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García-Chávez D, Domínguez-Martín E, Kawasaki L, Ongay-Larios L, Ruelas-Ramírez H, Mendoza-Martinez AE, Pardo JP, Funes S, Coria R. Prohibitins, Phb1 and Phb2, function as Atg8 receptors to support yeast mitophagy and also play a negative regulatory role in Atg32 processing. Autophagy 2024:1-12. [PMID: 38964378 DOI: 10.1080/15548627.2024.2371717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/19/2024] [Indexed: 07/06/2024] Open
Abstract
The prohibitins Phb1 and Phb2 assemble at the mitochondrial inner membrane to form a multi-dimeric complex. These scaffold proteins are highly conserved in eukaryotic cells, from yeast to mammals, and have been implicated in a variety of mitochondrial functions including aging, proliferation, and degenerative and metabolic diseases. In mammals, PHB2 regulates PINK1-PRKN mediated mitophagy by interacting with lipidated MAP1LC3B/LC3B. Despite their high conservation, prohibitins have not been linked to mitophagy in budding yeasts. In this study, we demonstrate that both Phb1 and Phb2 are required to sustain mitophagy in Saccharomyces cerevisiae. Prohibitin-dependent mitophagy requires formation of the Phb1-Phb2 complex and a conserved AIM/LIR-like motif identified in both yeast prohibitins. Furthermore, both Phb1 and Phb2 interact and exhibit mitochondrial colocalization with Atg8. Interestingly, we detected a basal C terminus processing of the mitophagy receptor Atg32 that depends on the presence of the i-AAA Yme1. In the absence of prohibitins this processing is highly enhanced but reverted by the inactivation of the rhomboid protease Pcp1. Together our results revealed a novel role of yeast prohibitins in mitophagy through its interaction with Atg8 and regulating an Atg32 proteolytic event. Abbreviation: AIM/LIR: Atg8-family interacting motif/LC3-interacting region; ANOVA: analysis of variance; ATG/Atg: autophagy related; C terminus/C-terminal: carboxyl terminus/carboxyl-terminal; GFP: green fluorescent protein; HA: human influenza hemagglutinin; Idh1: isocitrate dehydrogenase 1; MAP1C3B/LC3B: microtubule associated protein 1 light chain 3 beta; mCh: mCherry; MIM: mitochondrial inner membrane; MOM: mitochondrial outer membrane; N starvation: nitrogen starvation; N terminus: amino terminus; PARL: presenilin associated rhomboid like; Pcp1: processing of cytochrome c peroxidase 1; PCR: polymerase chain reaction; PGAM5: PGAM family member 5 mitochondrial serine/threonine protein phosphatase; PHBs/Phb: prohibitins; PINK1: PTEN induced kinase 1; PMSF: phenylmethylsulfonyl fluoride; PRKN: parkin RBR E3 ubiquitin protein ligase; SD: synthetic defined medium; SDS: sodium dodecyl sulfate; SMD-N: synthetic defined medium lacking nitrogen; WB: western blot; WT: wild type; Yme1: yeast mitochondrial escape 1; YPD: yeast extract-peptone-dextrose medium; YPLac: yeast extract-peptone-lactate medium.
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Affiliation(s)
- Diana García-Chávez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Mexico City, México
| | - Eunice Domínguez-Martín
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Laura Kawasaki
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Mexico City, México
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Mexico City, México
| | - Hilario Ruelas-Ramírez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Mexico City, México
| | | | - Juan P Pardo
- Departamento de Bioquímica, Facultad de Medicina, Mexico City, México
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Mexico City, México
| | - Roberto Coria
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Mexico City, México
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2
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Frumenzio G, Chandramouli B, Besker N, Grottesi A, Talarico C, Frigerio F, Emerson A, Musiani F. Conformational response to ligand binding of TMPRSS2, a protease involved in SARS-CoV-2 infection: Insights through computational modeling. Proteins 2023; 91:1288-1297. [PMID: 37409524 DOI: 10.1002/prot.26548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
Thanks to the considerable research which has been undertaken in the last few years to improve our understanding of the biology and mechanism of action of SARS-CoV-2, we know how the virus uses its surface spike protein to infect host cells. The transmembrane prosthesis, serine 2 (TMPRSS2) protein, located on the surface of human cells, recognizes the cleavage site in the spike protein, leading to the release of the fusion peptide and entry of the virus into the host cells. Because of its role, TMPRSS2 has been proposed as a drug target to prevent infection by the virus. In this study, we aim to increase our understanding of TMPRSS2 using long scale microsecond atomistic molecular dynamics simulations, focusing on the conformational changes over time. The comparison between simulations conducted on the protein in the native (apo) and inhibited form (holo), has shown that in the holo form the inhibitor stabilizes the catalytic site and induces rearrangements in the extracellular domain of the protein. In turn, it leads to the formation of a new cavity in the vicinity of the ligand binding pocket that is stable in the microsecond time scale. Given the low specificity of known protease inhibitors, these findings suggest a new potential drug target site that can be used to improve TMPRSS2 specific recognition by newly designed inhibitors.
