1
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John A, Krämer M, Lehmann M, Kunz HH, Aarabi F, Alseekh S, Fernie A, Sommer F, Schroda M, Zimmer D, Mühlhaus T, Peisker H, Gutbrod K, Dörmann P, Neunzig J, Philippar K, Neuhaus HE. Degradation of FATTY ACID EXPORT PROTEIN1 by RHOMBOID-LIKE PROTEASE11 contributes to cold tolerance in Arabidopsis. THE PLANT CELL 2024; 36:1937-1962. [PMID: 38242838 PMCID: PMC11062452 DOI: 10.1093/plcell/koae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Plants need to acclimate to different stresses to optimize growth under unfavorable conditions. In Arabidopsis (Arabidopsis thaliana), the abundance of the chloroplast envelope protein FATTY ACID EXPORT PROTEIN1 (FAX1) decreases after the onset of low temperatures. However, how FAX1 degradation occurs and whether altered FAX1 abundance contributes to cold tolerance in plants remains unclear. The rapid cold-induced increase in RHOMBOID-LIKE PROTEASE11 (RBL11) transcript levels, the physical interaction of RBL11 with FAX1, the specific FAX1 degradation after RBL11 expression, and the absence of cold-induced FAX1 degradation in rbl11 loss-of-function mutants suggest that this enzyme is responsible for FAX1 degradation. Proteomic analyses showed that rbl11 mutants have higher levels of FAX1 and other proteins involved in membrane lipid homeostasis, suggesting that RBL11 is a key element in the remodeling of membrane properties during cold conditions. Consequently, in the cold, rbl11 mutants show a shift in lipid biosynthesis toward the eukaryotic pathway, which coincides with impaired cold tolerance. To test whether cold sensitivity is due to increased FAX1 levels, we analyzed FAX1 overexpressors. The rbl11 mutants and FAX1 overexpressor lines show superimposable phenotypic defects upon exposure to cold temperatures. Our re-sults show that the cold-induced degradation of FAX1 by RBL11 is critical for Arabidop-sis to survive cold and freezing periods.
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Affiliation(s)
- Annalisa John
- Plant Physiology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Moritz Krämer
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried 82152, Germany
| | - Martin Lehmann
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried 82152, Germany
| | - Hans-Henning Kunz
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried 82152, Germany
| | - Fayezeh Aarabi
- Max Planck Institut for Molecular Plant Physiology, Central Metabolism, Potsdam D-14476, Germany
| | - Saleh Alseekh
- Max Planck Institut for Molecular Plant Physiology, Central Metabolism, Potsdam D-14476, Germany
| | - Alisdair Fernie
- Max Planck Institut for Molecular Plant Physiology, Central Metabolism, Potsdam D-14476, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - David Zimmer
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Helga Peisker
- Institute for Molecular Physiology and Biotechnology of Plants, IMBIO, University of Bonn, Bonn D-53115, Germany
| | - Katharina Gutbrod
- Institute for Molecular Physiology and Biotechnology of Plants, IMBIO, University of Bonn, Bonn D-53115, Germany
| | - Peter Dörmann
- Institute for Molecular Physiology and Biotechnology of Plants, IMBIO, University of Bonn, Bonn D-53115, Germany
| | - Jens Neunzig
- Plant Biology, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken D-66123, Germany
| | - Katrin Philippar
- Plant Biology, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken D-66123, Germany
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2
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Kandel RR, Neal SE. The role of rhomboid superfamily members in protein homeostasis: Mechanistic insight and physiological implications. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118793. [PMID: 32645330 PMCID: PMC7434706 DOI: 10.1016/j.bbamcr.2020.118793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/30/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022]
Abstract
Cells are equipped with protein quality control pathways in order to maintain a healthy proteome; a process known as protein homeostasis. Dysfunction in protein homeostasis leads to the development of many diseases that are associated with proteinopathies. Recently, the rhomboid superfamily has attracted much attention concerning their involvement in protein homeostasis. While their functional role has become much clearer in the last few years, their systemic significance in mammals remains elusive. Here we delineate the current knowledge of rhomboids in protein quality control and how these functions are integrated at the organismal level.
