Protein lipidation is a post-translational modification that confers hydrophobicity on protein substrates to control their cellular localization, mediate protein trafficking, and regulate protein function. In particular, protein prenylation is a C-terminal modification on proteins bearing canonical motifs catalyzed by prenyltransferases. Prenylated proteins have been of interest due to their numerous associations with various diseases. Chemical proteomic approaches have been pursued over the last decade to define prenylated proteomes (prenylome) and probe their responses to perturbations in various cellular systems. Here, we describe the discovery of prenylation of a non-canonical prenylated protein, ALDH9A1, which lacks any apparent prenylation motif. This enzyme was initially identified through chemical proteomic profiling of prenylomes in various cell lines. Metabolic labeling with an isoprenoid probe using overexpressed ALDH9A1 revealed that this enzyme can be prenylated inside cells but does not respond to inhibition by prenyltransferase inhibitors. Site-directed mutagenesis of the key residues involved in ALDH9A1 activity indicates that the catalytic C288 bears the isoprenoid modification likely through an NAD+-dependent mechanism. Furthermore, the isoprenoid modification is also susceptible to hydrolysis, indicating a reversible modification. We hypothesize that this modification originates from endogenous farnesal or geranygeranial, the established degradation products of prenylated proteins and results in a thioester form that accumulates. This novel reversible prenoyl modification on ALDH9A1 expands the current paradigm of protein prenylation by illustrating a potentially new type of protein-lipid modification that may also serve as a novel mechanism for controlling enzyme function.

Department of Chemistry University of Minnesota Minneapolis MN 55455 USA

Department of Experimental and Clinical Pharmacology University of Minnesota Minneapolis MN 55455 USA

Department of Experimental Biology Faculty of Science Palacký University CZ 78371 Czech Republic

Department of Medicinal Chemistry University of Minnesota Minneapolis MN 55455 USA

Institute of Organic Chemistry Faculty of Chemistry Lodz University of Technology Łódź Poland

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Marshall C. J. Science. 1993;259:1865–1866. doi: 10.1126/science.8456312. PubMed DOI

Zhang F. L. Casey P. J. Annu. Rev. Biochem. 1996;65:241–269. doi: 10.1146/annurev.bi.65.070196.001325. PubMed DOI

Blanden M. J. Suazo K. F. Hildebrandt E. R. Hardgrove D. S. Patel M. Saunders W. P. Distefano M. D. Schmidt W. K. Hougland J. L. J. Biol. Chem. 2017;293:2770–2785. doi: 10.1074/jbc.M117.805770. PubMed DOI PMC

Ashok S. Hildebrandt E. R. Ruiz C. S. Hardgrove D. S. Coreno D. W. Schmidt W. K. Hougland J. L. Biochemistry. 2020;59:1149–1162. doi: 10.1021/acs.biochem.0c00081. PubMed DOI PMC

Schey G. L. Buttery P. H. Hildebrandt E. R. Novak S. X. Schmidt W. K. Hougland J. L. Distefano M. D. Int. J. Mol. Sci. 2021;22:12042. doi: 10.3390/ijms222112042. PubMed DOI PMC

Kinsella B. T. Maltese W. A. J. Biol. Chem. 1992;267:3940–3945. doi: 10.1016/S0021-9258(19)50616-0. PubMed DOI

Kuchay S. Wang H. Marzio A. Jain K. Homer H. Fehrenbacher N. Philips M. R. Zheng N. Pagano M. Nat. Struct. Mol. Biol. 2019;26:628–636. doi: 10.1038/s41594-019-0249-3. PubMed DOI PMC

Shirakawa R. Goto-Ito S. Goto K. Wakayama S. Kubo H. Sakata N. Trinh D. A. Yamagata A. Sato Y. Masumoto H. Cheng J. Fujimoto T. Fukai S. Horiuchi H. EMBO J. 2020;39:e104120. doi: 10.15252/embj.2019104120. PubMed DOI PMC

Tate E. W. Kalesh K. A. Lanyon-Hogg T. Storck E. M. Thinon E. Curr. Opin. Chem. Biol. 2015;24:48–57. doi: 10.1016/j.cbpa.2014.10.016. PubMed DOI PMC

Suazo K. F. Schey G. Schaber C. Odom John A. R. Distefano M. D. Mass Spectrom. Chem. Proteomics. 2019:317–347.