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Affiliation(s)
- Giorgia Frumenzio
- Super Computing Applications and Innovation, Department HPC, CINECA, Casalecchio di Reno, Italy
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | | | | | | | - Andrew Emerson
- Super Computing Applications and Innovation, Department HPC, CINECA, Casalecchio di Reno, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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3
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Zhu X, Hua Y, Kong X, Li X, Chen Y, Zhang C. Characterization of proteases from Irpex lacteus grown on minimally denatured soybean meal. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1800-1809. [PMID: 36317244 DOI: 10.1002/jsfa.12301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Acid and thermal stabilities are important properties for the preparation of acidic protein beverage. It is an important method for enzymatic modification to improve the functional properties of protein. Irpex lacteus protease showed a selective hydrolysis to soy proteins. The purpose of this study was to investigate the mechanism of enzymatic hydrolysis and its effects on acid and thermal stabilities of soy proteins. RESULTS The I. lacteus protease selectively hydrolyzed the α and α' subunits of the native soybean β-conglycinin (7S globulin) to produce products that presented as the 55 kDa band upon sodium dodecyl sulfate polyacrylamide gel electrophoresis. The amino acid sequences of 55 kDa polypeptides were analyzed in gel multi-enzyme digestion followed by liquid chromatography-mass spectrometry. By matching the multi-enzyme digestion peptides with the published polypeptide chain sequences of the α and α' subunits, it was confirmed that the 55 kDa polypeptides were formed by eliminating amino acid residues on both sides of the N- and C-terminals. From the published protein structure database (https://www.uniprot.org/), it is known that the cleaved peptide bonds were in extension regions. Non-selective enzyme hydrolysis of both β-conglycinin (7S globulin) and glycinin (11S globulin), with corresponding drastic increases in the degree of hydrolysis, was observed when the substrates were preheated to the denaturation degree of 40% and above. However, 55 kDa hydrolyzed products and B polypeptides showed some extent of resistance to the proteolysis by I. lacteus protease even if denaturation degree was 100%. Both selective and non-selective hydrolysis of soy proteins by I. lacteus protease improved the acid and heat stabilities under the same hydrolysis conditions (enzyme/substrate ratio, time, and temperature). CONCLUSION Enzymatic hydrolysis of soybean proteins by the I. lacteus protease can effectively improve the acid and thermal stabilities of proteins. This discovery is significant to avoid aggregation during processing in the beverage industry. In the near future, the protease has potential application value for modification of other proteins. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xiaoxu Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Yufei Hua
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Xiangzhen Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Xingfei Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Yeming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Caimeng Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
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4
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Olenic S, Heo L, Feig M, Kroos L. Inhibitory proteins block substrate access by occupying the active site cleft of Bacillus subtilis intramembrane protease SpoIVFB. eLife 2022; 11:74275. [PMID: 35471152 PMCID: PMC9042235 DOI: 10.7554/elife.74275] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/25/2022] [Indexed: 12/16/2022] Open
Abstract
Intramembrane proteases (IPs) function in numerous signaling pathways that impact health, but elucidating the regulation of membrane-embedded proteases is challenging. We examined inhibition of intramembrane metalloprotease SpoIVFB by proteins BofA and SpoIVFA. We found that SpoIVFB inhibition requires BofA residues in and near a predicted transmembrane segment (TMS). This segment of BofA occupies the SpoIVFB active site cleft based on cross-linking experiments. SpoIVFB inhibition also requires SpoIVFA. The inhibitory proteins block access of the substrate N-terminal region to the membrane-embedded SpoIVFB active site, based on additional cross-linking experiments; however, the inhibitory proteins did not prevent interaction between the substrate C-terminal region and the SpoIVFB soluble domain. We built a structural model of SpoIVFB in complex with BofA and parts of SpoIVFA and substrate, using partial homology and constraints from cross-linking and co-evolutionary analyses. The model predicts that conserved BofA residues interact to stabilize a TMS and a membrane-embedded C-terminal region. The model also predicts that SpoIVFA bridges the BofA C-terminal region and SpoIVFB, forming a membrane-embedded inhibition complex. Our results reveal a novel mechanism of IP inhibition with clear implications for relief from inhibition in vivo and design of inhibitors as potential therapeutics.