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Affiliation(s)
- Rachel R Kandel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States of America.
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3
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Liu G, Beaton SE, Grieve AG, Evans R, Rogers M, Strisovsky K, Armstrong FA, Freeman M, Exley RM, Tang CM. Bacterial rhomboid proteases mediate quality control of orphan membrane proteins. EMBO J 2020; 39:e102922. [PMID: 32337752 PMCID: PMC7232013 DOI: 10.15252/embj.2019102922] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023] Open
Abstract
Although multiprotein membrane complexes play crucial roles in bacterial physiology and virulence, the mechanisms governing their quality control remain incompletely understood. In particular, it is not known how unincorporated, orphan components of protein complexes are recognised and eliminated from membranes. Rhomboids, the most widespread and largest superfamily of intramembrane proteases, are known to play key roles in eukaryotes. In contrast, the function of prokaryotic rhomboids has remained enigmatic. Here, we show that the Shigella sonnei rhomboid proteases GlpG and the newly identified Rhom7 are involved in membrane protein quality control by specifically targeting components of respiratory complexes, with the metastable transmembrane domains (TMDs) of rhomboid substrates protected when they are incorporated into a functional complex. Initial cleavage by GlpG or Rhom7 allows subsequent degradation of the orphan substrate. Given the occurrence of this strategy in an evolutionary ancient organism and the presence of rhomboids in all domains of life, it is likely that this form of quality control also mediates critical events in eukaryotes and protects cells from the damaging effects of orphan proteins.
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Affiliation(s)
- Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Stephen E Beaton
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Adam G Grieve
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rhiannon Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Miranda Rogers
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Praha 6, Czech Republic
| | | | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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4
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Began J, Cordier B, Březinová J, Delisle J, Hexnerová R, Srb P, Rampírová P, Kožíšek M, Baudet M, Couté Y, Galinier A, Veverka V, Doan T, Strisovsky K. Rhomboid intramembrane protease YqgP licenses bacterial membrane protein quality control as adaptor of FtsH AAA protease. EMBO J 2020; 39:e102935. [PMID: 31930742 PMCID: PMC7231995 DOI: 10.15252/embj.2019102935] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/18/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
Magnesium homeostasis is essential for life and depends on magnesium transporters, whose activity and ion selectivity need to be tightly controlled. Rhomboid intramembrane proteases pervade the prokaryotic kingdom, but their functions are largely elusive. Using proteomics, we find that Bacillus subtilis rhomboid protease YqgP interacts with the membrane‐bound ATP‐dependent processive metalloprotease FtsH and cleaves MgtE, the major high‐affinity magnesium transporter in B. subtilis. MgtE cleavage by YqgP is potentiated in conditions of low magnesium and high manganese or zinc, thereby protecting B. subtilis from Mn2+/Zn2+ toxicity. The N‐terminal cytosolic domain of YqgP binds Mn2+ and Zn2+ ions and facilitates MgtE cleavage. Independently of its intrinsic protease activity, YqgP acts as a substrate adaptor for FtsH, a function that is necessary for degradation of MgtE. YqgP thus unites protease and pseudoprotease function, hinting at the evolutionary origin of rhomboid pseudoproteases such as Derlins that are intimately involved in eukaryotic ER‐associated degradation (ERAD). Conceptually, the YqgP‐FtsH system we describe here is analogous to a primordial form of “ERAD” in bacteria and exemplifies an ancestral function of rhomboid‐superfamily proteins.
