1
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Lu F, Zhao H, Dai Y, Wang Y, Lee CH, Freeman M. Cryo-EM reveals that iRhom2 restrains ADAM17 protease activity to control the release of growth factor and inflammatory signals. Mol Cell 2024; 84:2152-2165.e5. [PMID: 38781971 PMCID: PMC11248996 DOI: 10.1016/j.molcel.2024.04.025] [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: 08/29/2023] [Revised: 02/09/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
A disintegrin and metalloprotease 17 (ADAM17) is a membrane-tethered protease that triggers multiple signaling pathways. It releases active forms of the primary inflammatory cytokine tumor necrosis factor (TNF) and cancer-implicated epidermal growth factor (EGF) family growth factors. iRhom2, a rhomboid-like, membrane-embedded pseudoprotease, is an essential cofactor of ADAM17. Here, we present cryoelectron microscopy (cryo-EM) structures of the human ADAM17/iRhom2 complex in both inactive and active states. These reveal three regulatory mechanisms. First, exploiting the rhomboid-like hallmark of TMD recognition, iRhom2 interacts with the ADAM17 TMD to promote ADAM17 trafficking and enzyme maturation. Second, a unique iRhom2 extracellular domain unexpectedly retains the cleaved ADAM17 inhibitory prodomain, safeguarding against premature activation and dysregulated proteolysis. Finally, loss of the prodomain from the complex mobilizes the ADAM17 protease domain, contributing to its ability to engage substrates. Our results reveal how a rhomboid-like pseudoprotease has been repurposed during evolution to regulate a potent membrane-tethered enzyme, ADAM17, ensuring the fidelity of inflammatory and growth factor signaling.
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Affiliation(s)
- Fangfang Lu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Hongtu Zhao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Yaxin Dai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yingdi Wang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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2
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Schwarzer E, Skorokhod O. Post-Translational Modifications of Proteins of Malaria Parasites during the Life Cycle. Int J Mol Sci 2024; 25:6145. [PMID: 38892332 PMCID: PMC11173270 DOI: 10.3390/ijms25116145] [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: 05/01/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Post-translational modifications (PTMs) are essential for regulating protein functions, influencing various fundamental processes in eukaryotes. These include, but are not limited to, cell signaling, protein trafficking, the epigenetic control of gene expression, and control of the cell cycle, as well as cell proliferation, differentiation, and interactions between cells. In this review, we discuss protein PTMs that play a key role in the malaria parasite biology and its pathogenesis. Phosphorylation, acetylation, methylation, lipidation and lipoxidation, glycosylation, ubiquitination and sumoylation, nitrosylation and glutathionylation, all of which occur in malarial parasites, are reviewed. We provide information regarding the biological significance of these modifications along all phases of the complex life cycle of Plasmodium spp. Importantly, not only the parasite, but also the host and vector protein PTMs are often crucial for parasite growth and development. In addition to metabolic regulations, protein PTMs can result in epitopes that are able to elicit both innate and adaptive immune responses of the host or vector. We discuss some existing and prospective results from antimalarial drug discovery trials that target various PTM-related processes in the parasite or host.
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Affiliation(s)
- Evelin Schwarzer
- Department of Oncology, University of Turin, Via Santena 5 bis, 10126 Turin, Italy;
| | - Oleksii Skorokhod
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina, 13, 10123 Turin, Italy
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3
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Zhang Y, Huang X, Zhang L, Gao W, Ma J, Chen T, Yang D. Genome-wide identification, gene expression and haplotype analysis of the rhomboid-like gene family in wheat (Triticum aestivum L.). THE PLANT GENOME 2024; 17:e20435. [PMID: 38348504 DOI: 10.1002/tpg2.20435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/08/2024] [Accepted: 01/23/2024] [Indexed: 07/02/2024]
Abstract
The rhomboid-like (RBL) gene encodes serine protease, which plays an important role in the response to cell development and diverse stresses. However, genome-wide identification, expression profiles, and haplotype analysis of the RBL family genes have not been performed in wheat (Triticum aestivum L.). This study investigated the phylogeny and diversity of the RBL family genes in the wheat genome through various approaches, including gene structure analysis, evolutionary relationship analysis, promoter cis-acting element analysis, expression pattern analysis, and haplotype analysis. The 41 TaRBL genes were identified and divided into five subfamilies in the wheat genome. RBL family genes were expanded through segmented duplication and purification selection. The cis-element analysis revealed their involvement in various stress responses and plant development. The results of RNA-seq and quantitative real-time-PCR showed that TaRBL genes displayed higher expression levels in developing spike/grain and were differentially regulated under polyethylene glycol, NaCl, and abscisic acid treatments, indicating their roles in grain development and abiotic stress response. A kompetitive allele-specific PCR molecular marker was developed to confirm the single nucleotide polymorphism of TaRBL14a gene in 263 wheat accessions. We found that the elite haplotype TaRBL14a-Hap2 showed a significantly higher 1000-grain weight than TaRBL14a-Hap11 in at least three environments, and the TaRBL14a-Hap2 was positively selected in wheat breeding. The findings will provide a good insight into the evolutionary and functional characteristics of the TaRBL genes family in wheat and lay the foundation for future exploration of the regulatory mechanisms of TaRBL genes in plant growth and development, as well as their response to abiotic stresses.
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Affiliation(s)
- Yanyan Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoya Huang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Long Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weidong Gao
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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4
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Talukdar S, Mal S, Kundu P. Physico-chemical features and functional relevance of tomato rhomboid proteases. Int J Biol Macromol 2024; 272:132681. [PMID: 38806088 DOI: 10.1016/j.ijbiomac.2024.132681] [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: 03/08/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
In plants, regulated intramembrane proteolysis (RIP) is crucial for proper growth, development, and stress management. Rhomboid proteases (RPs) residing in the membrane play a vital role in orchestrating RIP. Although RPs can be found in most sequenced genomes, tomato rhomboids (SlRPs) have not yet been studied. Using alternative and comprehensive strategies, we found ten SlRPs encoded in the tomato genome. These SlRPs possess signature motifs and transmembrane domains, showing structural similarity to other members of the RP family. Also, SlRPs are genetically related to other known RPs of the Solanaceae family. Seven of the SlRPs retain serine-histidine catalytic dyads, making them proteolytically active, while three iRhoms lack the dyad and other structural motifs. Although SlRPs could have functional redundancy, their distribution and expression pattern indicate tissue specificity and responsiveness to specific external stimuli. The presence of development and stress-response-related cis-elements in the promoters of SlRPs supports this view. Furthermore, our strategically designed substrate-reporter assay shows that SlRPs have proteolytic activity similar to that of known RPs. This study provides a detailed understanding of all SlRPs and their physico-chemical features, shedding light on their involvement in physiological processes.
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Affiliation(s)
- Sushmita Talukdar
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India
| | - Sayan Mal
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India
| | - Pallob Kundu
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India.
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5
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Yao J, Hong H. Steric trapping strategy for studying the folding of helical membrane proteins. Methods 2024; 225:1-12. [PMID: 38428472 PMCID: PMC11107808 DOI: 10.1016/j.ymeth.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024] Open
Abstract
Elucidating the folding energy landscape of membrane proteins is essential to the understanding of the proteins' stabilizing forces, folding mechanisms, biogenesis, and quality control. This is not a trivial task because the reversible control of folding is inherently difficult in a lipid bilayer environment. Recently, novel methods have been developed, each of which has a unique strength in investigating specific aspects of membrane protein folding. Among such methods, steric trapping is a versatile strategy allowing a reversible control of membrane protein folding with minimal perturbation of native protein-water and protein-lipid interactions. In a nutshell, steric trapping exploits the coupling of spontaneous denaturation of a doubly biotinylated protein to the simultaneous binding of bulky monovalent streptavidin molecules. This strategy has been evolved to investigate key elements of membrane protein folding such as thermodynamic stability, spontaneous denaturation rates, conformational features of the denatured states, and cooperativity of stabilizing interactions. In this review, we describe the critical methodological advancement, limitation, and outlook of the steric trapping strategy.
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Affiliation(s)
- Jiaqi Yao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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6
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Knopf JD, Steigleder SS, Korn F, Kühnle N, Badenes M, Tauber M, Theobald SJ, Rybniker J, Adrain C, Lemberg MK. RHBDL4-triggered downregulation of COPII adaptor protein TMED7 suppresses TLR4-mediated inflammatory signaling. Nat Commun 2024; 15:1528. [PMID: 38453906 PMCID: PMC10920636 DOI: 10.1038/s41467-024-45615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024] Open
Abstract
The toll-like receptor 4 (TLR4) is a central regulator of innate immunity that primarily recognizes bacterial lipopolysaccharide cell wall constituents to trigger cytokine secretion. We identify the intramembrane protease RHBDL4 as a negative regulator of TLR4 signaling. We show that RHBDL4 triggers degradation of TLR4's trafficking factor TMED7. This counteracts TLR4 transport to the cell surface. Notably, TLR4 activation mediates transcriptional upregulation of RHBDL4 thereby inducing a negative feedback loop to reduce TLR4 trafficking to the plasma membrane. This secretory cargo tuning mechanism prevents the over-activation of TLR4-dependent signaling in an in vitro Mycobacterium tuberculosis macrophage infection model and consequently alleviates septic shock in a mouse model. A hypomorphic RHBDL4 mutation linked to Kawasaki syndrome, an ill-defined inflammatory disorder in children, further supports the pathophysiological relevance of our findings. In this work, we identify an RHBDL4-mediated axis that acts as a rheostat to prevent over-activation of the TLR4 pathway.
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Affiliation(s)
- Julia D Knopf
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Susanne S Steigleder
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Friederike Korn
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Nathalie Kühnle
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Marina Badenes
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
- Faculty of Veterinary Medicine, Lusofona University and Faculty of Veterinary Nursing, Polytechnic Institute of Lusofonia, Lisbon, Portugal
| | - Marina Tauber
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931, Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931, Cologne, Germany
| | - Colin Adrain
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
- Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany.
