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Cortesio CL, Lewellyn EB, Drubin DG. Control of lipid organization and actin assembly during clathrin-mediated endocytosis by the cytoplasmic tail of the rhomboid protein Rbd2. Mol Biol Cell 2015; 26:1509-22. [PMID: 25694450 PMCID: PMC4395130 DOI: 10.1091/mbc.e14-11-1540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/09/2015] [Indexed: 12/13/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) requires precise regulation of the actin cytoskeleton. The yeast rhomboid protein Rbd2 controls the timing of actin polymerization during CME through its cytoplasmic tail and a PtdIns(4,5)P2-dependent mechanism. Clathrin-mediated endocytosis (CME) is facilitated by a precisely regulated burst of actin assembly. PtdIns(4,5)P2 is an important signaling lipid with conserved roles in CME and actin assembly regulation. Rhomboid family multipass transmembrane proteins regulate diverse cellular processes; however, rhomboid-mediated CME regulation has not been described. We report that yeast lacking the rhomboid protein Rbd2 exhibit accelerated endocytic-site dynamics and premature actin assembly during CME through a PtdIns(4,5)P2-dependent mechanism. Combined genetic and biochemical studies showed that the cytoplasmic tail of Rbd2 binds directly to PtdIns(4,5)P2 and is sufficient for Rbd2's role in actin regulation. Analysis of an Rbd2 mutant with diminished PtdIns(4,5)P2-binding capacity indicates that this interaction is necessary for the temporal regulation of actin assembly during CME. The cytoplasmic tail of Rbd2 appears to modulate PtdIns(4,5)P2 distribution on the cell cortex. The syndapin-like F-BAR protein Bzz1 functions in a pathway with Rbd2 to control the timing of type 1 myosin recruitment and actin polymerization onset during CME. This work reveals that the previously unstudied rhomboid protein Rbd2 functions in vivo at the nexus of three highly conserved processes: lipid regulation, endocytic regulation, and cytoskeletal function.
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Affiliation(s)
- Christa L Cortesio
- Department of Molecular- and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Eric B Lewellyn
- Department of Molecular- and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - David G Drubin
- Department of Molecular- and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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2
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Ghasriani H, Kwok JKC, Sherratt AR, Foo ACY, Qureshi T, Goto NK. Micelle-Catalyzed Domain Swapping in the GlpG Rhomboid Protease Cytoplasmic Domain. Biochemistry 2014; 53:5907-15. [DOI: 10.1021/bi500919v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Houman Ghasriani
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Jason K. C. Kwok
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Allison R. Sherratt
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Alexander C. Y. Foo
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Tabussom Qureshi
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | - Natalie K. Goto
- Department of Chemistry and ‡Department of Biochemistry, Microbiology
and
Immunology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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3
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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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4
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Abstract
Rhomboid protease was first discovered in Drosophila. Mutation of the fly gene interfered with growth factor signaling and produced a characteristic phenotype of a pointed head skeleton. The name rhomboid has since been widely used to describe a large family of related membrane proteins that have diverse biological functions but share a common catalytic core domain composed of six membrane-spanning segments. Most rhomboid proteases cleave membrane protein substrates near the N terminus of their transmembrane domains. How these proteases function within the confines of the membrane is not completely understood. Recent progress in crystallographic analysis of the Escherichia coli rhomboid protease GlpG in complex with inhibitors has provided new insights into the catalytic mechanism of the protease and its conformational change. Improved biochemical assays have also identified a substrate sequence motif that is specifically recognized by many rhomboid proteases.
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Affiliation(s)
- Ya Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA.
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5
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Rather P. Role of rhomboid proteases in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2849-54. [PMID: 23518036 DOI: 10.1016/j.bbamem.2013.03.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/28/2013] [Accepted: 03/07/2013] [Indexed: 11/20/2022]
Abstract
The first member of the rhomboid family of intramembrane serine proteases in bacteria was discovered almost 20years ago. It is now known that rhomboid proteins are widely distributed in bacteria, with some bacteria containing multiple rhomboids. At the present time, only a single rhomboid-dependent function in bacteria has been identified, which is the cleavage of TatA in Providencia stuartii. Mutational analysis has shown that loss of the GlpG rhomboid in Escherichia coli alters cefotaxime resistance, loss of the YqgP (GluP) rhomboid in Bacillus subtilis alters cell division and glucose uptake, and loss of the MSMEG_5036 and MSMEG_4904 genes in Mycobacterium smegmatis results in altered colony morphology, biofilm formation and antibiotic susceptibilities. However, the cellular substrates for these proteins have not been identified. In addition, analysis of the rhombosortases, together with their possible Gly-Gly CTERM substrates, may shed new light on the role of these proteases in bacteria. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Philip Rather
- Department of Microbiology and Immunology, 3001 Rollins Research Bldg, Emory University School of Medicine, Atlanta, GA 30322, USA; Atlanta VA Medical Center, Decatur, GA, USA.