Storck E. M. Morales-Sanfrutos J. Serwa R. A. Panyain N. Lanyon-Hogg T. Tolmachova T. Ventimiglia L. N. Martin-Serrano J. Seabra M. C. Wojciak-Stothard B. Tate E. W. Nat. Chem. 2019;11:552–561. doi: 10.1038/s41557-019-0237-6. PubMed DOI PMC

Suazo K. F. Jeong A. Ahmadi M. Brown C. Qu W. Li L. Distefano M. D. Sci. Rep. 2021;11:4367. doi: 10.1038/s41598-021-83666-3. PubMed DOI PMC

Suazo K. F. Park K.-Y. Distefano M. D. Chem. Rev. 2021;121:7178–7248. doi: 10.1021/acs.chemrev.0c01108. PubMed DOI PMC

Qu W. Suazo K. F. Liu W. Cheng S. Jeong A. Hottman D. Yuan L.-L. Distefano M. D. Li L. Mol. Neurobiol. 2021;58:1128–1144. doi: 10.1007/s12035-020-02169-w. PubMed DOI PMC

Charron G. Li M. M. H. MacDonald M. R. Hang H. C. Proc. Natl. Acad. Sci. U. S. A. 2013;110:11085–11090. doi: 10.1073/pnas.1302564110. PubMed DOI PMC

Končitíková R. Vigouroux A. Kopečná M. Šebela M. Moréra S. Kopečný D. Biosci. Rep. 2019;39:BSR20190558. doi: 10.1042/BSR20190558. PubMed DOI PMC

Wyatt J. W. Korasick D. A. Qureshi I. A. Campbell A. C. Gates K. S. Tanner J. J. Arch. Biochem. Biophys. 2020;691:108477. doi: 10.1016/j.abb.2020.108477. PubMed DOI PMC

Kuzuguchi T. Morita Y. Sagami I. Sagami H. Ogura K. J. Biol. Chem. 1999;274:5888–5894. doi: 10.1074/jbc.274.9.5888. PubMed DOI

Palsuledesai C. C. Ochocki J. D. Kuhns M. M. Wang Y.-C. Warmka J. K. Chernick D. S. Wattenberg E. V. Li L. Arriaga E. A. Distefano M. D. ACS Chem. Biol. 2016;11:2820–2828. doi: 10.1021/acschembio.6b00421. PubMed DOI PMC

Lerner E. C. Qian Y. Hamilton A. D. Sebti S. M. J. Biol. Chem. 1995;270:26770–26773. doi: 10.1074/jbc.270.45.26770. PubMed DOI

Gisselberg J. E. Zhang L. Elias J. E. Yeh E. Mol. Cell. Proteomics. 2017;16:S54–S64. doi: 10.1074/mcp.M116.064550. PubMed DOI PMC

Kaźmierczak A. Kusy D. Niinivehmas S. P. Gmach J. Joachimiak Ł. Pentikäinen O. T. Gendaszewska-Darmach E. Błażewska K. M. J. Med. Chem. 2017;60:8781–8800. doi: 10.1021/acs.jmedchem.7b00811. PubMed DOI

Joachimiak Ł. Marchwicka A. Gendaszewska-Darmach E. Błażewska K. M. ChemMedChem. 2018;13:842–851. doi: 10.1002/cmdc.201700791. PubMed DOI

Coxon F. P. Joachimiak Ł. Najumudeen A. K. Breen G. Gmach J. Oetken-Lindholm C. Way R. Dunford J. E. Abankwa D. Błażewska K. M. Eur. J. Med. Chem. 2014;84:77–89. doi: 10.1016/j.ejmech.2014.06.062. PubMed DOI

Sophos N. A. Vasiliou V. Chem. – Biol. Interact. 2003;143–144:5–22. doi: 10.1016/S0009-2797(02)00163-1. PubMed DOI