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Affiliation(s)
- Jakub Began
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Baptiste Cordier
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Jana Březinová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jordan Delisle
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Petra Rampírová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Mathieu Baudet
- CEA, Inserm, IRIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Yohann Couté
- CEA, Inserm, IRIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Thierry Doan
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France.,Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7255, Aix Marseille Univ, Marseille Cedex 20, France
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
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5
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Arutyunova E, Jiang Z, Yang J, Kulepa AN, Young HS, Verhelst S, O’Donoghue AJ, Lemieux MJ. An internally quenched peptide as a new model substrate for rhomboid intramembrane proteases. Biol Chem 2018; 399:1389-1397. [DOI: 10.1515/hsz-2018-0255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022]
Abstract
AbstractRhomboids are ubiquitous intramembrane serine proteases that cleave transmembrane substrates. Their functions include growth factor signaling, mitochondrial homeostasis, and parasite invasion. A recent study revealed that theEscherichia colirhomboid protease EcGlpG is essential for its extraintestinal pathogenic colonization within the gut. Crystal structures of EcGlpG and theHaemophilus influenzaerhomboid protease HiGlpG have deciphered an active site that is buried within the lipid bilayer but exposed to the aqueous environment via a cavity at the periplasmic face. A lack of physiological transmembrane substrates has hampered progression for understanding their catalytic mechanism and screening inhibitor libraries. To identify a soluble substrate for use in the study of rhomboid proteases, an array of internally quenched peptides were assayed with HiGlpG, EcGlpG and PsAarA fromProvidencia stuartti. One substrate was identified that was cleaved by all three rhomboid proteases, with HiGlpG having the highest cleavage efficiency. Mass spectrometry analysis determined that all enzymes hydrolyze this substrate between norvaline and tryptophan. Kinetic analysis in both detergent and bicellular systems demonstrated that this substrate can be cleaved in solution and in the lipid environment. The substrate was subsequently used to screen a panel of benzoxazin-4-one inhibitors to validate its use in inhibitor discovery.
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6
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Lichtenthaler SF, Lemberg MK, Fluhrer R. Proteolytic ectodomain shedding of membrane proteins in mammals-hardware, concepts, and recent developments. EMBO J 2018; 37:e99456. [PMID: 29976761 PMCID: PMC6068445 DOI: 10.15252/embj.201899456] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/05/2018] [Accepted: 06/18/2018] [Indexed: 12/14/2022] Open
Abstract
Proteolytic removal of membrane protein ectodomains (ectodomain shedding) is a post-translational modification that controls levels and function of hundreds of membrane proteins. The contributing proteases, referred to as sheddases, act as important molecular switches in processes ranging from signaling to cell adhesion. When deregulated, ectodomain shedding is linked to pathologies such as inflammation and Alzheimer's disease. While proteases of the "a disintegrin and metalloprotease" (ADAM) and "beta-site APP cleaving enzyme" (BACE) families are widely considered as sheddases, in recent years a much broader range of proteases, including intramembrane and soluble proteases, were shown to catalyze similar cleavage reactions. This review demonstrates that shedding is a fundamental process in cell biology and discusses the current understanding of sheddases and their substrates, molecular mechanisms and cellular localizations, as well as physiological functions of protein ectodomain shedding. Moreover, we provide an operational definition of shedding and highlight recent conceptual advances in the field. While new developments in proteomics facilitate substrate discovery, we expect that shedding is not a rare exception, but rather the rule for many membrane proteins, and that many more interesting shedding functions await discovery.
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Affiliation(s)
- Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, Klinikum rechts der Isar, School of Medicine, and Institute for Advanced Study, Technical University Munich, Munich, Germany
- Munich Center for Systems Neurology (SyNergy), Munich, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Regina Fluhrer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedizinisches Centrum (BMC), Ludwig-Maximilians University of Munich, Munich, Germany
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7
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Costa MI, Cerletti M, Paggi RA, Trötschel C, De Castro RE, Poetsch A, Giménez MI. Haloferax volcanii Proteome Response to Deletion of a Rhomboid Protease Gene. J Proteome Res 2018; 17:961-977. [PMID: 29301397 DOI: 10.1021/acs.jproteome.7b00530] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhomboids are conserved intramembrane serine proteases involved in cell signaling processes. Their role in prokaryotes is scarcely known and remains to be investigated in Archaea. We previously constructed a rhomboid homologue deletion mutant (ΔrhoII) in Haloferax volcanii, which showed reduced motility, increased novobiocin sensitivity, and an N- glycosylation defect. To address the impact of rhoII deletion on H. volcanii physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. A total of 1847 proteins were identified (45.8% of H. volcanii predicted proteome), from which 103 differed in amount. Additionally, the mutant strain evidenced 99 proteins with altered electrophoretic migration, which suggested differential post-translational processing/modification. Integral membrane proteins that evidenced variations in concentration, electrophoretic migration, or semitryptic cleavage in the mutant were considered as potential RhoII targets. These included a PrsW protease homologue (which was less stable in the mutant strain), a predicted halocyanin, and six integral membrane proteins potentially related to the mutant glycosylation (S-layer glycoprotein, Agl15) and cell adhesion/motility (flagellin1, HVO_1153, PilA1, and PibD) defects. This study investigated for the first time the impact of a rhomboid protease on the whole proteome of an organism.