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7
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Dulloo I, Tellier M, Levet C, Chikh A, Zhang B, Blaydon DC, Webb CM, Kelsell DP, Freeman M. Cleavage of the pseudoprotease iRhom2 by the signal peptidase complex reveals an ER-to-nucleus signaling pathway. Mol Cell 2024; 84:277-292.e9. [PMID: 38183983 DOI: 10.1016/j.molcel.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 09/18/2023] [Accepted: 12/08/2023] [Indexed: 01/08/2024]
Abstract
iRhoms are pseudoprotease members of the rhomboid-like superfamily and are cardinal regulators of inflammatory and growth factor signaling; they function primarily by recognizing transmembrane domains of their clients. Here, we report a mechanistically distinct nuclear function of iRhoms, showing that both human and mouse iRhom2 are non-canonical substrates of signal peptidase complex (SPC), the protease that removes signal peptides from secreted proteins. Cleavage of iRhom2 generates an N-terminal fragment that enters the nucleus and modifies the transcriptome, in part by binding C-terminal binding proteins (CtBPs). The biological significance of nuclear iRhom2 is indicated by elevated levels in skin biopsies of patients with psoriasis, tylosis with oesophageal cancer (TOC), and non-epidermolytic palmoplantar keratoderma (NEPPK); increased iRhom2 cleavage in a keratinocyte model of psoriasis; and nuclear iRhom2 promoting proliferation of keratinocytes. Overall, this work identifies an unexpected SPC-dependent ER-to-nucleus signaling pathway and demonstrates that iRhoms can mediate nuclear signaling.
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Affiliation(s)
- Iqbal Dulloo
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Michael Tellier
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Clémence Levet
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Anissa Chikh
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Boyan Zhang
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Diana C Blaydon
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Catherine M Webb
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - David P Kelsell
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Matthew Freeman
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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8
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Shao L, Zhang M, Liu Y, Peng J, Zhang X, He L. Fish Rhbdd3 positively regulates IFN response through RIG-I signaling pathway. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109102. [PMID: 37758095 DOI: 10.1016/j.fsi.2023.109102] [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: 04/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Rhomboid domain-containing protein 3 (Rhbdd3) is a member of the rhomboid family, which can modulate the innate immune response in mammals. Nonetheless, the function and regulatory mechanism of fish Rhbdd3 during viral infection have not been characterized. In this study, Rhbdd3 was firstly cloned from common carp (Cyprinus carpio) and nominated as CcRhbdd3. Phylogenetically characterization showed that CcRhbdd3 shared a relatively long evolutionary distance with its mammalian homologs. In vivo experiment demonstrated that spring viraemia of carp virus (SVCV) infection promoted the expression of CcRhbdd3 in the liver, spleen, kidney and muscle tissues. Furthermore, overexpression of CcRhbdd3 significantly inhibited SVCV propagation, whereas knockdown of CcRhbdd3 markedly promoted SVCV replication in susceptible cells. RNA-seq and following validation showed that CcRhbdd3 overexpression upregulated the expression of several RIG-I signaling related genes, including TRIM25, TRAF2, MDA5, LGP2, IFN1, IFN3, RIG-I, IRF3 and ISG15. Moreover, CcRhbdd3 promoted the expression of NF-κB, a central immune regulator. Subcellular localization experiments showed that CcRhbdd3 was primarily distributed in the cytoplasm and co-localized with Rab5 in the early endosomes. Truncation experiments further demonstrated that the C-terminus containing the ubiquitin-binding associated domain, was crucial for both the subcellular localization and antiviral activity of CcRhbdd3. The findings in this study provide new insight into the host antiviral mechanism against aquatic RNA virus infection, and will facilitate the development of therapeutic strategies for the infection of SVCV.
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Affiliation(s)
- Ling Shao
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai, 200433, China.
| | - Minghui Zhang
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai, 200433, China
| | - Yanan Liu
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai, 200433, China
| | - Junhui Peng
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai, 200433, China
| | - Xiaoming Zhang
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai, 200433, China
| | - Lan He
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai, 200433, China
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9
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Lagergren J, Pavicic M, Chhetri HB, York LM, Hyatt D, Kainer D, Rutter EM, Flores K, Bailey-Bale J, Klein M, Taylor G, Jacobson D, Streich J. Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0072. [PMID: 37519935 PMCID: PMC10380552 DOI: 10.34133/plantphenomics.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Plant phenotyping is typically a time-consuming and expensive endeavor, requiring large groups of researchers to meticulously measure biologically relevant plant traits, and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population scale. In this work, we address these challenges by leveraging few-shot learning with convolutional neural networks to segment the leaf body and visible venation of 2,906 Populus trichocarpa leaf images obtained in the field. In contrast to previous methods, our approach (a) does not require experimental or image preprocessing, (b) uses the raw RGB images at full resolution, and (c) requires very few samples for training (e.g., just 8 images for vein segmentation). Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools, validated using real-world physical measurements, and used to conduct a genome-wide association study to identify genes controlling the traits. In this way, the current work is designed to provide the plant phenotyping community with (a) methods for fast and accurate image-based feature extraction that require minimal training data and (b) a new population-scale dataset, including 68 different leaf phenotypes, for domain scientists and machine learning researchers. All of the few-shot learning code, data, and results are made publicly available.
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Affiliation(s)
- John Lagergren
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mirko Pavicic
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hari B Chhetri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Larry M York
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Doug Hyatt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - David Kainer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Erica M Rutter
- Department of Applied Mathematics, University of California, Merced, CA, USA
| | - Kevin Flores
- Department of Mathematics, North Carolina State University, Raleigh, NC, USA
| | - Jack Bailey-Bale
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Marie Klein
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Gail Taylor
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jared Streich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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10
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Kahveci-Türköz S, Bläsius K, Wozniak J, Rinkens C, Seifert A, Kasparek P, Ohm H, Oltzen S, Nieszporek M, Schwarz N, Babendreyer A, Preisinger C, Sedlacek R, Ludwig A, Düsterhöft S. A structural model of the iRhom-ADAM17 sheddase complex reveals functional insights into its trafficking and activity. Cell Mol Life Sci 2023; 80:135. [PMID: 37119365 PMCID: PMC10148629 DOI: 10.1007/s00018-023-04783-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 05/01/2023]
Abstract
Several membrane-anchored signal mediators such as cytokines (e.g. TNFα) and growth factors are proteolytically shed from the cell surface by the metalloproteinase ADAM17, which, thus, has an essential role in inflammatory and developmental processes. The membrane proteins iRhom1 and iRhom2 are instrumental for the transport of ADAM17 to the cell surface and its regulation. However, the structure-function determinants of the iRhom-ADAM17 complex are poorly understood. We used AI-based modelling to gain insights into the structure-function relationship of this complex. We identified different regions in the iRhom homology domain (IRHD) that are differentially responsible for iRhom functions. We have supported the validity of the predicted structure-function determinants with several in vitro, ex vivo and in vivo approaches and demonstrated the regulatory role of the IRHD for iRhom-ADAM17 complex cohesion and forward trafficking. Overall, we provide mechanistic insights into the iRhom-ADAM17-mediated shedding event, which is at the centre of several important cytokine and growth factor pathways.
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Affiliation(s)
- Selcan Kahveci-Türköz
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Katharina Bläsius
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Justyna Wozniak
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Cindy Rinkens
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Anke Seifert
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Petr Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Henrike Ohm
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Shixin Oltzen
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Martin Nieszporek
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Nicole Schwarz
- Institute of Molecular and Cellular Anatomy, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Aaron Babendreyer
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | | | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andreas Ludwig
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Stefan Düsterhöft
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
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11
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Bhaduri S, Scott NA, Neal SE. The Role of the Rhomboid Superfamily in ER Protein Quality Control: From Mechanisms and Functions to Diseases. Cold Spring Harb Perspect Biol 2023; 15:a041248. [PMID: 35940905 PMCID: PMC9899648 DOI: 10.1101/cshperspect.a041248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The endoplasmic reticulum (ER) is an essential organelle in eukaryotic cells and is a major site for protein folding, modification, and lipid synthesis. Perturbations within the ER, such as protein misfolding and high demand for protein folding, lead to dysregulation of the ER protein quality control network and ER stress. Recently, the rhomboid superfamily has emerged as a critical player in ER protein quality control because it has diverse cellular functions, including ER-associated degradation (ERAD), endosome Golgi-associated degradation (EGAD), and ER preemptive quality control (ERpQC). This breadth of function both illustrates the importance of the rhomboid superfamily in health and diseases and emphasizes the necessity of understanding their mechanisms of action. Because dysregulation of rhomboid proteins has been implicated in various diseases, such as neurological disorders and cancers, they represent promising potential therapeutic drug targets. This review provides a comprehensive account of the various roles of rhomboid proteins in the context of ER protein quality control and discusses their significance in health and disease.
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Affiliation(s)
- Satarupa Bhaduri
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Nicola A Scott
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
| | - Sonya E Neal
- School of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093, USA
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Kandel R, Jung J, Syau D, Kuo T, Songster L, Horn C, Chapman C, Aguayo A, Duttke S, Benner C, Neal SE. Yeast derlin Dfm1 employs a chaperone-like function to resolve misfolded membrane protein stress. PLoS Biol 2023; 21:e3001950. [PMID: 36689475 PMCID: PMC9894555 DOI: 10.1371/journal.pbio.3001950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/02/2023] [Accepted: 12/07/2022] [Indexed: 01/24/2023] Open
Abstract
Protein aggregates are a common feature of diseased and aged cells. Membrane proteins comprise a quarter of the proteome, and yet, it is not well understood how aggregation of membrane proteins is regulated and what effects these aggregates can have on cellular health. We have determined in yeast that the derlin Dfm1 has a chaperone-like activity that influences misfolded membrane protein aggregation. We establish that this function of Dfm1 does not require recruitment of the ATPase Cdc48 and it is distinct from Dfm1's previously identified function in dislocating misfolded membrane proteins from the endoplasmic reticulum (ER) to the cytosol for degradation. Additionally, we assess the cellular impacts of misfolded membrane proteins in the absence of Dfm1 and determine that misfolded membrane proteins are toxic to cells in the absence of Dfm1 and cause disruptions to proteasomal and ubiquitin homeostasis.
