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How intramembrane proteases bury hydrolytic reactions in the membrane

Abstract

Intramembrane proteolysis is increasingly seen as a regulatory step in a range of diverse processes, including development, organelle shaping, metabolism, pathogenicity and degenerative disease. Initial scepticism over the existence of intramembrane proteases was soon replaced by intense exploration of their catalytic mechanisms, substrate specificities, regulation and structures. Crystal structures of metal-dependent and serine intramembrane proteases have revealed active sites embedded in the plane of the membrane but accessible by water, a requirement for hydrolytic reactions. Efforts to understand how these membrane-bound proteases carry out their reactions have started to yield results.

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Figure 1: I-CLiP families and their signalling-related functions.
Figure 2: Secondary structure of presenilin and SPP.
Figure 3: Structure of Methanocaldococcus jannaschii S2P (mjS2P).
Figure 4: Structure of Escherichia coli GlpG.

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References

  1. Dodson, G. & Chothia, C. Fifty years of pepsin crystals. Nature 309, 309 (1984).

    ADS  CAS  PubMed  Google Scholar 

  2. Protein Data Bank Newsletter <ftp://ftp.wwpdb.org/pub/pdb/doc/newsletters/bnl/news01_sep74.pdf> (1974).

  3. Southan, C. A genomic perspective on human proteases as drug targets. Drug Discov. Today 6, 681–688 (2001).

    CAS  PubMed  Google Scholar 

  4. 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). This paper presents the first identification of an I-CLiP.

    CAS  PubMed  Google Scholar 

  5. 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).

    CAS  PubMed  Google Scholar 

  6. Urban, S. & Freeman, M. Intramembrane proteolysis controls diverse signalling pathways throughout evolution. Curr. Opin. Genet. Dev. 12, 512–518 (2002).

    CAS  PubMed  Google Scholar 

  7. Lewis, A. P. & Thomas, P. J. A novel clan of zinc metallopeptidases with possible intramembrane cleavage properties. Protein Sci. 8, 439–442 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Rudner, D. Z., Fawcett, P. & Losick, R. A family of membrane-embedded metalloproteases involved in regulated proteolysis of membrane-associated transcription factors. Proc. Natl Acad. Sci. USA 96, 14765–14770 (1999).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  9. 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).

    CAS  PubMed  Google Scholar 

  10. Alba, B. M. & Gross, C. A. Regulation of the Escherichia coli sigma-dependent envelope stress response. Mol. Microbiol. 52, 613–619 (2004).

    CAS  PubMed  Google Scholar 

  11. Ellermeier, C. D. & Losick, R. Evidence for a novel protease governing regulated intramembrane proteolysis and resistance to antimicrobial peptides in Bacillus subtilis . Genes Dev. 20, 1911–1922 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Kinch, L. N., Ginalski, K. & Grishin, N. V. Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade. Protein Sci. 15, 84–93 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Koonin, E. V. et al. The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. Genome Biol. 4, R19 (2003).

    PubMed  PubMed Central  Google Scholar 

  14. Lemberg, M. K. & Freeman, M. Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases. Genome Res. 17, 1634–1646 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Mayer, U. & Nüsslein-Volhard, C. A group of genes required for pattern formation in the ventral ectoderm of the Drosophila embryo. Genes Dev. 2, 1496–1511 (1988).

    CAS  PubMed  Google Scholar 

  16. Urban, S., Lee, J. R. & Freeman, M. Drosophila rhomboid-1 defines a family of putative intramembrane serine proteases. Cell 107, 173–182 (2001). This paper describes the first demonstration of cleavage activity by a rhomboid protease.

    CAS  PubMed  Google Scholar 

  17. Lee, J. R., Urban, S., Garvey, C. F. & Freeman, M. Regulated intracellular ligand transport and proteolysis control EGF signal activation in Drosophila . Cell 107, 161–171 (2001).

    CAS  PubMed  Google Scholar 

  18. Pascall, J. C. & Brown, K. D. Intramembrane cleavage of ephrinB3 by the human rhomboid family protease, RHBDL2. Biochem. Biophys. Res. Commun. 317, 244–252 (2004).

