Abstract
Hedgehog (Hh) is a morphogen that binds to its receptor Patched 1 and activates Smoothened (SMO), thereby governing embryonic development and postnatal tissue homeostasis. Cholesterol can bind and covalently conjugate to the luminal cysteine-rich domain (CRD) of human SMO at the D95 residue (D99 in mouse). The reaction mechanism and biological function of SMO cholesterylation have not been elucidated. Here, we show that the SMO-CRD undergoes auto-cholesterylation which is boosted by calcium and involves an intramolecular ester intermediate. In cells, Hh stimulation elevates local calcium concentration in the SMO-localized endosomes through store-operated calcium entry. In addition, we identify the signaling-incompetent SMO D95E mutation, and the D95E mutant SMO can bind cholesterol but cannot be modified or activated by cholesterol. The homozygous SmoD99E/D99E knockin mice are embryonic lethal with severe developmental delay, demonstrating that cholesterylation of CRD is required for full-length SMO activation. Our work reveals the unique autocatalytic mechanism of SMO cholesterylation and an unprecedented role of calcium in Hh signaling.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Vorechovsky, I. et al. Somatic mutations in the human homologue of Drosophila patched in primitive neuroectodermal tumours. Oncogene 15, 361–366 (1997).
Bale, A. E. Hedgehog signaling and human disease. Ann. Rev. Genom. Human Genet. 3, 47–65 (2002).
Reifenberger, J. et al. Somatic mutations in the PTCH, SMOH, SUFUH and TP53 genes in sporadic basal cell carcinomas. Br. J. Dermatol. 152, 43–51 (2005).
Hu, A. & Song, B. L. The interplay of Patched, Smoothened and cholesterol in Hedgehog signaling. Curr. Opin. Cell Biol. 61, 31–38 (2019).
Cong, Q., Xu, R. & Yang, Y. Galphas signaling in skeletal development, homeostasis and diseases. Curr. Top. Dev. Biol. 133, 281–307 (2019).
Ruiz i Altaba, A. Combinatorial Gli gene function in floor plate and neuronal inductions by Sonic Hedgehog. Development 125, 2203–2212 (1998).
Corbit, K. C. et al. Vertebrate Smoothened functions at the primary cilium. Nature 437, 1018–1021 (2005).
Huangfu, D. et al. Hedgehog signalling in the mouse requires intraflagellar transport proteins. Nature 426, 83–87 (2003).
Porter, J. A., Young, K. E. & Beachy, P. A. Cholesterol modification of Hedgehog signaling proteins in animal development. Science 274, 255–259 (1996).
Creanga, A. et al. Scube/You activity mediates release of dually lipid-modified Hedgehog signal in soluble form. Genes Dev. 26, 1312–1325 (2012).
Tukachinsky, H., Kuzmickas, R. P., Jao, C. Y., Liu, J. & Salic, A. Dispatched and scube mediate the efficient secretion of the cholesterol-modified Hedgehog ligand. Cell Rep. 2, 308–320 (2012).
Huang, P. et al. Cellular cholesterol directly activates Smoothened in hedgehog signaling. Cell 166, 1176–1187. e14 (2016).
Luchetti, G. et al. Cholesterol activates the G-protein coupled receptor Smoothened to promote Hedgehog signaling. eLife 5, e20304 (2016).
Xiao, X. et al. Cholesterol modification of Smoothened is required for Hedgehog signaling. Mol. Cell 66, 154–162. e10 (2017).
Kinnebrew, M. et al. Cholesterol accessibility at the ciliary membrane controls Hedgehog signaling. Elife 8, e50051 (2019).
Deshpande, I. et al. Smoothened stimulation by membrane sterols drives Hedgehog pathway activity. Nature 571, 284–288 (2019).
Qi, X., Friedberg, L., De Bose-Boyd, R., Long, T. & Li, X. Sterols in an intramolecular channel of Smoothened mediate Hedgehog signaling. Nat. Chem. Biol. 16, 1368–1375 (2020).
Hu, A., Zhou, M. & Song, B. L. Analysis of protein cholesterylation by biorthogonal labeling. Methods Mol. Biol. 2374, 27–36 (2022).
Zhang, X. M., Ramalho-Santos, M. & McMahon, A. P. Smoothened mutants reveal redundant roles for Shh and Ihh signaling including regulation of L/R asymmetry by the mouse node. Cell 105, 781–792 (2001).
Qiu, Z. P., Hu, A. & Song, B. L. The 3-beta-hydroxysteroid-Delta(8), Delta(7)-isomerase EBP inhibits cholesterylation of Smoothened. Biochim. Biophys. Acta. Mol. Cell Biol. Lipids 1866, 159041 (2021).
