1
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Phosphatidylglyerol Lipid Binding at the Active Site of an Intramembrane Protease. J Membr Biol 2020; 253:563-576. [PMID: 33210155 PMCID: PMC7688093 DOI: 10.1007/s00232-020-00152-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 10/25/2022]
Abstract
Transmembrane substrate cleavage by the small Escherichia coli rhomboid protease GlpG informs on mechanisms by which lipid interactions shape reaction coordinates of membrane-embedded enzymes. Here, I review and discuss new work on the molecular picture of protein-lipid interactions that might govern the formation of the substrate-enzyme complex in fluid lipid membranes. Negatively charged PG-type lipids are of particular interest, because they are a major component of bacterial membranes. Atomistic computer simulations indicate POPG and DOPG lipids bridge remote parts of GlpG and might pre-occupy the substrate-docking site. Inhibition of catalytic activity by PG lipids could arise from ligand-like lipid binding at the active site, which could delay or prevent substrate docking. Dynamic protein-lipid H-bond networks, water access to the active site, and fluctuations in the orientation of GlpG suggest that GlpG has lipid-coupled dynamics that could shape the energy landscape of transmembrane substrate docking.
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2
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Almeida-Hernandez Y, Tidow H. Soluble Regions of GlpG Influence Protein–Lipid Interactions and Lipid Distribution. J Phys Chem B 2019; 123:7852-7858. [DOI: 10.1021/acs.jpcb.9b06943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasser Almeida-Hernandez
- Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, Hamburg D-20146, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, Hamburg D-22761, Germany
| | - Henning Tidow
- Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, Hamburg D-20146, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, Hamburg D-22761, Germany
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3
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Abstract
Membranes surrounding the biological cell and its internal compartments host proteins that catalyze chemical reactions essential for the functioning of the cell. Rather than being a passive structural matrix that holds membrane-embedded proteins in place, the membrane can largely shape the conformational energy landscape of membrane proteins and impact the energetics of their chemical reaction. Here, we highlight the challenges in understanding how lipids impact the conformational energy landscape of macromolecular membrane complexes whose functioning involves chemical reactions including proton transfer. We review here advances in our understanding of how chemical reactions occur at membrane interfaces gleaned with both theoretical and experimental advances using simple protein systems as guides. Our perspective is that of bridging experiments with theory to understand general physicochemical principles of membrane reactions, with a long term goal of furthering our understanding of the role of the lipids on the functioning of complex macromolecular assemblies at the membrane interface.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin , Department of Physics, Theoretical Molecular Biophysics Group , Arnimallee 14 , D-14195 Berlin , Germany
| | - M Joanne Lemieux
- University of Alberta , Department of Biochemistry, Membrane Protein Disease Research Group , Edmonton , Alberta T6G 2H7 , Canada
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4
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Shokhen M, Albeck A. How does the exosite of rhomboid protease affect substrate processing and inhibition? Protein Sci 2017; 26:2355-2366. [PMID: 28884847 DOI: 10.1002/pro.3294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 09/03/2017] [Indexed: 12/24/2022]
Abstract
Rhomboid proteases constitute a family of intramembrane serine proteases ubiquitous in all forms of life. They differ in many aspects from their soluble counterparts. We applied molecular dynamics (MD) computational approach to address several challenging issues regarding their catalytic mechanism: How does the exosite of GlpG rhomboid protease control the kinetics efficiency of substrate hydrolysis? What is the mechanism of inhibition by the non-competitive peptidyl aldehyde inhibitors bound to the GlpG rhomboid active site (AS)? What is the underlying mechanism that explains the hypothesis that GlpG rhomboid protease is not adopted for the hydrolysis of short peptides that do not contain a transmembrane domain (TMD)? Two fundamental features of rhomboid catalysis, the enzyme recognition and discrimination of substrates by TMD interactions in the exosite, and the concerted mechanism of non-covalent pre-catalytic complex to covalent tetrahedral complex (TC) conversion, provide answers to these mechanistic questions.
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Affiliation(s)
- Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel
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5
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Langosch D, Steiner H. Substrate processing in intramembrane proteolysis by γ-secretase - the role of protein dynamics. Biol Chem 2017; 398:441-453. [PMID: 27845877 DOI: 10.1515/hsz-2016-0269] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/08/2016] [Indexed: 01/31/2023]
Abstract
Intramembrane proteases comprise a number of different membrane proteins with different types of catalytic sites. Their common denominator is cleavage within the plane of the membrane, which usually results in peptide bond scission within the transmembrane helices of their substrates. Despite recent progress in the determination of high-resolution structures, as illustrated here for the γ-secretase complex and its substrate C99, it is still unknown how these enzymes function and how they distinguish between substrates and non-substrates. In principle, substrate/non-substrate discrimination could occur at the level of substrate binding and/or cleavage. Focusing on the γ-secretase/C99 pair, we will discuss recent observations suggesting that global motions within a substrate transmembrane helix may be much more important for defining a substrate than local unraveling at cleavage sites.
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6
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The Rhomboid Protease GlpG Promotes the Persistence of Extraintestinal Pathogenic Escherichia coli within the Gut. Infect Immun 2017; 85:IAI.00866-16. [PMID: 28373355 PMCID: PMC5442614 DOI: 10.1128/iai.00866-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/27/2017] [Indexed: 12/22/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are typically benign within the mammalian gut but can disperse to extraintestinal sites to cause diseases like urinary tract infections and sepsis. As occupation of the intestinal tract is often a prerequisite for ExPEC-mediated pathogenesis, we set out to understand how ExPEC colonizes this niche. A screen using transposon sequencing (Tn-seq) was performed to search for genes within ExPEC isolate F11 that are important for growth in intestinal mucus, which is thought to be a major source of nutrients for E. coli in the gut. Multiple genes that contribute to ExPEC fitness in mucus broth were identified, with genes that are directly or indirectly associated with fatty acid beta-oxidation pathways being especially important. One of the identified mucus-specific fitness genes encodes the rhomboid protease GlpG. In vitro, we found that the disruption of glpG had polar effects on the downstream gene glpR, which encodes a transcriptional repressor of factors that catalyze glycerol degradation. Mutation of either glpG or glpR impaired ExPEC growth in mucus and on plates containing the long-chain fatty acid oleate as the sole carbon source. In contrast, in a mouse gut colonization model in which the natural microbiota is unperturbed, the disruption of glpG but not glpR significantly reduced ExPEC survival. This work reveals a novel biological role for a rhomboid protease and highlights new avenues for defining mechanisms by which ExPEC strains colonize the mammalian gastrointestinal tract.
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7
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Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux MJ. Reversible Unfolding of Rhomboid Intramembrane Proteases. Biophys J 2016; 110:1379-90. [PMID: 27028647 DOI: 10.1016/j.bpj.2016.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022] Open
Abstract
Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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8
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Bondar AN. Biophysical mechanism of rhomboid proteolysis: Setting a foundation for therapeutics. Semin Cell Dev Biol 2016; 60:46-51. [DOI: 10.1016/j.semcdb.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 08/12/2016] [Accepted: 09/12/2016] [Indexed: 11/16/2022]
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9
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Urban S. A guide to the rhomboid protein superfamily in development and disease. Semin Cell Dev Biol 2016; 60:1-4. [PMID: 27751777 DOI: 10.1016/j.semcdb.2016.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/13/2016] [Indexed: 11/28/2022]
Abstract
Rhomboid proteins are considered to be the most widespread membrane proteins across all forms of life. This superfamily comprises both active intramembrane serine proteases that catalyze the release of factors from the membrane, and a eukaryotic subset of non-catalytic members in which rhomboid architecture supports deviating functions. Although rhomboid was discovered in genetic studies of insect development, rhomboid research has broadened dramatically over the past 15 years; rhomboid enzymes are now the best biophysically understood of all intramembrane proteases, and are considered promising therapeutic targets for diseases ranging from parasitic infections to Parkinsonian neurodegeneration. Perhaps the most rapid progress has come with the catalytically inert rhomboid proteins, some of which regulate protein trafficking and/or function, and their prominence is underscored by clinical mutations. Such a diverse collection of advances mark an excellent point to review the state of this vibrant area of research, not because central questions have been answered, but instead because a firm grip in key areas has been established, and the field is now poised for breakthroughs.