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6
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Lazareno-Saez C, Arutyunova E, Coquelle N, Lemieux MJ. Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease. J Mol Biol 2013; 425:1127-42. [PMID: 23353827 DOI: 10.1016/j.jmb.2013.01.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/14/2013] [Accepted: 01/16/2013] [Indexed: 01/01/2023]
Abstract
Rhomboids are membrane-embedded serine proteases that cleave membrane protein substrates. Escherichia coli rhomboid GlpG (ecGlpG) consists of an N-terminal cytoplasmic domain and a membrane domain containing the active site. We determined the crystal structure of the soluble cytoplasmic domain of ecGlpG at 1.35Å resolution and examined whether this domain affected the catalytic activity of the enzyme. The structure revealed that the ecGlpG cytoplasmic domain exists as a dimer with extensive domain swapping between the two monomers. Domain-swapped dimers can be isolated from the full-length protein, suggesting that this is a physiologically relevant structure. An extensive steady-state kinetic analysis of the full-length ecGlpG and its membrane domain using soluble and transmembrane model protein substrates resulted in an unexpected conclusion: removal of the cytoplasmic domain does not alter the catalytic parameters for detergent-solubilized rhomboid for both substrates.
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Affiliation(s)
- Christelle Lazareno-Saez
- Membrane Protein Disease Research Group, Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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7
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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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Worrall LJ, Vuckovic M, Strynadka NCJ. Crystal structure of the C-terminal domain of the Salmonella type III secretion system export apparatus protein InvA. Protein Sci 2010; 19:1091-6. [PMID: 20306492 DOI: 10.1002/pro.382] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
InvA is a prominent inner-membrane component of the Salmonella type III secretion system (T3SS) apparatus, which is responsible for regulating virulence protein export in pathogenic bacteria. InvA is made up of an N-terminal integral membrane domain and a C-terminal cytoplasmic domain that is proposed to form part of a docking platform for the soluble export apparatus proteins notably the T3SS ATPase InvC. Here, we report the novel crystal structure of the C-terminal domain of Salmonella InvA which shows a compact structure composed of four subdomains. The overall structure is unique although the first and second subdomains exhibit structural similarity to the peripheral stalk of the A/V-type ATPase and a ring building motif found in other T3SS proteins respectively.
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Affiliation(s)
- Liam J Worrall
- Centre for Blood Research, Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, British Columbia, Canada V6T 1Z3
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Lei X, Li YM. The Processing of Human Rhomboid Intramembrane Serine Protease RHBDL2 Is Required for Its Proteolytic Activity. J Mol Biol 2009; 394:815-25. [DOI: 10.1016/j.jmb.2009.10.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Revised: 10/08/2009] [Accepted: 10/14/2009] [Indexed: 11/26/2022]
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Sherratt AR, Braganza MV, Nguyen E, Ducat T, Goto NK. Insights into the effect of detergents on the full-length rhomboid protease from Pseudomonas aeruginosa and its cytosolic domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2444-53. [DOI: 10.1016/j.bbamem.2009.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 08/19/2009] [Accepted: 09/06/2009] [Indexed: 11/16/2022]
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Freeman M. Rhomboids: 7 years of a new protease family. Semin Cell Dev Biol 2009; 20:231-9. [PMID: 19022390 DOI: 10.1016/j.semcdb.2008.10.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 10/13/2008] [Indexed: 12/24/2022]
Abstract
Drosophila Rhomboid-1 was discovered to be the first known intramembrane serine protease about 7 years ago. The study of the rhomboid-like family has since blossomed, and the purpose of this review is to take stock of where the field is, and how it may progress in the next few years. Three major themes are the increasing understanding of the biological roles of rhomboids, the detailed information we now have about their function and mechanism, and the promising leads they offer as medical targets.