Bygrave, F. L. & Benedetti, A. What is the concentration of calcium ions in the endoplasmic reticulum? Cell Calcium 19, 547–551 (1996).
Luo, J., Yang, H. & Song, B. L. Mechanisms and regulation of cholesterol homeostasis. Nat. Rev. Mol. Cell Biol. 21, 225–245 (2020).
Guan, C. et al. Structural insights into the inhibition mechanism of human sterol O-acyltransferase 1 by a competitive inhibitor. Nat. Commun. 11, 2478 (2020).
Qi, X., Schmiege, P., Coutavas, E. & Li, X. Two Patched molecules engage distinct sites on Hedgehog yielding a signaling-competent complex. Science 362, eaas8843 (2018).
Gong, X. et al. Structural basis for the recognition of Sonic Hedgehog by human Patched 1. Science 361, 568 (2018).
Allen, G. J. & Sanders, D. Two voltage-gated, calcium release channels coreside in the vacuolar membrane of broad bean guard cells. Plant Cell 6, 685–694 (1994).
Lansman, J. B. Blockade of current through single calcium channels by trivalent lanthanide cations. Effect of ionic radius on the rates of ion entry and exit. J. Gen. Physiol. 95, 679–696 (1990).
Nishitani, W. S., Saif, T. A. & Wang, Y. Calcium signaling in live cells on elastic gels under mechanical vibration at subcellular levels. PLoS One 6, e26181 (2011).
Liou, J. et al. STIM is a Ca2+ sensor essential for Ca2+-store-depletion-triggered Ca2+ influx. Curr. Biol. 15, 1235–1241 (2005).
Parekh, A. B. Store-operated CRAC channels: function in health and disease. Nat. Rev. Drug Discov. 9, 399–410 (2010).
Brandman, O., Liou, J., Park, W. S. & Meyer, T. STIM2 is a feedback regulator that stabilizes basal cytosolic and endoplasmic reticulum Ca2+ levels. Cell 131, 1327–1339 (2007).
Luik, R. M., Wang, B., Prakriya, M., Wu, M. M. & Lewis, R. S. Oligomerization of STIM1 couples ER calcium depletion to CRAC channel activation. Nature 454, 538–542 (2008).
Luo, C. et al. A genetically encoded ratiometric calcium sensor enables quantitative measurement of the local calcium microdomain in the endoplasmic reticulum. Biophys. Rep. 5, 31–42 (2019).
Tertyshnikova, S. & Fein, A. Inhibition of inositol 1,4,5-trisphosphate-induced Ca2+ release by cAMP-dependent protein kinase in a living cell. Proc. Natl. Acad. Sci. USA 95, 1613–1617 (1998).
Belgacem, Y. H. & Borodinsky, L. N. Sonic hedgehog signaling is decoded by calcium spike activity in the developing spinal cord. Proc. Natl. Acad. Sci. USA 108, 4482–4487 (2011).
Ogden, S. K. et al. G protein Galphai functions immediately downstream of Smoothened in Hedgehog signalling. Nature 456, 967–970 (2008).
Qi, X. et al. Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric Gi. Nature 571, 279–283 (2019).
Byrne, E. F. X. et al. Structural basis of Smoothened regulation by its extracellular domains. Nature 535, 517–522 (2016).
Guadiana, S. M. et al. Arborization of dendrites by developing neocortical neurons is dependent on primary cilia and type 3 adenylyl cyclase. J. Neurosci. 33, 2626–2638 (2013).
Nachtergaele, S. et al. Oxysterols are allosteric activators of the oncoprotein Smoothened. Nat. Chem. Biol. 8, 211–220 (2012).
Klatt Shaw, D. et al. Intracellular calcium mobilization is required for Sonic Hedgehog signaling. Dev. Cell 45, 512–525. e5 (2018).
Moore, B. S. et al. Cilia have high cAMP levels that are inhibited by Sonic Hedgehog-regulated calcium dynamics. Proc. Natl. Acad. Sci. USA 113, 13069–13074 (2016).
Gwack, Y. et al. Biochemical and functional characterization of Orai proteins. J. Biol. Chem. 282, 16232–16243 (2007).
Zhang, Y. et al. Structural basis for cholesterol transport-like activity of the Hedgehog receptor Patched. Cell 175, 1352–1364. e14 (2018).
Kinnebrew, M. et al. Patched 1 reduces the accessibility of cholesterol in the outer leaflet of membranes. eLife 10, e70504 (2021).
Milenkovic, L., Scott, M. P. & Rohatgi, R. Lateral transport of Smoothened from the plasma membrane to the membrane of the cilium. J. Cell Biol. 187, 365–374 (2009).
Qi, X., Schmiege, P., Coutavas, E., Wang, J. & Li, X. Structures of human Patched and its complex with native palmitoylated sonic hedgehog. Nature 560, 128–132 (2018).