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Affiliation(s)
- Sandra Olenic
- Michigan State University, East Lansing, United States
| | - Lim Heo
- Michigan State University, East Lansing, United States
| | - Michael Feig
- Michigan State University, East Lansing, United States
| | - Lee Kroos
- Michigan State University, East Lansing, United States
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Eimeria maxima Rhomboid-like Protein 5 Provided Partial Protection against Homologous Challenge in Forms of Recombinant Protein and DNA Plasmid in Chickens. Vaccines (Basel) 2021; 10:vaccines10010032. [PMID: 35062693 PMCID: PMC8781051 DOI: 10.3390/vaccines10010032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
Eimeria maxima (E. maxima) is one of the most prevalent species that causes chicken coccidiosis on chicken farms. During apicomplexan protozoa invasion, rhomboid-like proteins (ROMs) cleave microneme proteins (MICs), allowing the parasites to fully enter the host cells, which suggests that ROMs have the potential to be candidate antigens for the development of subunit or DNA vaccines against coccidiosis. In this study, a recombinant protein of E. maxima ROM5 (rEmROM5) was expressed and purified and was used as a subunit vaccine. The eukaryotic expression plasmid of pVAX-EmROM5 was constructed and was used as a DNA vaccine. Chickens who were two weeks old were vaccinated with the rEmROM5 and pVAX-EmROM5 vaccines twice, with a one-week interval separating the vaccination periods. The transcription and expression of pVAX-EmROM5 in the injected sites were detected through reverse transcription PCR (RT-PCR) and Western blot (WB) assays. The cellular and humoral immune responses that were induced by EmROM5 were determined by detecting the proportion of CD4+ and CD8+ T lymphocytes, the cytokine levels, and the serum antibody levels. Finally, vaccination-challenge trials were conducted to evaluate the protective efficacy of EmROM5 in forms of the recombinant protein (rEmROM5) and in the DNA plasmid (pVAX-EmROM5) separately. The results showed that rEmROM5 was about 53.64 kDa, which was well purified and recognized by the His-Tag Mouse Monoclonal antibody and the chicken serum against E. maxima separately. After vaccination, pVAX-EmROM5 was successfully transcribed and expressed in the injected sites of the chickens. Vaccination with rEmROM5 or pVAX-EmROM5 significantly promoted the proportion of CD4+/CD3+ and CD8+/CD3+ T lymphocytes, the mRNA levels of the cytokines IFN-γ, IL-2, IL-4, IL-17, TNF SF15, and IL-10, and specific IgG antibody levels compared to the control groups. The immunization also significantly reduced the weight loss, oocyst production, and intestinal lesions that are caused by E. maxima infection. The anticoccidial index (ACI)s of the vaccinated groups were beyond 160, showing moderate protection against E. maxima infection. In summary, EmROM5 was able to induce a robust immune response and effective protection against E. maxima in chickens in the form of both a recombinant protein and DNA plasmid. Hence, EmROM5 could be used as a candidate antigen for DNA vaccines and subunit vaccines against avian coccidiosis.
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6
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Caengprasath N, Theerapanon T, Porntaveetus T, Shotelersuk V. MBTPS2, a membrane bound protease, underlying several distinct skin and bone disorders. J Transl Med 2021; 19:114. [PMID: 33743732 PMCID: PMC7981912 DOI: 10.1186/s12967-021-02779-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/08/2021] [Indexed: 12/27/2022] Open
Abstract
The MBTPS2 gene on the X-chromosome encodes the membrane-bound transcription factor protease, site-2 (MBTPS2) or site-2 protease (S2P) which cleaves and activates several signaling and regulatory proteins from the membrane. The MBTPS2 is critical for a myriad of cellular processes, ranging from the regulation of cholesterol homeostasis to unfolded protein responses. While its functional role has become much clearer in the recent years, how mutations in the MBTPS2 gene lead to several human disorders with different phenotypes including Ichthyosis Follicularis, Atrichia and Photophobia syndrome (IFAP) with or without BRESHECK syndrome, Keratosis Follicularis Spinulosa Decalvans (KFSD), Olmsted syndrome, and Osteogenesis Imperfecta type XIX remains obscure. This review presents the biological role of MBTPS2 in development, summarizes its mutations and implicated disorders, and discusses outstanding unanswered questions.
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Affiliation(s)
- Natarin Caengprasath
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Thanakorn Theerapanon
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thantrira Porntaveetus
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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7
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Akiyama K, Hizukuri Y, Akiyama Y. Involvement of a conserved GFG motif region in substrate binding by RseP, an E
scherichia coli
S2P protease. Mol Microbiol 2017; 104:737-751. [DOI: 10.1111/mmi.13659] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Koichiro Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University; Kyoto 606-8507 Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University; Kyoto 606-8507 Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University; Kyoto 606-8507 Japan
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8
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Levytskyy RM, Germany EM, Khalimonchuk O. Mitochondrial Quality Control Proteases in Neuronal Welfare. J Neuroimmune Pharmacol 2016; 11:629-644. [PMID: 27137937 PMCID: PMC5093085 DOI: 10.1007/s11481-016-9683-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/27/2016] [Indexed: 01/01/2023]
Abstract
The functional integrity of mitochondria is a critical determinant of neuronal health and compromised mitochondrial function is a commonly recognized factor that underlies a plethora of neurological and neurodegenerative diseases. Metabolic demands of neural cells require high bioenergetic outputs that are often associated with enhanced production of reactive oxygen species. Unopposed accumulation of these respiratory byproducts over time leads to oxidative damage and imbalanced protein homeostasis within mitochondrial subcompartments, which in turn may result in cellular demise. The post-mitotic nature of neurons and their vulnerability to these stress factors necessitate strict protein homeostatic control to prevent such scenarios. A series of evolutionarily conserved proteases is one of the central elements of mitochondrial quality control. These versatile proteolytic enzymes conduct a multitude of activities to preserve normal mitochondrial function during organelle biogenesis, metabolic remodeling and stress. In this review we discuss neuroprotective aspects of mitochondrial quality control proteases and neuropathological manifestations arising from defective proteolysis within the mitochondrion.
