SPRING licenses S1P-mediated cleavage of SREBP2 by displacing an inhibitory pro-domain.
Sterol Regulatory Element Binding Protein 2
/ metabolism
Humans
Protein Domains
Serine Endopeptidases
/ metabolism
Endoplasmic Reticulum
/ metabolism
Cryoelectron Microscopy
Golgi Apparatus
/ metabolism
Proprotein Convertases
/ metabolism
Cholesterol
/ metabolism
Animals
HEK293 Cells
Signal Transduction
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
09 Jul 2024
09 Jul 2024
Historique:
received:
17
02
2024
accepted:
28
06
2024
medline:
9
7
2024
pubmed:
9
7
2024
entrez:
8
7
2024
Statut:
epublish
Résumé
Site-one protease (S1P) conducts the first of two cleavage events in the Golgi to activate Sterol regulatory element binding proteins (SREBPs) and upregulate lipogenic transcription. S1P is also required for a wide array of additional signaling pathways. A zymogen serine protease, S1P matures through autoproteolysis of two pro-domains, with one cleavage event in the endoplasmic reticulum (ER) and the other in the Golgi. We recently identified the SREBP regulating gene, (SPRING), which enhances S1P maturation and is necessary for SREBP signaling. Here, we report the cryo-EM structures of S1P and S1P-SPRING at sub-2.5 Å resolution. SPRING activates S1P by dislodging its inhibitory pro-domain and stabilizing intra-domain contacts. Functionally, SPRING licenses S1P to cleave its cognate substrate, SREBP2. Our findings reveal an activation mechanism for S1P and provide insights into how spatial control of S1P activity underpins cholesterol homeostasis.
Identifiants
pubmed: 38977690
doi: 10.1038/s41467-024-50068-8
pii: 10.1038/s41467-024-50068-8
doi:
Substances chimiques
Sterol Regulatory Element Binding Protein 2
0
membrane-bound transcription factor peptidase, site 1
EC 3.4.21.112
Serine Endopeptidases
EC 3.4.21.-
Proprotein Convertases
EC 3.4.21.-
Cholesterol
97C5T2UQ7J
SREBF2 protein, human
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
5732Subventions
Organisme : U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
ID : R00GM141261
Organisme : Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
ID : NWO; 016.176.643
Organisme : Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
ID : NWO; 016.176.643
Organisme : Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
ID : M.22.034; GENESIS
Informations de copyright
© 2024. The Author(s).
Références
Seidah, N. G. & Prat, A. The biology and therapeutic targeting of the proprotein convertases. Nat. Rev. Drug Discov. 11, 367–383 (2012).
pubmed: 22679642
doi: 10.1038/nrd3699
Danyukova, T., Schöneck, K. & Pohl, S. Site-1 and site-2 proteases: A team of two in regulated proteolysis. Biochimica et. Biophysica Acta (BBA) - Mol. Cell Res. 1869, 119138 (2022).
doi: 10.1016/j.bbamcr.2021.119138
Sakai, J. et al. Molecular Identification of the Sterol-Regulated Luminal Protease that Cleaves SREBPs and Controls Lipid Composition of Animal Cells. Mol. Cell 2, 505–514 (1998).
pubmed: 9809072
doi: 10.1016/S1097-2765(00)80150-1
Brown, M. S. & Goldstein, J. L. Cholesterol feedback: from Schoenheimer’s bottle to Scap’s MELADL. J. Lipid Res. 50, S15–S27 (2009).
pubmed: 18974038
pmcid: 2674699
doi: 10.1194/jlr.R800054-JLR200
Yang, J. et al. Decreased lipid synthesis in livers of mice with disrupted Site-1 protease gene. Proc. Natl Acad. Sci. 98, 13607–13612 (2001).
pubmed: 11717426
pmcid: 61088
doi: 10.1073/pnas.201524598
Schlombs, K., Wagner, T. & Scheel, J. Site-1 protease is required for cartilage development in zebrafish. Proc. Natl Acad. Sci. 100, 14024–14029 (2003).
