Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases

Abstract

SUMMARY The gut microbiota modulate host biology in numerous ways, but little is known about the molecular mediators of these interactions. Previously, we found a widely distributed family of nonribosomal peptide synthetase gene clusters in gut bacteria. Here, by expressing a subset of these clusters in Escherichia coli or Bacillus subtilis, we show that they encode pyrazinones and dihydropyrazinones. At least one of the 47 clusters is present in 88% of the NIH HMP stool samples, and they are transcribed under conditions of host colonization. We present evidence that the active form of these molecules is the initially released peptide aldehyde, which bears potent protease inhibitory activity and selectively targets a subset of cathepsins in human cell proteomes. Our findings show that an approach combining bioinformatics and heterologous gene cluster expression can rapidly expand our knowledge of the metabolic potential of the microbiota while avoiding the challenges of cultivating fastidious commensals.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

“…Those studies have also bolstered gene discovery efforts, particularly for biofuel and biotransformation applications and secondary metabolites [49][50][51] . New species, strains and clusters arising from the uncultivated majority are now complemented by our Resource of cultivated microbe genomes.…”

Accessing chemical diversity from the uncultivated symbionts of small marine animals

“…However, only two examples employing this strategy exist, one involving marine animals, 4 and the other the uncultivated human microbiota, 5,6 leaving substantial hurdles to accessing chemical novelty. Collectively, such systems feature hundreds or thousands of biosynthetic pathways to bioactive compounds, only a few of which have been accessed.…”

Gut Microbiota: Small Molecules Modulate Host Cellular Functions

“…Now in a recent paper in Cell, Guo et al [8] attempt to identify the most commonly shared BGC family in the human microbiome by mining the NIH Human Microbiome Project Phase I dataset, a large study profiling the 'healthy' human-gut microbiome in Americans, and then subsequently determining the function of this BGC family [8,9]. This synergistic approach couples computational analysis of large metagenomic datasets, synthetic biology to express genetic elements from uncultured bacteria in laboratory strains, and chemistry to identify and interpret the BGC products.…”

“…Several of these BGCs, derived from Grampositive bacteria, were not only transcribed but also shown to produce unique smallmolecule products in E. coli driven by an E. coli promoter, an encouraging result that shows it is possible to have functioning BGCs even when they're expressed in vastly divergent bacteria [8]. With these 14 BGCs reconstructed in vivo, the next step was to elucidate their cognate small molecule products.…”

“…With these 14 BGCs reconstructed in vivo, the next step was to elucidate their cognate small molecule products. Liquid chromatography-mass spectrometry was used to identify new peaks that show up in the BGC product-7 out of the 14 BGCs produced new peaks that corresponded to 32 unique compounds [8].…”