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Affiliation(s)
- Roman M Levytskyy
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Edward M Germany
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Nebraska Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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9
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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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10
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Strisovsky K. Why cells need intramembrane proteases - a mechanistic perspective. FEBS J 2016; 283:1837-45. [DOI: 10.1111/febs.13638] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/19/2015] [Accepted: 12/24/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Prague Czech Republic
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11
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Akiyama K, Mizuno S, Hizukuri Y, Mori H, Nogi T, Akiyama Y. Roles of the membrane-reentrant β-hairpin-like loop of RseP protease in selective substrate cleavage. eLife 2015; 4. [PMID: 26447507 PMCID: PMC4597795 DOI: 10.7554/elife.08928] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/10/2015] [Indexed: 11/13/2022] Open
Abstract
Molecular mechanisms underlying substrate recognition and cleavage by Escherichia coli RseP, which belongs to S2P family of intramembrane-cleaving proteases, remain unclear. We examined the function of a conserved region looped into the membrane domain of RseP to form a β-hairpin-like structure near its active site in substrate recognition and cleavage. We observed that mutations disturbing the possible β-strand conformation of the loop impaired RseP proteolytic activity and that some of these mutations resulted in the differential cleavage of different substrates. Co-immunoprecipitation and crosslinking experiments suggest that the loop directly interacts with the transmembrane segments of substrates. Helix-destabilising mutations in the transmembrane segments of substrates suppressed the effect of loop mutations in an allele-specific manner. These results suggest that the loop promotes substrate cleavage by selectively recognising the transmembrane segments of substrates in an extended conformation and by presenting them to the proteolytic active site, which contributes to substrate discrimination.
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Affiliation(s)
| | - Shinya Mizuno
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Yohei Hizukuri
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Hiroyuki Mori
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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12
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Zoll S, Stanchev S, Began J, Skerle J, Lepšík M, Peclinovská L, Majer P, Strisovsky K. Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate-peptide complex structures. EMBO J 2014; 33:2408-21. [PMID: 25216680 PMCID: PMC4253528 DOI: 10.15252/embj.201489367] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The mechanisms of intramembrane proteases are incompletely understood due to the lack of structural data on substrate complexes. To gain insight into substrate binding by rhomboid proteases, we have synthesised a series of novel peptidyl-chloromethylketone (CMK) inhibitors and analysed their interactions with Escherichia coli rhomboid GlpG enzymologically and structurally. We show that peptidyl-CMKs derived from the natural rhomboid substrate TatA from bacterium Providencia stuartii bind GlpG in a substrate-like manner, and their co-crystal structures with GlpG reveal the S1 to S4 subsites of the protease. The S1 subsite is prominent and merges into the 'water retention site', suggesting intimate interplay between substrate binding, specificity and catalysis. Unexpectedly, the S4 subsite is plastically formed by residues of the L1 loop, an important but hitherto enigmatic feature of the rhomboid fold. We propose that the homologous region of members of the wider rhomboid-like protein superfamily may have similar substrate or client-protein binding function. Finally, using molecular dynamics, we generate a model of the Michaelis complex of the substrate bound in the active site of GlpG.
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Affiliation(s)
- Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jakub Began
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Skerle
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Peclinovská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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13
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Kroos L, Akiyama Y. Biochemical and structural insights into intramembrane metalloprotease mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2873-85. [PMID: 24099006 DOI: 10.1016/j.bbamem.2013.03.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/07/2013] [Accepted: 03/27/2013] [Indexed: 01/11/2023]
Abstract
Intramembrane metalloproteases are nearly ubiquitous in living organisms and they function in diverse processes ranging from cholesterol homeostasis and the unfolded protein response in humans to sporulation, stress responses, and virulence of bacteria. Understanding how these enzymes function in membranes is a challenge of fundamental interest with potential applications if modulators can be devised. Progress is described toward a mechanistic understanding, based primarily on molecular genetic and biochemical studies of human S2P and bacterial SpoIVFB and RseP, and on the structure of the membrane domain of an archaeal enzyme. Conserved features of the enzymes appear to include transmembrane helices and loops around the active site zinc ion, which may be near the membrane surface. Extramembrane domains such as PDZ (PSD-95, DLG, ZO-1) or CBS (cystathionine-β-synthase) domains govern substrate access to the active site, but several different mechanisms of access and cleavage site selection can be envisioned, which might differ depending on the substrate and the enzyme. More work is needed to distinguish between these mechanisms, both for enzymes that have been relatively well-studied, and for enzymes lacking PDZ and CBS domains, which have not been studied. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Lee Kroos
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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14
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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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15
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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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16
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Xue Y, Ha Y. Large lateral movement of transmembrane helix S5 is not required for substrate access to the active site of rhomboid intramembrane protease. J Biol Chem 2013; 288:16645-16654. [PMID: 23609444 DOI: 10.1074/jbc.m112.438127] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Rhomboids represent an evolutionarily ancient protease family. Unlike most other proteases, they are polytopic membrane proteins and specialize in cleaving transmembrane protein substrates. The polar active site of rhomboid protease is embedded in the membrane and normally closed. For the bacterial rhomboid GlpG, it has been proposed that one of the transmembrane helices (S5) of the protease can rotate to open a lateral gate, enabling substrate to enter the protease from inside the membrane. Here, we studied the conformational change in GlpG by solving the cocrystal structure of the protease with a mechanism-based inhibitor. We also examined the lateral gating model by cross-linking S5 to a neighboring helix (S2). The crystal structure shows that inhibitor binding displaces a capping loop (L5) from the active site but causes only minor shifts in the transmembrane helices. Cross-linking S5 and S2, which not only restricts the lateral movement of S5 but also prevents substrate from passing between the two helices, does not hinder the ability of the protease to cleave a membrane protein substrate in detergent solution and in reconstituted membrane vesicles. Taken together, these data suggest that a large lateral movement of the S5 helix is not required for substrate access to the active site of rhomboid protease.
