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Madera D, Alonso-Gómez A, Delgado MJ, Valenciano AI, Alonso-Gómez ÁL. Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression. Int J Mol Sci 2023; 25:54. [PMID: 38203224 PMCID: PMC10779419 DOI: 10.3390/ijms25010054] [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: 10/30/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
The aim of this work is the full characterization of all the nocturnin (noc) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of noc in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for noc-a (noc-aa and noc-ab) with two splice variants (I and II), and only one for noc-b (noc-bb) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three noc isoforms. A synteny analysis based on the localization of noc genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of noc in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the noc paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization.
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Affiliation(s)
| | | | | | | | - Ángel Luis Alonso-Gómez
- Departamento de Genética, Fisiología y Microbiología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.M.); (A.A.-G.); (M.J.D.); (A.I.V.)
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2
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Czaplewska P, Bogucka A, Macur K, Rybicka M, Rychłowski M, Fiołka MJ. Proteomic response of A549 lung cancer cell line to protein-polysaccharide complex Venetin-1 isolated from earthworm coelomic fluid. Front Mol Biosci 2023; 10:1128320. [PMID: 37377864 PMCID: PMC10292018 DOI: 10.3389/fmolb.2023.1128320] [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: 12/20/2022] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
Earthworms' celomic fluid has long attracted scientists' interest due to their toxic properties. It has been shown that the elimination of coelomic fluid cytotoxicity to normal human cells was crucial for the generation of the non-toxic Venetin-1 protein-polysaccharide complex, which exhibits selective activity against Candida albicans cells as well as A549 non-small cell lung cancer cells. To find the molecular mechanisms behind the anti-cancer properties of the preparation, this research investigated the proteome response of A549 cells to the presence of Venetin-1. The sequential window acquisition of all theoretical mass spectra (SWATH-MS) methodology was used for the analysis, which allows for a relative quantitative analysis to be carried out without radiolabelling. The results showed that the formulation did not induce significant proteome responses in normal BEAS-2B cells. In the case of the tumour line, 31 proteins were up regulated, and 18 proteins down regulated. Proteins with increased expression in neoplastic cells are mainly associated with the mitochondrion, membrane transport and the endoplasmic reticulum. In the case of altered proteins, Venetin-1 interferes with proteins that stabilise the structures, i.e., keratin, glycolysis/gluconeogenesis and metabolic processes.
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Affiliation(s)
- Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Aleksandra Bogucka
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
- Institute of Biochemistry, Justus Liebig University of Giessen, Giessen, Germany
| | - Katarzyna Macur
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Magda Rybicka
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Michał Rychłowski
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Marta J. Fiołka
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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3
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Taskin AA, Moretti DN, Vögtle FN, Meisinger C. Isolation and Quality Control of Yeast Mitochondria. Methods Mol Biol 2023; 2615:41-55. [PMID: 36807783 DOI: 10.1007/978-1-0716-2922-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The isolation of organelles devoid of other cellular compartments is crucial for studying organellar proteomes and the localization of newly identified proteins, as well as for assessing specific organellar functions. Here, we describe a protocol for the isolation of crude and highly pure mitochondria from Saccharomyces cerevisiae and provide methods for testing the functional integrity of the isolated organelles.
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Affiliation(s)
- Asli Aras Taskin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Daiana Nerina Moretti
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - F Nora Vögtle
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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4
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Bayne AN, Dong J, Amiri S, Farhan SMK, Trempe JF. MTSviewer: A database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures. PLoS One 2023; 18:e0284541. [PMID: 37093842 PMCID: PMC10124841 DOI: 10.1371/journal.pone.0284541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/02/2023] [Indexed: 04/25/2023] Open
Abstract
Mitochondrial dysfunction is implicated in a wide array of human diseases ranging from neurodegenerative disorders to cardiovascular defects. The coordinated localization and import of proteins into mitochondria are essential processes that ensure mitochondrial homeostasis. The localization and import of most mitochondrial proteins are driven by N-terminal mitochondrial targeting sequences (MTS's), which interact with import machinery and are removed by the mitochondrial processing peptidase (MPP). The recent discovery of internal MTS's-those which are distributed throughout a protein and act as import regulators or secondary MPP cleavage sites-has expanded the role of both MTS's and MPP beyond conventional N-terminal regulatory pathways. Still, the global mutational landscape of MTS's remains poorly characterized, both from genetic and structural perspectives. To this end, we have integrated a variety of tools into one harmonized R/Shiny database called MTSviewer (https://neurobioinfo.github.io/MTSvieweR/), which combines MTS predictions, cleavage sites, genetic variants, pathogenicity predictions, and N-terminomics data with structural visualization using AlphaFold models of human and yeast mitochondrial proteomes. Using MTSviewer, we profiled all MTS-containing proteins across human and yeast mitochondrial proteomes and provide multiple case studies to highlight the utility of this database.