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Affiliation(s)
- Mariana I Costa
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
| | - Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
| | - Christian Trötschel
- Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum , 44801 Bochum, Germany
| | - Rosana E De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
| | - Ansgar Poetsch
- Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum , 44801 Bochum, Germany.,School of Biomedical and Healthcare Sciences, Plymouth University , Plymouth PL4 8AA, United Kingdom
| | - María I Giménez
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
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8
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Abstract
Rhomboids are ubiquitous intramembrane serine proteases that are involved in various signaling pathways. This fascinating class of proteases harbors an active site buried within the lipid milieu. High-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed the catalytic mechanism for rhomboid-mediated proteolysis; however, a quantitative characterization was lacking. Assessing an enzyme's catalytic parameters is important for understanding the details of its proteolytic reaction and regulatory mechanisms. To assay rhomboid protease activity, many challenges exist such as the lipid environment and lack of known substrates. Here, we summarize various enzymatic assays developed over the last decade to study rhomboid protease activity. We present detailed protocols for gel-shift and FRET-based assays, and calculation of KM and Vmax to measure catalytic parameters, using detergent solubilized rhomboids with TatA, the only known substrate for bacterial rhomboids, and the model substrate fluorescently labeled casein.
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9
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Lemberg MK, Adrain C. Inactive rhomboid proteins: New mechanisms with implications in health and disease. Semin Cell Dev Biol 2016; 60:29-37. [PMID: 27378062 DOI: 10.1016/j.semcdb.2016.06.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/25/2016] [Accepted: 06/30/2016] [Indexed: 12/23/2022]
Abstract
Rhomboids, proteases containing an unusual membrane-integral serine protease active site, were first identified in Drosophila, where they fulfill an essential role in epidermal growth factor receptor signaling, by cleaving membrane-tethered growth factor precursors. It has recently become apparent that eukaryotic genomes harbor conserved catalytically inactive rhomboid protease homologs, including derlins and iRhoms. Here we highlight how loss of proteolytic activity was followed in evolution by impressive functional diversification, enabling these pseudoproteases to fulfill crucial roles within the secretory pathway, including protein degradation, trafficking regulation, and inflammatory signaling. We distil the current understanding of the roles of rhomboid pseudoproteases in development and disease. Finally, we address mechanistically how versatile features of proteolytically active rhomboids have been elaborated to serve the sophisticated functions of their pseudoprotease cousins. By comparing functional and structural clues, we highlight common principles shared by the rhomboid superfamily, and make mechanistic predictions.
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Affiliation(s)
- Marius K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Colin Adrain
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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10
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Avci D, Lemberg MK. Clipping or Extracting: Two Ways to Membrane Protein Degradation. Trends Cell Biol 2016; 25:611-622. [PMID: 26410407 DOI: 10.1016/j.tcb.2015.07.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/18/2015] [Accepted: 07/17/2015] [Indexed: 12/20/2022]
Abstract
Protein degradation is a fundamentally important process that allows cells to recognize and remove damaged protein species and to regulate protein abundance according to functional need. A fundamental challenge is to understand how membrane proteins are recognized and removed from cellular organelles. While most of our understanding of this mechanism comes from studies on p97/Cdc48-mediated protein dislocation along the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, recent studies have revealed intramembrane proteolysis to be an additional mechanism that can extract transmembrane segments. Here, we review these two principles in membrane protein degradation and discuss how intramembrane proteolysis, which introduces an irreversible step in protein dislocation, is used to drive regulated protein turnover.
