Environmental DNA-encoded antibiotics fasamycins A and B inhibit FabF in type II fatty acid biosynthesis.
In a recent study of polyketide biosynthetic gene clusters cloned directly from soil, we isolated two antibiotics, fasamycins A and B, which showed activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. To identify the target of the fasamycins, mutants with elevated fasamycin A minimum inhibitory concentrations were selected from a wild-type culture of E. faecalis OG1RF. Next-generation sequencing of these mutants, in conjunction with in vitro biochemical assays, showed that the fasamycins inhibit FabF of type II fatty acid biosynthesis (FASII). Candidate gene overexpression studies also showed that fasamycin resistance is conferred by fabF overexpression. On the basis of comparisons with known FASII inhibitors and in silico docking studies, the chloro-gem-dimethyl-anthracenone substructure seen in the fasamycins is predicted to represent a naturally occurring FabF-specific antibiotic pharmacophore. Optimization of this pharmacophore should yield FabF-specific antibiotics with increased potencies and differing spectra of activity. This study demonstrates that culture-independent antibiotic discovery methods have the potential to provide access to novel metabolites with modes of action that differ from those of antibiotics currently in clinical use.
Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.
Zhiyang
Z
Feng
Debjani
D
Chakraborty
Scott B
SB
Dewell
Boojala Vijay B
BV
Reddy
Sean F
SF
Brady
D015099:3-Oxoacyl-(Acyl-Carrier-Protein) Synthase / Q000187:drug effects*; D000900:Anti-Bacterial Agents / Q000737:chemistry*; D001426:Bacterial Proteins / Q000187:drug effects*; D001483:Base Sequence; D001671:Biochemistry / Q000379:methods; D001713:Biphenyl Compounds / Q000138:chemical synthesis*; D002626:Chemistry, Pharmaceutical / Q000379:methods*; D002845:Chromatography / Q000379:methods; D003001:Cloning, Molecular; D004247:DNA / Q000737:chemistry*; D017931:DNA Primers / Q000235:genetics; D013293:Enterococcus faecalis / Q000378:metabolism*; D005227:Fatty Acids / Q000378:metabolism*; D015723:Gene Library; D006801:Humans; D020128:Inhibitory Concentration 50; D008956:Models, Chemical; D008969:Molecular Sequence Data; D005810:Multigene Family; D009154:Mutation; D011084:Polycyclic Aromatic Hydrocarbons / Q000138:chemical synthesis*
D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D001713:Biphenyl Compounds; D017931:DNA Primers; D005227:Fatty Acids; D011084:Polycyclic Aromatic Hydrocarbons; C573598:fasamycin A; C573599:fasamycin B; D004247:DNA; D015099:3-Oxoacyl-(Acyl-Carrier-Protein) Synthase; C490370:FabF protein, Enterococcus faecalis