A palmitoyl transferase chemical–genetic system to map ZDHHC-specific S-acylation

Cory A. Ocasio; Marc P. Baggelaar; James Sipthorp; Ana Losada de la Lastra; Manuel Tavares; Jana Volarić; Christelle Soudy; Elisabeth M. Storck; Jack W. Houghton; Susana A. Palma-Duran; James I. MacRae; Goran Tomić; Lotte Carr; Julian Downward; Ulrike S. Eggert; Edward W. Tate

doi:10.1038/s41587-023-02030-0

A palmitoyl transferase chemical–genetic system to map ZDHHC-specific S-acylation

Cory A. Ocasio, Marc P. Baggelaar, James Sipthorp, Ana Losada de la Lastra, Manuel Tavares, Jana Volarić, Christelle Soudy, Elisabeth M. Storck, Jack W. Houghton, Susana A. Palma-Duran, James I. MacRae, Goran Tomić, Lotte Carr, Julian Downward, Ulrike S. Eggert, Edward W. Tate^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

20 Citations (Scopus)

Abstract

The 23 human zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S-acyltransferases catalyze long-chain S-acylation at cysteine residues across an extensive network of hundreds of proteins important for normal physiology or dysregulated in disease. Here we present a technology to directly map the protein substrates of a specific ZDHHC at the whole-proteome level, in intact cells. Structure-guided engineering of paired ZDHHC ‘hole’ mutants and ‘bumped’ chemically tagged fatty acid probes enabled probe transfer to specific protein substrates with excellent selectivity over wild-type ZDHHCs. Chemical–genetic systems were exemplified for five human ZDHHCs (3, 7, 11, 15 and 20) and applied to generate de novo ZDHHC substrate profiles, identifying >300 substrates and S-acylation sites for new functionally diverse proteins across multiple cell lines. We expect that this platform will elucidate S-acylation biology for a wide range of models and organisms.

Original language	English
Pages (from-to)	1548-1558
Number of pages	11
Journal	Nature Biotechnology
Volume	42
Issue number	10
Early online date	8 Jan 2024
DOIs	https://doi.org/10.1038/s41587-023-02030-0
Publication status	Published - Oct 2024

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Ocasio, C. A., Baggelaar, M. P., Sipthorp, J., Losada de la Lastra, A., Tavares, M., Volarić, J., Soudy, C., Storck, E. M., Houghton, J. W., Palma-Duran, S. A., MacRae, J. I., Tomić, G., Carr, L., Downward, J., Eggert, U. S., & Tate, E. W. (2024). A palmitoyl transferase chemical–genetic system to map ZDHHC-specific S-acylation. Nature Biotechnology, 42(10), 1548-1558. https://doi.org/10.1038/s41587-023-02030-0

@article{4b4afae1f357417a95ba707d48386338,

title = "A palmitoyl transferase chemical–genetic system to map ZDHHC-specific S-acylation",

abstract = "The 23 human zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S-acyltransferases catalyze long-chain S-acylation at cysteine residues across an extensive network of hundreds of proteins important for normal physiology or dysregulated in disease. Here we present a technology to directly map the protein substrates of a specific ZDHHC at the whole-proteome level, in intact cells. Structure-guided engineering of paired ZDHHC {\textquoteleft}hole{\textquoteright} mutants and {\textquoteleft}bumped{\textquoteright} chemically tagged fatty acid probes enabled probe transfer to specific protein substrates with excellent selectivity over wild-type ZDHHCs. Chemical–genetic systems were exemplified for five human ZDHHCs (3, 7, 11, 15 and 20) and applied to generate de novo ZDHHC substrate profiles, identifying >300 substrates and S-acylation sites for new functionally diverse proteins across multiple cell lines. We expect that this platform will elucidate S-acylation biology for a wide range of models and organisms.",

author = "Ocasio, {Cory A.} and Baggelaar, {Marc P.} and James Sipthorp and {Losada de la Lastra}, Ana and Manuel Tavares and Jana Volari{\'c} and Christelle Soudy and Storck, {Elisabeth M.} and Houghton, {Jack W.} and Palma-Duran, {Susana A.} and MacRae, {James I.} and Goran Tomi{\'c} and Lotte Carr and Julian Downward and Eggert, {Ulrike S.} and Tate, {Edward W.}",