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Affiliation(s)
- Siniša Urban
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD, 21205, USA.
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10
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Zer Aviv P, Shubely M, Moskovits Y, Viskind O, Albeck A, Vertommen D, Ruthstein S, Shokhen M, Gruzman A. A New Oxopiperazin-Based Peptidomimetic Molecule Inhibits Prostatic Acid Phosphatase Secretion and Induces Prostate Cancer Cell Apoptosis. ChemistrySelect 2016. [DOI: 10.1002/slct.201600987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pinchas Zer Aviv
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Moran Shubely
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Yoni Moskovits
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Olga Viskind
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Amnon Albeck
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Didier Vertommen
- de Duve Institute; Université catholique de Louvain; Brussels 1200 Belgium
| | - Sharon Ruthstein
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Michael Shokhen
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Arie Gruzman
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
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11
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Hwang J, Ribbens D, Raychaudhuri S, Cairns L, Gu H, Frost A, Urban S, Espenshade PJ. A Golgi rhomboid protease Rbd2 recruits Cdc48 to cleave yeast SREBP. EMBO J 2016; 35:2332-2349. [PMID: 27655872 DOI: 10.15252/embj.201693923] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 09/06/2016] [Indexed: 12/26/2022] Open
Abstract
Hypoxic growth of fungi requires sterol regulatory element-binding protein (SREBP) transcription factors, and human opportunistic fungal pathogens require SREBP activation for virulence. Proteolytic release of fission yeast SREBPs from the membrane in response to low oxygen requires the Golgi membrane-anchored Dsc E3 ligase complex. Using genetic interaction arrays, we identified Rbd2 as a rhomboid family protease required for SREBP proteolytic processing. Rbd2 is an active, Golgi-localized protease that cleaves the transmembrane segment of the TatA rhomboid model substrate. Epistasis analysis revealed that the Dsc E3 ligase acts on SREBP prior to cleavage by Rbd2. Using APEX2 proximity biotinylation, we demonstrated that Rbd2 binds the AAA-ATPase Cdc48 through a C-terminal SHP box. Interestingly, SREBP cleavage required Rbd2 binding of Cdc48, consistent with Cdc48 acting to recruit ubiquitinylated substrates. In support of this claim, overexpressing a Cdc48-binding mutant of Rbd2 bypassed the Cdc48 requirement for SREBP cleavage, demonstrating that Cdc48 likely plays a role in SREBP recognition. In the absence of functional Rbd2, SREBP precursor is degraded by the proteasome, indicating that Rbd2 activity controls the balance between SREBP activation and degradation.
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Affiliation(s)
- Jiwon Hwang
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Diedre Ribbens
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leah Cairns
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - He Gu
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Siniša Urban
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter J Espenshade
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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Functional Implications of Domain Organization Within Prokaryotic Rhomboid Proteases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 883:107-17. [PMID: 26621464 DOI: 10.1007/978-3-319-23603-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Intramembrane proteases are membrane embedded enzymes that cleave transmembrane substrates. This interesting class of enzyme and its water mediated substrate cleavage mechanism occurring within the hydrophobic lipid bilayer has drawn the attention of researchers. Rhomboids are a family of ubiquitous serine intramembrane proteases. Bacterial forms of rhomboid proteases are mainly composed of six transmembrane helices that are preceded by a soluble N-terminal domain. Several crystal structures of the membrane domain of the E. coli rhomboid protease ecGlpG have been solved. Independently, the ecGlpG N-terminal cytoplasmic domain structure was solved using both NMR and protein crystallography. Despite these structures, we still do not know the structure of the full-length protein, nor do we know the functional role of these domains in the cell. This chapter will review the structural and functional roles of the different domains associated with prokaryotic rhomboid proteases. Lastly, we will address questions remaining in the field.
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13
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Lau JB, Stork S, Moog D, Schulz J, Maier UG. Protein-protein interactions indicate composition of a 480 kDa SELMA complex in the second outermost membrane of diatom complex plastids. Mol Microbiol 2016; 100:76-89. [PMID: 26712034 DOI: 10.1111/mmi.13302] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 02/04/2023]
Abstract
Most secondary plastids of red algal origin are surrounded by four membranes and nucleus-encoded plastid proteins have to traverse these barriers. Translocation across the second outermost plastid membrane, the periplastidal membrane (PPM), is facilitated by a ERAD-(ER-associated degradation) derived machinery termed SELMA (symbiont-specific ERAD-like machinery). In the last years, important subunits of this translocator have been identified, which clearly imply compositional similarities between SELMA and ERAD. Here we investigated, via protein-protein interaction studies, if the composition of SELMA is comparable to the known ERAD complex. As a result, our data suggest that the membrane proteins of SELMA, the derlin proteins, are linked to the soluble sCdc48 complex via the UBX protein sUBX. This is similar to the ERAD machinery whereas the additional SELMA components, sPUB und a second Cdc48 copy might indicate the influence of functional constraints in developing a translocation machinery from ERAD-related factors. In addition, we show for the first time that a rhomboid protease is a central interaction partner of the membrane proteins of the SELMA system in complex plastids.
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Affiliation(s)
- Julia B Lau
- Laboratory for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Simone Stork
- Laboratory for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Moog
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Germany
| | - Julian Schulz
- Laboratory for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Uwe G Maier
- Laboratory for Cell Biology, Philipps-Universität Marburg, Marburg, Germany.,LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Germany
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14
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015; 55:1680-4. [DOI: 10.1002/anie.201507772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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15
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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16
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Nguyen MTN, Kersavond TV, Verhelst SHL. Chemical Tools for the Study of Intramembrane Proteases. ACS Chem Biol 2015; 10:2423-34. [PMID: 26473325 DOI: 10.1021/acschembio.5b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intramembrane proteases (IMPs) reside inside lipid bilayers and perform peptide hydrolysis in transmembrane or juxtamembrane regions of their substrates. Many IMPs are involved in crucial regulatory pathways and human diseases, including Alzheimer's disease, Parkinson's disease, and diabetes. In the past, chemical tools have been instrumental in the study of soluble proteases, enabling biochemical and biomedical research in complex environments such as tissue lysates or living cells. However, IMPs place special challenges on probe design and applications, and progress has been much slower than for soluble proteases. In this review, we will give an overview of the available chemical tools for IMPs, including activity-based probes, affinity-based probes, and synthetic substrates. We will discuss how these have been used to increase our structural and functional understanding of this fascinating group of enzymes, and how they might be applied to address future questions and challenges.
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Affiliation(s)
- Minh T. N. Nguyen
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Tim Van Kersavond
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Steven H. L. Verhelst
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
- KU Leuven − University of Leuven, Department
of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 Box 802, 3000 Leuven, Belgium
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17
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Bae HE, Gotfryd K, Thomas J, Hussain H, Ehsan M, Go J, Loland CJ, Byrne B, Chae PS. Deoxycholate-Based Glycosides (DCGs) for Membrane Protein Stabilisation. Chembiochem 2015; 16:1454-9. [PMID: 25953685 DOI: 10.1002/cbic.201500151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Indexed: 12/16/2022]
Abstract
Detergents are an absolute requirement for studying the structure of membrane proteins. However, many conventional detergents fail to stabilise denaturation-sensitive membrane proteins, such as eukaryotic proteins and membrane protein complexes. New amphipathic agents with enhanced efficacy in stabilising membrane proteins will be helpful in overcoming the barriers to studying membrane protein structures. We have prepared a number of deoxycholate-based amphiphiles with carbohydrate head groups, designated deoxycholate-based glycosides (DCGs). These DCGs are the hydrophilic variants of previously reported deoxycholate-based N-oxides (DCAOs). Membrane proteins in these agents, particularly the branched diglucoside-bearing amphiphiles DCG-1 and DCG-2, displayed favourable behaviour compared to previously reported parent compounds (DCAOs) and conventional detergents (LDAO and DDM). Given their excellent properties, these agents should have significant potential for membrane protein studies.