Marchitti S. A. Brocker C. Stagos D. Vasiliou V. Expert Opin. Drug Metab. Toxicol. 2008;4:697–720. doi: 10.1517/17425255.4.6.697. PubMed DOI PMC

Koppaka V. Thompson D. C. Chen Y. Ellermann M. Nicolaou K. C. Juvonen R. O. Petersen D. Deitrich R. A. Hurley T. D. Vasiliou V. Pharmacol. Rev. 2012;64:520–539. doi: 10.1124/pr.111.005538. PubMed DOI PMC

Chern M. K. Pietruszko R. Biochem. Biophys. Res. Commun. 1995;213:561–568. doi: 10.1006/bbrc.1995.2168. PubMed DOI

Vaz F. M. Fouchier S. W. Ofman R. Sommer M. Wanders R. J. A. J. Biol. Chem. 2000;275:7390–7394. doi: 10.1074/jbc.275.10.7390. PubMed DOI

Kurys G. Ambroziak W. Pietruszko R. J. Biol. Chem. 1989;264:4715–4721. doi: 10.1016/S0021-9258(18)83802-9. PubMed DOI

Zhang Y. Wang M. Lin H. ACS Chem. Biol. 2020;15:28–32. doi: 10.1021/acschembio.9b00662. PubMed DOI PMC

Kitamura T. Takagi S. Naganuma T. Kihara A. Biochem. J. 2014;465:79–87. doi: 10.1042/BJ20140624. PubMed DOI

Fink A. L. Folding Des. 1998;3:R9–R23. doi: 10.1016/S1359-0278(98)00002-9. PubMed DOI

Bentinger M. Grünler J. Peterson E. Swiezewska E. Dallner G. Arch. Biochem. Biophys. 1998;353:191–198. doi: 10.1006/abbi.1998.0611. PubMed DOI

Tschantz W. R. Digits J. A. Pyun H.-J. Coates R. M. Casey P. J. J. Biol. Chem. 2001;276:2321–2324. doi: 10.1074/jbc.C000616200. PubMed DOI

Petenkova A. Auger S. A. Lamb J. Quellier D. Carter C. To O. T. Milosevic J. Barghout R. Kugadas A. Lu X. Geddes-McAlister J. Fichorova R. Sykes D. B. Distefano M. D. Gadjeva M. Nat. Commun. 2023;14:2761. doi: 10.1038/s41467-023-38447-z. PubMed DOI PMC

Hao P. Ren Y. Alpert A. J. Sze S. K. Mol. Cell. Proteomics. 2011;10:O111.009381. doi: 10.1074/mcp.O111.009381. PubMed DOI PMC

Ji Y. Leymarie N. Haeussler D. J. Bachschmid M. M. Costello C. E. Lin C. Anal. Chem. 2013;85:11952–11959. doi: 10.1021/ac402850s. PubMed DOI PMC

Mullen D. G. Kyro K. Hauser M. Gustavsson M. Veglia G. Becker J. M. Naider F. Distefano M. D. Bioorg. Med. Chem. 2011;19:490–497. doi: 10.1016/j.bmc.2010.11.006. PubMed DOI PMC

Tate E. W. J. Chem. Biol. 2008;1:17–26. doi: 10.1007/s12154-008-0002-6. PubMed DOI PMC

Tars K. Rumnieks J. Zeltins A. Kazaks A. Kotelovica S. Leonciks A. Sharipo J. Viksna A. Kuka J. Liepinsh E. Dambrova M. Biochem. Biophys. Res. Commun. 2010;398:634–639. doi: 10.1016/j.bbrc.2010.06.121. PubMed DOI

Morrison H. in Enzyme Active Sites and their Reaction Mechanisms, ed. H. Morrison, Academic Press, New York, 2021, pp.21–26

Morgan C. A. Parajuli B. Buchman C. D. Dria K. Hurley T. D. Chem. – Biol. Interact. 2015;234:18–28. doi: 10.1016/j.cbi.2014.12.008. PubMed DOI PMC

Kikonyogo A. Abriola D. P. Dryjanski M. Pietruszko R. Eur. J. Biochem. 1999;262:704–712. doi: 10.1046/j.1432-1327.1999.00415.x. PubMed DOI