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Affiliation(s)
- Yi Xue
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520
| | - Ya Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520.
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17
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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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18
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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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19
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Rawson RB. The site-2 protease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2801-7. [PMID: 23571157 DOI: 10.1016/j.bbamem.2013.03.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/06/2013] [Accepted: 03/25/2013] [Indexed: 12/19/2022]
Abstract
The site-2 protease (S2P) is an unusually-hydrophobic integral membrane protease. It cleaves its substrates, which are membrane-bound transcription factors, within membrane-spanning helices. Although structural information for S2P from animals is lacking, the available data suggest that cleavage may occur at or within the lipid bilayer. In mammalian cells, S2P is essential owing to its activation of the sterol regulatory element binding proteins (SREBPs); in the absence of exogenous lipid, cells lacking S2P cannot survive. S2P is also important in the endoplasmic reticulum (ER) stress response, activating several different membrane-bound transcription factors. Human patients harboring reduction-of-function mutations in S2P exhibit an array of pathologies ranging from skin defects to neurological abnormalities. Surprisingly, Drosophila melanogaster lacking S2P are viable and fertile. This article is part of a Special Issue entitled: Intramembrane Proteases.
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20
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Ahmedli NB, Gribanova Y, Njoku CC, Naidu A, Young A, Mendoza E, Yamashita CK, Özgül RK, Johnson JE, Fox DA, Farber DB. Dynamics of the rhomboid-like protein RHBDD2 expression in mouse retina and involvement of its human ortholog in retinitis pigmentosa. J Biol Chem 2013; 288:9742-9754. [PMID: 23386608 DOI: 10.1074/jbc.m112.419960] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The novel rhomboid-like protein RHBDD2 is distantly related to rhomboid proteins, a group of highly specialized membrane-bound proteases that catalyze regulated intramembrane proteolysis. In retina, RHBDD2 is expressed from embryonic stages to adulthood, and its levels show age-dependent changes. RHBDD2 is distinctly abundant in the perinuclear region of cells, and it localizes to their Golgi. A glycine zipper motif present in one of the transmembrane domains of RHBDD2 is important for its packing into the Golgi membranes. Its deletion causes dislodgment of RHBDD2 from the Golgi. A specific antibody against RHBDD2 recognizes two forms of the protein, one with low (39 kDa; RHBDD2(L)) and the other with high (117 kDa; RHBDD2H) molecular masses in mouse retinal extracts. RHBDD2(L) seems to be ubiquitously expressed in all retinal cells. In contrast, RHBDD2H seems to be present only in the outer segments of cone photoreceptors and may correspond to a homotrimer of RHBDD2(L). This protein consistently co-localizes with S- and M-types of cone opsins. We identified a homozygous mutation in the human RHBDD2 gene, R85H, that co-segregates with disease in affected members of a family with autosomal recessive retinitis pigmentosa. Our findings suggest that the RHBDD2 protein plays important roles in the development and normal function of the retina.
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Affiliation(s)
| | | | - Collins C Njoku
- Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | - Akash Naidu
- Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | - Alejandra Young
- Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | | | | | - Riza Köksal Özgül
- Department of Molecular Biology, Hacettepe University, 06230 Beytepe-Ankara, Turkey
| | - Jerry E Johnson
- Department of Natural Sciences, University of Houston-Downtown, Houston, Texas 77002
| | - Donald A Fox
- College of Optometry, University of Houston, Houston, Texas 77004; Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004; Department of Pharmacology and Pharmaceutical Sciences, University of Houston, Houston, Texas 77004
| | - Debora B Farber
- Jules Stein Eye Institute, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095; Brain Research Institute, UCLA, Los Angeles, California 90095
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21
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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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22
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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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23
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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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24
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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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25
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Liao HJ, Carpenter G. Regulated intramembrane cleavage of the EGF receptor. Traffic 2012; 13:1106-12. [PMID: 22531034 DOI: 10.1111/j.1600-0854.2012.01371.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 04/19/2012] [Accepted: 04/24/2012] [Indexed: 11/28/2022]
Abstract
Following the addition of EGF or ionomycin to A431 cells, protease activity mediates cleavage of the EGF receptor producing a 60 kDa fragment that includes the intracellular domain (ICD). This fragment is located in both membrane and nuclear fractions. On the basis of sensitivity to chemical inhibitors and overexpression of cDNAs, the rhomboid intramembrane proteases, not γ-secretase proteases, are identified as responsible for the cleavage event. Agonist-initiated cleavage occurs slowly over 3-24 h. Inhibition of calpain protease activity significantly increased the detectable level of ICD fragment.