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Affiliation(s)
- Rachel Kandel
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Jasmine Jung
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Della Syau
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Tiffany Kuo
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Livia Songster
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Casey Horn
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Claire Chapman
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Analine Aguayo
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Sascha Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Christopher Benner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Sonya E. Neal
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
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13
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Chen S, Cai K, Zheng D, Liu Y, Li L, He Z, Sun C, Yu C. RHBDL2 promotes the proliferation, migration, and invasion of pancreatic cancer by stabilizing the N1ICD via the OTUD7B and activating the Notch signaling pathway. Cell Death Dis 2022; 13:945. [PMID: 36351890 PMCID: PMC9646733 DOI: 10.1038/s41419-022-05379-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Pancreatic cancer (PC) is one of the most malignant types of cancer, and is characterized by early metastasis, limited response to chemotherapeutics, and poor prognosis. Therefore, there is an urgent need to explore new therapeutic strategies for PC treatment. Human rhomboid-like 2 (RHBDL2) is differentially expressed in cervical and breast cancer. However, the correlation between RHBDL2 and PC remains unclear. We found that RHBDL2 is highly expressed in human PC cells and tissues and is significantly associated with distant metastasis and poor survival of patients with PC. Gain- and loss-of-function assays indicated that RHBDL2 could accelerate PC cell proliferation and mobility in vitro and in vivo. The RNA-Seq results suggest that RHBDL2 may be involved in the activation of Notch signaling pathway. IMR-1 could restore the proliferation and metastatic capacity of PC cells mediated by RHBDL2. RHBDL2 interacted with and cleaved Notch1, resulting in the release of N1ICD. RHBDL2 decreased the ubiquitination level of N1ICD and collaborated with Ovarian tumor domain-containing 7B (OTUD7B) to stabilize N1ICD via the ubiquitin-proteasome pathway. RHBDL2 facilitated PC cell proliferation and mobility by stabilizing the N1ICD via the OTUD7B and activating the Notch signaling pathway. Thus, targeting this novel pathway may be a potential therapeutic strategy for PC.
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Affiliation(s)
- Shiyu Chen
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Kun Cai
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Dijie Zheng
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Yanqing Liu
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Lin Li
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Translational Medicine, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Zhiwei He
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Chengyi Sun
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
| | - Chao Yu
- grid.452244.1Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004 China ,Guizhou Provincial Institute of Hepatobiliary, Pancreatic and Splenic Diseases, Guiyang, Guizhou 550004 China ,Guizhou Provincial Clinical Medical Research Center of Hepatobiliary Surgery, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Key Laboratory of Liver, Gallbladder, Pancreas and Spleen of Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, Guiyang, Guizhou 550004 China ,grid.413458.f0000 0000 9330 9891Department of Surgery, College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550004 China
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Hodges SL, Bouza AA, Isom LL. Therapeutic Potential of Targeting Regulated Intramembrane Proteolysis Mechanisms of Voltage-Gated Ion Channel Subunits and Cell Adhesion Molecules. Pharmacol Rev 2022; 74:1028-1048. [PMID: 36113879 PMCID: PMC9553118 DOI: 10.1124/pharmrev.121.000340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/13/2022] [Indexed: 10/03/2023] Open
Abstract
Several integral membrane proteins undergo regulated intramembrane proteolysis (RIP), a tightly controlled process through which cells transmit information across and between intracellular compartments. RIP generates biologically active peptides by a series of proteolytic cleavage events carried out by two primary groups of enzymes: sheddases and intramembrane-cleaving proteases (iCLiPs). Following RIP, fragments of both pore-forming and non-pore-forming ion channel subunits, as well as immunoglobulin super family (IgSF) members, have been shown to translocate to the nucleus to function in transcriptional regulation. As an example, the voltage-gated sodium channel β1 subunit, which is also an IgSF-cell adhesion molecule (CAM), is a substrate for RIP. β1 RIP results in generation of a soluble intracellular domain, which can regulate gene expression in the nucleus. In this review, we discuss the proposed RIP mechanisms of voltage-gated sodium, potassium, and calcium channel subunits as well as the roles of their generated proteolytic products in the nucleus. We also discuss other RIP substrates that are cleaved by similar sheddases and iCLiPs, such as IgSF macromolecules, including CAMs, whose proteolytically generated fragments function in the nucleus. Importantly, dysfunctional RIP mechanisms are linked to human disease. Thus, we will also review how understanding RIP events and subsequent signaling processes involving ion channel subunits and IgSF proteins may lead to the discovery of novel therapeutic targets. SIGNIFICANCE STATEMENT: Several ion channel subunits and immunoglobulin superfamily molecules have been identified as substrates of regulated intramembrane proteolysis (RIP). This signal transduction mechanism, which generates polypeptide fragments that translocate to the nucleus, is an important regulator of gene transcription. RIP may impact diseases of excitability, including epilepsy, cardiac arrhythmia, and sudden death syndromes. A thorough understanding of the role of RIP in gene regulation is critical as it may reveal novel therapeutic strategies for the treatment of previously intractable diseases.
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Affiliation(s)
- Samantha L Hodges
- Departments of Pharmacology (S.L.H., A.A.B., L.L.I.), Neurology (L.L.I.), and Molecular & Integrative Physiology (L.L.I.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Alexandra A Bouza
- Departments of Pharmacology (S.L.H., A.A.B., L.L.I.), Neurology (L.L.I.), and Molecular & Integrative Physiology (L.L.I.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Lori L Isom
- Departments of Pharmacology (S.L.H., A.A.B., L.L.I.), Neurology (L.L.I.), and Molecular & Integrative Physiology (L.L.I.), University of Michigan Medical School, Ann Arbor, Michigan
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15
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Siebert V, Silber M, Heuten E, Muhle-Goll C, Lemberg MK. Cleavage of mitochondrial homeostasis regulator PGAM5 by the intramembrane protease PARL is governed by transmembrane helix dynamics and oligomeric state. J Biol Chem 2022; 298:102321. [PMID: 35921890 PMCID: PMC9436811 DOI: 10.1016/j.jbc.2022.102321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/07/2022] Open
Abstract
The intramembrane protease PARL acts as a crucial mitochondrial safeguard by cleaving the mitophagy regulators PINK1 and PGAM5. Depending on the stress level, PGAM5 can either stimulate cell survival or cell death. In contrast to PINK1, which is constantly cleaved in healthy mitochondria and only active when the inner mitochondrial membrane is depolarized, PGAM5 processing is inversely regulated. However, determinants of PGAM5 that indicate it as a conditional substrate for PARL have not been rigorously investigated, and it is unclear how uncoupling the mitochondrial membrane potential affects its processing compared to that of PINK1. Here, we show that several polar transmembrane residues in PGAM5 distant from the cleavage site serve as determinants for its PARL-catalyzed cleavage. Our NMR analysis indicates that a short N-terminal amphipathic helix, followed by a kink and a C-terminal transmembrane helix harboring the scissile peptide bond are key for a productive interaction with PARL. Furthermore, we also show that PGAM5 is stably inserted into the inner mitochondrial membrane until uncoupling the membrane potential triggers its disassembly into monomers, which are then cleaved by PARL. In conclusion, we propose a model in which PGAM5 is slowly processed by PARL-catalyzed cleavage that is influenced by multiple hierarchical substrate features, including a membrane potential–dependent oligomeric switch.
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16
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Metal cofactor stabilization by a partner protein is a widespread strategy employed for amidase activation. Proc Natl Acad Sci U S A 2022; 119:e2201141119. [PMID: 35733252 PMCID: PMC9245657 DOI: 10.1073/pnas.2201141119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Construction and remodeling of the bacterial peptidoglycan (PG) cell wall must be carefully coordinated with cell growth and division. Central to cell wall construction are hydrolases that cleave bonds in peptidoglycan. These enzymes also represent potential new antibiotic targets. One such hydrolase, the amidase LytH in Staphylococcus aureus, acts to remove stem peptides from PG, controlling where substrates are available for insertion of new PG strands and consequently regulating cell size. When it is absent, cells grow excessively large and have division defects. For activity, LytH requires a protein partner, ActH, that consists of an intracellular domain, a large rhomboid protease domain, and three extracellular tetratricopeptide repeats (TPRs). Here, we demonstrate that the amidase-activating function of ActH is entirely contained in its extracellular TPRs. We show that ActH binding stabilizes metals in the LytH active site and that LytH metal binding in turn is needed for stable complexation with ActH. We further present a structure of a complex of the extracellular domains of LytH and ActH. Our findings suggest that metal cofactor stabilization is a general strategy used by amidase activators and that ActH houses multiple functions within a single protein.
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17
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Erland LAE, Dumigan CR, Forsyth JA, Frolova L, Yasunaga AB, Pun W, Li ITS, Deyholos MK, Murch SJ. Mammalian Melatonin Agonist Pharmaceuticals Stimulate Rhomboid Proteins in Plants. Biomolecules 2022; 12:biom12070882. [PMID: 35883439 PMCID: PMC9313243 DOI: 10.3390/biom12070882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/04/2022] Open
Abstract
Melatonin is a human neurotransmitter and plant signalling metabolite that perceives and directs plant metabolism. The mechanisms of melatonin action in plants remain undefined. We hypothesized that roots have a melatonin-specific receptor and/or transporter that can respond to melatonin-mediating pharmaceuticals. To test this hypothesis Arabidopsis seedlings were grown with melatonin pharmaceutical receptor agonists: ramelteon and tasimelteon, and/or antagonists: luzindole and 4-P-PDOT. Ramelteon was found both to mimic and competitively inhibit melatonin metabolism in plants. Due to the higher selectivity of ramelteon for the MT1 receptor type in humans, a sequence homology search for MT1 in Arabidopsis identified the rhomboid-like protein 7 (RBL7). In physiological studies, Arabidopsis rbl7 mutants were less responsive to ramelteon and melatonin. Quantum dot visualizations of the effects of ramelteon on melatonin binding to root cell membranes revealed a potential mechanism. We propose that RBL7 is a melatonin-interacting protein that directs root architecture and growth in a mechanism that is responsive to environmental factors.
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Affiliation(s)
- Lauren A. E. Erland
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (L.A.E.E.); (J.A.F.); (L.F.); (A.B.Y.); (W.P.); (I.T.S.L.)
