Helical stability of the GnTV transmembrane domain impacts on SPPL3 dependent cleavage.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
05 12 2022
05 12 2022
Historique:
received:
22
04
2022
accepted:
21
11
2022
entrez:
5
12
2022
pubmed:
6
12
2022
medline:
10
12
2022
Statut:
epublish
Résumé
Signal-Peptide Peptidase Like-3 (SPPL3) is an intramembrane cleaving aspartyl protease that causes secretion of extracellular domains from type-II transmembrane proteins. Numerous Golgi-localized glycosidases and glucosyltransferases have been identified as physiological SPPL3 substrates. By SPPL3 dependent processing, glycan-transferring enzymes are deactivated inside the cell, as their active site-containing domain is cleaved and secreted. Thus, SPPL3 impacts on glycan patterns of many cellular and secreted proteins and can regulate protein glycosylation. However, the characteristics that make a substrate a favourable candidate for SPPL3-dependent cleavage remain unknown. To gain insights into substrate requirements, we investigated the function of a GxxxG motif located in the transmembrane domain of N-acetylglucosaminyltransferase V (GnTV), a well-known SPPL3 substrate. SPPL3-dependent secretion of the substrate's ectodomain was affected by mutations disrupting the GxxxG motif. Using deuterium/hydrogen exchange and NMR spectroscopy, we studied the effect of these mutations on the helix flexibility of the GnTV transmembrane domain and observed that increased flexibility facilitates SPPL3-dependent shedding and vice versa. This study provides first insights into the characteristics of SPPL3 substrates, combining molecular biology, biochemistry, and biophysical techniques and its results will provide the basis for better understanding the characteristics of SPPL3 substrates with implications for the substrates of other intramembrane proteases.
Identifiants
pubmed: 36470941
doi: 10.1038/s41598-022-24772-8
pii: 10.1038/s41598-022-24772-8
pmc: PMC9722940
doi:
Substances chimiques
Aspartic Acid Endopeptidases
EC 3.4.23.-
Membrane Proteins
0
Polysaccharides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
20987Informations de copyright
© 2022. The Author(s).
Références
Steiner, H., Fluhrer, R. & Haass, C. Intramembrane proteolysis by gamma-secretase. J. Biol. Chem. 283, 29627–29631 (2008).
doi: 10.1074/jbc.R800010200
Rawson, R. B. et al. Complementation cloning of S2P, a gene encoding a putative metalloprotease required for intramembrane cleavage of SREBPs. Mol. Cell 1, 47–57 (1997).
doi: 10.1016/S1097-2765(00)80006-4
Langosch, D. & Steiner, H. Substrate processing in intramembrane proteolysis by gamma-secretase - the role of protein dynamics. Biol. Chem. 398, 441–453 (2017).
doi: 10.1515/hsz-2016-0269
Grigorenko, A. P., Moliaka, Y. K., Korovaitseva, G. I. & Rogaev, E. I. Novel class of polytopic proteins with domains associated with putative protease activity. Biochem. Biokhimiia 67, 826–835 (2002).
doi: 10.1023/A:1016365227942
Ponting, C. P. et al. Identification of a novel family of presenilin homologues. Hum. Mol. Genet. 11, 1037–1044 (2002).
doi: 10.1093/hmg/11.9.1037
Weihofen, A., Binns, K., Lemberg, M. K., Ashman, K. & Martoglio, B. Identification of signal peptide peptidase, a presenilin-type aspartic protease. Science 296, 2215–2218 (2002).
doi: 10.1126/science.1070925
Wolfe, M. S. Toward the structure of presenilin/gamma-secretase and presenilin homologs. Biochem. Biophys. Acta 1828, 2886–2897 (2013).
doi: 10.1016/j.bbamem.2013.04.015
Levy-Lahad, E. et al. Candidate gene for the chromosome 1 familial Alzheimer’s disease locus. Science 269, 973–977 (1995).
doi: 10.1126/science.7638622
Levy-Lahad, E. et al. A familial Alzheimer’s disease locus on chromosome 1. Science 269, 970–973 (1995).
doi: 10.1126/science.7638621
Rogaev, E. I. et al. Familial Alzheimer’s disease in kindreds with missense mutations in a gene on chromosome 1 related to the Alzheimer’s disease type 3 gene. Nature 376, 775–778 (1995).
doi: 10.1038/376775a0
Sherrington, R. et al. Cloning of a gene bearing missense mutations in early-onset familial Alzheimer’s disease. Nature 375, 754–760 (1995).
doi: 10.1038/375754a0
Wolfe, M. S. Intramembrane-cleaving proteases. J. Biol. Chem. 284, 13969–13973 (2009).