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Affiliation(s)
- Hong-Jun Liao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
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26
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Xue Y, Chowdhury S, Liu X, Akiyama Y, Ellman J, Ha Y. Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S' subsites. Biochemistry 2012; 51:3723-31. [PMID: 22515733 DOI: 10.1021/bi300368b] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhomboid protease conducts proteolysis inside the hydrophobic environment of the membrane. The conformational flexibility of the protease is essential for the enzyme mechanism, but the nature of this flexibility is not completely understood. Here we describe the crystal structure of rhomboid protease GlpG in complex with a phosphonofluoridate inhibitor, which is covalently bonded to the catalytic serine and extends into the S' side of the substrate binding cleft. Inhibitor binding causes subtle but extensive changes in the membrane protease. Many transmembrane helices tilt and shift positions, and the gap between S2 and S5 is slightly widened so that the inhibitor can bind between them. The side chain of Phe-245 from a loop (L5) that acts as a cap rotates and uncovers the opening of the substrate binding cleft to the lipid bilayer. A concurrent turn of the polypeptide backbone at Phe-245 moves the rest of the cap and exposes the catalytic serine to the aqueous solution. This study, together with earlier crystallographic investigation of smaller inhibitors, suggests a simple model for explaining substrate binding to rhomboid 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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27
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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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28
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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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29
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Li J, Zheng J, Gong P, Zhang X. Efficacy of Eimeria tenella rhomboid-like protein as a subunit vaccine in protective immunity against homologous challenge. Parasitol Res 2011; 110:1139-45. [DOI: 10.1007/s00436-011-2603-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 08/04/2011] [Indexed: 11/25/2022]
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30
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Post-liberation cleavage of signal peptides is catalyzed by the site-2 protease (S2P) in bacteria. Proc Natl Acad Sci U S A 2011; 108:13740-5. [PMID: 21810987 DOI: 10.1073/pnas.1108376108] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A signal peptide (SP) is cleaved off from presecretory proteins by signal peptidase during or immediately after insertion into the membrane. In metazoan cells, the cleaved SP then receives proteolysis by signal peptide peptidase, an intramembrane-cleaving protease (I-CLiP). However, bacteria lack any signal peptide peptidase member I-CLiP, and little is known about the metabolic fate of bacterial SPs. Here we show that Escherichia coli RseP, an site-2 protease (S2P) family I-CLiP, introduces a cleavage into SPs after their signal peptidase-mediated liberation from preproteins. A Bacillus subtilis S2P protease, RasP, is also shown to be involved in SP cleavage. These results uncover a physiological role of bacterial S2P proteases and update the basic knowledge about the fate of signal peptides in bacterial cells.
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31
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Huang X, Lee S, Chen X. Design of "smart" probes for optical imaging of apoptosis. AMERICAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING 2011; 1:3-17. [PMID: 22514789 PMCID: PMC3327302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 06/18/2011] [Indexed: 05/31/2023]
Abstract
Apoptosis is a mode of programmed cell death in multicellular organisms and plays a central role in controlling embryonic development, growth and differentiation and monitoring the induction of tumor cell death through anticancer therapy. Since the most effective chemotherapeutics rely on apoptosis, imaging apoptotic processes can be an invaluable tool to monitor therapeutic intervention and discover new drugs modulating apoptosis. The most attractive target for developing specific apoptosis imaging probes is caspases, crucial mediators of apoptosis. Up to now, various optical imaging strategies for apoptosis have been developed as an easy and economical modality. However, current optical applications are limited by poor sensitivity and specificity. A subset of molecular imaging contrast agents known as "activatable" or "smart" molecular probes allow for very high signal-to-background ratios compared to conventional targeted contrast agents and open up the possibility of imaging intracellular targets. In this review, we will discuss the unique design strategies and applications of activatable probes recently developed for fluorescence and bioluminescence imaging of caspase activity.
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Affiliation(s)
- Xinglu Huang
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), Bethesda, MD, USA
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Hu J, Xue Y, Lee S, Ha Y. The crystal structure of GXGD membrane protease FlaK. Nature 2011; 475:528-31. [PMID: 21765428 DOI: 10.1038/nature10218] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 05/18/2011] [Indexed: 11/09/2022]
Abstract
The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 Å resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.
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Affiliation(s)
- Jian Hu
- Department of Pharmacology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
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Abstract
Regulated intramembrane proteolysis is an evolutionarily conserved mechanism by which membrane-anchored bioactive molecules are released from cellular membranes. In eukaryotic cells, intramembrane proteases are found in different cellular organelles ranging from the endosomal system to mitochondria and chloroplasts. These proteases function in diverse processes such as transcription control, regulated growth factor secretion and recently even a role in the control of mitophagy has been suggested. Genomic annotation has predicted 13 different intramembrane proteases in humans. Apart from few studied examples, very little is known about their function. This review describes emerging principles of how intramembrane proteases contribute to the regulation of cellular protein trafficking in eukaryotic cells and raises the important question of how their activity is controlled.