- Department of Agriculture, University of the Fraser Valley, Chilliwack, BC V6T 1Z4, Canada
| | - Christopher R. Dumigan
- Department of Biology, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (C.R.D.); (M.K.D.)
| | - Jillian A. Forsyth
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (L.A.E.E.); (J.A.F.); (L.F.); (A.B.Y.); (W.P.); (I.T.S.L.)
| | - Liubov Frolova
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (L.A.E.E.); (J.A.F.); (L.F.); (A.B.Y.); (W.P.); (I.T.S.L.)
| | - Adam B. Yasunaga
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (L.A.E.E.); (J.A.F.); (L.F.); (A.B.Y.); (W.P.); (I.T.S.L.)
| | - Winnie Pun
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (L.A.E.E.); (J.A.F.); (L.F.); (A.B.Y.); (W.P.); (I.T.S.L.)
| | - Isaac T. S. Li
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (L.A.E.E.); (J.A.F.); (L.F.); (A.B.Y.); (W.P.); (I.T.S.L.)
| | - Michael K. Deyholos
- Department of Biology, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (C.R.D.); (M.K.D.)
| | - Susan J. Murch
- Department of Chemistry, University of British Columbia, Kelowna, BC V1V 1V7, Canada; (L.A.E.E.); (J.A.F.); (L.F.); (A.B.Y.); (W.P.); (I.T.S.L.)
- Correspondence:
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18
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Lastun VL, Levet C, Freeman M. The mammalian rhomboid protein RHBDL4 protects against endoplasmic reticulum stress by regulating the morphology and distribution of ER sheets. J Biol Chem 2022; 298:101935. [PMID: 35436469 PMCID: PMC9136127 DOI: 10.1016/j.jbc.2022.101935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
In metazoans, the architecture of the endoplasmic reticulum (ER) differs between cell types and undergoes major changes throughout the cell cycle and according to physiological needs. Although much is known about how the different ER morphologies are generated and maintained, especially ER tubules, how context-dependent changes in ER shape and distribution are regulated and the factors involved are less well characterized, as are the factors that contribute to the positioning of the ER within the cell. By overexpression and KO experiments, we show that the levels of RHBDL4, an ER-resident rhomboid protease, modulate the shape and distribution of the ER, especially during conditions that require rapid changes in the ER sheet distribution, such as ER stress. We demonstrate that RHBDL4 interacts with cytoskeleton-linking membrane protein 63 (CLIMP-63), a protein involved in ER sheet stabilization, as well as with the cytoskeleton. Furthermore, we found that mice lacking RHBDL4 are sensitive to ER stress and develop liver steatosis, a phenotype associated with unresolved ER stress. Taken together, these data suggest a new physiological role for RHBDL4 and also imply that this function does not require its enzymatic activity.
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19
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Ji R, Shi Q, Cao Y, Zhang J, Zhao C, Zhao H, Sayyed Y, Fu L, Li LY. Alternative splicing of the human rhomboid family-1 gene RHBDF1 inhibits epidermal growth factor receptor activation. J Biol Chem 2022; 298:102033. [PMID: 35595096 PMCID: PMC9190019 DOI: 10.1016/j.jbc.2022.102033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 12/01/2022] Open
Abstract
The human rhomboid-5 homolog-1 (RHBDF1) is a multi-transmembrane protein present mainly on the endoplasmic reticulum. RHBDF1 has been implicated in the activation of epidermal growth factor receptor (EGFR)–derived cell growth signals and other activities critical to cellular responses to stressful conditions, but details of this activation mechanism are unclear. Here, we report a RHBDF1 mRNA transcript alternative splicing variant X6 (RHBDF1 X6 or RHX6) that antagonizes RHBDF1 activities. We found that while the RHBDF1 gene is marginally expressed in breast tumor-adjacent normal tissues, it is markedly elevated in the tumor tissues. In sharp contrast, the RHX6 mRNA represents the primary RHBDF1 variant in normal breast epithelial cells and tumor-adjacent normal tissues but is diminished in breast cancer cells and tumors. We demonstrate that, functionally, RHX6 acts as an inhibitor of RHBDF1 activities. We show that artificially overexpressing RHX6 in breast cancer cells leads to retarded proliferation, migration, and decreased production of epithelial–mesenchymal transition-related adhesion molecules. Mechanically, RHX6 is able to inhibit the maturation of TACE, a protease that processes pro-TGFα, a pro-ligand of EGFR, and to prevent intracellular transportation of pro-TGFα to the cell surface. Additionally, we show that the production of RHX6 is under the control of the alternative splicing regulator RNA binding motif protein-4 (RBM4). Our findings suggest that differential splicing of the RHBDF1 gene transcript may have a regulatory role in the development of epithelial cell cancers.
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Affiliation(s)
- Renpeng Ji
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | - Qianqian Shi
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical university, Tianjin, 300060, China
| | - Yixin Cao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | - Jingyue Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical university, Tianjin, 300060, China
| | - Cancan Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | - Huanyu Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | - Yasra Sayyed
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical university, Tianjin, 300060, China
| | - Lu-Yuan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China.
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Calvanese E, Gu Y. Towards understanding inner nuclear membrane protein degradation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2266-2274. [PMID: 35139191 DOI: 10.1093/jxb/erac037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
The inner nuclear membrane (INM) hosts a unique set of membrane proteins that play essential roles in various aspects of the nuclear function. However, overaccumulation or malfunction of INM protein has been associated with a range of rare genetic diseases; therefore, maintaining the homeostasis and integrity of INM proteins by active removal of aberrantly accumulated proteins and replacing defective molecules through proteolysis is of critical importance. Within the last decade, it has been shown that INM proteins are degraded in yeasts by a process very similar to endoplasmic reticulum-associated degradation (ERAD), which is accomplished by retrotranslocation of membrane substrates followed by proteasome-dependent proteolysis, and this process was named inner nuclear membrane-associated degradation (INMAD). INMAD is distinguished from ERAD by specific INM-localized E3 ubiquitin ligases and proteolysis regulators. While much is yet to be determined about the INMAD pathway in yeasts, virtually no knowledge of it exists for higher eukaryotes, and only very recently have several critical regulators that participate in INM protein degradation been discovered in plants. Here, we review key molecular components of the INMAD pathway and draw parallels between the yeast and plant system to discuss promising directions in the future study of the plant INMAD process.
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Affiliation(s)
- Enrico Calvanese
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
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21
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Luenenschloss A, Ter Veld F, Albaum SP, Neddermann TM, Wendisch VF, Poetsch A. Functional Genomics Uncovers Pleiotropic Role of Rhomboids in Corynebacterium glutamicum. Front Microbiol 2022; 13:771968. [PMID: 35265054 PMCID: PMC8899591 DOI: 10.3389/fmicb.2022.771968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/17/2022] [Indexed: 11/14/2022] Open
Abstract
The physiological role of ubiquitous rhomboid proteases, membrane-integral proteins that cleave their substrates inside the lipid bilayer, is still ill-defined in many prokaryotes. The two rhomboid genes cg0049 and cg2767 of Corynebacterium glutamicum were mutated and it was the aim of this study to investigate consequences in respect to growth phenotype, stress resistance, transcriptome, proteome, and lipidome composition. Albeit increased amount of Cg2767 upon heat stress, its absence did not change the growth behavior of C. glutamicum during exponential and stationary phase. Quantitative shotgun mass spectrometry was used to compare the rhomboid mutant with wild type strain and revealed that proteins covering diverse cellular functions were differentially abundant with more proteins affected in the stationary than in the exponential growth phase. An observation common to both growth phases was a decrease in ribosomal subunits and RNA polymerase, differences in iron uptake proteins, and abundance changes in lipid and mycolic acid biosynthesis enzymes that suggested a functional link of rhomboids to cell envelope lipid biosynthesis. The latter was substantiated by shotgun lipidomics in the stationary growth phase, where in a strain-dependent manner phosphatidylglycerol, phosphatidic acid, diacylglycerol and phosphatidylinositol increased irrespective of cultivation temperature.
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Affiliation(s)
| | - Frank Ter Veld
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stefan P Albaum
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias M Neddermann
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany.,Department of Marine Biology, Ocean University of China, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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22
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Tang S, Beattie AT, Kafkova L, Petris G, Huguenin-Dezot N, Fiedler M, Freeman M, Chin JW. Mechanism-based traps enable protease and hydrolase substrate discovery. Nature 2022; 602:701-707. [PMID: 35173328 PMCID: PMC8866121 DOI: 10.1038/s41586-022-04414-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/07/2022] [Indexed: 12/28/2022]
Abstract
Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets1. However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond2; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. 3,4). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. 5) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.
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Affiliation(s)
- Shan Tang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Adam T Beattie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Lucie Kafkova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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23
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Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion. Microorganisms 2022; 10:microorganisms10010114. [PMID: 35056563 PMCID: PMC8778405 DOI: 10.3390/microorganisms10010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 01/18/2023] Open
Abstract
Rhomboids are intramembrane serine proteases highly conserved in the three domains of life. Their key roles in eukaryotes are well understood but their contribution to bacterial physiology is still poorly characterized. Here we demonstrate that Brucella abortus, the etiological agent of the zoonosis called brucellosis, encodes an active rhomboid protease capable of cleaving model heterologous substrates like Drosophila melanogaster Gurken and Providencia stuartii TatA. To address the impact of rhomboid deletion on B. abortus physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. About 50% of the B. abortus predicted proteome was identified by quantitative proteomics under two experimental conditions and 108 differentially represented proteins were detected. Membrane associated proteins that showed variations in concentration in the mutant were considered as potential rhomboid targets. This class included nitric oxide reductase subunit C NorC (Q2YJT6) and periplasmic protein LptC involved in LPS transport to the outer membrane (Q2YP16). Differences in secretory proteins were also addressed. Differentially represented proteins included a putative lytic murein transglycosylase (Q2YIT4), nitrous-oxide reductase NosZ (Q2YJW2) and high oxygen affinity Cbb3-type cytochrome c oxidase subunit (Q2YM85). Deletion of rhomboid had no obvious effect in B. abortus virulence. However, rhomboid overexpression had a negative impact on growth under static conditions, suggesting an effect on denitrification enzymes and/or high oxygen affinity cytochrome c oxidase required for growth in low oxygen tension conditions.