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Affiliation(s)
- Dönem Avci
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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11
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Feige MJ, Hendershot LM. Quality control of integral membrane proteins by assembly-dependent membrane integration. Mol Cell 2013; 51:297-309. [PMID: 23932713 DOI: 10.1016/j.molcel.2013.07.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/28/2013] [Accepted: 07/09/2013] [Indexed: 02/07/2023]
Abstract
Cell-surface multiprotein complexes are synthesized in the endoplasmic reticulum (ER), where they undergo cotranslational membrane integration and assembly. The quality control mechanisms that oversee these processes remain poorly understood. We show that less hydrophobic transmembrane (TM) regions derived from several single-pass TM proteins can enter the ER lumen completely. Once mislocalized, they are recognized by the Hsp70 chaperone BiP. In a detailed analysis for one of these proteins, the αβT cell receptor (αβTCR), we show that unassembled ER-lumenal subunits are rapidly degraded, whereas specific subunit interactions en route to the native receptor promote membrane integration of the less hydrophobic TM segments, thereby stabilizing the protein. For the TCR α chain, both complete ER import and subunit assembly depend on the same pivotal residue in its TM region. Thus, membrane integration linked to protein assembly allows cellular quality control of membrane proteins and connects the lumenal ER chaperone machinery to membrane protein biogenesis.
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Affiliation(s)
- Matthias J Feige
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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12
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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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13
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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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14
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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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15
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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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16
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Lemberg MK. Sampling the membrane: function of rhomboid-family proteins. Trends Cell Biol 2013; 23:210-7. [PMID: 23369641 DOI: 10.1016/j.tcb.2013.01.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/19/2012] [Accepted: 01/03/2013] [Indexed: 12/29/2022]
Abstract
Rhomboids constitute a conserved protein superfamily that specifically binds membrane proteins and directs them into various different cellular pathways ranging from regulated secretion to endoplasmic reticulum (ER)-associated degradation (ERAD). Rhomboid proteases are known to release protein domains from membranes by a cut in their membrane anchor, whereas an emerging new class of rhomboid-family proteins lacks key catalytic residues and is not proteolytically active. Recent work has shown that these rhomboid pseudoproteases, including iRhoms and derlins, bind membrane proteins to regulate their fate, but the underlying molecular mechanism is not known. This review summarizes recent advances in the molecular understanding of rhomboid-family proteins and discusses common principles in how they recognize and bind proteins in the plane of the membrane.
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Affiliation(s)
- Marius K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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17
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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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18
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Membrane proteases in the bacterial protein secretion and quality control pathway. Microbiol Mol Biol Rev 2012; 76:311-30. [PMID: 22688815 DOI: 10.1128/mmbr.05019-11] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Proteolytic cleavage of proteins that are permanently or transiently associated with the cytoplasmic membrane is crucially important for a wide range of essential processes in bacteria. This applies in particular to the secretion of proteins and to membrane protein quality control. Major progress has been made in elucidating the structure-function relationships of many of the responsible membrane proteases, including signal peptidases, signal peptide hydrolases, FtsH, the rhomboid protease GlpG, and the site 1 protease DegS. These enzymes employ very different mechanisms to cleave substrates at the cytoplasmic and extracytoplasmic membrane surfaces or within the plane of the membrane. This review highlights the different ways that bacterial membrane proteases degrade their substrates, with special emphasis on catalytic mechanisms and substrate delivery to the respective active sites.