Singh S. Brocker C. Koppaka V. Chen Y. Jackson B. C. Matsumoto A. Thompson D. C. Vasiliou V. Free Radicals Biol. Med. 2013;56:89–101. doi: 10.1016/j.freeradbiomed.2012.11.010. PubMed DOI PMC

Dinavahi S. S. Bazewicz C. G. Gowda R. Robertson G. P. Trends Pharmacol. Sci. 2019;40:774–789. doi: 10.1016/j.tips.2019.08.002. PubMed DOI

Johansson J. Fleetwood L. Jörnvall H. FEBS Lett. 1992;303:1–3. doi: 10.1016/0014-5793(92)80464-R. PubMed DOI

Ford B. Bateman L. A. Gutierrez-Palominos L. Park R. Nomura D. K. Cell Chem. Biol. 2017;24:133–140. doi: 10.1016/j.chembiol.2016.12.013. PubMed DOI

Whitby L. R. Obach R. S. Simon G. M. Hayward M. M. Cravatt B. F. ACS Chem. Biol. 2017;12:2040–2050. doi: 10.1021/acschembio.7b00346. PubMed DOI PMC

Huang Z. Ogasawara D. Seneviratne U. I. Cognetta 3rd A. B. Am Ende C. W. Nason D. M. Lapham K. Litchfield J. Johnson D. S. Cravatt B. F. ACS Chem. Biol. 2019;14:192–197. doi: 10.1021/acschembio.8b01097. PubMed DOI PMC

Almannai M. Alfadhel M. El-Hattab A. W. Molecules. 2019;24:3251. doi: 10.3390/molecules24183251. PubMed DOI PMC

Lin S. W. Chen J. C. Hsu L. C. Hsieh C.-L. Yoshida A. Genomics. 1996;34:376–380. doi: 10.1006/geno.1996.0300. PubMed DOI

Chew H. Solomon V. A. Fonteh A. N. Front. Physiol. 2020;11:598. doi: 10.3389/fphys.2020.00598. PubMed DOI PMC

Solas M. Puerta E. Ramirez J. M. Curr. Pharm. Des. 2015;21:4960–4971. doi: 10.2174/1381612821666150914121149. PubMed DOI

Jeong A. Auger S. A. Maity S. Fredriksen K. Zhong R. Li L. Distefano M. D. ACS Chem. Biol. 2022;17:2863–2876. doi: 10.1021/acschembio.2c00486. PubMed DOI PMC

Nunomura A. Perry G. Aliev G. Hirai K. Takeda A. Balraj E. K. Jones P. K. Ghanbari H. Wataya T. Shimohama S. Chiba S. Atwood C. S. Petersen R. B. Smith M. A. J. Neuropathol. Exp. Neurol. 2001;60:759–767. doi: 10.1093/jnen/60.8.759. PubMed DOI

Zhou Y. Prakash P. Liang H. Cho K.-J. Gorfe A. A. Hancock J. F. Cell. 2017;168:239–251.e16. doi: 10.1016/j.cell.2016.11.059. PubMed DOI PMC

Main A. Fuller W. FEBS J. 2022;289:861–882. doi: 10.1111/febs.15781. PubMed DOI

Suazo K. F. Hurben A. K. Liu K. Xu F. Thao P. Sudheer C. Li L. Distefano M. Curr. Protoc. Chem. Biol. 2018;10:e46. PubMed PMC

Morris G. M. Goodsell D. S. Halliday R. S. Huey R. Hart W. E. Belew R. K. Olson A. J. J. Comput. Chem. 1998;19:1639–1662. doi: 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B. DOI

Trott O. Olson A. J. J. Comput. Chem. 2010;31:455–461. PubMed PMC

Dallakyan S. and Olson A. J., in Chemical Biology: Methods and Protocols, ed. J. E. Hempel, C. H. Williams and C. C. Hong, Springer, New York, 2015, pp.243–250

Kopečný D. Končitíková R. Tylichová M. Vigouroux A. Moskalíková H. Soural M. Šebela M. Moréra S. J. Biol. Chem. 2013;288:9491–9507. doi: 10.1074/jbc.M112.443952. PubMed DOI PMC