, dashed if <600 similarity), spanning a network displayed in Cytoscape. Unknown metabolites (BinBase Metabolome Database numbers (48)) are added by mass spectral similarity (red edges, dashed if <600 similarity). Red node metabolites are significantly increased in concentration (p < 0.05), blue nodes mark decreased compounds, and yellow nodes (small print) are not regulated. Node size indicates magnitude of change.