pubmed: 14612568
pmcid: 283539
doi: 10.1073/pnas.2331794100
Carvalho, D. R., Speck-Martins, C. E., Brum, J. M., Ferreira, C. R. & Sobreira, N. L. M. Spondyloepimetaphyseal dysplasia with elevated plasma lysosomal enzymes caused by homozygous variant in MBTPS1. Am. J. Med. Genet. Part A 182, 1796–1800 (2020).
pubmed: 32420688
doi: 10.1002/ajmg.a.61614
Kondo, Y. et al. Site-1 protease deficiency causes human skeletal dysplasia due to defective inter-organelle protein trafficking. JCI Insight 3, e121596 (2018).
pubmed: 30046013
pmcid: 6124414
doi: 10.1172/jci.insight.121596
Lenz, O., ter Meulen, J., Klenk, H.-D., Seidah, N. G. & Garten, W. The Lassa virus glycoprotein precursor GP-C is proteolytically processed by subtilase SKI-1/S1P. Proc. Natl Acad. Sci. 98, 12701–12705 (2001).
pubmed: 11606739
pmcid: 60117
doi: 10.1073/pnas.221447598
Rojek, J. M., Lee, A. M., Nguyen, N., Spiropoulou, C. F. & Kunz, S. Site 1 protease is required for proteolytic processing of the glycoproteins of the South American hemorrhagic fever viruses Junin, Machupo, and Guanarito. J. Virol. 82, 6045–6051 (2008).
pubmed: 18400865
pmcid: 2395157
doi: 10.1128/JVI.02392-07
Seidah, N. G., Pasquato, A. & Andréo, U. How Do Enveloped Viruses Exploit the Secretory Proprotein Convertases to Regulate Infectivity and Spread? Viruses 13, 1229 (2021).
Olmstead, A. D., Knecht, W., Lazarov, I., Dixit, S. B. & Jean, F. Human Subtilase SKI-1/S1P Is a Master Regulator of the HCV Lifecycle and a Potential Host Cell Target for Developing Indirect-Acting Antiviral Agents. PLOS Pathog. 8, e1002468 (2012).
pubmed: 22241994
pmcid: 3252376
doi: 10.1371/journal.ppat.1002468
Marschner, K., Kollmann, K., Schweizer, M., Braulke, T. & Pohl, S. A Key Enzyme in the Biogenesis of Lysosomes Is a Protease That Regulates Cholesterol Metabolism. Science 333, 87–90 (2011).
pubmed: 21719679
doi: 10.1126/science.1205677
Ye, J. et al. ER Stress Induces Cleavage of Membrane-Bound ATF6 by the Same Proteases that Process SREBPs. Mol. Cell 6, 1355–1364 (2000).
pubmed: 11163209
doi: 10.1016/S1097-2765(00)00133-7
Sakai, J. et al. Sterol-Regulated Release of SREBP-2 from Cell Membranes Requires Two Sequential Cleavages, One Within a Transmembrane Segment. Cell 85, 1037–1046 (1996).
pubmed: 8674110
doi: 10.1016/S0092-8674(00)81304-5
Gensberg, K., Jan, S. & Matthews, G. M. Subtilisin-related serine proteases in the mammalian constitutive secretory pathway. Semin. Cell Developmental Biol. 9, 11–17 (1998).
doi: 10.1006/scdb.1997.0196
Wells, J. A. & Estell, D. A. Subtilisin — an enzyme designed to be engineered. Trends Biochem. Sci. 13, 291–297 (1988).
pubmed: 3154281
doi: 10.1016/0968-0004(88)90121-1
Bryan, P., Pantoliano, M. W., Quill, S. G., Hsiao, H. Y. & Poulos, T. Site-directed mutagenesis and the role of the oxyanion hole in subtilisin. Proc. Natl Acad. Sci. USA 83, 3743–3745 (1986).
pubmed: 3520553
pmcid: 323599
doi: 10.1073/pnas.83.11.3743
Seidah, N. G. et al. Mammalian subtilisin/kexin isozyme SKI-1: A widely expressed proprotein convertase with a unique cleavage specificity and cellular localization. Proc. Natl Acad. Sci. 96, 1321–1326 (1999).