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19
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Fleig L, Bergbold N, Sahasrabudhe P, Geiger B, Kaltak L, Lemberg M. Ubiquitin-Dependent Intramembrane Rhomboid Protease Promotes ERAD of Membrane Proteins. Mol Cell 2012; 47:558-69. [DOI: 10.1016/j.molcel.2012.06.008] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 03/22/2012] [Accepted: 06/08/2012] [Indexed: 11/27/2022]
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20
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Reddy T, Rainey JK. Multifaceted Substrate Capture Scheme of a Rhomboid Protease. J Phys Chem B 2012; 116:8942-54. [DOI: 10.1021/jp305077k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tyler Reddy
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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Wan C, Fu J, Wang Y, Miao S, Song W, Wang L. Exosome-related multi-pass transmembrane protein TSAP6 is a target of rhomboid protease RHBDD1-induced proteolysis. PLoS One 2012; 7:e37452. [PMID: 22624035 PMCID: PMC3356283 DOI: 10.1371/journal.pone.0037452] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 04/21/2012] [Indexed: 11/18/2022] Open
Abstract
We have previously reported that rhomboid domain containing 1 (RHBDD1), a mammalian rhomboid protease highly expressed in the testis, can cleave the Bcl-2 protein Bik. In this study, we identified a multi-pass transmembrane protein, tumor suppressor activated pathway-6 (TSAP6) as a potential substrate of RHBDD1. RHBDD1 was found to induce the proteolysis of TSAP6 in a dose- and activity-dependent manner. The cleavage of TSAP6 was not restricted to its glycosylated form and occurred in three different regions. In addition, mass spectrometry and mutagenesis analyses both indicated that the major cleavage site laid in the C-terminal of the third transmembrane domain of TSAP6. A somatic cell knock-in approach was used to genetically inactivate the endogenous RHBDD1 in HCT116 and RKO colon cancer cells. Exosome secretion was significantly elevated when RHBDD1 was inactivated in the two cells lines. The increased exosome secretion was verfied through the detection of certain exosomal components, including Tsg101, Tf-R, FasL and Trail. In addition, the elevation of exosome secretion by RHBDD1 inactivation was reduced when TSAP6 was knocked down, indicating that the role of RHBDD1 in regulating exosomal trafficking is very likely to be TSAP6-dependent. We found that the increase in FasL and Trail increased exosome-induced apoptosis in Jurkat cells. Taken together, our findings suggest that RHBDD1 is involved in the regulation of a nonclassical exosomal secretion pathway through the restriction of TSAP6.
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Affiliation(s)
- Chunhua Wan
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, China
- School of Public Health, Nantong University, Nantong, China
| | - Jun Fu
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, China
| | - Yong Wang
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, China
| | - Shiying Miao
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, China
| | - Wei Song
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, China
- * E-mail: (WS); (LW)
| | - Linfang Wang
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, China
- * E-mail: (WS); (LW)
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22
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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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23
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Luirink J, Yu Z, Wagner S, de Gier JW. Biogenesis of inner membrane proteins in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:965-76. [PMID: 22201544 DOI: 10.1016/j.bbabio.2011.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/05/2011] [Accepted: 12/12/2011] [Indexed: 11/26/2022]
Abstract
The inner membrane proteome of the model organism Escherichia coli is composed of inner membrane proteins, lipoproteins and peripherally attached soluble proteins. Our knowledge of the biogenesis of inner membrane proteins is rapidly increasing. This is in particular true for the early steps of biogenesis - protein targeting to and insertion into the membrane. However, our knowledge of inner membrane protein folding and quality control is still fragmentary. Furthering our knowledge in these areas will bring us closer to understand the biogenesis of individual inner membrane proteins in the context of the biogenesis of the inner membrane proteome of Escherichia coli as a whole. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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Affiliation(s)
- Joen Luirink
- Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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24
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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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25
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Xue Y, Ha Y. Catalytic mechanism of rhomboid protease GlpG probed by 3,4-dichloroisocoumarin and diisopropyl fluorophosphonate. J Biol Chem 2011; 287:3099-107. [PMID: 22130671 DOI: 10.1074/jbc.m111.310482] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhomboid proteases have many important biological functions. Unlike soluble serine proteases such as chymotrypsin, the active site of rhomboid protease, which contains a Ser-His catalytic dyad, is submerged in the membrane and surrounded by membrane-spanning helices. Previous crystallographic analyses of GlpG, a bacterial rhomboid protease, and its complex with isocoumarin have provided insights into the mechanism of the membrane protease. Here, we studied the interaction of GlpG with 3,4-dichloroisocoumarin and diisopropyl fluorophosphonate, both mechanism-based inhibitors for the serine protease, and describe the crystal structure of the covalent adduct between GlpG and diisopropyl fluorophosphonate, which mimics the oxyanion-containing tetrahedral intermediate of the hydrolytic reaction. The crystal structure confirms that the oxyanion is stabilized by the main chain amide of Ser-201 and by the side chains of His-150 and Asn-154. The phosphorylation of the catalytic Ser-201 weakens its interaction with His-254, causing the catalytic histidine to rotate away from the serine. The rotation of His-254 is accompanied by further rearrangement of the side chains of Tyr-205 and Trp-236 within the substrate-binding groove. The formation of the tetrahedral adduct is also accompanied by opening of the L5 cap and movement of transmembrane helix S5 toward S6 in a direction different from that predicted by the lateral gating model. Combining the new structural data with those on the isocoumarin complex sheds further light on the plasticity of the active site of rhomboid membrane protease.