doi: 10.1074/jbc.R800039200
Manolaridis, I. et al. Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1. Nature 504, 301–305 (2013).
doi: 10.1038/nature12754
Voss, M., Schroder, B. & Fluhrer, R. Mechanism, specificity, and physiology of signal peptide peptidase (SPP) and SPP-like proteases. Biochem. Biophys. Acta 1828, 2828–2839 (2013).
doi: 10.1016/j.bbamem.2013.03.033
Papadopoulou, A. A. & Fluhrer, R. Signaling functions of intramembrane aspartyl-proteases. Front. Cardiovasc. Med. 7, 591787 (2020).
doi: 10.3389/fcvm.2020.591787
Steiner, H. et al. Glycine 384 is required for presenilin-1 function and is conserved in bacterial polytopic aspartyl proteases. Nat. Cell. Biol. 2, 848–851 (2000).
doi: 10.1038/35041097
Zhou, R. et al. Recognition of the amyloid precursor protein by human gamma-secretase. Science 363(6428), eaaw0930 (2019).
doi: 10.1126/science.aaw0930
Mentrup, T., Cabrera-Cabrera, F., Fluhrer, R. & Schroder, B. Physiological functions of SPP/SPPL intramembrane proteases. Cell Mol Life Sci 77(15), 2959–2979 (2020).
doi: 10.1007/s00018-020-03470-6
Lichtenthaler, S. F., Lemberg, M. K. & Fluhrer, R. Proteolytic ectodomain shedding of membrane proteins in mammals-hardware, concepts, and recent developments. EMBO J 37(15), e99456 (2018).
doi: 10.15252/embj.201899456
Voss, M. et al. Foamy virus envelope protein is a substrate for signal peptide peptidase-like 3 (SPPL3). J. Biol. Chem. 287, 43401–43409 (2012).
doi: 10.1074/jbc.M112.371369
Voss, M. et al. Shedding of glycan-modifying enzymes by signal peptide peptidase-like 3 (SPPL3) regulates cellular N-glycosylation. EMBO J. 33, 2890–2905 (2014).
doi: 10.15252/embj.201488375
Spitz, C. et al. Non-canonical shedding of TNFalpha by SPPL2a Is determined by the conformational flexibility of its transmembrane helix. iScience 23, 101775 (2020).
doi: 10.1016/j.isci.2020.101775
Kuhn, P. H. et al. Secretome analysis identifies novel signal Peptide peptidase-like 3 (Sppl3) substrates and reveals a role of Sppl3 in multiple Golgi glycosylation pathways. Mol. Cell Proteomics 14, 1584–1598 (2015).
doi: 10.1074/mcp.M115.048298
Strisovsky, K. Mechanism and inhibition of rhomboid proteases. Methods Enzymol. 584, 279–293 (2017).
doi: 10.1016/bs.mie.2016.10.014
Martin, L., Fluhrer, R. & Haass, C. Substrate requirements for SPPL2b-dependent regulated intramembrane proteolysis. J. Biol. Chem. 284, 5662–5670 (2009).
doi: 10.1074/jbc.M807485200
Lemberg, M. K. & Martoglio, B. Requirements for signal peptide peptidase-catalyzed intramembrane proteolysis. Mol. Cell 10, 735–744 (2002).
doi: 10.1016/S1097-2765(02)00655-X
Fluhrer, R. et al. The alpha-helical content of the transmembrane domain of the British dementia protein-2 (Bri2) determines its processing by signal peptide peptidase-like 2b (SPPL2b). J. Biol. Chem. 287, 5156–5163 (2012).
doi: 10.1074/jbc.M111.328104
Langosch, D., Scharnagl, C., Steiner, H. & Lemberg, M. K. Understanding intramembrane proteolysis: From protein dynamics to reaction kinetics. Trends Biochem. Sci. 40, 318–327 (2015).
doi: 10.1016/j.tibs.2015.04.001
Yang, G. et al. Structural basis of Notch recognition by human gamma-secretase. Nature 565, 192–197 (2019).
doi: 10.1038/s41586-018-0813-8
Gotz, A. et al. Modulating hinge flexibility in the APP transmembrane domain alters gamma-secretase cleavage. Biophys. J. 116, 2103–2120 (2019).
doi: 10.1016/j.bpj.2019.04.030
Scharnagl, C. et al. Side-chain to main-chain hydrogen bonding controls the intrinsic backbone dynamics of the amyloid precursor protein transmembrane helix. Biophys. J. 106, 1318–1326 (2014).
doi: 10.1016/j.bpj.2014.02.013
Teese, M. G. & Langosch, D. Role of GxxxG motifs in transmembrane domain interactions. Biochemistry 54, 5125–5135 (2015).
