title: Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.
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.
authors.affiliation: Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
authors.forename: Chun-Jun
authors.initials: CJ
authors.lastname: Guo
authors.affiliation: Department of Biological Engineering and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02115, USA.
authors.forename: Fang-Yuan
authors.initials: FY
authors.lastname: Chang
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Wyche
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92307, USA.
authors.forename: Keriann M
authors.initials: KM
authors.lastname: Backus
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Acker
authors.affiliation: Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
authors.forename: Masanori
authors.initials: M
authors.lastname: Funabashi
authors.affiliation: Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
authors.forename: Mao
authors.initials: M
authors.lastname: Taketani
authors.affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Mohamed S
authors.initials: MS
authors.lastname: Donia
authors.affiliation: Integrative Program in Quantitative Biology, Gladstone Institutes, and Division of Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Nayfach
authors.affiliation: Integrative Program in Quantitative Biology, Gladstone Institutes, and Division of Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Katherine S
authors.initials: KS
authors.lastname: Pollard
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
authors.forename: Charles S
authors.initials: CS
authors.lastname: Craik
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92307, USA.
authors.forename: Benjamin F
authors.initials: BF
authors.lastname: Cravatt
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Jon
authors.initials: J
authors.lastname: Clardy
authors.affiliation: Department of Biological Engineering and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02115, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Voigt
authors.affiliation: Department 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.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Fischbach
mesh_terms: D000818:Animals; D001412:Bacillus subtilis / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D006801:Humans; D064307:Microbiota; D010453:Peptide Synthases / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D011719:Pyrazines / Q000378:metabolism*
chemical_list: D011719:Pyrazines; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase
keywords: biosynthetic gene cluster; metagenomics; microbiome; natural products; peptide aldehyde; protease inhibitor; synthetic biology