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AIG1 and ADTRP are atypical integral membrane hydrolases that degrade bioactive FAHFAs

Nature Chemical Biology volume 12, pages 367–372 (2016)Cite this article

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Abstract

Enzyme classes may contain outlier members that share mechanistic, but not sequence or structural, relatedness with more common representatives. The functional annotation of such exceptional proteins can be challenging. Here, we use activity-based profiling to discover that the poorly characterized multipass transmembrane proteins AIG1 and ADTRP are atypical hydrolytic enzymes that depend on conserved threonine and histidine residues for catalysis. Both AIG1 and ADTRP hydrolyze bioactive fatty acid esters of hydroxy fatty acids (FAHFAs) but not other major classes of lipids. We identify multiple cell-active, covalent inhibitors of AIG1 and show that these agents block FAHFA hydrolysis in mammalian cells. These results indicate that AIG1 and ADTRP are founding members of an evolutionarily conserved class of transmembrane threonine hydrolases involved in bioactive lipid metabolism. More generally, our findings demonstrate how chemical proteomics can excavate potential cases of convergent or parallel protein evolution that defy conventional sequence- and structure-based predictions.

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Figure 1: Discovery and characterization of AIG1 and ADTRP as FP-reactive proteins in the human proteome.
Figure 2: Identification of Thr and His residues critical for FP labeling of AIG1 and ADTRP.
Figure 3: AIG1 and ADTRP are FAHFA hydrolases.
Figure 4: Discovery of inhibitors and structurally related inactive control compounds for AIG1.
Figure 5: AIG1 inhibitors block FAHFA hydrolysis in mammalian cells.

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Acknowledgements

We are grateful to K. Masuda and L. Bar-Peled for discussions on and assistance with cloning; M. Dix, J. Wu and K. Lum for discussions and technical expertise in designing and analyzing proteomics experiments; J. Teijaro for providing T cells; G. Simon for assistance with the HHpred analysis; and C. Walsh and M. Niphakis for numerous helpful discussions. This work was supported by the US National Institutes of Health (DA033760, DK909810), The Leona M. and Harry B. Helmsley Charitable Trust (grant no. 2012-PG-MED002 to A.S.), National Cancer Institute Cancer Center Support grant P30 (CA014195 MASS core, A.S.), Dr. Frederick Paulsen Chair/Ferring Pharmaceuticals (A.S.), a Hewitt Foundation for Medical Research Fellowship (to W.H.P.), a Chapman Charitable Trust Fellowship (to M.J.K.), UCSD Medical Scientist Training Program funding (T32 GM007198 to M.J.K.) and an Irving S. Sigal postdoctoral fellowship from the American Chemical Society (to S.S.K.).

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Author notes

  1. William H Parsons and Matthew J Kolar: These authors contributed equally to this work.

  2. Enrique Saez, Barbara B Kahn, Alan Saghatelian and Benjamin F Cravatt: These authors jointly supervised this work.

Authors and Affiliations

  1. Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA

    William H Parsons, Siddhesh S Kamat, Armand B Cognetta III, Jonathan J Hulce, Enrique Saez & Benjamin F Cravatt

  2. Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California, USA

    Matthew J Kolar & Alan Saghatelian

  3. Division of Endocrinology, Department of Medicine, Diabetes & Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA

    Barbara B Kahn

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Contributions

W.H.P., M.J.K., A.S. and B.F.C. conceived the project. W.H.P., M.J.K., S.S.K., A.S. and B.F.C. designed experiments. W.H.P. performed the molecular biology and proteomics experiments. W.H.P., A.B.C., J.J.H. and A.S. synthesized compounds. M.J.K., S.S.K. and W.H.P. performed substrate assays and biochemical experiments. W.H.P., M.J.K., S.S.K., E.S., B.B.K., A.S. and B.F.C. analyzed and interpreted the data. W.H.P. and B.F.C. wrote the paper. M.J.K., S.S.K. and A.S. edited the paper.

Corresponding authors

Correspondence to Alan Saghatelian or Benjamin F Cravatt.

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Competing interests

B.F.C. is a founder and advisor to Abide Therapeutics, a biotechnology company interested in developing serine hydrolase inhibitors and therapeutics.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–18, Supplementary Table 1 and 2 captions, and Supplementary Tables 3 and 4. (PDF 3492 kb)

Supplementary Note

Synthetic Procedures. (PDF 270 kb)

Supplementary Table 1

Complete ABPP-SILAC data sets. (XLSX 5746 kb)

Supplementary Table 2

HHpred search results for AIG1/ADTRP alignment. (XLSX 20 kb)

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Parsons, W., Kolar, M., Kamat, S. et al. AIG1 and ADTRP are atypical integral membrane hydrolases that degrade bioactive FAHFAs. Nat Chem Biol 12, 367–372 (2016). https://doi.org/10.1038/nchembio.2051

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