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Affiliation(s)
- Hyoung Eun Bae
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea)
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology, University of Copenhagen, Nørre Alle 20, 2200 Copenhagen (Denmark).,Present address: Department of Biomedical Sciences, University of Copenhagen, Nørre Alle 20, 2200 Copenhagen (Denmark)
| | - Jennifer Thomas
- Present address: MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 OQH (UK).,Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ (UK)
| | - Hazrat Hussain
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea)
| | - Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea)
| | - Juyeon Go
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea)
| | - Claus J Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, Nørre Alle 20, 2200 Copenhagen (Denmark)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ (UK)
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea).
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18
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Stangl M, Schneider D. Functional competition within a membrane: Lipid recognition vs. transmembrane helix oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1886-96. [PMID: 25791349 DOI: 10.1016/j.bbamem.2015.03.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 12/27/2022]
Abstract
Binding of specific lipids to large, polytopic membrane proteins is well described, and it is clear that such lipids are crucial for protein stability and activity. In contrast, binding of defined lipid species to individual transmembrane helices and regulation of transmembrane helix monomer-oligomer equilibria by binding of distinct lipids is a concept, which has emerged only lately. Lipids bind to single-span membrane proteins, both in the juxta-membrane region as well as in the hydrophobic membrane core. While some interactions counteract transmembrane helix oligomerization, in other cases lipid binding appears to enhance oligomerization. As reversible oligomerization is involved in activation of many membrane proteins, binding of defined lipids to single-span transmembrane proteins might be a mechanism to regulate and/or fine-tune the protein activity. But how could lipid binding trigger the activity of a protein? How can binding of a single lipid molecule to a transmembrane helix affect the structure of a transmembrane helix oligomer, and consequently its signaling state? These questions are discussed in the present article based on recent results obtained with simple, single-span transmembrane proteins. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Michael Stangl
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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Dickey SW, Baker RP, Cho S, Urban S. Proteolysis inside the membrane is a rate-governed reaction not driven by substrate affinity. Cell 2014; 155:1270-81. [PMID: 24315097 DOI: 10.1016/j.cell.2013.10.053] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/04/2013] [Accepted: 10/28/2013] [Indexed: 10/25/2022]
Abstract
Enzymatic cleavage of transmembrane anchors to release proteins from the membrane controls diverse signaling pathways and is implicated in more than a dozen diseases. How catalysis works within the viscous, water-excluding, two-dimensional membrane is unknown. We developed an inducible reconstitution system to interrogate rhomboid proteolysis quantitatively within the membrane in real time. Remarkably, rhomboid proteases displayed no physiological affinity for substrates (K(d) ~190 μM/0.1 mol%). Instead, ~10,000-fold differences in proteolytic efficiency with substrate mutants and diverse rhomboid proteases were reflected in k(cat) values alone. Analysis of gate-open mutant and solvent isotope effects revealed that substrate gating, not hydrolysis, is rate limiting. Ultimately, a single proteolytic event within the membrane normally takes minutes. Rhomboid intramembrane proteolysis is thus a slow, kinetically controlled reaction not driven by transmembrane protein-protein affinity. These properties are unlike those of other studied proteases or membrane proteins but are strikingly reminiscent of one subset of DNA-repair enzymes, raising important mechanistic and drug-design implications.
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Affiliation(s)
- Seth W Dickey
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
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Ohki Y, Shimada N, Tominaga A, Osawa S, Higo T, Yokoshima S, Fukuyama T, Tomita T, Iwatsubo T. Binding of longer Aβ to transmembrane domain 1 of presenilin 1 impacts on Aβ42 generation. Mol Neurodegener 2014; 9:7. [PMID: 24410857 PMCID: PMC3896738 DOI: 10.1186/1750-1326-9-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/10/2014] [Indexed: 11/18/2022] Open
Abstract
Background Amyloid-β peptide ending at 42nd residue (Aβ42) is believed as a pathogenic peptide for Alzheimer disease. Although γ-secretase is a responsible protease to generate Aβ through a processive cleavage, the proteolytic mechanism of γ-secretase at molecular level is poorly understood. Results We found that the transmembrane domain (TMD) 1 of presenilin (PS) 1, a catalytic subunit for the γ-secretase, as a key modulatory domain for Aβ42 production. Aβ42-lowering and -raising γ-secretase modulators (GSMs) directly targeted TMD1 of PS1 and affected its structure. A point mutation in TMD1 caused an aberrant secretion of longer Aβ species including Aβ45 that are the precursor of Aβ42. We further found that the helical surface of TMD1 is involved in the binding of Aβ45/48 and that the binding was altered by GSMs as well as TMD1 mutation. Conclusions Binding between PS1 TMD1 and longer Aβ is critical for Aβ42 production.
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Affiliation(s)
| | | | | | | | | | | | | | - Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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21
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Untangling structure-function relationships in the rhomboid family of intramembrane proteases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2862-72. [PMID: 24099005 DOI: 10.1016/j.bbamem.2013.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/04/2013] [Accepted: 05/04/2013] [Indexed: 12/30/2022]
Abstract
Rhomboid proteases are a family of integral membrane proteins that have been implicated in critical regulatory roles in a wide array of cellular processes and signaling events. The determination of crystal structures of the prokaryotic rhomboid GlpG from Escherichia coli and Haemophilus influenzae has ushered in an era of unprecedented understanding into molecular aspects of intramembrane proteolysis by this fascinating class of protein. A combination of structural studies by X-ray crystallography, and biophysical and spectroscopic analyses, combined with traditional enzymatic and functional analysis has revealed fundamental aspects of rhomboid structure, substrate recognition and the catalytic mechanism. This review summarizes these remarkable advances by examining evidence for the proposed catalytic mechanism derived from inhibitor co-crystal structures, conflicting models of rhomboid-substrate interaction, and recent work on the structure and function of rhomboid cytosolic domains. In addition to exploring progress on aspects of rhomboid structure, areas for future research and unaddressed questions are emphasized and highlighted. This article is part of a Special Issue entitled: Intramembrane Proteases.
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22
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Intramembrane proteolysis by rhomboids: catalytic mechanisms and regulatory principles. Curr Opin Struct Biol 2013; 23:851-8. [DOI: 10.1016/j.sbi.2013.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/06/2013] [Accepted: 07/19/2013] [Indexed: 12/20/2022]
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Chae PS, Kruse AC, Gotfryd K, Rana RR, Cho KH, Rasmussen SGF, Bae HE, Chandra R, Gether U, Guan L, Kobilka BK, Loland CJ, Byrne B, Gellman SH. Novel tripod amphiphiles for membrane protein analysis. Chemistry 2013; 19:15645-51. [PMID: 24123610 PMCID: PMC3947462 DOI: 10.1002/chem.201301423] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/15/2013] [Indexed: 11/08/2022]
Abstract
Integral membrane proteins play central roles in controlling the flow of information and molecules across membranes. Our understanding of membrane protein structures and functions, however, is seriously limited, mainly due to difficulties in handling and analysing these proteins in aqueous solution. The use of a detergent or other amphipathic agents is required to overcome the intrinsic incompatibility between the large lipophilic surfaces displayed by the membrane proteins in their native forms and the polar solvent molecules. Here, we introduce new tripod amphiphiles displaying favourable behaviours toward several membrane protein systems, leading to an enhanced protein solubilisation and stabilisation compared to both conventional detergents and previously described tripod amphiphiles.