    CAS  PubMed  Google Scholar 

  19. Lohi, O., Urban, S. & Freeman, M. Diverse substrate recognition mechanisms for rhomboids: thrombomodulin is cleaved by mammalian rhomboids. Curr. Biol. 14, 236–241 (2004).

    CAS  PubMed  Google Scholar 

  20. Stevenson, L. G. et al. Rhomboid protease AarA mediates quorum-sensing in Providencia stuartii by activating TatA of the twin-arginine translocase. Proc. Natl Acad. Sci. USA 104, 1003–1008 (2007).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  21. Dowse, T. J., Koussis, K., Blackman, M. J. & Soldati-Favre, D. Roles of proteases during invasion and egress by Plasmodium and Toxoplasma . Subcell. Biochem. 47, 121–139 (2008).

    PubMed  Google Scholar 

  22. Herlan, M., Vogel, F., Bornhovd, C., Neupert, W. & Reichert, A. S. Processing of Mgm1 by the rhomboid-type protease Pcp1 is required for maintenance of mitochondrial morphology and of mitochondrial DNA. J. Biol. Chem. 278, 27781–27788 (2003).

    CAS  PubMed  Google Scholar 

  23. McQuibban, G. A., Saurya, S. & Freeman, M. Mitochondrial membrane remodelling regulated by a conserved rhomboid protease. Nature 423, 537–541 (2003).

    ADS  CAS  PubMed  Google Scholar 

  24. Cipolat, S. et al. Mitochondrial rhomboid PARL regulates cytochrome c release during apoptosis via OPA1-dependent cristae remodelling. Cell 126, 163–175 (2006).

    CAS  PubMed  Google Scholar 

  25. Chao, J. R. et al. Hax1-mediated processing of HtrA2 by Parl allows survival of lymphocytes and neurons. Nature 452, 98–102 (2008).

    ADS  CAS  PubMed  Google Scholar 

  26. Hulko, M., Lupas, A. N. & Martin, J. Inherent chaperone-like activity of aspartic proteases reveals a distant evolutionary relation to double-ψ barrel domains of AAA-ATPases. Protein Sci. 16, 644–653 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Spiess, C., Beil, A. & Ehrmann, M. A temperature-dependent switch from chaperone to protease in a widely conserved heat shock protein. Cell 97, 339–347 (1999).

    CAS  PubMed  Google Scholar 

  28. 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). Human SPP was isolated by affinity purification and the protein identified in this paper.

    ADS  CAS  PubMed  Google Scholar 

  29. Sato, T. et al. Signal peptide peptidase: biochemical properties and modulation by nonsteroidal antiinflammatory drugs. Biochemistry 45, 8649–8656 (2006).

    CAS  PubMed  Google Scholar 

  30. De Strooper, B. et al. Deficiency of presenilin-1 inhibits the normal cleavage of amyloid precursor protein. Nature 391, 387–390 (1998). This paper links intramembrane proteolysis and Alzheimer's disease.

    ADS  CAS  PubMed  Google Scholar 

  31. Wolfe, M. S. et al. Two transmembrane aspartates in presenilin-1 required for presenilin endoproteolysis and γ-secretase activity. Nature 398, 513–517 (1999). This paper shows that the transmembrane aspartates in presenilin are critical for its function.

    ADS  CAS  PubMed  Google Scholar 

  32. Sato, T. et al. Active γ-secretase complexes contain only one of each component. J. Biol. Chem. 282, 33985–33993 (2007).

    CAS  PubMed  Google Scholar 

  33. Osenkowski, P. et al. Cryoelectron microscopy structure of purified γ-secretase at 12 Å resolution. J. Mol. Biol. 385, 642–652 (2009).

    CAS  PubMed  Google Scholar 

  34. Schroeter, E. H. et al. A presenilin dimer at the core of the γ-secretase enzyme: insights from parallel analysis of Notch 1 and APP proteolysis. Proc. Natl Acad. Sci. USA 100, 13075–13080 (2003).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  35. Tolia, A. & De Strooper, B. Structure and function of γ-secretase. Semin. Cell Dev. Biol. 20, 211–218 (2009).