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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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EGY2, a chloroplast membrane metalloprotease, plays a role in hypocotyl elongation in Arabidopsis. Mol Biol Rep 2011; 39:2147-55. [PMID: 21643750 DOI: 10.1007/s11033-011-0962-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
Intramembrane proteases control many important processes in a wide variety of organisms through regulated intramembrane proteolysis (RIP). However, very few intramembrane proteases have been characterized in plants. Intriguingly, EGY2 in Arabidopsis belongs to the Site-2 protease (S2P) family that performs RIP. It contains the conserved catalytic motifs, HExxH and NPDG on its multiple transmembrane helices. Four egy2 knockout mutants have significantly shorter hypocotyls and accumulate lower levels of fatty acids in seedlings. Accumulation of fatty acid biosynthesis enzymes in seedlings are also decreased in egy2 knockout mutants. EGY2 protein resides in the chloroplast and EGY2 transcripts are found throughout the plant except root. Recombinant EGY2 protein cleaves β-casein in an ATP-independent manner. These results together suggest that EGY2 metalloprotease plays a role in hypocotyl elongation likely through a RIP dependent process to regulate the coordinated expression of nuclear- and plastid-encoded genes.
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Abstract
The mitochondrial rhomboid protease Parl governs apoptosis, morphology, metabolism and might be implicated in Parkinson's disease, but the structural basis of its activity and complex regulation remain unknown. We report the discovery of γ-cleavage, a proteolytic event on the loop connecting the first transmembrane helix (TMH) of Parl to the 6-TMH catalytic rhomboid domain of the protease. This cleavage disrupts the '1+6' structure that defines every mitochondrial rhomboid and generates a new form of Parl, PROD (Parl-rhomboid-domain). Structure-function analysis of Parl suggests that γ-cleavage could be implicated in eliminating Parl proteolytic activity, and structural modeling of PROD reveals structural conservation with the bacterial rhomboid GlpG. However, unlike bacterial rhomboids, which employ a diad-based mechanism of catalysis, Parl appears to use a conserved mitochondrial rhomboid-specific Asp residue on TMH-5 in a triad-based mechanism of catalysis. This work provides unexpected insights into the structural determinants regulating Parl stability and activity in vivo, and reveals a complex cascade of proteolytic events controlling the function of the protease in the mitochondrion.
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Chen G, Zhang X. New insights into S2P signaling cascades: regulation, variation, and conservation. Protein Sci 2011; 19:2015-30. [PMID: 20836086 DOI: 10.1002/pro.496] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Regulated intramembrane proteolysis (RIP) is a conserved mechanism that regulates signal transduction across the membrane by recruiting membrane-bound proteases to cleave membrane-spanning regulatory proteins. As the first identified protease that performs RIP, the metalloprotease site-2 protease (S2P) has received extensive study during the past decade, and an increasing number of S2P-like proteases have been identified and studied in different organisms; however, some of their substrates and the related S1Ps remain elusive. Here, we review recent research on S2P cascades, including human S2P, E. coli RseP, B. subtilis SpoIVFB and the newly identified S2P homologs. We also discuss the variation and conservation of characterized S2P cascades. The conserved catalytic motif of S2P and prevalence of amino acids of low helical propensity in the transmembrane segments of the substrates suggest a conserved catalytic conformation and mechanism within the S2P family. The review also sheds light on future research on S2P cascades.
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Affiliation(s)
- Gu Chen
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China.
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37
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Structure of rhomboid protease in a lipid environment. J Mol Biol 2011; 407:232-47. [PMID: 21256137 PMCID: PMC3093617 DOI: 10.1016/j.jmb.2011.01.029] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 01/12/2011] [Accepted: 01/13/2011] [Indexed: 11/24/2022]
Abstract
Structures of the prokaryotic homologue of rhomboid proteases reveal a core of six transmembrane helices, with the active-site residues residing in a hydrophilic cavity. The native environment of rhomboid protease is a lipid bilayer, yet all the structures determined thus far are in a nonnative detergent environment. There remains a possibility of structural artefacts arising from the use of detergents. In an attempt to address the effect of detergents on the structure of rhomboid protease, crystals of GlpG, an Escherichia coli rhomboid protease in a lipid environment, were obtained using two alternative approaches. The structure of GlpG refined to 1. 7-Å resolution was obtained from crystals grown in the presence of lipid bicelles. This structure reveals well-ordered and partly ordered lipid molecules forming an annulus around the protein. Lipid molecules adapt to the surface features of protein and arrange such that they match the hydrophobic thickness of GlpG. Virtually identical two-dimensional crystals were also obtained after detergent removal by dialysis. A comparison of an equivalent structure determined in a completely delipidated detergent environment provides insights on how detergent substitutes for lipid. A detergent molecule is also observed close to the active site, helping to postulate a model for substrate binding and hydrolysis in rhomboids.
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Sequence analysis and verification of Eimeria tenella rhomboid bait plasmid suitability for CytoTrap yeast two-hybrid system. Parasitol Res 2010; 108:253-9. [DOI: 10.1007/s00436-010-2076-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 09/16/2010] [Indexed: 10/19/2022]
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Vinothkumar KR, Strisovsky K, Andreeva A, Christova Y, Verhelst S, Freeman M. The structural basis for catalysis and substrate specificity of a rhomboid protease. EMBO J 2010; 29:3797-809. [PMID: 20890268 DOI: 10.1038/emboj.2010.243] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 09/06/2010] [Indexed: 12/28/2022] Open
Abstract
Rhomboids are intramembrane proteases that use a catalytic dyad of serine and histidine for proteolysis. They are conserved in both prokaryotes and eukaryotes and regulate cellular processes as diverse as intercellular signalling, parasitic invasion of host cells, and mitochondrial morphology. Their widespread biological significance and consequent medical potential provides a strong incentive to understand the mechanism of these unusual enzymes for identification of specific inhibitors. In this study, we describe the structure of Escherichia coli rhomboid GlpG covalently bound to a mechanism-based isocoumarin inhibitor. We identify the position of the oxyanion hole, and the S₁- and S₂'-binding subsites of GlpG, which are the key determinants of substrate specificity. The inhibitor-bound structure suggests that subtle structural change is sufficient for catalysis, as opposed to large changes proposed from previous structures of unliganded GlpG. Using bound inhibitor as a template, we present a model for substrate binding at the active site and biochemically test its validity. This study provides a foundation for a structural explanation of rhomboid specificity and mechanism, and for inhibitor design.