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Affiliation(s)
- Pil Seok Chae
- Department of Bionano Engineering, Hanyang University
Ansan, 426-791, (Korea), Fax: (+) 81 31 436 8146
| | - Andrew C. Kruse
- Molecular and Cellular Physiology, Stanford University
Stanford, CA, 94305 (USA)
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology University of
Copenhagen, 2200 Copenhagen (Denmark)
| | - Rohini R. Rana
- Department of Life Sciences, Imperial College London
London, SW7 2AZ, (UK)
| | - Kyung Ho Cho
- Department of Bionano Engineering, Hanyang University
Ansan, 426-791, (Korea), Fax: (+) 81 31 436 8146
| | | | - Hyoung Eun Bae
- Department of Bionano Engineering, Hanyang University
Ansan, 426-791, (Korea), Fax: (+) 81 31 436 8146
| | - Richa Chandra
- Molecular and Cellular Physiology, Stanford University
Stanford, CA, 94305 (USA)
| | - Ulrik Gether
- Department of Neuroscience and Pharmacology University of
Copenhagen, 2200 Copenhagen (Denmark)
| | - Lan Guan
- Molecular and Cellular Physiology, Stanford University
Stanford, CA, 94305 (USA)
| | - Brian K. Kobilka
- Molecular and Cellular Physiology, Stanford University
Stanford, CA, 94305 (USA)
| | - Claus J. Loland
- Department of Neuroscience and Pharmacology University of
Copenhagen, 2200 Copenhagen (Denmark)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London
London, SW7 2AZ, (UK)
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison
1101, University Avenue, Madison, WI 53706 (USA)
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Hildebrandt ER, Davis DM, Deaton J, Krishnankutty RK, Lilla E, Schmidt WK. Topology of the yeast Ras converting enzyme as inferred from cysteine accessibility studies. Biochemistry 2013; 52:6601-14. [PMID: 23972033 DOI: 10.1021/bi400647c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Ras converting enzyme (Rce1p) is an endoprotease that is involved in the post-translational processing of the Ras GTPases and other isoprenylated proteins. Its role in Ras biosynthesis marks Rce1p as an anticancer target. By assessing the chemical accessibility of cysteine residues substituted throughout the Saccharomyces cerevisiae Rce1p sequence, we have determined that yeast Rce1p has eight segments that are protected from chemical modification. Notably, the three residues that are essential for yeast Rce1p function (E156, H194, and H248) are all chemically inaccessible and associated with separate protected segments. By specifically assessing the chemical reactivity and glycosylation potential of the NH2 and COOH termini of Rce1p, we further demonstrate that Rce1p has an odd number of transmembrane spans. Substantial evidence that the most NH2-terminal segment functions as a transmembrane segment with the extreme NH2 terminus projecting into the endoplasmic reticulum (ER) lumen is presented. Because each of the remaining seven segments is too short to contain two spans and is flanked by chemically reactive positions, we infer that these segments are not transmembrane segments but rather represent compact structural features and/or hydrophobic loops that penetrate but do not fully span the bilayer (i.e., re-entrant helices). We thus propose a topological model in which yeast Rce1p contains a single transmembrane helix localized at its extreme NH2 terminus and one or more re-entrant helices and/or compact structural domains that populate the cytosolic face of the ER membrane. Lastly, we demonstrate that the natural cysteine residues of Rce1p are chemically inaccessible and fully dispensable for in vivo enzyme activity, formally eliminating the possibility of a cysteine-based enzymatic mechanism for this protease.
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Affiliation(s)
- Emily R Hildebrandt
- Department of Biochemistry and Molecular Biology, The University of Georgia , Athens, Georgia 30602, United States
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25
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Olzmann JA, Kopito RR, Christianson JC. The mammalian endoplasmic reticulum-associated degradation system. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a013185. [PMID: 23232094 DOI: 10.1101/cshperspect.a013185] [Citation(s) in RCA: 253] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The endoplasmic reticulum (ER) is the site of synthesis for nearly one-third of the eukaryotic proteome and is accordingly endowed with specialized machinery to ensure that proteins deployed to the distal secretory pathway are correctly folded and assembled into native oligomeric complexes. Proteins failing to meet this conformational standard are degraded by ER-associated degradation (ERAD), a complex process through which folding-defective proteins are selected and ultimately degraded by the ubiquitin-proteasome system. ERAD proceeds through four tightly coupled steps involving substrate selection, dislocation across the ER membrane, covalent conjugation with polyubiquitin, and proteasomal degradation. The ERAD machinery shows a modular organization with central ER membrane-embedded ubiquitin ligases linking components responsible for recognition in the ER lumen to the ubiquitin-proteasome system in the cytoplasm. The core ERAD machinery is highly conserved among eukaryotes and much of our basic understanding of ERAD organization has been derived from genetic and biochemical studies of yeast. In this article we discuss how the core ERAD machinery is organized in mammalian cells.
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Affiliation(s)
- James A Olzmann
- Department of Biology, Stanford University, Stanford, California 94305, USA
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26
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Residues in conserved loops of intramembrane metalloprotease SpoIVFB interact with residues near the cleavage site in pro-σK. J Bacteriol 2013; 195:4936-46. [PMID: 23995631 DOI: 10.1128/jb.00807-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Intramembrane metalloproteases (IMMPs) control critical biological processes by cleaving membrane-associated proteins within a transmembrane segment or at a site near the membrane surface. Phylogenetic analysis divides IMMPs into four groups. SpoIVFB is a group III IMMP that regulates Bacillus subtilis endospore formation by cleaving Pro-σ(K) and releasing the active sigma factor from a membrane. To elucidate the enzyme-substrate interaction, single-cysteine versions of catalytically inactive SpoIVFB and C-terminally truncated Pro-σ(K)(1-126) (which can be cleaved by active SpoIVFB) were coexpressed in Escherichia coli, and proximity was tested by disulfide cross-linking in vivo. As expected, the results provided evidence that catalytic residue Glu-44 of SpoIVFB is near the cleavage site in the substrate. Also near the cleavage site were two residues of SpoIVFB in predicted conserved loops; Pro-135 in a short loop and Val-70 in a longer loop. Pro-135 corresponds to Pro-399 of RseP, a group I IMMP, and Pro-399 was reported previously to interact with substrate near the cleavage site, suggesting a conserved interaction across IMMP subfamilies. Val-70 follows a newly recognized conserved motif, PXGG (X is a large hydrophobic residue), which is in a hydrophobic region predicted to be a membrane reentrant loop. Following the hydrophobic region is a negatively charged region that is conserved in IMMPs of groups I and III. At least two residues with a negatively charged side chain are required in this region for activity of SpoIVFB. The region exhibits other features in IMMPs of groups II and IV. Its possible roles, as well as that of the short loop, are discussed. New insights into IMMP-substrate interaction build toward understanding how IMMPs function and may facilitate manipulation of their activity.
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27
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Features of Pro-σK important for cleavage by SpoIVFB, an intramembrane metalloprotease. J Bacteriol 2013; 195:2793-806. [PMID: 23585539 DOI: 10.1128/jb.00229-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intramembrane proteases regulate diverse processes by cleaving substrates within a transmembrane segment or near the membrane surface. Bacillus subtilis SpoIVFB is an intramembrane metalloprotease that cleaves Pro-σ(K) during sporulation. To elucidate features of Pro-σ(K) important for cleavage by SpoIVFB, coexpression of the two proteins in Escherichia coli was used along with cell fractionation. In the absence of SpoIVFB, a portion of the Pro-σ(K) was peripherally membrane associated. This portion was not observed in the presence of SpoIVFB, suggesting that it serves as the substrate. Deletion of Pro-σ(K) residues 2 to 8, addition of residues at its N terminus, or certain single-residue substitutions near the cleavage site impaired cleavage. Certain multiresidue substitutions near the cleavage site changed the position of cleavage, revealing preferences for a small residue preceding the cleavage site N-terminally (i.e., at the P1 position) and a hydrophobic residue at the second position following the cleavage site C-terminally (i.e., P2'). These features appear to be conserved among Pro-σ(K) orthologs. SpoIVFB did not tolerate an aromatic residue at P1 or P2' of Pro-σ(K). A Lys residue at P3' of Pro-σ(K) could not be replaced with Ala unless a Lys was provided farther C-terminally (e.g., at P9'). α-Helix-destabilizing residues near the cleavage site were not crucial for SpoIVFB to cleave Pro-σ(K). The preferences and tolerances of SpoIVFB are somewhat different from those of other intramembrane metalloproteases, perhaps reflecting differences in the interaction of the substrate with the membrane and the enzyme.
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28
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Pryor EE, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME. Structure of the integral membrane protein CAAX protease Ste24p. Science 2013; 339:1600-4. [PMID: 23539602 DOI: 10.1126/science.1232048] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Posttranslational lipidation provides critical modulation of the functions of some proteins. Isoprenoids (i.e., farnesyl or geranylgeranyl groups) are attached to cysteine residues in proteins containing C-terminal CAAX sequence motifs (where A is an aliphatic residue and X is any residue). Isoprenylation is followed by cleavage of the AAX amino acid residues and, in some cases, by additional proteolytic cuts. We determined the crystal structure of the CAAX protease Ste24p, a zinc metalloprotease catalyzing two proteolytic steps in the maturation of yeast mating pheromone a-factor. The Ste24p core structure is a ring of seven transmembrane helices enclosing a voluminous cavity containing the active site and substrate-binding groove. The cavity is accessible to the external milieu by means of gaps between splayed transmembrane helices. We hypothesize that cleavage proceeds by means of a processive mechanism of substrate insertion, translocation, and ejection.