    CAS  PubMed  Google Scholar 

  36. Friedmann, E. et al. Consensus analysis of signal peptide peptidase and homologous human aspartic proteases reveals opposite topology of catalytic domains compared with presenilins. J. Biol. Chem. 279, 50790–50798 (2004).

    CAS  PubMed  Google Scholar 

  37. Steiner, H., Fluhrer, R. & Haass, C. Intramembrane proteolysis by γ-secretase. J. Biol. Chem. 283, 29627–29631 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. De Strooper, B. et al. A presenilin-1-dependent gamma-secretase-like protease mediates release of Notch intracellular domain. Nature 398, 518–522 (1999).

    ADS  CAS  PubMed  Google Scholar 

  39. Struhl, G. & Greenwald, I. Presenilin is required for activity and nuclear access of Notch in Drosophila . Nature 398, 522–525 (1999).

    ADS  CAS  PubMed  Google Scholar 

  40. Ye, Y., Lukinova, N. & Fortini, M. E. Neurogenic phenotypes and altered Notch processing in Drosophila Presenilin mutants. Nature 398, 525–529 (1999).

    ADS  CAS  PubMed  Google Scholar 

  41. Hass, M. R., Sato, C., Kopan, R. & Zhao, G. Presenilin: RIP and beyond. Semin. Cell Dev. Biol. 20, 201–210 (2009).

    CAS  PubMed  Google Scholar 

  42. Lemberg, M. K. & Martoglio, B. Requirements for signal peptide peptidase-catalyzed intramembrane proteolysis. Mol. Cell 10, 735–744 (2002).

    CAS  PubMed  Google Scholar 

  43. Lemberg, M. K., Bland, F. A., Weihofen, A., Braud, V. M. & Martoglio, B. Intramembrane proteolysis of signal peptides: an essential step in the generation of HLA-E epitopes. J. Immunol. 167, 6441–6446 (2001).

    CAS  PubMed  Google Scholar 

  44. McLauchlan, J., Lemberg, M. K., Hope, G. & Martoglio, B. Intramembrane proteolysis promotes trafficking of hepatitis C virus core protein to lipid droplets. EMBO J. 21, 3980–3908 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Ponting, C. P. et al. Identification of a novel family of presenilin homologues. Hum. Mol. Genet. 11, 1037–1044 (2002).

    CAS  PubMed  Google Scholar 

  46. Friedmann, E. et al. SPPL2a and SPPL2b promote intramembrane proteolysis of TNF-α in activated dendritic cells to trigger IL-12 production. Nature Cell Biol. 8, 843–848 (2006).

    CAS  PubMed  Google Scholar 

  47. Fluhrer, R. et al. A γ-secretase-like intramembrane cleavage of TNF-α by the GxGD aspartyl protease SPPL2b. Nature Cell Biol. 8, 894–896 (2006).

    CAS  PubMed  Google Scholar 

  48. Carpenter, E. P., Beis, K., Cameron, A. D. & Iwata, S. Overcoming the challenges of membrane protein crystallography. Curr. Opin. Struct. Biol. 18, 581–586 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Feng, L. et al. Structure of a site-2 protease family intramembrane metalloprotease. Science 318, 1608–1612 (2007). This paper reports the first crystal structure of a metalloprotease.

    ADS  CAS  PubMed  Google Scholar 

  50. Matthews, B. W. Structural basis of the action of thermolysin and related zinc peptidases. Acc. Chem. Res. 21, 333–340 (1988).

    CAS  Google Scholar 

  51. Christianson, D. W. & Lipscomb, W. N. Carboxypeptidase A. Acc. Chem. Res. 22, 62–69 (1989).

    CAS  Google Scholar 

  52. Hausrath, A. C. & Matthews, B. W. Thermolysin in the absence of substrate has an open conformation. Acta Crystallogr. D 58, 1002–1007 (2002).