note = "Funding Information: We would like to thank B. Martin (Scorpion Therapeutics) and D. Sharp (Imperial College London) for engaging in discussions on ZDHHC chemical genetics and Y. Ohno and A. Kihara from Hokkaido University for sharing their complete set of human N-terminal FLAG-tagged ZDHHC constructs. We would also like to thank E. Thinon (Institut Europ{\'e}en de Chimie et Biologie, France) and H. Bakker (Hannover Medical School, Germany) for generously gifting Ifitm3, and VAMP3 and XXYLT1 plasmids, respectively. We thank B. Snijders, S. Howell, V. Encheva and J. Kirkpatrick (Francis Crick Institute) for their assistance and sharing of knowledge regarding LC–MS/MS as well as the Cell Services, Metabolomics, Light Microscopy and the Flow Cytometry Science Technology Platforms at the Francis Crick Institute for their support and sharing of knowledge. Schematic figures were generated using BioRender.com . Funding sources included the following: the CRUK/EPSRC Multidisciplinary Award to E.W.T. and J.D. (C29637/A27506 and NS/A000078/1); CRUK Programme Foundation Award to E.W.T. (C29637/A20183); CRUK Programme Award to E.W.T. (DRCNPG-Nov21/100001), with support from the Engineering and Physical Sciences Research Council; CRUK Convergence Science Centre studentship to A.L.L., E.W.T. and J.D. (C24523/A27435); Wellcome Trust Senior Investigator Award awarded to J.D. (103799/Z/14/Z) and Wellcome Trust Investigator award (110060/Z/15/Z) to U.S.E. Core funding from the Francis Crick Institute from Cancer Research UK (FC001070), the UK Medical Research Council (FC001070) and the Wellcome Trust (FC001070) was received by J.D. European Research Council Advanced Grant RASImmune was awarded to J.D. Funding Information: E.W.T. is a founder and shareholder in Myricx Pharma and receives consultancy or research funding from Kura Oncology, Pfizer, Samsara Therapeutics, Myricx Pharma, Merck Sharp and Dohme (MSD), Exscientia and Daiichi Sankyo. J.D. has acted as a consultant for AstraZeneca, Jubilant, Theras, BridgeBio and Vividion and receives research funding from Bristol Myers Squibb and Revolution Medicines. The other authors declare no competing interests. Publisher Copyright: {\textcopyright} 2024, The Author(s).",

year = "2024",

month = oct,

doi = "10.1038/s41587-023-02030-0",

language = "English",

volume = "42",

pages = "1548--1558",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "10",

}

Ocasio, CA, Baggelaar, MP, Sipthorp, J, Losada de la Lastra, A, Tavares, M, Volarić, J, Soudy, C, Storck, EM , Houghton, JW, Palma-Duran, SA, MacRae, JI, Tomić, G, Carr, L, Downward, J, Eggert, US & Tate, EW 2024, 'A palmitoyl transferase chemical–genetic system to map ZDHHC-specific S-acylation', Nature Biotechnology, vol. 42, no. 10, pp. 1548-1558. https://doi.org/10.1038/s41587-023-02030-0

TY - JOUR

T1 - A palmitoyl transferase chemical–genetic system to map ZDHHC-specific S-acylation

AU - Ocasio, Cory A.

AU - Baggelaar, Marc P.

AU - Sipthorp, James

AU - Losada de la Lastra, Ana

AU - Tavares, Manuel

AU - Volarić, Jana

AU - Soudy, Christelle

AU - Storck, Elisabeth M.

AU - Houghton, Jack W.

AU - Palma-Duran, Susana A.

AU - MacRae, James I.

AU - Tomić, Goran

AU - Carr, Lotte

AU - Downward, Julian

AU - Eggert, Ulrike S.

AU - Tate, Edward W.