pubmed: 9990022
pmcid: 15461
doi: 10.1073/pnas.96.4.1321
Espenshade, P. J., Cheng, D., Goldstein, J. L. & Brown, M. S. Autocatalytic Processing of Site-1 Protease Removes Propeptide and Permits Cleavage of Sterol Regulatory Element-binding Proteins. J. Biol. Chem. 274, 22795–22804 (1999).
pubmed: 10428864
doi: 10.1074/jbc.274.32.22795
Cheng, D. et al. Secreted Site-1 Protease Cleaves Peptides Corresponding to Luminal Loop of Sterol Regulatory Element-binding Proteins*. J. Biol. Chem. 274, 22805–22812 (1999).
pubmed: 10428865
doi: 10.1074/jbc.274.32.22805
da Palma, J. R. et al. Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*. J. Biol. Chem. 289, 35743–35756 (2014).
pubmed: 25378398
pmcid: 4276844
doi: 10.1074/jbc.M114.588525
Elagoz, A., Benjannet, S., Mammarbassi, A., Wickham, L. & Seidah, N. G. Biosynthesis and Cellular Trafficking of the Convertase SKI-1/S1P: ECTODOMAIN SHEDDING REQUIRES SKI-1 ACTIVITY*. J. Biol. Chem. 277, 11265–11275 (2002).
pubmed: 11756446
doi: 10.1074/jbc.M109011200
Brown, M. S., Radhakrishnan, A. & Goldstein, J. L. Retrospective on Cholesterol Homeostasis: The Central Role of Scap. Ann. Rev. Biochem. 87, 783–807 (2018).
Sakai, J. et al. Identification of Complexes between the COOH-terminal Domains of Sterol Regulatory Element-binding Proteins (SREBPs) and SREBP Cleavage-Activating Protein. J. Biol. Chem. 272, 20213–20221 (1997).
pubmed: 9242699
doi: 10.1074/jbc.272.32.20213
Nohturfft, A., DeBose-Boyd, R. A., Scheek, S., Goldstein, J. L. & Brown, M. S. Sterols regulate cycling of SREBP cleavage-activating protein (SCAP) between endoplasmic reticulum and Golgi. Proc. Natl Acad. Sci. 96, 11235–11240 (1999).
pubmed: 10500160
pmcid: 18017
doi: 10.1073/pnas.96.20.11235
Radhakrishnan, A., Goldstein, J. L., McDonald, J. G. & Brown, M. S. Switch-like control of SREBP-2 transport triggered by small changes in ER cholesterol: a delicate balance. Cell Metab. 8, 512–521 (2008).
pubmed: 19041766
pmcid: 2652870
doi: 10.1016/j.cmet.2008.10.008
Hua, X., Sakai, J., Brown, M. S. & Goldstein, J. L. Regulated Cleavage of Sterol Regulatory Element Binding Proteins Requires Sequences on Both Sides of the Endoplasmic Reticulum Membrane. J. Biol. Chem. 271, 10379–10384 (1996).
pubmed: 8626610
doi: 10.1074/jbc.271.17.10379
Duncan, E. A., Brown, M. S., Goldstein, J. L. & Sakai, J. Cleavage Site for Sterol-regulated Protease Localized to a Leu-Ser Bond in the Lumenal Loop of Sterol Regulatory Element-binding Protein-2. J. Biol. Chem. 272, 12778–12785 (1997).
pubmed: 9139737
doi: 10.1074/jbc.272.19.12778
Shao, W. & Espenshade, P. J. Sterol Regulatory Element-binding Protein (SREBP) Cleavage Regulates Golgi-to-Endoplasmic Reticulum Recycling of SREBP Cleavage-activating Protein (SCAP). J. Biol. Chem. 289, 7547–7557 (2014).
pubmed: 24478315
pmcid: 3953268
doi: 10.1074/jbc.M113.545699
Rawson, R. B., Cheng, D., Brown, M. S. & Goldstein, J. L. Isolation of Cholesterol-requiring Mutant Chinese Hamster Ovary Cells with Defects in Cleavage of Sterol Regulatory Element-binding Proteins at Site 1. J. Biol. Chem. 273, 28261–28269 (1998).