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29
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Bergbold N, Lemberg MK. Emerging role of rhomboid family proteins in mammalian biology and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2840-8. [PMID: 23562403 DOI: 10.1016/j.bbamem.2013.03.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 02/26/2013] [Accepted: 03/26/2013] [Indexed: 01/19/2023]
Abstract
From proteases that cleave peptide bonds in the plane of the membrane, rhomboids have evolved into a heterogeneous superfamily with a wide range of different mechanistic properties. In mammals 14 family members have been annotated based on a shared conserved membrane-integral rhomboid core domain, including intramembrane serine proteases and diverse proteolytically inactive homologues. While the function of rhomboid proteases is the proteolytic release of membrane-tethered factors, rhomboid pseudoproteases including iRhoms and derlins interact with their clients without cleaving them. It has become evident that specific recognition of membrane protein substrates and clients by the rhomboid fold reflects a spectrum of cellular functions ranging from growth factor activation, trafficking control to membrane protein degradation. This review summarizes recent progress on rhomboid family proteins in the mammalian secretory pathway and raises the question whether they can be seen as new drug targets for inflammatory diseases and cancer. This article is part of a special issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Nina Bergbold
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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30
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Chae PS, Rana RR, Gotfryd K, Rasmussen SGF, Kruse AC, Cho KH, Capaldi S, Carlsson E, Kobilka B, Loland CJ, Gether U, Banerjee S, Byrne B, Lee JK, Gellman SH. Glucose-neopentyl glycol (GNG) amphiphiles for membrane protein study. Chem Commun (Camb) 2013; 49:2287-9. [PMID: 23165475 PMCID: PMC3578972 DOI: 10.1039/c2cc36844g] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of a new class of surfactants for membrane protein manipulation, "GNG amphiphiles", is reported. These amphiphiles display promising behavior for membrane proteins, as demonstrated recently by the high resolution structure of a sodium-pumping pyrophosphatase reported by Kellosalo et al. (Science, 2012, 337, 473).
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Affiliation(s)
- Pil Seok Chae
- Department of Bionano Engineering, Hanyang University, Ansan, 426-791, Korea
| | - Rohini R. Rana
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Andrew C. Kruse
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Kyung Ho Cho
- Department of Bionano Engineering, Hanyang University, Ansan, 426-791, Korea
| | - Stefano Capaldi
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Emil Carlsson
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Brian Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Claus J. Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ulrik Gether
- Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - John K. Lee
- Department of Biochemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Making the cut: intramembrane cleavage by a rhomboid protease promotes ERAD. Nat Struct Mol Biol 2013; 19:979-81. [PMID: 23037595 DOI: 10.1038/nsmb.2398] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Endoplasmic reticulum–associated degradation (ERAD) is a cellular protein quality-control process that disposes of proteasomal substrates from the early secretory pathway. Recent work shows that the endoplasmic reticulum–resident rhomboid protease RHBDL4 facilitates ERAD by recognizing and cleaving integral membrane substrates. The work indicates that intramembrane proteolysis may have a general role in the extraction of misfolded membrane proteins from the endoplasmic reticulum.
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32
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Activity-based probes for rhomboid proteases discovered in a mass spectrometry-based assay. Proc Natl Acad Sci U S A 2013; 110:2472-7. [PMID: 23359682 DOI: 10.1073/pnas.1215076110] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rhomboid proteases are evolutionary conserved intramembrane serine proteases. Because of their emerging role in many important biological pathways, rhomboids are potential drug targets. Unfortunately, few chemical tools are available for their study. Here, we describe a mass spectrometry-based assay to measure rhomboid substrate cleavage and inhibition. We have identified isocoumarin inhibitors and developed activity-based probes for rhomboid proteases. The probes can distinguish between active and inactive rhomboids due to covalent, reversible binding of the active-site serine and stable modification of a histidine residue. Finally, the structure of an isocoumarin-based inhibitor with Escherichia coli rhomboid GlpG uncovers an unusual mode of binding at the active site and suggests that the interactions between the 3-substituent on the isocoumarin inhibitor and hydrophobic residues on the protease reflect S' subsite binding. Overall, these probes represent valuable tools for rhomboid study, and the structural insights may facilitate future inhibitor design.
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Moin SM, Urban S. Membrane immersion allows rhomboid proteases to achieve specificity by reading transmembrane segment dynamics. eLife 2012; 1:e00173. [PMID: 23150798 PMCID: PMC3494066 DOI: 10.7554/elife.00173] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 09/12/2012] [Indexed: 12/28/2022] Open
Abstract
Rhomboid proteases reside within cellular membranes, but the advantage of this unusual environment is unclear. We discovered membrane immersion allows substrates to be identified in a fundamentally-different way, based initially upon exposing ‘masked’ conformational dynamics of transmembrane segments rather than sequence-specific binding. EPR and CD spectroscopy revealed that the membrane restrains rhomboid gate and substrate conformation to limit proteolysis. True substrates evolved intrinsically-unstable transmembrane helices that both become unstructured when not supported by the membrane, and facilitate partitioning into the hydrophilic, active-site environment. Accordingly, manipulating substrate and gate dynamics in living cells shifted cleavage sites in a manner incompatible with extended sequence binding, but correlated with a membrane-and-helix-exit propensity scale. Moreover, cleavage of diverse non-substrates was provoked by single-residue changes that destabilize transmembrane helices. Membrane immersion thus bestows rhomboid proteases with the ability to identify substrates primarily based on reading their intrinsic transmembrane dynamics. DOI:http://dx.doi.org/10.7554/eLife.00173.001 Proteases are enzymes that break the peptide bonds that hold proteins together, and have a central role in many physiological processes, including digestion, blood clotting and programmed cell death. An important characteristic of proteases is that they are highly selective, only cutting proteins that contain well-defined sequences of amino acids in accessible regions. Proteases that are soluble in water have been studied for over a century and are now well understood, as are proteases that need to be tethered to the membrane of a cell to work properly. In 1997 researchers discovered a protease that was immersed in the cell membrane, and it soon became clear that these intramembrane proteases were widespread and involved in a wide range of processes in cells. Examples of intramembrane proteases include γ-secretase, which is implicated in Alzheimer's disease, and various site-2 proteases that regulate pathogenic circuits in bacteria. There are many similarities between soluble and intramembrane proteases. However, given that intramembrane proteases evolved within the hydrophobic environment of the membrane, whereas soluble proteases evolved in an aqueous environment, there should there should also be significant differences between them. The best understood intramembrane proteases in terms of their biochemistry are probably the rhomboid proteases. However, most studies of their function have been performed in detergent systems rather than in real membranes. Moin and Urban now report that the main strategy used by rhomboid proteases to identity the proteins that they selectively cut is completely different from that used by soluble proteases. Through a combination of biochemical and spectroscopic methods, they have discovered that rhomboid proteases identify the proteins they act on mainly by detecting changes in dynamic behavior: only those proteins that lose a stable helical structure when they exit the lipid phase to interact with the rhomboid protease will be cut by the rhomboid protease. Soluble proteases, on the other hand, achieve specificity by looking for proteins with a particular sequence of amino acids. The novel strategy used by rhomboid proteases allows them to patrol the membrane for unstable helices and selectively cut them. This discovery provides the first explanation of why these complicated enzymes evolved to have active sites immersed within the cell membrane. DOI:http://dx.doi.org/10.7554/eLife.00173.002
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Affiliation(s)
- Syed M Moin
- Department of Molecular Biology and Genetics , Howard Hughes Medical Institute, Johns Hopkins University , Baltimore , United States
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Knopf RR, Feder A, Mayer K, Lin A, Rozenberg M, Schaller A, Adam Z. Rhomboid proteins in the chloroplast envelope affect the level of allene oxide synthase in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:559-71. [PMID: 22738221 DOI: 10.1111/j.1365-313x.2012.05090.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rhomboids are intra-membrane serine proteases whose sequences are found in nearly all organisms. They are involved in a variety of biological functions in both eukaryotes and prokaryotes. Localization assays revealed that two Arabidopsis thaliana rhomboid-like proteases (AtRBL), AtRBL8 and AtRBL9, are targeted to the chloroplast. Using transgenic plants expressing epitope-tagged AtRBL9, we localized AtRBL9 to the chloroplast inner envelope membrane, with both its N- and C-termini facing the stroma. Mass spectrometry analyses confirmed this localization, and suggested that this is also the case for AtRBL8. Both are proteins of very low abundance. The results of size-exclusion chromatography implied that AtRBL9 forms homo-oligomers. In search of a putative function, a comparative proteomic analysis was performed on wild-type and double-knockout plants, lacking both AtRBL8 and AtRBL9, using the iTRAQ method. Of 180 envelope proteins, the level of only a few was either increased or decreased in the mutant line. One of the latter, allene oxide synthase, is involved in jasmonic acid biosynthesis. This observation provides an explanation for the recently reported aberration in flower morphology that is associated with the loss of AtRBL8.