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Affiliation(s)
- Andrew N Bayne
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - Jing Dong
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - Saeid Amiri
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Sali M K Farhan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
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5
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Shen X, Sun P, Zhang H, Yang H. Mitochondrial quality control in the brain: The physiological and pathological roles. Front Neurosci 2022; 16:1075141. [PMID: 36578825 PMCID: PMC9791200 DOI: 10.3389/fnins.2022.1075141] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
The human brain has high energetic expenses and consumes over 20% of total oxygen metabolism. Abnormal brain energy homeostasis leads to various brain diseases. Among multiple factors that contribute to these diseases, mitochondrial dysfunction is one of the most common causes. Maintenance of mitochondrial integrity and functionality is of pivotal importance to brain energy generation. Mitochondrial quality control (MQC), employing the coordination of multiple mechanisms, is evolved to overcome many mitochondrial defects. Thus, not surprisingly, aberrant mitochondrial quality control results in a wide range of brain disorders. Targeting MQC to preserve and restore mitochondrial function has emerged as a promising therapeutic strategy for the prevention and treatment of brain diseases. Here, we set out to summarize the current understanding of mitochondrial quality control in brain homeostasis. We also evaluate potential pharmaceutically and clinically relevant targets in MQC-associated brain disorders.
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6
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Garrido C, Wollman FA, Lafontaine I. The evolutionary history of peptidases involved in the processing of Organelle-Targeting Peptides. Genome Biol Evol 2022; 14:6618273. [PMID: 35758251 PMCID: PMC9291397 DOI: 10.1093/gbe/evac101] [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] [Accepted: 06/23/2022] [Indexed: 11/25/2022] Open
Abstract
Most of the proteins present in mitochondria and chloroplasts, the organelles acquired via endosymbiotic events, are encoded in the nucleus and translated into the cytosol. Most of such nuclear-encoded proteins are specifically recognized via an N-terminal-encoded targeting peptide (TP) and imported into the organelles via a translocon machinery. Once imported, the TP is degraded by a succession of cleavage steps ensured by dedicated peptidases. Here, we retrace the evolution of the families of the mitochondrial processing peptidase (MPP), stromal processing peptidase (SPP), presequence protease (PreP), and organellar oligo-peptidase (OOP) that play a central role in TP processing and degradation across the tree of life. Their bacterial distributions are widespread but patchy, revealing unsurprisingly complex history of lateral transfers among bacteria. We provide evidence for the eukaryotic acquisition of MPP, OOP, and PreP by lateral gene transfers from bacteria at the time of the mitochondrial endosymbiosis. We show that the acquisition of SPP and of a second copy of OOP and PreP at the time of the chloroplast endosymbiosis was followed by a differential loss of one PreP paralog in photosynthetic eukaryotes. We identified some contrasting sequence conservations between bacterial and eukaryotic homologs that could reflect differences in the functional context of their peptidase activity. The close vicinity of the eukaryotic peptidases MPP and OOP to those of several bacterial pathogens, showing antimicrobial resistance, supports a scenario where such bacteria were instrumental in the establishment of the proteolytic pathway for TP degradation in organelles. The evidence for their role in the acquisition of PreP is weaker, and none is observed for SPP, although it cannot be excluded by the present study.