    PubMed  Google Scholar 

  53. Wang, Y., Zhang, Y. & Ha, Y. Crystal structure of a rhomboid family intramembrane protease. Nature 444, 179–180 (2006). This paper reports the first crystal structure of the intramembrane serine protease GlpG.

    ADS  CAS  PubMed  Google Scholar 

  54. Wu, Z. et al. Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nature Struct. Mol. Biol. 13, 1084–1091 (2006).

    CAS  Google Scholar 

  55. Ben-Shem, A., Fass, D. & Bibi, E. Structural basis for intramembrane proteolysis by rhomboid serine proteases. Proc. Natl Acad. Sci. USA 104, 462–466 (2007). This paper describes the crystal structure of GlpG in two different conformations.

    ADS  CAS  PubMed  Google Scholar 

  56. Lemieux, M. J., Fischer, S. J., Cherney, M. M., Bateman, K. S. & James, M. N. The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis. Proc. Natl Acad. Sci. USA 104, 750–754 (2007).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  57. Wang, Y. & Ha, Y. Open-cap conformation of intramembrane protease GlpG. Proc. Natl Acad. Sci. USA 104, 2098–2102 (2007).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  58. Wang, Y., Maegawa, S., Akiyama, Y. & Ha, Y. The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. J. Mol. Biol. 374, 1104–1113 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Yernool, D., Boudker, O., Jin, Y. & Gouaux, E. Structure of a glutamate transporter homologue from Pyrococcus horikoshii . Nature 431, 811–818 (2004).

    ADS  CAS  PubMed  Google Scholar 

  60. Bondar, A. N., del Val, C. & White, S. H. Rhomboid protease dynamics and lipid interactions. Structure 17, 395–405 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Tolia, A., Chávez-Gutiérrez, L. & De Strooper, B. Contribution of presenilin transmembrane domains 6 and 7 to a water-containing cavity in the γ-secretase complex. J. Biol. Chem. 281, 27633–27642 (2006).

    CAS  PubMed  Google Scholar 

  62. Narayanan, S., Sato, T. & Wolfe, M. S. A C-terminal region of signal peptide peptidase defines a functional domain for intramembrane aspartic protease catalysis. J. Biol. Chem. 282, 20172–20179 (2007).

    CAS  PubMed  Google Scholar 

  63. Urban, S., Schlieper, D. & Freeman, M. Conservation of intramembrane proteolytic activity and substrate specificity in prokaryotic and eukaryotic rhomboids. Curr. Biol. 12, 1507–1512 (2002).

    CAS  PubMed  Google Scholar 

  64. Akiyama, Y. & Maegawa, S. Sequence features of substrates required for cleavage by GlpG, an Escherichia coli rhomboid protease. Mol. Microbiol. 64, 1028–1037 (2007).

    CAS  PubMed  Google Scholar 

  65. Urban, S. & Freeman, M. Substrate specificity of rhomboid intramembrane proteases is governed by helix-breaking residues in the substrate transmembrane domain. Mol. Cell 11, 1425–1434 (2003).

    CAS  PubMed  Google Scholar 

  66. Ye, J., Dave, U. P., Grishin, N. V., Goldstein, J. L. & Brown, M. S. Asparagine-proline sequence within membrane-spanning segment of SREBP triggers intramembrane cleavage by site-2 protease. Proc. Natl Acad. Sci. USA 97, 5123–5128 (2000).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  67. Beel, A. J. & Sanders, C. R. Substrate specificity of gamma-secretase and other intramembrane proteases. Cell. Mol. Life Sci. 65, 1311–1334 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Lichtenthaler, S. F. et al. Mechanism of the cleavage specificity of Alzheimer's disease γ-secretase identified by phenylalanine-scanning mutagenesis of the transmembrane domain of the amyloid precursor protein. Proc. Natl Acad. Sci. USA 96, 3053–3058 (1999).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  69. Duncan, E. A., Dave, U. P., Sakai, J., Goldstein, J. L. & Brown, M. S. Second-site cleavage in sterol regulatory element-binding protein occurs at transmembrane junction as determined by cysteine panning. J. Biol. Chem. 273, 17801–17809 (1998).