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24
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Conformational surveillance of Orai1 by a rhomboid intramembrane protease prevents inappropriate CRAC channel activation. Mol Cell 2021; 81:4784-4798.e7. [PMID: 34800360 PMCID: PMC8657799 DOI: 10.1016/j.molcel.2021.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/14/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
Calcium influx through plasma membrane calcium release-activated calcium (CRAC) channels, which are formed of hexamers of Orai1, is a potent trigger for many important biological processes, most notably in T cell-mediated immunity. Through a bioinformatics-led cell biological screen, we have identified Orai1 as a substrate for the rhomboid intramembrane protease RHBDL2. We show that RHBDL2 prevents stochastic calcium signaling in unstimulated cells through conformational surveillance and cleavage of inappropriately activated Orai1. A conserved disease-linked proline residue is responsible for RHBDL2’s recognizing the active conformation of Orai1, which is required to sharpen switch-like signaling triggered by store-operated calcium entry. Loss of RHBDL2 control of CRAC channel activity causes severe dysregulation of downstream CRAC channel effectors, including transcription factor activation, inflammatory cytokine expression, and T cell activation. We propose that this surveillance function may represent an ancient activity of rhomboid proteases in degrading unwanted signaling proteins. A screen for transmembrane substrates of the rhomboid intramembrane protease RHBDL2 RHBDL2 cleaves the CRAC channel protein Orai1 when it is inappropriately activated Conformational change in these calcium channels is recognized by RHBDL2 An Orai1 mutant that cannot be cleaved by RHBDL2 causes a human disease syndrome
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25
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Lavell A, Smith M, Xu Y, Froehlich JE, De La Mora C, Benning C. Proteins associated with the Arabidopsis thaliana plastid rhomboid-like protein RBL10. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1332-1345. [PMID: 34582071 PMCID: PMC9219029 DOI: 10.1111/tpj.15514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 05/07/2023]
Abstract
Rhomboid-like proteins are intramembrane proteases with a variety of regulatory roles in cells. Though many rhomboid-like proteins are predicted in plants, their detailed molecular mechanisms or cellular functions are not yet known. Of the 13 predicted rhomboids in Arabidopsis thaliana, one, RBL10, affects lipid metabolism in the chloroplast, because in the respective rbl10 mutant the transfer of phosphatidic acid through the inner envelope membrane is disrupted. Here we show that RBL10 is part of a high-molecular-weight complex of 250 kDa or greater in size. Nine likely components of this complex are identified by two independent methods and include Acyl Carrier Protein 4 (ACP4) and Carboxyltransferase Interactor1 (CTI1), which have known roles in chloroplast lipid metabolism. The acp4 mutant has decreased C16:3 fatty acid content of monogalactosyldiacylglycerol, similar to the rbl10 mutant, prompting us to offer a mechanistic model of how an interaction between ACP4 and RBL10 might affect chloroplast lipid assembly. We also demonstrate the presence of a seventh transmembrane domain in RBL10, refining the currently accepted topology of this protein. Taken together, the identity of possible RBL10 complex components as well as insights into RBL10 topology and distribution in the membrane provide a stepping-stone towards a deeper understanding of RBL10 function in Arabidopsis lipid metabolism.
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Affiliation(s)
- Anastasiya Lavell
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - Montgomery Smith
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
- Department of Chemical Engineering and Material Science, Michigan State University, East Lansing, MI 48824
| | - Yang Xu
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - John E. Froehlich
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - Cameron De La Mora
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
- Dept. of Molecular & Cellular Biology, Illinois State University, Normal, IL 61761
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
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26
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Wang L, Liu XX, Yang YM, Wang Y, Song YY, Gao S, Li LY, Zhang ZS. RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression. Cancer Cell Int 2021; 21:590. [PMID: 34736454 PMCID: PMC8567583 DOI: 10.1186/s12935-021-02277-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023] Open
Abstract
Background The rhomboids are a family of multi-transmembrane proteins, many of which have been implicated in facilitating tumor progression. Little is yet known, however, about rhomboid-associated biomarkers in cancers. An analysis of such biomarkers could yield important insights into the role of the rhomboids in cancer pathology. Methods In this study, we carried out the univariate Cox regression analysis and compared gene expression patterns of several rhomboid genes in 30 types of cancers by using The Cancer Genome Atlas (TCGA) database and the methods delineated in Gene Expression Profiling Interactive Analysis (GEPIA). We then used datasets GSE47032, GSE126964, GSE68417 and 75 paired pathological specimens to verify the influences of the rhomboid genes in cancer progression. Moreover, we carried out Weighted Gene Correlation Network Analysis (WGCNA) to investigate gene-related functions and we exploited potential correlations between rhomboid genes expression and immune cell infiltration in cancer tissues. Furthermore, we constructed gene-knockdown cancer cell lines to investigate rhomboid gene functions. Results We find that kidney renal clear cell carcinoma (KIRC) disease progression is affected by fluctuations in the expression of a number of the rhomboid family of genes and, more specifically, high levels of RHBDF2 gene expression are a good indicator of poor prognosis of the disease, as patients with high RHBDF2 expression levels exhibit less favorable survival rates compared to those with low RHBDF2 levels. Silencing of the RHBDF2 gene in KIRC cell lines leads to significantly diminished cell proliferation and migration; this is in good agreement with the identification of an enhanced presence of a number of cell growth and migration promoting signaling molecules in KIRC tumors. We found that, although high level of RHBDF2 correlated with increased infiltration of lymphocytes in cancer tissues, artificially overexpressed RHBDF2 led to an inhibition of the activity of the infiltrated immune cells through sustaining PD-L1 protein level. Furthermore, we show that RHBDF2 related cell migration and PD-L1 regulation were potentially mediated by EGFR signaling pathway. Conclusions RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression and may serve as a critical prognostic biomarker for the disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02277-0.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Xiu-Xiu Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Yu-Meng Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Yan Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Yuan-Yuan Song
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Shan Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Lu-Yuan Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
| | - Zhi-Song Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
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27
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Nejatfard A, Wauer N, Bhaduri S, Conn A, Gourkanti S, Singh N, Kuo T, Kandel R, Amaro RE, Neal SE. Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates. Cell Rep 2021; 37:109840. [PMID: 34686332 PMCID: PMC8641752 DOI: 10.1016/j.celrep.2021.109840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/19/2021] [Accepted: 09/27/2021] [Indexed: 01/13/2023] Open
Abstract
Nearly one-third of proteins are initially targeted to the endoplasmic reticulum (ER) membrane, where they are correctly folded and then delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) moves these clients from the ER membrane to the cytosol, a process known as retrotranslocation. Our recent work in Saccharomyces cerevisiae reveals a derlin rhomboid pseudoprotease, Dfm1, is involved in the retrotranslocation of ubiquitinated ERAD membrane substrates. In this study, we identify conserved residues of Dfm1 that are critical for retrotranslocation. We find several retrotranslocation-deficient Loop 1 mutants that display impaired binding to membrane substrates. Furthermore, Dfm1 possesses lipid thinning function to facilitate in the removal of ER membrane substrates, and this feature is conserved in its human homolog, Derlin-1, further implicating that derlin-mediated retrotranslocation is a well-conserved process.
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Affiliation(s)
- Anahita Nejatfard
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Wauer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Satarupa Bhaduri
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam Conn
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Saroj Gourkanti
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Narinderbir Singh
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Tiffany Kuo
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Kandel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
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28
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Al-Salihi M, Bornikoel A, Zhuang Y, Stachura P, Scheller J, Lang KS, Lang PA. The role of ADAM17 during liver damage. Biol Chem 2021; 402:1115-1128. [PMID: 34192832 DOI: 10.1515/hsz-2021-0149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022]
Abstract
A disintegrin and metalloprotease (ADAM) 17 is a membrane bound protease, involved in the cleavage and thus regulation of various membrane proteins, which are critical during liver injury. Among ADAM17 substrates are tumor necrosis factor α (TNFα), tumor necrosis factor receptor 1 and 2 (TNFR1, TNFR2), the epidermal growth factor receptor (EGFR) ligands amphiregulin (AR) and heparin-binding-EGF-like growth factor (HB-EGF), the interleukin-6 receptor (IL-6R) and the receptor for a hepatocyte growth factor (HGF), c-Met. TNFα and its binding receptors can promote liver injury by inducing apoptosis and necroptosis in liver cells. Consistently, hepatocyte specific deletion of ADAM17 resulted in increased liver cell damage following CD95 stimulation. IL-6 trans-signaling is critical for liver regeneration and can alleviate liver damage. EGFR ligands can prevent liver damage and deletion of amphiregulin and HB-EGF can result in increased hepatocyte death and reduced proliferation. All of which indicates that ADAM17 has a central role in liver injury and recovery from it. Furthermore, inactive rhomboid proteins (iRhom) are involved in the trafficking and maturation of ADAM17 and have been linked to liver damage. Taken together, ADAM17 can contribute in a complex way to liver damage and injury.
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Affiliation(s)
- Mazin Al-Salihi
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
- School of Medicine, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Anna Bornikoel
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Yuan Zhuang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Pawel Stachura
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Jürgen Scheller
- Department of Biochemistry and Molecular Biology II, Medical Faculty, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Karl S Lang
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, D-45147 Essen, Germany
| | - Philipp A Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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29
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Koch L, Kespohl B, Agthe M, Schumertl T, Düsterhöft S, Lemberg MK, Lokau J, Garbers C. Interleukin-11 (IL-11) receptor cleavage by the rhomboid protease RHBDL2 induces IL-11 trans-signaling. FASEB J 2021; 35:e21380. [PMID: 33566379 DOI: 10.1096/fj.202002087r] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Interleukin-11 (IL-11) is a pleiotropic cytokine with both pro- and anti-inflammatory properties. It activates its target cells via binding to the membrane-bound IL-11 receptor (IL-11R), which then recruits a homodimer of the ubiquitously expressed, signal-transducing receptor gp130. Besides this classic signaling pathway, IL-11 can also bind to soluble forms of the IL-11R (sIL-11R), and IL-11/sIL-11R complexes activate cells via the induction of gp130 homodimerization (trans-signaling). We have previously reported that the metalloprotease ADAM10 cleaves the membrane-bound IL-11R and thereby generates sIL-11R. In this study, we identify the rhomboid intramembrane protease RHBDL2 as a so far unrecognized alternative sheddase that can efficiently trigger IL-11R secretion. We determine the cleavage site used by RHBDL2, which is located in the extracellular part of the receptor in close proximity to the plasma membrane, between Ala-370 and Ser-371. Furthermore, we identify critical amino acid residues within the transmembrane helix that are required for IL-11R proteolysis. We also show that ectopically expressed RHBDL2 is able to cleave the IL-11R within the early secretory pathway and not only at the plasma membrane, indicating that its subcellular localization plays a central role in controlling its activity. Moreover, RHBDL2-derived sIL-11R is biologically active and able to perform IL-11 trans-signaling. Finally, we show that the human mutation IL-11R-A370V does not impede IL-11 classic signaling, but prevents RHBDL2-mediated IL-11R cleavage.
