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Cell. 2017 Jan 26;168(3):517-526.e18. doi: 10.1016/j.cell.2016.12.021. Epub 2017 Jan 19.

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.

Author information

  • 1Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
  • 2Department of Biological Engineering and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02115, USA.
  • 3Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
  • 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92307, USA.
  • 5Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
  • 6Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
  • 7Integrative Program in Quantitative Biology, Gladstone Institutes, and Division of Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA.
  • 8Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: fischbach@fischbachgroup.org.

Abstract

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 National Institutes of Health Human Microbiome Project (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, synthetic biology, 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.

KEYWORDS:

biosynthetic gene cluster; metagenomics; microbiome; natural products; peptide aldehyde; protease inhibitor; synthetic biology

PMID:
28111075
PMCID:
PMC5302092
[Available on 2018-01-26]
DOI:
10.1016/j.cell.2016.12.021
[PubMed - in process]
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