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Downregulation of an Entamoeba histolytica rhomboid protease reveals roles in regulating parasite adhesion and phagocytosis. EUKARYOTIC CELL 2010; 9:1283-93. [PMID: 20581296 DOI: 10.1128/ec.00015-10] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Entamoeba histolytica is a deep-branching eukaryotic pathogen. Rhomboid proteases are intramembrane serine proteases, which cleave transmembrane proteins in, or in close proximity to, their transmembrane domain. We have previously shown that E. histolytica contains a single functional rhomboid protease (EhROM1) and has unique substrate specificity. EhROM1 is present on the trophozoite surface and relocalizes to internal vesicles during erythrophagocytosis and to the base of the cap during surface receptor capping. In order to further examine the biological function of EhROM1 we downregulated EhROM1 expression by >95% by utilizing the epigenetic silencing mechanism of the G3 parasite strain. Despite the observation that EhROM1 relocalized to the cap during surface receptor capping, EhROM1 knockdown [ROM(KD)] parasites had no gross changes in cap formation or complement resistance. However, ROM(KD) parasites demonstrated decreased host cell adhesion, a result recapitulated by treatment of wild-type parasites with DCI, a serine protease inhibitor with activity against rhomboid proteases. The reduced adhesion phenotype of ROM(KD) parasites was noted exclusively with healthy cells, and not with apoptotic cells. Additionally, ROM(KD) parasites had decreased phagocytic ability with reduced ingestion of healthy cells, apoptotic cells, and rice starch. Decreased phagocytic ability is thus independent of the reduced adhesion phenotype, since phagocytosis of apoptotic cells was reduced despite normal adhesion levels. The defect in host cell adhesion was not explained by altered expression or localization of the heavy subunit of the Gal/GalNAc surface lectin. These results suggest no significant role of EhROM1 in complement resistance but unexpected roles in parasite adhesion and phagocytosis.
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Erez E, Bibi E. Cleavage of a multispanning membrane protein by an intramembrane serine protease. Biochemistry 2010; 48:12314-22. [PMID: 19919105 DOI: 10.1021/bi901648g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
All intramembrane proteases are known to cleave membrane proteins with a single transmembrane helix. Such cleavages often release anchored soluble domains, which play a role in physiologically important inter- and intracellular processes. However, in many cases the physiological roles/substrates of intramembrane proteases are not known. It is interesting that no multispanning substrates were identified so far, despite the fact that intramembrane proteases have promiscuous substrate recognition and cleavage capabilities. Here we determined whether, in a synthetic experimental system, intramembrane proteases have the capability to interact with and cleave multispanning membrane proteins. We utilized the Escherichia coli rhomboid GlpG, an intramembrane serine protease, and truncated versions of the E. coli multidrug transporter MdfA as model multispanning membrane proteins. On the basis of in vivo and in vitro studies on the association of GlpG with various MdfA constructs and their cleavage, we conclude that GlpG is able to recognize and cleave truncated forms of MdfA but not the intact protein. We propose that GlpG has the capacity to act on unfolded multispanning membrane proteins, thus providing an incentive for investigating possible physiological consequences.
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Affiliation(s)
- Elinor Erez
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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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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Strisovsky K, Sharpe HJ, Freeman M. Sequence-specific intramembrane proteolysis: identification of a recognition motif in rhomboid substrates. Mol Cell 2009; 36:1048-59. [PMID: 20064469 PMCID: PMC2941825 DOI: 10.1016/j.molcel.2009.11.006] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 08/27/2009] [Accepted: 09/23/2009] [Indexed: 11/21/2022]
Abstract
Members of the widespread rhomboid family of intramembrane proteases cleave transmembrane domain (TMD) proteins to regulate processes as diverse as EGF receptor signaling, mitochondrial dynamics, and invasion by apicomplexan parasites. However, lack of information about their substrates means that the biological role of most rhomboids remains obscure. Knowledge of how rhomboids recognize their substrates would illuminate their mechanism and might also allow substrate prediction. Previous work has suggested that rhomboid substrates are specified by helical instability in their TMD. Here we demonstrate that rhomboids instead primarily recognize a specific sequence surrounding the cleavage site. This recognition motif is necessary for substrate cleavage, it determines the cleavage site, and it is more strictly required than TM helix-destabilizing residues. Our work demonstrates that intramembrane proteases can be sequence specific and that genome-wide substrate prediction based on their recognition motifs is feasible.
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Affiliation(s)
- Kvido Strisovsky
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Hayley J. Sharpe
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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