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Affiliation(s)
- Lydia Koch
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Birte Kespohl
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Maria Agthe
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Tim Schumertl
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Stefan Düsterhöft
- Institute of Molecular Pharmacology, RWTH Aachen University, Aachen, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Juliane Lokau
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Christoph Garbers
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
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30
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Düsterhöft S, Kahveci-Türköz S, Wozniak J, Seifert A, Kasparek P, Ohm H, Liu S, Kopkanova J, Lokau J, Garbers C, Preisinger C, Sedlacek R, Freeman M, Ludwig A. The iRhom homology domain is indispensable for ADAM17-mediated TNFα and EGF receptor ligand release. Cell Mol Life Sci 2021; 78:5015-5040. [PMID: 33950315 PMCID: PMC8233286 DOI: 10.1007/s00018-021-03845-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/29/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022]
Abstract
Membrane-tethered signalling proteins such as TNFα and many EGF receptor ligands undergo shedding by the metalloproteinase ADAM17 to get released. The pseudoproteases iRhom1 and iRhom2 are important for the transport, maturation and activity of ADAM17. Yet, the structural and functional requirements to promote the transport of the iRhom-ADAM17 complex have not yet been thoroughly investigated. Utilising in silico and in vitro methods, we here map the conserved iRhom homology domain (IRHD) and provide first insights into its structure and function. By focusing on iRhom2, we identified different structural and functional factors within the IRHD. We found that the structural integrity of the IRHD is a key factor for ADAM17 binding. In addition, we identified a highly conserved motif within an unstructured region of the IRHD, that, when mutated, restricts the transport of the iRhom-ADAM17 complex through the secretory pathway in in vitro, ex vivo and in vivo systems and also increases the half-life of iRhom2 and ADAM17. Furthermore, the disruption of this IRHD motif was also reflected by changes in the yet undescribed interaction profile of iRhom2 with proteins involved in intracellular vesicle transport. Overall, we provide the first insights into the forward trafficking of iRhoms which is critical for TNFα and EGF receptor signalling.
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Affiliation(s)
- Stefan Düsterhöft
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
| | - Selcan Kahveci-Türköz
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Justyna Wozniak
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Anke Seifert
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Petr Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Henrike Ohm
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Shixin Liu
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Jana Kopkanova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Juliane Lokau
- Department of Pathology, Medical Faculty, Otto Von Guericke University Magdeburg, Magdeburg, Germany
| | - Christoph Garbers
- Department of Pathology, Medical Faculty, Otto Von Guericke University Magdeburg, Magdeburg, Germany
| | | | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Andreas Ludwig
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
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31
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Chao-Chu J, Murtough S, Zaman N, Pennington DJ, Blaydon DC, Kelsell DP. iRHOM2: A Regulator of Palmoplantar Biology, Inflammation, and Viral Susceptibility. J Invest Dermatol 2021; 141:722-726. [PMID: 33080304 PMCID: PMC7568177 DOI: 10.1016/j.jid.2020.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/04/2022]
Abstract
The palmoplantar epidermis is a specialized area of the skin that undergoes high levels of mechanical stress. The palmoplantar keratinization and esophageal cancer syndrome, tylosis with esophageal cancer, is linked to mutations in RHBDF2 encoding the proteolytically inactive rhomboid protein, iRhom2. Subsequently, iRhom2 was found to affect palmoplantar thickening to modulate the stress keratin response and to mediate context-dependent stress pathways by p63. iRhom2 is also a direct regulator of the sheddase, ADAM17, and the antiviral adaptor protein, stimulator of IFN genes. In this perspective, the pleiotropic functions of iRhom2 are discussed with respect to the skin, inflammation, and the antiviral response.
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Affiliation(s)
- Jennifer Chao-Chu
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Stephen Murtough
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Najwa Zaman
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Daniel J Pennington
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Diana C Blaydon
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - David P Kelsell
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.
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The repertoire of serine rhomboid proteases of piroplasmids of importance to animal and human health. Int J Parasitol 2021; 51:455-462. [PMID: 33610524 DOI: 10.1016/j.ijpara.2020.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Babesia, Theileria and Cytauxzoon are tick-borne apicomplexan protozoans of the order Piroplasmida, notorious for the diseases they cause in livestock, pets and humans. Host cell invasion is their Achilles heel, allowing for the development of drug or vaccine-based therapies. In other apicomplexans, cleavage of the transmembrane domain of adhesins by the serine rhomboid proteinase ROM4 is required for successful completion of invasion. In this study, we record and classify the rhomboid repertoire encoded in the genomes of 10 piroplasmid species pertaining to the lineages Babesia sensu stricto (s.s., Clade VI), Theileria sensu stricto (Clade IV), Theileria equi (Clade IV), Cytauxzoon felis (Clade IIIb) and Babesia microti (Clade I), as defined by Schnittger et al. (2012). Fifty-six piroplasmid rhomboid-like proteins were assigned by phylogenetic analysis and bidirectional best hit to the ROM4, ROM6, ROM7 or ROM8 groups, and their crucial motifs for conformation and function were identified. Forty-four of these rhomboids had either been incorrectly classified or misannotated. Babesia s.s. encode five or three ROM4 proteinase paralogs, whereas the remaining piroplasmids encode two ROM4 paralogs. All piroplasmids encode a single ROM6, ROM7 and ROM8. Thus, an increased paralog number of ROM4 is the only feature distinguishing Babesia s.s. from other piroplasmid lineages. Piroplasmid ROM6 is related to the mammalian mitochondrial rhomboid and, accordingly, N-terminal mitochondrial targeting signal sequences was found in some cases. ROM6 is the only rhomboid encoded by piroplasmids that is ubiquitous in other organisms. ROM8 represents a pseudoproteinase that is highly conserved between studied piroplasmids, suggesting that it is important in regulatory functions. ROM4, ROM6, ROM7 and ROM8 are exclusively present in Aconoidasida, which comprises piroplasmids and Plasmodium, suggesting a relevant functional role in erythrocyte invasion. The correct classification and designation of piroplasmid rhomboids presented in this study facilitates an informed choice for future in-depth study of their functions.
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Lysyk L, Brassard R, Arutyunova E, Siebert V, Jiang Z, Takyi E, Morrison M, Young HS, Lemberg MK, O'Donoghue AJ, Lemieux MJ. Insights into the catalytic properties of the mitochondrial rhomboid protease PARL. J Biol Chem 2021; 296:100383. [PMID: 33556373 PMCID: PMC7966987 DOI: 10.1016/j.jbc.2021.100383] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The rhomboid protease PARL is a critical regulator of mitochondrial homeostasis through its cleavage of substrates such as PINK1, PGAM5, and Smac/Diablo, which have crucial roles in mitochondrial quality control and apoptosis. However, the catalytic properties of PARL, including the effect of lipids on the protease, have never been characterized in vitro. To address this, we isolated human PARL expressed in yeast and used FRET-based kinetic assays to measure proteolytic activity in vitro. We show that PARL activity in detergent is enhanced by cardiolipin, a lipid enriched in the mitochondrial inner membrane. Significantly higher turnover rates were observed for PARL reconstituted in proteoliposomes, with Smac/Diablo being cleaved most rapidly at a rate of 1 min−1. In contrast, PGAM5 is cleaved with the highest efficiency (kcat/KM) compared with PINK1 and Smac/Diablo. In proteoliposomes, a truncated β-cleavage form of PARL, a physiological form known to affect mitochondrial fragmentation, is more active than the full-length enzyme for hydrolysis of PINK1, PGAM5, and Smac/Diablo. Multiplex profiling of 228 peptides reveals that PARL prefers substrates with a bulky side chain such as Phe in P1, which is distinct from the preference for small side chain residues typically found with bacterial rhomboid proteases. This study using recombinant PARL provides fundamental insights into its catalytic activity and substrate preferences that enhance our understanding of its role in mitochondrial function and has implications for specific inhibitor design.
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Affiliation(s)
- Laine Lysyk
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Raelynn Brassard
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Verena Siebert
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Emmanuella Takyi
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Melissa Morrison
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Howard S Young
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada.
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Van Kersavond T, Konopatzki R, van der Plassche MAT, Yang J, Verhelst SHL. Rapid synthesis of internal peptidyl α-ketoamides by on resin oxidation for the construction of rhomboid protease inhibitors. RSC Adv 2021; 11:4196-4199. [PMID: 35424368 PMCID: PMC8694341 DOI: 10.1039/d0ra10614c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/01/2021] [Accepted: 01/08/2021] [Indexed: 11/21/2022] Open
Abstract
Rhomboid proteases are intramembrane serine proteases, which are involved in a wide variety of biological processes and have been implied in various human diseases. Recently, peptidyl α-ketoamides have been reported as rhomboid inhibitors with high potency and selectivity – owing to their interaction with both the primed and non-primed site of the target protease. However, their synthesis has been performed by solution phase chemistry. Here, we report a solid phase strategy towards ketoamides as rhomboid protease inhibitors, allowing rapid synthesis and optimization. We found that the primed site binding part of inhibitors is crucial for potency. Rhomboid intramembrane serine proteases are involved in various biological processes. A solid phase synthesis of internal α-ketoamides reported here shows that primed site elements are crucial for rhomboid protease inhibition.![]()
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Affiliation(s)
| | | | | | - Jian Yang
- KU Leuven
- Department of Cellular and Molecular Medicine
- Laboratory of Chemical Biology
- 3000 Leuven
- Belgium
| | - Steven H. L. Verhelst
- Leibniz Institute for Analytical Sciences ISAS
- 44227 Dortmund
- Germany
- KU Leuven
- Department of Cellular and Molecular Medicine
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35
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Adrain C, Cavadas M. The complex life of rhomboid pseudoproteases. FEBS J 2020; 287:4261-4283. [DOI: 10.1111/febs.15548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Colin Adrain
- Instituto Gulbenkian de Ciência (IGC) Oeiras Portugal
- Centre for Cancer Research and Cell Biology Queen's University Belfast UK
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36
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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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37
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iRhom2: An Emerging Adaptor Regulating Immunity and Disease. Int J Mol Sci 2020; 21:ijms21186570. [PMID: 32911849 PMCID: PMC7554728 DOI: 10.3390/ijms21186570] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
The rhomboid family are evolutionary conserved intramembrane proteases. Their inactive members, iRhom in Drosophila melanogaster and iRhom1 and iRhom2 in mammals, lack the catalytic center and are hence labelled “inactive” rhomboid family members. In mammals, both iRhoms are involved in maturation and trafficking of the ubiquitous transmembrane protease a disintegrin and metalloprotease (ADAM) 17, which through cleaving many biologically active molecules has a critical role in tumor necrosis factor alpha (TNFα), epidermal growth factor receptor (EGFR), interleukin-6 (IL-6) and Notch signaling. Accordingly, with iRhom2 having a profound influence on ADAM17 activation and substrate specificity it regulates these signaling pathways. Moreover, iRhom2 has a role in the innate immune response to both RNA and DNA viruses and in regulation of keratin subtype expression in wound healing and cancer. Here we review the role of iRhom2 in immunity and disease, both dependent and independent of its regulation of ADAM17.