doi: 10.1021/acs.biochem.5b00495
Stelzer, W. & Langosch, D. Sequence-dependent backbone dynamics of a viral fusogen transmembrane helix. Protein Sci. 21, 1097–1102 (2012).
doi: 10.1002/pro.2094
Munter, L. M. et al. GxxxG motifs within the amyloid precursor protein transmembrane sequence are critical for the etiology of Abeta42. EMBO J. 26, 1702–1712 (2007).
doi: 10.1038/sj.emboj.7601616
Eggert, S., Midthune, B., Cottrell, B. & Koo, E. H. Induced dimerization of the amyloid precursor protein leads to decreased amyloid-beta protein production. J. Biol. Chem. 284, 28943–28952 (2009).
doi: 10.1074/jbc.M109.038646
Sykes, A. M. et al. The effects of transmembrane sequence and dimerization on cleavage of the p75 neurotrophin receptor by gamma-secretase. J. Biol. Chem. 287, 43810–43824 (2012).
doi: 10.1074/jbc.M112.382903
Pinho, S. S. & Reis, C. A. Glycosylation in cancer: Mechanisms and clinical implications. Nat. Rev. Cancer 15, 540–555 (2015).
doi: 10.1038/nrc3982
Schachter, H. The joys of HexNAc. The synthesis and function of N- and O-glycan branches. Glycoconj. J. 17, 465–483 (2000).
doi: 10.1023/A:1011010206774
Li, S. C. & Deber, C. M. A measure of helical propensity for amino acids in membrane environments. Nat. Struct. Biol. 1, 558 (1994).
doi: 10.1038/nsb0894-558
Hogel, P. et al. Glycine perturbs local and global conformational flexibility of a transmembrane helix. Biochemistry 57, 1326–1337 (2018).
doi: 10.1021/acs.biochem.7b01197
Cordes, F. S., Bright, J. N. & Sansom, M. S. Proline-induced distortions of transmembrane helices. J. Mol. Biol. 323, 951–960 (2002).
doi: 10.1016/S0022-2836(02)01006-9
Quint, S. et al. Residue-specific side-chain packing determines the backbone dynamics of transmembrane model helices. Biophys. J. 99, 2541–2549 (2010).
doi: 10.1016/j.bpj.2010.08.031
Kuhn, P. H. et al. Secretome protein enrichment identifies physiological BACE1 protease substrates in neurons. EMBO J. 31, 3157–3168 (2012).
doi: 10.1038/emboj.2012.173
Kitazume, S. et al. Screening a series of sialyltransferases for possible BACE1 substrates. Glycoconj. J. 23, 437–441 (2006).
doi: 10.1007/s10719-006-6671-x
Kitazume, S. et al. In vivo cleavage of alpha2,6-sialyltransferase by Alzheimer beta-secretase. J. Biol. Chem. 280, 8589–8595 (2005).
doi: 10.1074/jbc.M409417200
Zheng, J., Strutzenberg, T., Pascal, B. D. & Griffin, P. R. Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry. Curr. Opin. Struct. Biol. 58, 305–313 (2019).
doi: 10.1016/j.sbi.2019.06.007
Yucel, S. S. et al. The metastable XBP1u transmembrane domain defines determinants for intramembrane proteolysis by signal peptide peptidase. Cell Rep. 26, 3087-3099 e3011 (2019).
doi: 10.1016/j.celrep.2019.02.057
Stelzer, W. & Langosch, D. Conformationally flexible sites within the transmembrane helices of amyloid precursor protein and Notch1 receptor. Biochemistry 58, 3065–3068 (2019).
doi: 10.1021/acs.biochem.9b00505
Schutz, C. N. & Warshel, A. What are the dielectric “constants” of proteins and how to validate electrostatic models?. Proteins 44, 400–417 (2001).
doi: 10.1002/prot.1106
Tolia, A., Chavez-Gutierrez, L. & De Strooper, B. Contribution of presenilin transmembrane domains 6 and 7 to a water-containing cavity in the gamma-secretase complex. J. Biol. Chem. 281, 27633–27642 (2006).
doi: 10.1074/jbc.M604997200
Fierz, B., Reiner, A. & Kiefhaber, T. Local conformational dynamics in alpha-helices measured by fast triplet transfer. Proc. Natl. Acad. Sci. U. S. A. 106, 1057–1062 (2009).
doi: 10.1073/pnas.0808581106
Silber, M., Hitzenberger, M., Zacharias, M. & Muhle-Goll, C. Altered hinge conformations in APP transmembrane helix mutants may affect enzyme-substrate interactions of gamma-secretase. ACS Chem. Neurosci. 11, 4426–4433 (2020).