pubmed: 9774448
doi: 10.1074/jbc.273.43.28261
Kober, D. L. et al. Scap structures highlight key role for rotation of intertwined luminal loops in cholesterol sensing. Cell 184, 3689–3701.e22 (2021).
pubmed: 34139175
pmcid: 8277531
doi: 10.1016/j.cell.2021.05.019
Kober, D. L. et al. Identification of a degradation signal at the carboxy terminus of SREBP2: A new role for this domain in cholesterol homeostasis. Proc. Natl Acad. Sci. 117, 28080–28091 (2020).
pubmed: 33106423
pmcid: 7668084
doi: 10.1073/pnas.2018578117
Hendrix, S. & Zelcer, N. A new SPRING in lipid metabolism. Curr. Opin. Lipidol. 34, 201–207 (2023).
pubmed: 37548386
doi: 10.1097/MOL.0000000000000894
Loregger, A. et al. Haploid genetic screens identify SPRING/C12ORF49 as a determinant of SREBP signaling and cholesterol metabolism. Nat. Commun. 11, 1128 (2020).
pubmed: 32111832
pmcid: 7048761
doi: 10.1038/s41467-020-14811-1
Xiao, J. et al. POST1/C12ORF49 regulates the SREBP pathway by promoting site-1 protease maturation. Protein Cell 12, 279–296 (2020).
pubmed: 32666500
pmcid: 8019017
doi: 10.1007/s13238-020-00753-3
Bayraktar, E. C. et al. Metabolic coessentiality mapping identifies C12orf49 as a regulator of SREBP processing and cholesterol metabolism. Nat. Metab. 2, 487–498 (2020).
pubmed: 32694732
pmcid: 7384252
doi: 10.1038/s42255-020-0206-9
Aregger, M. et al. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Nat. Metab. 2, 499–513 (2020).
pubmed: 32694731
pmcid: 7566881
doi: 10.1038/s42255-020-0211-z
Hendrix, S. et al. SPRING is a Dedicated Licensing Factor for SREBP-Specific Activation by S1P. Mol. Cell. Biol. 44, 123–137 (2024).
pubmed: 38747374
doi: 10.1080/10985549.2024.2348711
DeBose-Boyd, R. A. et al. Transport-Dependent Proteolysis of SREBP. Cell 99, 703–712 (1999).
pubmed: 10619424
doi: 10.1016/S0092-8674(00)81668-2
Hendrix, S. et al. Hepatic SREBP signaling requires SPRING to govern systemic lipid metabolism in mice and humans. Nat. Commun. 14, 5181 (2023).
pubmed: 37626055
pmcid: 10457316
doi: 10.1038/s41467-023-40943-1
Touré, B. B. et al. Biosynthesis and Enzymatic Characterization of Human SKI-1/S1P and the Processing of Its Inhibitory Prosegment*. J. Biol. Chem. 275, 2349–2358 (2000).
pubmed: 10644685
doi: 10.1074/jbc.275.4.2349
Cunningham, D. et al. Structural and biophysical studies of PCSK9 and its mutants linked to familial hypercholesterolemia. Nat. Struct. Mol. Biol. 14, 413–419 (2007).
pubmed: 17435765
doi: 10.1038/nsmb1235
Piper, D. E. et al. The Crystal Structure of PCSK9: A Regulator of Plasma LDL-Cholesterol. Structure 15, 545–552 (2007).
pubmed: 17502100
doi: 10.1016/j.str.2007.04.004
Hampton, E. N. et al. The self-inhibited structure of full-length PCSK9 at 1.9 Å reveals structural homology with resistin within the C-terminal domain. Proc. Natl Acad. Sci. 104, 14604–14609 (2007).
pubmed: 17804797
pmcid: 1976225
doi: 10.1073/pnas.0703402104
Reeves, P. J., Callewaert, N., Contreras, R. & Khorana, H. G. Structure and function in rhodopsin: High-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc. Natl Acad. Sci. 99, 13419–13424 (2002).