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Affiliation(s)
- Yi Xue
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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26
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Affiliation(s)
- Ross E. Dalbey
- The Ohio State University, Department of Chemistry, Columbus, Ohio 43210;
| | - Peng Wang
- The Ohio State University, Department of Chemistry, Columbus, Ohio 43210;
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany;
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27
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Santos JM, Soldati-Favre D. Invasion factors are coupled to key signalling events leading to the establishment of infection in apicomplexan parasites. Cell Microbiol 2011; 13:787-96. [DOI: 10.1111/j.1462-5822.2011.01585.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Brooks CL, Lazareno-Saez C, Lamoureux JS, Mak MW, Lemieux MJ. Insights into substrate gating in H. influenzae rhomboid. J Mol Biol 2011; 407:687-97. [PMID: 21295583 DOI: 10.1016/j.jmb.2011.01.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 01/16/2023]
Abstract
Rhomboids are a remarkable class of serine proteases that are embedded in lipid membranes. These membrane-bound enzymes play key roles in cellular signaling events, and disruptions in these events can result in numerous disease pathologies, including hereditary blindness, type 2 diabetes, Parkinson's disease, and epithelial cancers. Recent crystal structures of rhomboids from Escherichia coli have focused on how membrane-bound substrates gain access to a buried active site. In E. coli, it has been shown that movements of loop 5, with smaller movements in helix 5 and loop 4, act as substrate gate, facilitating inhibitor access to rhomboid catalytic residues. Herein we present a new structure of the Haemophilus influenzae rhomboid hiGlpG, which reveals disorder in loop 5, helix 5, and loop 4, indicating that, together, they represent mobile elements of the substrate gate. Substrate cleavage assays by hiGlpG with amino acid substitutions in these mobile regions demonstrate that the flexibilities of both loop 5 and helix 5 are important for access of the substrates to the catalytic residues. Mutagenesis indicates that less mobility by loop 4 is required for substrate cleavage. A reexamination of the reaction mechanism of rhomboid substrates, whereby cleavage of the scissile bond occurs on the si-face of the peptide bond, is discussed.
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Affiliation(s)
- Cory L Brooks
- 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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Hill RB, Pellegrini L. The PARL family of mitochondrial rhomboid proteases. Semin Cell Dev Biol 2010; 21:582-92. [PMID: 20045481 DOI: 10.1016/j.semcdb.2009.12.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 12/10/2009] [Accepted: 12/18/2009] [Indexed: 10/20/2022]
Abstract
Rhomboids are an ancient and conserved family of intramembrane-cleaving proteases, a small group of proteolytic enzymes capable of hydrolyzing a peptide bond within a transmembrane helix that anchors a substrate protein to the membrane. Mitochondrial rhomboids evolved in eukaryotes to coordinate a critical aspect of cell biology, the regulation of mitochondrial membranes dynamics. This function appears to have required the emergence of a structural feature that is unique among all other rhomboids: an additional transmembrane helix (TMH) positioned at the N-terminus of six TMHs that form the core proteolytic domain of all prokaryotic and eukaryotic rhomboids. This "1+6" structure, which is shared only among mitochondrial rhomboids, defines a subfamily of rhomboids with the prototypical family member being mammalian Parl. Here, we present the findings that in 11 years have elevated mitochondrial rhomboids as the gatekeepers of mitochondrial dynamics and apoptosis; further, we discuss the aspects of their biology that are bound to introduce new paradigm shifts in our understanding of how the organelle uses this unique type of protease to govern stress, signaling to the nucleus, and other key mitochondrial activities in health and disease.
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Affiliation(s)
- R Blake Hill
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
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