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Affiliation(s)
- Clotilde Garrido
- UMR7141, Institut de Biologie Physico-Chimique (CNRS/Sorbonne Université), 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Francis André Wollman
- UMR7141, Institut de Biologie Physico-Chimique (CNRS/Sorbonne Université), 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Ingrid Lafontaine
- UMR7141, Institut de Biologie Physico-Chimique (CNRS/Sorbonne Université), 13 Rue Pierre et Marie Curie, 75005 Paris, France
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7
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Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition. Nat Commun 2022; 13:1833. [PMID: 35383169 PMCID: PMC8983764 DOI: 10.1038/s41467-022-29322-4] [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: 08/21/2020] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
Presequence protease (PreP), a 117 kDa mitochondrial M16C metalloprotease vital for mitochondrial proteostasis, degrades presequence peptides cleaved off from nuclear-encoded proteins and other aggregation-prone peptides, such as amyloid β (Aβ). PreP structures have only been determined in a closed conformation; thus, the mechanisms of substrate binding and selectivity remain elusive. Here, we leverage advanced vitrification techniques to overcome the preferential denaturation of one of two ~55 kDa homologous domains of PreP caused by air-water interface adsorption. Thereby, we elucidate cryoEM structures of three apo-PreP open states along with Aβ- and citrate synthase presequence-bound PreP at 3.3–4.6 Å resolution. Together with integrative biophysical and pharmacological approaches, these structures reveal the key stages of the PreP catalytic cycle and how the binding of substrates or PreP inhibitor drives a rigid body motion of the protein for substrate binding and catalysis. Together, our studies provide key mechanistic insights into M16C metalloproteases for future therapeutic innovations. Presequence protease (PreP) is essential to mitochondrial proteostasis. This study leverages advanced vitrification techniques to solve cryoEM structures of apo- and substrate-bound PreP and integrates these data with other analysis to reveal key stages and mechanistic insights of the PreP catalytic cycle.
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8
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Wikramanayake TC, Chéret J, Sevilla A, Birch-Machin M, Paus R. Targeting mitochondria in dermatological therapy: Beyond oxidative damage and skin aging. Expert Opin Ther Targets 2022; 26:233-259. [PMID: 35249436 DOI: 10.1080/14728222.2022.2049756] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The analysis of the role of the mitochondria in oxidative damage and skin aging is a significant aspect of dermatological research. Mitochondria generate most reactive oxygen species (ROS); however, excessive ROS are cytotoxic and DNA-damaging and promote (photo-)aging. ROS also possesses key physiological and regulatory functions and mitochondrial dysfunction is prominent in several skin diseases including skin cancers. Although many standard dermatotherapeutics modulate mitochondrial function, dermatological therapy rarely targets the mitochondria. Accordingly, there is a rationale for "mitochondrial dermatology"-based approaches to be applied to therapeutic research. AREAS COVERED This paper examines the functions of mitochondria in cutaneous physiology beyond energy (ATP) and ROS production. Keratinocyte differentiation and epidermal barrier maintenance, appendage morphogenesis and homeostasis, photoaging and skin cancer are considered. Based on related PubMed search results, the paper evaluates thyroid hormones, glucocorticoids, Vitamin D3 derivatives, retinoids, cannabinoid receptor agonists, PPARγ agonists, thyrotropin, and thyrotropin-releasing hormone as instructive lead compounds. Moreover, the mitochondrial protein MPZL3 as a promising new drug target for future "mitochondrial dermatology" is highlighted. EXPERT OPINION Future dermatological therapeutic research should have a mitochondrial medicine emphasis. Focusing on selected lead agents, protein targets, in silico drug design, and model diseases will fertilize a mito-centric approach.