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Affiliation(s)
- Ronit Rimon Knopf
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
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Karabadzhak AG, Weerakkody D, Wijesinghe D, Thakur MS, Engelman DM, Andreev OA, Markin VS, Reshetnyak YK. Modulation of the pHLIP transmembrane helix insertion pathway. Biophys J 2012; 102:1846-55. [PMID: 22768940 DOI: 10.1016/j.bpj.2012.03.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 02/24/2012] [Accepted: 03/12/2012] [Indexed: 12/15/2022] Open
Abstract
The membrane-associated folding/unfolding of pH (low) insertion peptide (pHLIP) provides an opportunity to study how sequence variations influence the kinetics and pathway of peptide insertion into bilayers. Here, we present the results of steady-state and kinetics investigations of several pHLIP variants with different numbers of charged residues, with attached polar cargoes at the peptide's membrane-inserting end, and with three single-Trp variants placed at the beginning, middle, and end of the transmembrane helix. Each pHLIP variant exhibits a pH-dependent interaction with a lipid bilayer. Although the number of protonatable residues at the inserting end does not affect the ultimate formation of helical structure across a membrane, it correlates with the time for peptide insertion, the number of intermediate states on the folding pathway, and the rates of unfolding and exit. The presence of polar cargoes at the peptide's inserting end leads to the appearance of intermediate states on the insertion pathway. Cargo polarity correlates with a decrease of the insertion rate. We conclude that the existence of intermediate states on the folding and unfolding pathways is not mandatory and, in the simple case of a polypeptide with a noncharged and nonpolar inserting end, the folding and unfolding appears as an all-or-none transition. We propose a model for membrane-associated insertion/folding and exit/unfolding and discuss the importance of these observations for the design of new delivery agents for direct translocation of polar therapeutic and diagnostic cargo molecules across cellular membranes.
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36
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Uritsky N, Shokhen M, Albeck A. The Catalytic Machinery of Rhomboid Proteases: Combined MD and QM Simulations. J Chem Theory Comput 2012; 8:4663-71. [DOI: 10.1021/ct3003767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Neta Uritsky
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Michael Shokhen
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Amnon Albeck
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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37
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Sherratt AR, Blais DR, Ghasriani H, Pezacki JP, Goto NK. Activity-Based Protein Profiling of the Escherichia coli GlpG Rhomboid Protein Delineates the Catalytic Core. Biochemistry 2012; 51:7794-803. [DOI: 10.1021/bi301087c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Allison R. Sherratt
- Department of Biochemistry,
Microbiology and Immunology, University of Ottawa, Health Sciences Campus, 451 Smyth Road, Ottawa, Canada K1H 8M5
| | - David R. Blais
- Steacie Institute for Molecular
Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Canada K1A 0R6
| | - Houman Ghasriani
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Canada
K1N 6N5
| | - John Paul Pezacki
- Department of Biochemistry,
Microbiology and Immunology, University of Ottawa, Health Sciences Campus, 451 Smyth Road, Ottawa, Canada K1H 8M5
- Steacie Institute for Molecular
Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Canada K1A 0R6
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Canada
K1N 6N5
| | - Natalie K. Goto
- Department of Biochemistry,
Microbiology and Immunology, University of Ottawa, Health Sciences Campus, 451 Smyth Road, Ottawa, Canada K1H 8M5
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Canada
K1N 6N5
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38
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Chae PS, Rasmussen SGF, Rana RR, Gotfryd K, Kruse AC, Manglik A, Cho KH, Nurva S, Gether U, Guan L, Loland CJ, Byrne B, Kobilka BK, Gellman SH. A new class of amphiphiles bearing rigid hydrophobic groups for solubilization and stabilization of membrane proteins. Chemistry 2012; 18:9485-90. [PMID: 22730191 PMCID: PMC3493560 DOI: 10.1002/chem.201200069] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Indexed: 12/24/2022]
Affiliation(s)
- Pil Seok Chae
- Department of Bionano Engineering, Hanyang University, Ansan, 426-791 (Korea)
| | | | - Rohini R. Rana
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen (Denmark)
| | - Andrew C. Kruse
- Molecular and Cellular Physiology, Stanford University Stanford, CA 94305 (USA)
| | - Aashish Manglik
- Molecular and Cellular Physiology, Stanford University Stanford, CA 94305 (USA)
| | - Kyung Ho Cho
- Department of Bionano Engineering, Hanyang University, Ansan, 426-791 (Korea)
| | - Shailika Nurva
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430 (USA)
| | - Ulrik Gether
- Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen (Denmark)
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430 (USA)
| | - Claus J. Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen (Denmark)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ (UK)
| | - Brian K. Kobilka
- Molecular and Cellular Physiology, Stanford University Stanford, CA 94305 (USA)
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706 (USA)
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39
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Architectural and thermodynamic principles underlying intramembrane protease function. Nat Chem Biol 2012; 8:759-68. [PMID: 22797666 PMCID: PMC4028635 DOI: 10.1038/nchembio.1021] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 06/07/2012] [Indexed: 12/18/2022]
Abstract
Intramembrane proteases hydrolyze peptide bonds within the membrane as a signaling paradigm universal to all life forms and with implications in disease. Deciphering the architectural strategies supporting intramembrane proteolysis is an essential but unattained goal. We integrated a new, quantitative and high-throughput thermal light-scattering technology, reversible equilibrium un/refolding, and quantitative protease assays to interrogate rhomboid architecture with 151 purified variants. Rhomboid proteases maintain low intrinsic thermodynamic stability (ΔG=2.1-4.5kcal/mol) resulting from a multitude of generally-weak transmembrane packing interactions, making them highly-responsive to their environment. Stability is consolidated by two buried glycines and several packing leucines, with a few multifaceted hydrogen bonds strategically-deployed to two peripheral regions. Opposite these regions lie transmembrane segment 5 and connected loops that are notably exempt of structural responsibility, suggesting intramembrane proteolysis involves considerable but localized protein dynamics. Our analyses provide a comprehensive ‘heat map’ of the physio-chemical anatomy underlying membrane-immersed enzyme function at unprecedented resolution.
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40
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Zhou Y, Moin SM, Urban S, Zhang Y. An internal water-retention site in the rhomboid intramembrane protease GlpG ensures catalytic efficiency. Structure 2012; 20:1255-63. [PMID: 22705210 DOI: 10.1016/j.str.2012.04.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 02/29/2012] [Accepted: 04/05/2012] [Indexed: 12/11/2022]
Abstract
Rhomboid proteases regulate key cellular pathways, but their biochemical mechanism including how water is made available to the membrane-immersed active site remains ambiguous. We performed four prolonged molecular dynamics simulations initiated from both gate-open and gate-closed states of Escherichia coli rhomboid GlpG in a phospholipid bilayer. GlpG was notably stable in both gating states, experiencing similar tilt and local membrane thinning, with no observable gating transitions, highlighting that gating is rate-limiting. Analysis of dynamics revealed rapid loss of crystallographic waters from the active site, but retention of a water cluster within a site formed by His141, Ser181, Ser185, and/or Gln189. Experimental interrogation of 14 engineered mutants revealed an essential role for at least Gln189 and Ser185 in catalysis with no effect on structural stability. Our studies indicate that spontaneous water supply to the intramembrane active site of rhomboid proteases is rare, but its availability for catalysis is ensured by an unanticipated active site element, the water-retention site.