N1 - Funding Information: We would like to thank B. Martin (Scorpion Therapeutics) and D. Sharp (Imperial College London) for engaging in discussions on ZDHHC chemical genetics and Y. Ohno and A. Kihara from Hokkaido University for sharing their complete set of human N-terminal FLAG-tagged ZDHHC constructs. We would also like to thank E. Thinon (Institut Européen de Chimie et Biologie, France) and H. Bakker (Hannover Medical School, Germany) for generously gifting Ifitm3, and VAMP3 and XXYLT1 plasmids, respectively. We thank B. Snijders, S. Howell, V. Encheva and J. Kirkpatrick (Francis Crick Institute) for their assistance and sharing of knowledge regarding LC–MS/MS as well as the Cell Services, Metabolomics, Light Microscopy and the Flow Cytometry Science Technology Platforms at the Francis Crick Institute for their support and sharing of knowledge. Schematic figures were generated using BioRender.com . Funding sources included the following: the CRUK/EPSRC Multidisciplinary Award to E.W.T. and J.D. (C29637/A27506 and NS/A000078/1); CRUK Programme Foundation Award to E.W.T. (C29637/A20183); CRUK Programme Award to E.W.T. (DRCNPG-Nov21/100001), with support from the Engineering and Physical Sciences Research Council; CRUK Convergence Science Centre studentship to A.L.L., E.W.T. and J.D. (C24523/A27435); Wellcome Trust Senior Investigator Award awarded to J.D. (103799/Z/14/Z) and Wellcome Trust Investigator award (110060/Z/15/Z) to U.S.E. Core funding from the Francis Crick Institute from Cancer Research UK (FC001070), the UK Medical Research Council (FC001070) and the Wellcome Trust (FC001070) was received by J.D. European Research Council Advanced Grant RASImmune was awarded to J.D. Funding Information: E.W.T. is a founder and shareholder in Myricx Pharma and receives consultancy or research funding from Kura Oncology, Pfizer, Samsara Therapeutics, Myricx Pharma, Merck Sharp and Dohme (MSD), Exscientia and Daiichi Sankyo. J.D. has acted as a consultant for AstraZeneca, Jubilant, Theras, BridgeBio and Vividion and receives research funding from Bristol Myers Squibb and Revolution Medicines. The other authors declare no competing interests. Publisher Copyright: © 2024, The Author(s).

PY - 2024/10

Y1 - 2024/10

N2 - The 23 human zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S-acyltransferases catalyze long-chain S-acylation at cysteine residues across an extensive network of hundreds of proteins important for normal physiology or dysregulated in disease. Here we present a technology to directly map the protein substrates of a specific ZDHHC at the whole-proteome level, in intact cells. Structure-guided engineering of paired ZDHHC ‘hole’ mutants and ‘bumped’ chemically tagged fatty acid probes enabled probe transfer to specific protein substrates with excellent selectivity over wild-type ZDHHCs. Chemical–genetic systems were exemplified for five human ZDHHCs (3, 7, 11, 15 and 20) and applied to generate de novo ZDHHC substrate profiles, identifying >300 substrates and S-acylation sites for new functionally diverse proteins across multiple cell lines. We expect that this platform will elucidate S-acylation biology for a wide range of models and organisms.

AB - The 23 human zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S-acyltransferases catalyze long-chain S-acylation at cysteine residues across an extensive network of hundreds of proteins important for normal physiology or dysregulated in disease. Here we present a technology to directly map the protein substrates of a specific ZDHHC at the whole-proteome level, in intact cells. Structure-guided engineering of paired ZDHHC ‘hole’ mutants and ‘bumped’ chemically tagged fatty acid probes enabled probe transfer to specific protein substrates with excellent selectivity over wild-type ZDHHCs. Chemical–genetic systems were exemplified for five human ZDHHCs (3, 7, 11, 15 and 20) and applied to generate de novo ZDHHC substrate profiles, identifying >300 substrates and S-acylation sites for new functionally diverse proteins across multiple cell lines. We expect that this platform will elucidate S-acylation biology for a wide range of models and organisms.

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U2 - 10.1038/s41587-023-02030-0

DO - 10.1038/s41587-023-02030-0

M3 - Article

AN - SCOPUS:85181695602

SN - 1087-0156

VL - 42

SP - 1548

EP - 1558

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 10

ER -

A palmitoyl transferase chemical–genetic system to map ZDHHC-specific S-acylation

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