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Affiliation(s)
- Tongyu C Wikramanayake
- Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, U.S.A.,Molecular Cell and Developmental Biology Program, University of Miami Miller School of Medicine, Miami, FL, U.S.A
| | - Jérémy Chéret
- Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, U.S.A
| | - Alec Sevilla
- Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, U.S.A
| | - Mark Birch-Machin
- Dermatological Sciences, Translational and Clinical Research Institute, and The UK National Innovation Centre for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Ralf Paus
- Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, U.S.A.,Monasterium Laboratory, Münster, Germany.,Centre for Dermatology Research, University of Manchester, and NIHR Manchester Biomedical Research Centre, Manchester, UK
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9
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Kunová N, Havalová H, Ondrovičová G, Stojkovičová B, Bauer JA, Bauerová-Hlinková V, Pevala V, Kutejová E. Mitochondrial Processing Peptidases-Structure, Function and the Role in Human Diseases. Int J Mol Sci 2022; 23:1297. [PMID: 35163221 PMCID: PMC8835746 DOI: 10.3390/ijms23031297] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial proteins are encoded by both nuclear and mitochondrial DNA. While some of the essential subunits of the oxidative phosphorylation (OXPHOS) complexes responsible for cellular ATP production are synthesized directly in the mitochondria, most mitochondrial proteins are first translated in the cytosol and then imported into the organelle using a sophisticated transport system. These proteins are directed mainly by targeting presequences at their N-termini. These presequences need to be cleaved to allow the proper folding and assembly of the pre-proteins into functional protein complexes. In the mitochondria, the presequences are removed by several processing peptidases, including the mitochondrial processing peptidase (MPP), the inner membrane processing peptidase (IMP), the inter-membrane processing peptidase (MIP), and the mitochondrial rhomboid protease (Pcp1/PARL). Their proper functioning is essential for mitochondrial homeostasis as the disruption of any of them is lethal in yeast and severely impacts the lifespan and survival in humans. In this review, we focus on characterizing the structure, function, and substrate specificities of mitochondrial processing peptidases, as well as the connection of their malfunctions to severe human diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Eva Kutejová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (H.H.); (G.O.); (B.S.); (J.A.B.); (V.B.-H.); (V.P.)
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10
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Dissecting the molecular mechanisms of mitochondrial import and maturation of peroxiredoxins from yeast and mammalian cells. Biophys Rev 2022; 13:983-994. [PMID: 35059022 DOI: 10.1007/s12551-021-00899-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/01/2021] [Indexed: 12/26/2022] Open
Abstract
Peroxiredoxins (Prxs) are cysteine-based peroxidases that play a central role in keeping the H2O2 at physiological levels. Eukaryotic cells express different Prxs isoforms, which differ in their subcellular locations and substrate specificities. Mitochondrial Prxs are synthesized in the cytosol as precursor proteins containing N-terminal cleavable presequences that act as mitochondrial targeting signals. Due to the fact that presequence controls the import of the vast majority of mitochondrial matrix proteins, the mitochondrial Prxs were initially predicted to be localized exclusively in the matrix. However, recent studies showed that mitochondrial Prxs are also targeted to the intermembrane space by mechanisms that remain poorly understood. While in yeast the IMP complex can translocate Prx1 to the intermembrane space, the maturation of yeast Prx1 and mammalian Prdx3 and Prdx5 in the matrix has been associated with sequential cleavages of the presequence by MPP and Oct1/MIP proteases. In this review, we describe the state of the art of the molecular mechanisms that control the mitochondrial import and maturation of Prxs of yeast and human cells. Once mitochondria are considered the major intracellular source of H2O2, understanding the mitochondrial Prx biogenesis pathways is essential to increase our knowledge about the H2O2-dependent cellular signaling, which is relevant to the pathophysiology of some human diseases.