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Affiliation(s)
- Yanzi Zhou
- Department of Chemistry, New York University, New York, NY 10003, USA
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41
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Barrett PJ, Song Y, Van Horn WD, Hustedt EJ, Schafer JM, Hadziselimovic A, Beel AJ, Sanders CR. The amyloid precursor protein has a flexible transmembrane domain and binds cholesterol. Science 2012; 336:1168-71. [PMID: 22654059 PMCID: PMC3528355 DOI: 10.1126/science.1219988] [Citation(s) in RCA: 371] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
C99 is the transmembrane carboxyl-terminal domain of the amyloid precursor protein that is cleaved by γ-secretase to release the amyloid-β polypeptides, which are associated with Alzheimer's disease. Nuclear magnetic resonance and electron paramagnetic resonance spectroscopy show that the extracellular amino terminus of C99 includes a surface-embedded "N-helix" followed by a short "N-loop" connecting to the transmembrane domain (TMD). The TMD is a flexibly curved α helix, making it well suited for processive cleavage by γ-secretase. Titration of C99 reveals a binding site for cholesterol, providing mechanistic insight into how cholesterol promotes amyloidogenesis. Membrane-buried GXXXG motifs (G, Gly; X, any amino acid), which have an established role in oligomerization, were also shown to play a key role in cholesterol binding. The structure and cholesterol binding properties of C99 may aid in the design of Alzheimer's therapeutics.
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Affiliation(s)
- Paul J. Barrett
- Dept. of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yuanli Song
- Dept. of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Wade D. Van Horn
- Dept. of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Eric J. Hustedt
- Dept. of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Johanna M. Schafer
- Dept. of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Arina Hadziselimovic
- Dept. of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew J. Beel
- Dept. of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Charles R. Sanders
- Dept. of Biochemistry, Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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42
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Thompson EP, Smith SGL, Glover BJ. An Arabidopsis rhomboid protease has roles in the chloroplast and in flower development. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3559-70. [PMID: 22416142 PMCID: PMC3388827 DOI: 10.1093/jxb/ers012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 01/03/2012] [Accepted: 01/08/2012] [Indexed: 05/23/2023]
Abstract
Increasing numbers of cellular pathways are now recognized to be regulated via proteolytic processing events. The rhomboid family of serine proteases plays a pivotal role in a diverse range of pathways, activating and releasing proteins via regulated intramembrane proteolysis. The prototype rhomboid protease, rhomboid-1 in Drosophila, is the key activator of epidermal growth factor (EGF) receptor pathway signalling in the fly and thus affects multiple aspects of development. The role of the rhomboid family in plants is explored and another developmental phenotype, this time in a mutant of an Arabidopsis chloroplast-localized rhomboid, is reported here. It is confirmed by GFP-protein fusion that this protease is located in the envelope of chloroplasts and of chlorophyll-free plastids elsewhere in the plant. Mutant plants lacking this organellar rhomboid demonstrate reduced fertility, as documented previously with KOM-the one other Arabidopsis rhomboid mutant that has been reported in the literature-along with aberrant floral morphology.
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Affiliation(s)
- Elinor P Thompson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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43
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Jeyaraju DV, Sood A, Laforce-Lavoie A, Pellegrini L. Rhomboid proteases in mitochondria and plastids: keeping organelles in shape. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:371-80. [PMID: 22634239 DOI: 10.1016/j.bbamcr.2012.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 05/10/2012] [Accepted: 05/17/2012] [Indexed: 01/16/2023]
Abstract
Rhomboids constitute the most widespread and conserved family of intramembrane cleaving proteases. They are key regulators of critical cellular processes in bacteria and animals, and are poised to play an equally important role also in plants. Among eukaryotes, a distinct subfamily of rhomboids, prototyped by the mammalian mitochondrial protein Parl, ensures the maintenance of the structural and functional integrity of mitochondria and plastids. Here, we discuss the studies that in the past decade have unveiled the role, regulation, and structure of this unique group of rhomboid proteases. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Danny V Jeyaraju
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, Canada
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44
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Abstract
Rhomboids are ubiquitous intramembrane serine proteases the sequences of which are found in nearly all sequenced genomes, including those of plants. They were molecularly characterized in a number of organisms, and were found to play a role in a variety of biological functions including signaling, development, apoptosis, mitochondrial integrity, parasite invasion and more. Although rhomboid sequences are found in plants, very little is known about their function. Here, we present the current knowledge in the rhomboids field in general, and in plant rhomboids in particular. In addition, we discuss possible physiological roles of different plant rhomboids.
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Affiliation(s)
- Ronit Rimon Knopf
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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45
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Teixeira PF, Glaser E. Processing peptidases in mitochondria and chloroplasts. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:360-70. [PMID: 22495024 DOI: 10.1016/j.bbamcr.2012.03.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/21/2012] [Accepted: 03/22/2012] [Indexed: 12/12/2022]
Abstract
Most of the mitochondrial and chloroplastic proteins are nuclear encoded and synthesized in the cytosol as precursor proteins with N-terminal extensions called targeting peptides. Targeting peptides function as organellar import signals, they are recognized by the import receptors and route precursors through the protein translocons across the organellar membranes. After the fulfilled function, targeting peptides are proteolytically cleaved off inside the organelles by different processing peptidases. The processing of mitochondrial precursors is catalyzed in the matrix by the Mitochondrial Processing Peptidase, MPP, the Mitochondrial Intermediate Peptidase, MIP (recently called Octapeptidyl aminopeptidase 1, Oct1) and the Intermediate cleaving peptidase of 55kDa, Icp55. Furthermore, different inner membrane peptidases (Inner Membrane Proteases, IMPs, Atp23, rhomboids and AAA proteases) catalyze additional processing functions, resulting in intra-mitochondrial sorting of proteins, the targeting to the intermembrane space or in the assembly of proteins into inner membrane complexes. Chloroplast targeting peptides are cleaved off in the stroma by the Stromal Processing Peptidase, SPP. If the protein is further translocated to the thylakoid lumen, an additional thylakoid-transfer sequence is removed by the Thylakoidal Processing Peptidase, TPP. Proper function of the D1 protein of Photosystem II reaction center requires its C-terminal processing by Carboxy-terminal processing protease, CtpA. Both in mitochondria and in chloroplasts, the cleaved targeting peptides are finally degraded by the Presequence Protease, PreP. The organellar proteases involved in precursor processing and targeting peptide degradation constitute themselves a quality control system ensuring the correct maturation and localization of proteins as well as assembly of protein complexes, contributing to sustenance of organelle functions. Dysfunctions of several mitochondrial processing proteases have been shown to be associated with human diseases. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Pedro Filipe Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-106 91 Stockholm, Sweden
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46
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Phosphatidylglycerol::prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane. J Bacteriol 2012; 194:2142-51. [PMID: 22287519 DOI: 10.1128/jb.06641-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lgt of Escherichia coli catalyzes the transfer of an sn-1,2-diacylglyceryl group from phosphatidylglycerol to prolipoproteins. The enzyme is essential for growth, as demonstrated here by the analysis of an lgt depletion strain. Cell fractionation demonstrated that Lgt is an inner membrane protein. Its membrane topology was determined by fusing Lgt to β-galactosidase and alkaline phosphatase and by substituted cysteine accessibility method (SCAM) studies. The data show that Lgt is embedded in the membrane by seven transmembrane segments, that its N terminus faces the periplasm, and that its C terminus faces the cytoplasm. Highly conserved amino acids in Lgt of both Gram-negative and Gram-positive bacteria were identified. Lgt enzymes are characterized by a so-called Lgt signature motif in which four residues are invariant. Ten conserved residues were replaced with alanine, and the activity of these Lgt variants was analyzed by their ability to complement the lgt depletion strain. Residues Y26, N146, and G154 are absolutely required for Lgt function, and R143, E151, R239, and E243 are important. The results demonstrate that the majority of the essential residues of Lgt are located in the membrane and that the Lgt signature motif faces the periplasm.