doi: 10.1021/acschemneuro.0c00640
Shen, Y., Delaglio, F., Cornilescu, G. & Bax, A. TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J. Biomol. NMR 44, 213–223 (2009).
doi: 10.1007/s10858-009-9333-z
Butterfield, S. M., Patel, P. R. & Waters, M. L. Contribution of aromatic interactions to alpha-helix stability. J. Am. Chem. Soc. 124, 9751–9755 (2002).
doi: 10.1021/ja026668q
Tyndall, J. D., Nall, T. & Fairlie, D. P. Proteases universally recognize beta strands in their active sites. Chem. Rev. 105, 973–999 (2005).
doi: 10.1021/cr040669e
Popot, J. L. & Engelman, D. M. Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem. 69, 881–922 (2000).
doi: 10.1146/annurev.biochem.69.1.881
Huttl, S. et al. Substrate determinants of signal peptide peptidase-like 2a (SPPL2a)-mediated intramembrane proteolysis of the invariant chain CD74. Biochem. J. 473, 1405–1422 (2016).
doi: 10.1042/BCJ20160156
Zoll, S. et al. Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate-peptide complex structures. EMBO J. 33, 2408–2421 (2014).
doi: 10.15252/embj.201489367
Fukumori, A., Fluhrer, R., Steiner, H. & Haass, C. Three-amino acid spacing of presenilin endoproteolysis suggests a general stepwise cleavage of gamma-secretase-mediated intramembrane proteolysis. J. Neurosci. 30, 7853–7862 (2010).
doi: 10.1523/JNEUROSCI.1443-10.2010
Lemberg, M. K. et al. Mechanism of intramembrane proteolysis investigated with purified rhomboid proteases. EMBO J. 24, 464–472 (2005).
doi: 10.1038/sj.emboj.7600537
Brown, M. S., Ye, J., Rawson, R. B. & Goldstein, J. L. Regulated intramembrane proteolysis: A control mechanism conserved from bacteria to humans. Cell 100, 391–398 (2000).
doi: 10.1016/S0092-8674(00)80675-3
Gotz, A. et al. Increased H-bond stability relates to altered epsilon-cleavage efficiency and abeta levels in the I45T familial Alzheimer’s disease mutant of APP. Sci. Rep. 9, 5321 (2019).
doi: 10.1038/s41598-019-41766-1
Deatherage, C. L. et al. Structural and biochemical differences between the Notch and the amyloid precursor protein transmembrane domains. Sci. Adv. 3, e1602794 (2017).
doi: 10.1126/sciadv.1602794
Madala, P. K., Tyndall, J. D., Nall, T. & Fairlie, D. P. Update 1 of: Proteases universally recognize beta strands in their active sites. Chem. Rev. 110, PR1–PR31 (2010).
doi: 10.1021/cr900368a
Belushkin, A. A. et al. Sequence-derived structural features driving proteolytic processing. Proteomics 14, 42–50 (2014).
doi: 10.1002/pmic.201300416
Kamp, F. et al. Intramembrane proteolysis of beta-amyloid precursor protein by gamma-secretase is an unusually slow process. Biophys. J. 108, 1229–1237 (2015).
doi: 10.1016/j.bpj.2014.12.045
Bolduc, D. M., Montagna, D. R., Gu, Y., Selkoe, D. J. & Wolfe, M. S. Nicastrin functions to sterically hinder gamma-secretase-substrate interactions driven by substrate transmembrane domain. Proc. Natl. Acad. Sci. U. S. A. 113, E509-518 (2016).
doi: 10.1073/pnas.1512952113
Jesus, C. S. H., Cruz, P. F., Arnaut, L. G., Brito, R. M. M. & Serpa, C. One peptide reveals the two faces of alpha-helix unfolding-folding dynamics. J. Phys. Chem. B 122, 3790–3800 (2018).
doi: 10.1021/acs.jpcb.8b00229
Niemeyer, J. et al. The intramembrane protease SPPL2c promotes male germ cell development by cleaving phospholamban. EMBO Rep. 20(3), e46449 (2019).
doi: 10.15252/embr.201846449
Bohm, G., Muhr, R. & Jaenicke, R. Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng. 5, 191–195 (1992).
doi: 10.1093/protein/5.3.191
Vranken, W. F. et al. The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins 59, 687–696 (2005).
doi: 10.1002/prot.20449
Wishart, D. S. Interpreting protein chemical shift data. Prog. Nucl. Magn. Reson. Spectrosc. 58, 62–87 (2011).
doi: 10.1016/j.pnmrs.2010.07.004
Rieping, W. et al. ARIA2: Automated NOE assignment and data integration in NMR structure calculation. Bioinformatics 23, 381–382 (2007).
doi: 10.1093/bioinformatics/btl589