    CAS  PubMed  Google Scholar 

  70. Maegawa, S., Ito, K. & Akiyama, Y. Proteolytic action of GlpG, a rhomboid protease in the Escherichia coli cytoplasmic membrane. Biochemistry 44, 13543–13552 (2005).

    CAS  PubMed  Google Scholar 

  71. Baker, R. P., Young, K., Feng, L., Shi, Y. & Urban, S. Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate. Proc. Natl Acad. Sci. USA 104, 8257–8262 (2007).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  72. Tsruya, R. et al. Rhomboid cleaves Star to regulate the levels of secreted Spitz. EMBO J. 26, 1211–1220 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Schroeter, E. H., Kisslinger, J. A. & Kopan, R. Notch-1 signalling requires ligand-induced proteolytic release of intracellular domain. Nature 393, 382–386 (1998).

    ADS  CAS  PubMed  Google Scholar 

  74. Shen, J. & Prywes, R. Dependence of site-2 protease cleavage of ATF6 on prior site-1 protease digestion is determined by the size of the luminal domain of ATF6. J. Biol. Chem. 279, 43046–43051 (2004).

    CAS  PubMed  Google Scholar 

  75. Goldstein, J. L., Rawson, R. B. & Brown, M. S. Mutant mammalian cells as tools to delineate the sterol regulatory element-binding protein pathway for feedback regulation of lipid synthesis. Arch. Biochem. Biophys. 397, 139–148 (2002).

    CAS  PubMed  Google Scholar 

  76. Freeman, M. Rhomboids: 7 years of a new protease family. Semin. Cell Dev. Biol. 20, 231–239 (2009).

    CAS  PubMed  Google Scholar 

  77. Weihofen, A. & Martoglio, B. Intramembrane-cleaving proteases: controlled liberation of proteins and bioactive peptides. Trends Cell Biol. 13, 71–78 (2003).

    CAS  PubMed  Google Scholar 

  78. Akiyama, Y., Kanehara, K. & Ito, K. RseP (YaeL), an Escherichia coli RIP protease, cleaves transmembrane sequences. EMBO J. 23, 4434–4442 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Daley, D. O. et al. Global topology analysis of the Escherichia coli inner membrane proteome. Science 308, 1321–1323 (2005).

    ADS  CAS  PubMed  Google Scholar 

  80. An, F. Y., Sulavik, M. C. & Clewell, D. B. Identification and characterization of a determinant (eep) on the Enterococcus faecalis chromosome that is involved in production of the peptide sex pheromone cAD1. J. Bacteriol. 181, 5915–5921 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Ni, C. Y., Murphy, M. P., Golde, T. E. & Carpenter, G. γ -Secretase cleavage and nuclear localization of ErbB-4 receptor tyrosine kinase. Science 294, 2179–2181 (2001).

    ADS  CAS  PubMed  Google Scholar 

  82. Okamoto, I. et al. Proteolytic release of CD44 intracellular domain and its role in the CD44 signaling pathway. J. Cell Biol. 155, 755–762 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Marambaud, P. et al. A presenilin-1/γ-secretase cleavage releases the E-cadherin intracellular domain and regulates disassembly of adherens junctions. EMBO J. 21, 1948–1956 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Targett-Adams, P. et al. Signal peptide peptidase cleavage of GB virus B core protein is required for productive infection in vivo. J. Biol. Chem. 281, 29221–29227 (2006).

    CAS  PubMed  Google Scholar 

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Acknowledgements

E.B. is supported by the Israel Science Foundation and the Yale-Weizmann Collaborative Program. D.F. acknowledges support from the Kimmelman Center for Macromolecular Assemblies.

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Correspondence should be addressed to D.F. (deborah.fass@weizmann.ac.il) or E.B. (e.bibi@weizmann.ac.il).

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Erez, E., Fass, D. & Bibi, E. How intramembrane proteases bury hydrolytic reactions in the membrane. Nature 459, 371–378 (2009). https://doi.org/10.1038/nature08146

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