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47
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Olivieri A, Collins CR, Hackett F, Withers-Martinez C, Marshall J, Flynn HR, Skehel JM, Blackman MJ. Juxtamembrane shedding of Plasmodium falciparum AMA1 is sequence independent and essential, and helps evade invasion-inhibitory antibodies. PLoS Pathog 2011; 7:e1002448. [PMID: 22194692 PMCID: PMC3240622 DOI: 10.1371/journal.ppat.1002448] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 11/04/2011] [Indexed: 12/16/2022] Open
Abstract
The malarial life cycle involves repeated rounds of intraerythrocytic replication interspersed by host cell rupture which releases merozoites that rapidly invade fresh erythrocytes. Apical membrane antigen-1 (AMA1) is a merozoite protein that plays a critical role in invasion. Antibodies against AMA1 prevent invasion and can protect against malaria in vivo, so AMA1 is of interest as a malaria vaccine candidate. AMA1 is efficiently shed from the invading parasite surface, predominantly through juxtamembrane cleavage by a membrane-bound protease called SUB2, but also by limited intramembrane cleavage. We have investigated the structural requirements for shedding of Plasmodium falciparum AMA1 (PfAMA1), and the consequences of its inhibition. Mutagenesis of the intramembrane cleavage site by targeted homologous recombination abolished intramembrane cleavage with no effect on parasite viability in vitro. Examination of PfSUB2-mediated shedding of episomally-expressed PfAMA1 revealed that the position of cleavage is determined primarily by its distance from the parasite membrane. Certain mutations at the PfSUB2 cleavage site block shedding, and parasites expressing these non-cleavable forms of PfAMA1 on a background of expression of the wild type gene invade and replicate normally in vitro. The non-cleavable PfAMA1 is also functional in invasion. However – in contrast to the intramembrane cleavage site - mutations that block PfSUB2-mediated shedding could not be stably introduced into the genomic pfama1 locus, indicating that some shedding of PfAMA1 by PfSUB2 is essential. Remarkably, parasites expressing shedding-resistant forms of PfAMA1 exhibit enhanced sensitivity to antibody-mediated inhibition of invasion. Drugs that inhibit PfSUB2 activity should block parasite replication and may also enhance the efficacy of vaccines based on AMA1 and other merozoite surface proteins. The malaria parasite invades red blood cells. During invasion several parasite proteins, including a vaccine candidate called PfAMA1, are clipped from the parasite surface. Most of this clipping is performed by an enzyme called PfSUB2, but some also occurs through intramembrane cleavage. The function of this shedding is unknown. We have examined the requirements for shedding of PfAMA1, and the effects of mutations that block shedding. Mutations that block intramembrane cleavage have no effect on the parasite. We then show that PfSUB2 does not recognise a specific amino acid sequence in PfAMA1, but rather cleaves it at a position determined primarily by its distance from the parasite membrane. Certain mutations at the PfSUB2 cleavage site prevent shedding, and parasites expressing non-cleavable PfAMA1 along with unmodified PfAMA1 grow normally. However, these mutations cannot be introduced into the parasite's genome, showing that some shedding by PfSUB2 is essential for parasite survival. Parasites expressing shedding-resistant mutants of PfAMA1 show enhanced sensitivity to invasion-inhibitory antibodies, suggesting that shedding of surface proteins during invasion helps the parasite to evade potentially protective antibodies. Drugs that inhibit PfSUB2 may prevent disease and enhance the efficacy of vaccines based on PfAMA1.
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Affiliation(s)
- Anna Olivieri
- Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Christine R. Collins
- Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Fiona Hackett
- Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | | | - Joshua Marshall
- Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Helen R. Flynn
- Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, Hertfordshire, United Kingdom
| | - J. Mark Skehel
- Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, Hertfordshire, United Kingdom
| | - Michael J. Blackman
- Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, Hertfordshire, United Kingdom
- * E-mail:
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48
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Haft DH, Varghese N. GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. PLoS One 2011; 6:e28886. [PMID: 22194940 PMCID: PMC3237569 DOI: 10.1371/journal.pone.0028886] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 11/16/2011] [Indexed: 11/30/2022] Open
Abstract
The rhomboid family of serine proteases occurs in all domains of life. Its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. The model member GlpG from Escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple X-ray crystal studies, yet its relationship to endogenous substrates is not well understood. Here we describe an apparent membrane anchoring C-terminal homology domain that appears in numerous genera including Shewanella, Vibrio, Acinetobacter, and Ralstonia, but excluding Escherichia and Haemophilus. Individual genomes encode up to thirteen members, usually homologous to each other only in this C-terminal region. The domain's tripartite architecture consists of motif, transmembrane helix, and cluster of basic residues at the protein C-terminus, as also seen with the LPXTG recognition sequence for sortase A and the PEP-CTERM recognition sequence for exosortase. Partial Phylogenetic Profiling identifies a distinctive rhomboid-like protease subfamily almost perfectly co-distributed with this recognition sequence. This protease subfamily and its putative target domain are hereby renamed rhombosortase and GlyGly-CTERM, respectively. The protease and target are encoded by consecutive genes in most genomes with just a single target, but far apart otherwise. The signature motif of the Rhombo-CTERM domain, often SGGS, only partially resembles known cleavage sites of rhomboid protease family model substrates. Some protein families that have several members with C-terminal GlyGly-CTERM domains also have additional members with LPXTG or PEP-CTERM domains instead, suggesting there may be common themes to the post-translational processing of these proteins by three different membrane protein superfamilies.
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Affiliation(s)
- Daniel H Haft
- Department of Bioinformatics, J. Craig Venter Institute, Rockville, Maryland, United States of America.
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49
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M Santos J, Graindorge A, Soldati-Favre D. New insights into parasite rhomboid proteases. Mol Biochem Parasitol 2011; 182:27-36. [PMID: 22173057 DOI: 10.1016/j.molbiopara.2011.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 11/24/2011] [Accepted: 11/28/2011] [Indexed: 11/16/2022]
Abstract
The rhomboid-like proteins constitute a large family of intramembrane serine proteases that are present in all branches of life. First studied in Drosophila, these enzymes catalyse the release of the active forms of proteins from the membrane and hence trigger signalling events. In protozoan parasites, a limited number of rhomboid-like proteases have been investigated and some of them are associated to pathogenesis. In Apicomplexans, rhomboid-like protease activity is involved in shedding adhesins from the surface of the zoites during motility and host cell entry. Recently, a Toxoplasma gondii rhomboid was also implicated in an intracellular signalling mechanism leading to parasite proliferation. In Entamoeba histolytica, the capacity to adhere to host cells and to phagocytose cells is potentiated by a rhomboid-like protease. Survey of a small number of protozoan parasite genomes has uncovered species-specific rhomboid-like protease genes, many of which are predicted to encode inactive enzymes. Functional investigation of the rhomboid-like proteases in other protozoan parasites will likely uncover novel and unexpected implications for this family of proteases.
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Affiliation(s)
- Joana M Santos
- Department of Microbiology, Faculty of Medicine, University of Geneva, 1 Rue-Michel Servet, 1211 Geneva 4, Switzerland
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50
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Abstract
Summary Rhomboid proteases are the largest family of enzymes that hydrolyze peptide bonds within the cell membrane. Although discovered to be serine proteases only a decade ago, rhomboid proteases are already considered to be the best understood intramembrane proteases. The presence of rhomboid proteins in all domains of life emphasizes their importance but makes their evolutionary history difficult to chart with confidence. Phylogenetics nevertheless offers three guiding principles for interpreting rhomboid function. The near ubiquity of rhomboid proteases across evolution suggests broad, organizational roles that are not directly essential for cell survival. Functions have been deciphered in only about a dozen organisms and fall into four general categories: initiating cell signaling in animals, facilitating bacterial quorum sensing, regulating mitochondrial homeostasis, and dismantling adhesion complexes of parasitic protozoa. Although in no organism has the full complement of rhomboid function yet been elucidated, links to devastating human disease are emerging rapidly, including to Parkinson's disease, type II diabetes, cancer, and bacterial and malaria infection. Rhomboid proteases are unlike most proteolytic enzymes, because they are membrane-immersed; understanding how the membrane immersion affects their function remains a key challenge.
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Affiliation(s)
- Sinisa Urban
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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