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38
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Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme. Proc Natl Acad Sci U S A 2020; 117:22146-22156. [PMID: 32848056 DOI: 10.1073/pnas.1917770117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Packing interaction is a critical driving force in the folding of helical membrane proteins. Despite the importance, packing defects (i.e., cavities including voids, pockets, and pores) are prevalent in membrane-integral enzymes, channels, transporters, and receptors, playing essential roles in function. Then, a question arises regarding how the two competing requirements, packing for stability vs. cavities for function, are reconciled in membrane protein structures. Here, using the intramembrane protease GlpG of Escherichia coli as a model and cavity-filling mutation as a probe, we tested the impacts of native cavities on the thermodynamic stability and function of a membrane protein. We find several stabilizing mutations which induce substantial activity reduction without distorting the active site. Notably, these mutations are all mapped onto the regions of conformational flexibility and functional importance, indicating that the cavities facilitate functional movement of GlpG while compromising the stability. Experiment and molecular dynamics simulation suggest that the stabilization is induced by the coupling between enhanced protein packing and weakly unfavorable lipid desolvation, or solely by favorable lipid solvation on the cavities. Our result suggests that, stabilized by the relatively weak interactions with lipids, cavities are accommodated in membrane proteins without severe energetic cost, which, in turn, serve as a platform to fine-tune the balance between stability and flexibility for optimal activity.
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39
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Lysyk L, Brassard R, Touret N, Lemieux MJ. PARL Protease: A Glimpse at Intramembrane Proteolysis in the Inner Mitochondrial Membrane. J Mol Biol 2020; 432:5052-5062. [DOI: 10.1016/j.jmb.2020.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 01/07/2023]
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40
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Adamiec M, Misztal L, Kasprowicz-Maluśki A, Luciński R. EGY3: homologue of S2P protease located in chloroplasts. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:735-743. [PMID: 31886945 DOI: 10.1111/plb.13087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
The EGY3 protein is a homologue of site-2 proteases, which are intramembrane zinc metalloproteases. EGY3 itself lacks proteolytic activity due to the absence of a zinc-binding motif. Plentiful evidence indicates that such intramembrane 'pseudoproteases' play significant roles in many diverse processes occurring within the cell. However, the physiological functions of EGY3, as well as its subcellular localization, remain unknown. The subcellular localization of EGY3 protein was investigated using Arabidopsis thaliana protoplasts transformed with EGY3-GFP fusion protein, and immunoblot experiments using the total leaf protein extract, as well as highly purified chloroplasts and fractions of stroma, envelope and thylakoid membrane proteins. The physiological role of EGY3 was studied using two A. thaliana mutant lines devoid of EGY3 protein. Chlorophyll a fluorescence measurement was performed and the egy3 mutant sensitivity to photoinhibition was investigated. Additionally, the abundance of thylakoid membrane complexes was established using blue native gel electrophoresis. We present experimental evidence for thylakoid membrane localization of the EGY3 protein. We show that egy3 mutants display increased value of the non-photochemical quenching parameter and significantly slower recovery rate after photoinhibitory treatment. This was associated with a decrease in the level of proteases involved in photosystem II recovery, Deg1 and FtsH2/8.
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Affiliation(s)
- M Adamiec
- Department of Plant Physiology, Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - L Misztal
- Department of Plant Physiology, Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - A Kasprowicz-Maluśki
- Department of Molecular and Cellular Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - R Luciński
- Department of Plant Physiology, Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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41
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Differential effects of 'resurrecting' Csp pseudoproteases during Clostridioides difficile spore germination. Biochem J 2020; 477:1459-1478. [PMID: 32242623 PMCID: PMC7200643 DOI: 10.1042/bcj20190875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 01/02/2023]
Abstract
Clostridioides difficile is a spore-forming bacterial pathogen that is the leading cause of hospital-acquired gastroenteritis. C. difficile infections begin when its spore form germinates in the gut upon sensing bile acids. These germinants induce a proteolytic signaling cascade controlled by three members of the subtilisin-like serine protease family, CspA, CspB, and CspC. Notably, even though CspC and CspA are both pseudoproteases, they are nevertheless required to sense germinants and activate the protease, CspB. Thus, CspC and CspA are part of a growing list of pseudoenzymes that play important roles in regulating cellular processes. However, despite their importance, the structural properties of pseudoenzymes that allow them to function as regulators remain poorly understood. Our recently solved crystal structure of CspC revealed that its pseudoactive site residues align closely with the catalytic triad of CspB, suggesting that it might be possible to ‘resurrect' the ancestral protease activity of the CspC and CspA pseudoproteases. Here, we demonstrate that restoring the catalytic triad to these pseudoproteases fails to resurrect their protease activity. We further show that the pseudoactive site substitutions differentially affect the stability and function of the CspC and CspA pseudoproteases: the substitutions destabilized CspC and impaired spore germination without affecting CspA stability or function. Thus, our results surprisingly reveal that the presence of a catalytic triad does not necessarily predict protease activity. Since homologs of C. difficile CspA occasionally carry an intact catalytic triad, our results indicate that bioinformatic predictions of enzyme activity may underestimate pseudoenzymes in rare cases.
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42
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Palma S, Raffa CI, Garcia-Fabiani MB, Ferretti VA, Zwenger A, Perez Verdera PV, Llontop A, Rojas Bilbao E, Cuartero V, Abba MC, Lacunza E. RHBDD2 overexpression promotes a chemoresistant and invasive phenotype to rectal cancer tumors via modulating UPR and focal adhesion genes. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165810. [PMID: 32339641 DOI: 10.1016/j.bbadis.2020.165810] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/07/2020] [Accepted: 04/19/2020] [Indexed: 12/29/2022]
Abstract
The current standard of care for locally advanced rectal cancer (RC) is neoadjuvant radio-chemotherapy (NRC) with 5-fluorouracil (5Fu) as the main drug, followed by surgery and adjuvant chemotherapy. While a group of patients will achieve a pathological complete response, a significant percentage will not respond to the treatment. The Unfolding Protein Response (UPR) pathway is generally activated in tumors and results in resistance to radio-chemotherapy. We previously showed that RHBDD2 gene is overexpressed in the advanced stages of colorectal cancer (CRC) and that it could modulate the UPR pathway. Moreover, RHBDD2 expression is induced by 5Fu. In this study, we demonstrate that the overexpression of RHBDD2 in CACO2 cell line confers resistance to 5Fu, favors cell migration, adhesion and proliferation and has a profound impact on the expression of both, the UPR genes BiP, PERK and CHOP, and on the cell adhesion genes FAK and PXN. We also determined that RHBDD2 binds to BiP protein, the master UPR regulator. Finally, we confirmed that a high expression of RHBDD2 in RC tumors after NRC treatment is associated with the development of local or distant metastases. The collected evidence positions RHBDD2 as a promising prognostic biomarker to predict the response to neoadjuvant therapy in patients with RC.
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Affiliation(s)
- S Palma
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - C I Raffa
- Gastroenterology and Proctology Department, Instituto de Oncología Angel H. Roffo, University of Buenos Aires, Buenos Aires, Argentina
| | - M B Garcia-Fabiani
- Instituto de Investigaciones Bioquímicas de La Plata Rodolfo R. Brenner, CONICET, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - V A Ferretti
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - A Zwenger
- Grupo Oncológico Cooperativo del Sur (GOCS), Neuquén, Argentina
| | | | - A Llontop
- Pathology Department, Instituto de Oncología Angel H. Roffo, University of Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - E Rojas Bilbao
- Pathology Department, Instituto de Oncología Angel H. Roffo, University of Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - V Cuartero
- Clinic Oncology Department, Functional Unit of Digestive Tumors, Instituto de Oncología Angel H. Roffo, University of Buenos Aires, Buenos Aires, Argentina
| | - M C Abba
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - E Lacunza
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
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43
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Dulloo I, Muliyil S, Freeman M. The molecular, cellular and pathophysiological roles of iRhom pseudoproteases. Open Biol 2020; 9:190003. [PMID: 30890028 PMCID: PMC6451368 DOI: 10.1098/rsob.190003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
iRhom proteins are catalytically inactive relatives of rhomboid intramembrane proteases. There is a rapidly growing body of evidence that these pseudoenzymes have a central function in regulating inflammatory and growth factor signalling and consequent roles in many diseases. iRhom pseudoproteases have evolved new domains from their proteolytic ancestors, which are integral to their modular regulation and functions. Although we cannot yet conclude the full extent of their molecular and cellular mechanisms, there is a clearly emerging theme that they regulate the stability and trafficking of other membrane proteins. In the best understood case, iRhoms act as regulatory cofactors of the ADAM17 protease, controlling its function of shedding cytokines and growth factors. It seems likely that as the involvement of iRhoms in human diseases is increasingly recognized, they will become the focus of pharmaceutical interest, and here we discuss what is known about their molecular mechanisms and relevance in known pathologies.
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Affiliation(s)
- Iqbal Dulloo
- Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE , UK
| | - Sonia Muliyil
- Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE , UK
| | - Matthew Freeman
- Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE , UK
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44
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Gipson AB, Giloteaux L, Hanson MR, Bentolila S. Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PLANTS 2020; 9:plants9030307. [PMID: 32121603 PMCID: PMC7154859 DOI: 10.3390/plants9030307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023]
Abstract
OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins.