pubmed: 12370423
pmcid: 129688
doi: 10.1073/pnas.212519299
da Palma, J. R., Cendron, L., Seidah, N. G., Pasquato, A. & Kunz, S. Mechanism of Folding and Activation of Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P). J. Biol. Chem. 291, 2055–2066 (2016).
pubmed: 26645686
doi: 10.1074/jbc.M115.677757
Ye, J. Transcription factors activated through RIP (regulated intramembrane proteolysis) and RAT (regulated alternative translocation). J. Biol. Chem. 295, 10271–10280 (2020).
pubmed: 32487748
pmcid: 7383392
doi: 10.1074/jbc.REV120.012669
Varadi, M. et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50, D439–D444 (2021).
pmcid: 8728224
doi: 10.1093/nar/gkab1061
Beatson, S. & Ponting, C. P. GIFT domains: linking eukaryotic intraflagellar transport and glycosylation to bacterial gliding. Trends Biochem. Sci. 29, 396–399 (2004).
pubmed: 15288869
doi: 10.1016/j.tibs.2004.06.002
Than, M. E. et al. The endoproteinase furin contains two essential Ca2+ ions stabilizing its N-terminus and the unique S1 specificity pocket. Acta Crystallogr. Sect. D. 61, 505–512 (2005).
doi: 10.1107/S0907444905002556
Kiessling, L. L. & Diehl, R. C. CH−π Interactions in Glycan Recognition. ACS Chem. Biol. 16, 1884–1893 (2021).
pubmed: 34615357
pmcid: 9004545
doi: 10.1021/acschembio.1c00413
Petrilli, W. L. et al. From Screening to Targeted Degradation: Strategies for the Discovery and Optimization of Small Molecule Ligands for PCSK9. Cell Chem. Biol. 27, 32–40.e3 (2020).
pubmed: 31653597
doi: 10.1016/j.chembiol.2019.10.002
Holm, L. DALI and the persistence of protein shape. Protein Sci. 29, 128–140 (2020).
pubmed: 31606894
doi: 10.1002/pro.3749
Pearce, K. H. et al. BacMam production and crystal structure of nonglycosylated apo human furin at 1.89 A resolution. Acta Crystallogr. Sect. F. 75, 239–245 (2019).
doi: 10.1107/S2053230X19001419
Hay, B. A. et al. Aminopyrrolidineamide inhibitors of site-1 protease. Bioorg. Medicinal Chem. Lett. 17, 4411–4414 (2007).
doi: 10.1016/j.bmcl.2007.06.031
Burri, D. J. et al. Molecular Characterization of the Processing of Arenavirus Envelope Glycoprotein Precursors by Subtilisin Kexin Isozyme-1/Site-1 Protease. J. Virol. 86, 4935–4946 (2012).
pubmed: 22357276
pmcid: 3347368
doi: 10.1128/JVI.00024-12
Pullikotil, P., Vincent, M., Nichol, S. T. & Seidah, N. G. Development of Protein-based Inhibitors of the Proprotein of Convertase SKI-1/S1P: PROCESSING OF SREBP-2, ATF6, AND A VIRAL GLYCOPROTEIN*. J. Biol. Chem. 279, 17338–17347 (2004).
pubmed: 14970232
doi: 10.1074/jbc.M313764200
Morales-Perez, C. L., Noviello, C. M. & Hibbs, R. E. Manipulation of Subunit Stoichiometry in Heteromeric Membrane Proteins. Structure 24, 797–805 (2016).
pubmed: 27041595
pmcid: 4856541
doi: 10.1016/j.str.2016.03.004
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
pubmed: 16182563
doi: 10.1016/j.jsb.2005.07.007
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473
doi: 10.1038/nmeth.4169
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Croll, T. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. Sect. D. 74, 519–530 (2018).
doi: 10.1107/S2059798318002425
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. Sect. D. 74, 531–544 (2018).
doi: 10.1107/S2059798318006551
Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, W320–W324 (2014).
pubmed: 24753421
pmcid: 4086106
doi: 10.1093/nar/gku316