MATE transport of the E. coli-derived genotoxin colibactin

  • Nature Microbiology 1, Article number: 15009 (2016)
  • doi:10.1038/nmicrobiol.2015.9
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Various forms of cancer have been linked to the carcinogenic activities of microorganisms1,​2,​3. The virulent gene island polyketide synthase (pks) produces the secondary metabolite colibactin, a genotoxic molecule(s) causing double-stranded DNA breaks4 and enhanced colorectal cancer development5,6. Colibactin biosynthesis involves a prodrug resistance strategy where an N-terminal prodrug scaffold (precolibactin) is assembled, transported into the periplasm and cleaved to release the mature product7,​8,​9,​10. Here, we show that ClbM, a multidrug and toxic compound extrusion (MATE) transporter, is a key component involved in colibactin activity and transport. Disruption of clbM attenuated pks+ E. coli-induced DNA damage in vitro and significantly decreased the DNA damage response in gnotobiotic Il10−/− mice. Colonization experiments performed in mice or zebrafish animal models indicate that clbM is not implicated in E. coli niche establishment. The X-ray structure of ClbM shows a structural motif common to the recently described MATE family. The 12-transmembrane ClbM is characterized as a cation-coupled antiporter, and residues important to the cation-binding site are identified. Our data identify ClbM as a precolibactin transporter and provide the first structure of a MATE transporter with a defined and specific biological function.

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This work was supported by funding from R01 DK73338 (C.J.), R01DK47700 (C.J.), R01 GM0865700 (S.D.B.) and by the University of Florida (S.D.B.) and the UF DoM Gatorade Fund (C.J.). The authors thank V. de Crecy-Lagard for discussions.

Author information

Author notes

    • Jarrod J. Mousa
    •  & Ye Yang

    These authors contributed equally to this work.


  1. Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA

    • Jarrod J. Mousa
    • , Rachel C. Newsome
    • , Prabhanshu Tripathi
    •  & Steven D. Bruner
  2. Department of Medicine, University of Florida, Gainesville, Florida 32611, USA

    • Ye Yang
    • , Sarah Tomkovich
    •  & Christian Jobin
  3. INRA, USC 1360, F-31300 Toulouse, France

    • Ayaka Shima
    •  & Eric Oswald
  4. Inserm, UMR1043, F-31300 Toulouse, France

    • Ayaka Shima
    •  & Eric Oswald
  5. CNRS, UMR5282, F-31400 Toulouse, France

    • Ayaka Shima
    •  & Eric Oswald
  6. Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), F-31400 Toulouse, France

    • Ayaka Shima
    •  & Eric Oswald
  7. CHU Toulouse, Hôpital Purpan, Service de bactériologie-Hygiène, F-31059 Toulouse, France

    • Ayaka Shima
    •  & Eric Oswald
  8. Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida 32611, USA

    • Christian Jobin


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C.J., S.D.B. and E.O. conceived the project and designed the experiments. J.J.M., Y.Y., S.D.B. and C.J. wrote the manuscript. J.J.M. purified, crystallized, collected data and solved the structure of ClbM. J.J.M. and R.C.N. performed the ethidium fluorescence assay and LC-MS analysis of compound 1 accumulation. J.J.M., P.T. and Y.Y. performed the ClbM cellular localization experiment. Y.Y. made ΔclbM and ΔacrA in NC101 and performed the in vitro infection and mouse colonization studies. S.T. carried out the zebrafish colonization study. A.S. constructed MGpks+ and MGpks+ mutants and examined minimal inhibitory concentrations of various antibiotics and toxic compounds. Y.Y. performed statistical analyses. J.J.M. and Y.Y. contributed equally to this work.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Steven D. Bruner or Christian Jobin.

Supplementary information

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  1. 1.

    Supplementary Information

    Supplementary Figures 1–9 and Tables 1,2.


  1. 1.

    Supplementary Video 1

    NC101-colonized, fixed 6-d.p.f. zebrafish. Reconstruction from z-stack images; DAPI stained whole mount zebrafish with tdTomato-labelled bacteria.

  2. 2.

    Supplementary Video 2

    ΔclbM-colonized, fixed 6-d.p.f. zebrafish. Reconstruction from z-stack images; DAPI stained whole mount zebrafish with tdTomato-labelled bacteria.