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Levy R, Levet C, Cohen K, Freeman M, Mott R, Iraqi F, Gabet Y. A genome-wide association study in mice reveals a role for Rhbdf2 in skeletal homeostasis. Sci Rep 2020; 10:3286. [PMID: 32094386 PMCID: PMC7039944 DOI: 10.1038/s41598-020-60146-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 02/06/2020] [Indexed: 12/16/2022] Open
Abstract
Low bone mass and an increased risk of fracture are predictors of osteoporosis. Individuals who share the same bone-mineral density (BMD) vary in their fracture risk, suggesting that microstructural architecture is an important determinant of skeletal strength. Here, we utilized the rich diversity of the Collaborative Cross mice to identify putative causal genes that contribute to the risk of fractures. Using microcomputed tomography, we examined key structural features that pertain to bone quality in the femoral cortical and trabecular compartments of male and female mice. We estimated the broad-sense heritability to be 50–60% for all examined traits, and we identified five quantitative trait loci (QTL) significantly associated with six traits. We refined each QTL by combining information inferred from the ancestry of the mice, ranging from RNA-Seq data and published literature to shortlist candidate genes. We found strong evidence for new candidate genes, particularly Rhbdf2, whose close association with the trabecular bone volume fraction and number was strongly suggested by our analyses. We confirmed our findings with mRNA expression assays of Rhbdf2 in extreme-phenotype mice, and by phenotyping bones of Rhbdf2 knockout mice. Our results indicate that Rhbdf2 plays a decisive role in bone mass accrual and microarchitecture.
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Affiliation(s)
- Roei Levy
- Department of Anatomy and Anthropology, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Clemence Levet
- Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Keren Cohen
- Department of Anatomy and Anthropology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Matthew Freeman
- Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Richard Mott
- UCL Genetics Institute, University College London, Gower St., London, WC1E 6BT, UK
| | - Fuad Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Yankel Gabet
- Department of Anatomy and Anthropology, Tel Aviv University, Tel Aviv, 69978, Israel
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Kim JH, Hwang SW, Koh J, Chun J, Lee C, Im JP, Kim JS. Inactive Rhomboid Protein 2 Mediates Intestinal Inflammation by Releasing Tumor Necrosis Factor-α. Inflamm Bowel Dis 2020; 26:242-253. [PMID: 31586441 DOI: 10.1093/ibd/izz239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Tumor necrosis factor (TNF)-α is a major proinflammatory cytokine that plays a key role in inflammatory bowel disease (IBD). Inactive rhomboid protein 2 (iRhom2) is essential for activating TNF-α-converting enzyme (TACE) in immune cells, which regulates TNF-α release. The aim of the study was to investigate the role of iRhom2 in intestinal inflammation in IBD. METHODS The expression of iRhom2 and TACE in lipopolysaccharide (LPS)-stimulated COLO 205 and RAW 264.7 cells was assessed by reverse transcription polymerase chain reaction (RT-PCR) and Western blot analysis. The expression of iRhom2 and TACE in the colonic tissue of IBD patients and 2,4,6-trinitrobenzenesulfonic acid solution (TNBS)-treated mice was determined by RT-PCR and immunohistochemistry. To assess the role of iRhom2 in intestinal inflammation, colitis was induced in wild-type and iRhom2-/- mice by the administration of TNBS enema. RESULTS In LPS-stimulated COLO 205 and RAW 264.7 cells, the mRNA and protein levels of TACE and iRhom2 were upregulated. The expression of TACE and iRhom2 in the colon of the IBD patients and TNBS-treated mice was significantly enhanced. The inflammatory cells that expressed high levels of iRhom2 in the colon were identified as macrophages. Finally, iRhom2 deficiency ameliorated TNBS-induced colitis by inhibiting TNF-α release. CONCLUSIONS iRhom2 has an important role in intestinal inflammation through TNF-α secretion in immune cells, which suggests that iRhom2 could be a novel therapeutic target for IBD.
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Affiliation(s)
- Jee Hyun Kim
- Department of Gastroenterology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Republic of Korea
| | - Sung Wook Hwang
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Jaemoon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jaeyoung Chun
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Changhyun Lee
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jong Pil Im
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Joo Sung Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Republic of Korea
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Beard HA, Barniol-Xicota M, Yang J, Verhelst SHL. Discovery of Cellular Roles of Intramembrane Proteases. ACS Chem Biol 2019; 14:2372-2388. [PMID: 31287658 DOI: 10.1021/acschembio.9b00404] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intramembrane proteases (IMPs) are localized within lipid bilayers of membranes-either the cell membrane or membranes of various organelles. Cleavage of substrates often results in release from the membrane, leading to a downstream biological effect. This mechanism allows different signaling events to happen through intramembrane proteolysis. Over the years, various mechanistically distinct families of IMPs have been discovered, but the research progress has generally been slower than for soluble proteases due to the challenges associated with membrane proteins. In this review we summarize how each mechanistic family of IMPs was discovered, which chemical tools are available for the study of IMPs, and which techniques have been developed for the discovery of IMP substrates. Finally, we discuss the various roles in cellular physiology of some of these IMPs.
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Affiliation(s)
- Hester A. Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Marta Barniol-Xicota
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Jian Yang
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
| | - Steven H. L. Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49, 3000 Leuven, Belgium
- Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
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48
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Lavell A, Froehlich J, Baylis O, Rotondo A, Benning C. A predicted plastid rhomboid protease affects phosphatidic acid metabolism in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:978-987. [PMID: 31062431 PMCID: PMC6711814 DOI: 10.1111/tpj.14377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/22/2019] [Accepted: 05/01/2019] [Indexed: 05/23/2023]
Abstract
The thylakoid membranes of the chloroplast harbor the photosynthetic machinery that converts light into chemical energy. Chloroplast membranes are unique in their lipid makeup, which is dominated by the galactolipids mono- and digalactosyldiacylglycerol (MGDG and DGDG). The most abundant galactolipid, MGDG, is assembled through both plastid and endoplasmic reticulum (ER) pathways in Arabidopsis, resulting in distinguishable molecular lipid species. Phosphatidic acid (PA) is the first glycerolipid formed by the plastid galactolipid biosynthetic pathway. It is converted to substrate diacylglycerol (DAG) for MGDG Synthase (MGD1) which adds to it a galactose from UDP-Gal. The enzymatic reactions yielding these galactolipids have been well established. However, auxiliary or regulatory factors are largely unknown. We identified a predicted rhomboid-like protease 10 (RBL10), located in plastids of Arabidopsis thaliana, that affects galactolipid biosynthesis likely through intramembrane proteolysis. Plants with T-DNA disruptions in RBL10 have greatly decreased 16:3 (acyl carbons:double bonds) and increased 18:3 acyl chain abundance in MGDG of leaves. Additionally, rbl10-1 mutants show reduced [14 C]-acetate incorporation into MGDG during pulse-chase labeling, indicating a reduced flux through the plastid galactolipid biosynthesis pathway. While plastid MGDG biosynthesis is blocked in rbl10-1 mutants, they are capable of synthesizing PA, as well as producing normal amounts of MGDG by compensating with ER-derived lipid precursors. These findings link this predicted protease to the utilization of PA for plastid galactolipid biosynthesis potentially revealing a regulatory mechanism in chloroplasts.
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Affiliation(s)
- A. Lavell
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - J.E. Froehlich
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - O. Baylis
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - A. Rotondo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - C. Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
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Saad MI, Rose-John S, Jenkins BJ. ADAM17: An Emerging Therapeutic Target for Lung Cancer. Cancers (Basel) 2019; 11:E1218. [PMID: 31438559 PMCID: PMC6769596 DOI: 10.3390/cancers11091218] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/07/2019] [Accepted: 08/17/2019] [Indexed: 12/23/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality, which histologically is classified into small-cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC accounts for approximately 85% of all lung cancer diagnoses, with the majority of patients presenting with lung adenocarcinoma (LAC). KRAS mutations are a major driver of LAC, and are closely related to cigarette smoking, unlike mutations in the epidermal growth factor receptor (EGFR) which arise in never-smokers. Although the past two decades have seen fundamental progress in the treatment and diagnosis of NSCLC, NSCLC still is predominantly diagnosed at an advanced stage when therapeutic interventions are mostly palliative. A disintegrin and metalloproteinase 17 (ADAM17), also known as tumour necrosis factor-α (TNFα)-converting enzyme (TACE), is responsible for the protease-driven shedding of more than 70 membrane-tethered cytokines, growth factors and cell surface receptors. Among these, the soluble interleukin-6 receptor (sIL-6R), which drives pro-inflammatory and pro-tumourigenic IL-6 trans-signaling, along with several EGFR family ligands, are the best characterised. This large repertoire of substrates processed by ADAM17 places it as a pivotal orchestrator of a myriad of physiological and pathological processes associated with the initiation and/or progression of cancer, such as cell proliferation, survival, regeneration, differentiation and inflammation. In this review, we discuss recent research implicating ADAM17 as a key player in the development of LAC, and highlight the potential of ADAM17 inhibition as a promising therapeutic strategy to tackle this deadly malignancy.
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Affiliation(s)
- Mohamed I Saad
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3168, Australia
| | - Stefan Rose-John
- Institute of Biochemistry, Christian-Albrechts-University, D-24098 Kiel, Germany
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3168, Australia.
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Kühnle N, Dederer V, Lemberg MK. Intramembrane proteolysis at a glance: from signalling to protein degradation. J Cell Sci 2019; 132:132/16/jcs217745. [DOI: 10.1242/jcs.217745] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT
Over the last two decades, a group of unusual proteases, so-called intramembrane proteases, have become increasingly recognized for their unique ability to cleave peptide bonds within cellular membranes. They are found in all kingdoms of life and fulfil versatile functions ranging from protein maturation, to activation of signalling molecules, to protein degradation. In this Cell Science at a Glance article and the accompanying poster, we focus on intramembrane proteases in mammalian cells. By comparing intramembrane proteases in different cellular organelles, we set out to review their functions within the context of the roles of individual cellular compartments. Additionally, we exemplify their mode of action in relation to known substrates by distinguishing cleavage events that promote degradation of substrate from those that release active domains from the membrane bilayer.
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Affiliation(s)
- Nathalie Kühnle
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Verena Dederer
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marius K. Lemberg
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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