Hurwitz, S. Homeostatic control of plasma calcium concentration. Crit. Rev. Biochem. Mol. Biol. 31, 41–100 (1996).
Maxfield, F. R. & Wustner, D. Intracellular cholesterol transport. J. Clin. Invest. 110, 891–898 (2002).
Albrecht, T., Zhao, Y., Nguyen, T. H., Campbell, R. E. & Johnson, J. D. Fluorescent biosensors illuminate calcium levels within defined beta-cell endosome subpopulations. Cell Calcium 57, 263–274 (2015).
Myers, B. R., Neahring, L., Zhang, Y., Roberts, K. J. & Beachy, P. A. Rapid, direct activity assays for Smoothened reveal Hedgehog pathway regulation by membrane cholesterol and extracellular sodium. Proc. Natl. Acad. Sci. USA 114, E11141–E11150 (2017).
Bernatik, O., Paclikova, P., Kotrbova, A., Bryja, V. & Cajanek, L. Primary cilia formation does not rely on WNT/beta-catenin signaling. Front. Cell Dev. Biol. 9, 623753 (2021).
Zhao, Y., Tong, C. & Jiang, J. Hedgehog regulates smoothened activity by inducing a conformational switch. Nature 450, 252–258 (2007).
Li, S. et al. Hedgehog-regulated ubiquitination controls smoothened trafficking and cell surface expression in Drosophila. PLoS Biol. 10, e1001239 (2012).
Kim, J. et al. The role of ciliary trafficking in Hedgehog receptor signaling. Sci. Signal. 8, ra55 (2015).
Kovalchuk, S. I., Jensen, O. N. & Rogowska-Wrzesinska, A. FlashPack: fast and simple preparation of ultrahigh-performance capillary columns for LC-MS. Mol. Cell Proteomics 18, 383–390 (2019).
Zhou, Y. et al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509, 487–491 (2014).
Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).
Ovchinnikov, D. Alcian blue/alizarin red staining of cartilage and bone in mouse. Cold Spring Harbor Protocols 2009, pdb. prot5170 (2009).
Zhao, Y. & Truhlar, D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Accounts 120, 215–241 (2008).
Frisch M. J. et al. Gaussian 16, Revision A.03, (Gaussian, Inc., 2016).
Acknowledgements
We thank Ms. Dan Liang for technical assistance, Dr. Wei Qi (ShanghaiTech University) for revising the manuscript. We appreciate the helpful discussion with Drs. Guo-Yin Yin (Wuhan University) and Yun Zhao (Shanghai Institutes for Biological Sciences). This work was supported by grants from the National Natural Science Foundation of China (22077035, 91753204, 31690102, 91957103), Ministry of Science and Technology of China (2018YFA0800700, 2019YFA0802701), and Fountain-Valley Life Sciences Fund of University of Chinese Academy of Sciences Education Foundation. B.-L.S. acknowledges the support from the Tencent Foundation through the XPLORER PRIZE.
Author information
Authors and Affiliations
Contributions
B.-L.S. conceived the project. J.-Z.Z., C.-C.L, J.W. and W.-W.Q. designed and synthesized cholesterol analogs. A.H. and B.-L.S. designed the experiments. A.H., Z.-C.L., Z.-P.Q., and H.-Y.L. performed the experiments. P.-C.W. performed the structural remodeling. M.Y., G.D. and X.Z. did MS/MS. X.-W.W. and X.H. performed quantum mechanical calculations. A.H. and B.-L.S. analyzed the data. A.H., J.W., W.-W.Q. and B.-L.S. wrote the paper with input from others.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Supplementary information
Rights and permissions
About this article
Cite this article
Hu, A., Zhang, JZ., Wang, J. et al. Cholesterylation of Smoothened is a calcium-accelerated autoreaction involving an intramolecular ester intermediate. Cell Res 32, 288–301 (2022). https://doi.org/10.1038/s41422-022-00622-0
Received:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s41422-022-00622-0
This article is cited by
-
Genome-wide identification and functional characterization of GPCR family genes reveal their key roles in the vitellarium development and egg production in Schistosoma japonicum
Parasites & Vectors (2025)
-
A Novel Heterozygous IHH c.331_333del Mutation Identified in a Fetus with Brachydactyly Type A1 Causes IHH Protein Maturation Failure in HEK293T Cells
Phenomics (2025)
-
Protein lipidation in health and disease: molecular basis, physiological function and pathological implication
Signal Transduction and Targeted Therapy (2024)
-
Regulation of autophagy by protein lipidation
Advanced Biotechnology (2024)
-
Bile acids-mediated intracellular cholesterol transport promotes intestinal cholesterol absorption and NPC1L1 recycling
Nature Communications (2023)