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Affiliation(s)
- Matthew Freeman
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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Calcium regulation of mitochondria motility and morphology. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1787:1363-73. [PMID: 19138660 DOI: 10.1016/j.bbabio.2008.12.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 12/10/2008] [Accepted: 12/10/2008] [Indexed: 12/21/2022]
Abstract
In the Fifties, electron microscopy studies on neuronal cells showed that mitochondria typically cluster at synaptic terminals, thereby introducing the concept that proper mitochondria trafficking and partitioning inside the cell could provide functional support to the execution of key physiological processes. Today, the notion that a central event in the life of every eukaryotic cell is to configure, maintain, and reorganize the mitochondrial network at sites of high energy demand in response to environmental and cellular cues is well established, and the challenge ahead is to define the underlying molecular mechanisms and regulatory pathways. Recent pioneering studies have further contributed to place mitochondria at the center of the cell biology by showing that the machinery governing remodeling of mitochondria shape and structure regulates the functional output of the organelle as the powerhouse of the cell, the gateway to programmed cell death, and the platform for Ca(2+) signaling. Thus, a raising issue is to identify the cues integrating mitochondria trafficking and dynamics into cell physiology and metabolism. Given the versatile function of calcium as a second messenger and of the role of mitochondria as a major calcium store, evidences are emerging linking Ca(2+) transients to the modulation of mitochondrial activities. This review focuses on calcium as a switch controlling mitochondria motility and morphology in steady state, stressed, and pathological conditions.
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Abstract
Rhomboids were only discovered to be novel proteases in 2001, but progress on understanding this newest family of intramembrane proteases has been rapid. They are now the best characterized of these rather mysterious enzymes that cleave transmembrane domains within the lipid bilayer. In particular, the biochemical analysis of solubilized rhomboids and, most recently, a flurry of high-resolution crystal structures, have led to real insight into their enzymology. Long-standing questions about how it is possible for a water-requiring proteolytic reaction to occur in the lipid bilayer are now answered for the rhomboids. Intramembrane proteases, which control many medically important biological processes, have made the transition from rather heretical outsiders to novel enzymes that are becoming well understood.
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Nauli S, Farr S, Lee YJ, Kim HY, Faham S, Bowie JU. Polymer-driven crystallization. Protein Sci 2007; 16:2542-51. [PMID: 17962407 PMCID: PMC2211692 DOI: 10.1110/ps.073074207] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
Obtaining well-diffracting crystals of macromolecules remains a significant barrier to structure determination. Here we propose and test a new approach to crystallization, in which the crystallization target is fused to a polymerizing protein module, so that polymer formation drives crystallization of the target. We test the approach using a polymerization module called 2TEL, which consists of two tandem sterile alpha motif (SAM) domains from the protein translocation Ets leukemia (TEL). The 2TEL module is engineered to polymerize as the pH is lowered, which allows the subtle modulation of polymerization needed for crystal formation. We show that the 2TEL module can drive the crystallization of 11 soluble proteins, including three that resisted prior crystallization attempts. In addition, the 2TEL module crystallizes in the presence of various detergents, suggesting that it might facilitate membrane protein crystallization. The crystal structures of two fusion proteins show that the TELSAM polymer is responsible for the majority of contacts in the crystal lattice. The results suggest that biological polymers could be designed as crystallization modules.
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Affiliation(s)
- Sehat Nauli
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles 90095-1570, USA
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Dancea F, Kami K, Overduin M. Lipid interaction networks of peripheral membrane proteins revealed by data-driven micelle docking. Biophys J 2007; 94:515-24. [PMID: 17890395 PMCID: PMC2157223 DOI: 10.1529/biophysj.107.115923] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Many signaling and trafficking proteins contain modular domains that bind reversibly to cellular membranes. The structural basis of the intermolecular interactions which mediate these membrane-targeting events remains elusive since protein-membrane complexes are not directly accessible to standard structural biology techniques. Here we report a fast protein-micelle docking methodology that yields three-dimensional model structures of proteins inserted into micelles, revealing energetically favorable orientations, convergent insertion angles, and an array of protein-lipid interactions at atomic resolution. The method is applied to two peripheral membrane proteins, the early endosome antigen 1 (EEA1) FYVE (a zinc finger domain found in the proteins Fab1, YOTB/ZK632.12, Vac1, and EEA1) and Vam7p phagocyte oxidase homology domains, which are revealed to form extensive networks of interactions with multiple phospholipid headgroups and acyl chains. The resulting structural models explain extensive published mutagenesis data and reveal novel binding determinants. The docking restraints used here were based on NMR data, but can be derived from any technique that detects insertion of protein residues into a membrane, and can be applied to virtually any peripheral membrane protein or membrane-like structure.
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Affiliation(s)
- Felician Dancea
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Birmingham B15 2TT, United Kingdom
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