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11
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Heidorn-Czarna M, Maziak A, Janska H. Protein Processing in Plant Mitochondria Compared to Yeast and Mammals. FRONTIERS IN PLANT SCIENCE 2022; 13:824080. [PMID: 35185991 PMCID: PMC8847149 DOI: 10.3389/fpls.2022.824080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 05/02/2023]
Abstract
Limited proteolysis, called protein processing, is an essential post-translational mechanism that controls protein localization, activity, and in consequence, function. This process is prevalent for mitochondrial proteins, mainly synthesized as precursor proteins with N-terminal sequences (presequences) that act as targeting signals and are removed upon import into the organelle. Mitochondria have a distinct and highly conserved proteolytic system that includes proteases with sole function in presequence processing and proteases, which show diverse mitochondrial functions with limited proteolysis as an additional one. In virtually all mitochondria, the primary processing of N-terminal signals is catalyzed by the well-characterized mitochondrial processing peptidase (MPP). Subsequently, a second proteolytic cleavage occurs, leading to more stabilized residues at the newly formed N-terminus. Lately, mitochondrial proteases, intermediate cleavage peptidase 55 (ICP55) and octapeptidyl protease 1 (OCT1), involved in proteolytic cleavage after MPP and their substrates have been described in the plant, yeast, and mammalian mitochondria. Mitochondrial proteins can also be processed by removing a peptide from their N- or C-terminus as a maturation step during insertion into the membrane or as a regulatory mechanism in maintaining their function. This type of limited proteolysis is characteristic for processing proteases, such as IMP and rhomboid proteases, or the general mitochondrial quality control proteases ATP23, m-AAA, i-AAA, and OMA1. Identification of processing protease substrates and defining their consensus cleavage motifs is now possible with the help of large-scale quantitative mass spectrometry-based N-terminomics, such as combined fractional diagonal chromatography (COFRADIC), charge-based fractional diagonal chromatography (ChaFRADIC), or terminal amine isotopic labeling of substrates (TAILS). This review summarizes the current knowledge on the characterization of mitochondrial processing peptidases and selected N-terminomics techniques used to uncover protease substrates in the plant, yeast, and mammalian mitochondria.
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Rosier K, McDevitt MT, Smet J, Floyd BJ, Verschoore M, Marcaida MJ, Bingman CA, Lemmens I, Dal Peraro M, Tavernier J, Cravatt BF, Gounko NV, Vints K, Monnens Y, Bhalla K, Aerts L, Rashan EH, Vanlander AV, Van Coster R, Régal L, Pagliarini DJ, Creemers JW. Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function. iScience 2021; 24:103460. [PMID: 34888501 PMCID: PMC8634043 DOI: 10.1016/j.isci.2021.103460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Deficiency of the serine hydrolase prolyl endopeptidase-like (PREPL) causes a recessive metabolic disorder characterized by neonatal hypotonia, feeding difficulties, and growth hormone deficiency. The pathophysiology of PREPL deficiency and the physiological substrates of PREPL remain largely unknown. In this study, we connect PREPL with mitochondrial gene expression and oxidative phosphorylation by analyzing its protein interactors. We demonstrate that the long PREPLL isoform localizes to mitochondria, whereas PREPLS remains cytosolic. Prepl KO mice showed reduced mitochondrial complex activities and disrupted mitochondrial gene expression. Furthermore, mitochondrial ultrastructure was abnormal in a PREPL-deficient patient and Prepl KO mice. In addition, we reveal that PREPL has (thio)esterase activity and inhibition of PREPL by Palmostatin M suggests a depalmitoylating function. We subsequently determined the crystal structure of PREPL, thereby providing insight into the mechanism of action. Taken together, PREPL is a (thio)esterase rather than a peptidase and PREPLL is involved in mitochondrial homeostasis.
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Affiliation(s)
- Karen Rosier
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Molly T. McDevitt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joél Smet
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Brendan J. Floyd
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Maxime Verschoore
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Maria J. Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irma Lemmens
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jan Tavernier
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Benjamin F. Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia V. Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Yenthe Monnens
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Kritika Bhalla
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Laetitia Aerts
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arnaud V. Vanlander
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Luc Régal
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Neurology and Metabolism, UZ Brussel, Brussels, Belgium
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Departments of Cell Biology and Physiology, Biochemistry and Molecular Biophysics, and Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - John W.M. Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
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13
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Dimogkioka AR, Lees J, Lacko E, Tokatlidis K. Protein import in mitochondria biogenesis: guided by targeting signals and sustained by dedicated chaperones. RSC Adv 2021; 11:32476-32493. [PMID: 35495482 PMCID: PMC9041937 DOI: 10.1039/d1ra04497d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/25/2021] [Indexed: 12/31/2022] Open
Abstract
Mitochondria have a central role in cellular metabolism; they are responsible for the biosynthesis of amino acids, lipids, iron-sulphur clusters and regulate apoptosis. About 99% of mitochondrial proteins are encoded by nuclear genes, so the biogenesis of mitochondria heavily depends on protein import pathways into the organelle. An intricate system of well-studied import machinery facilitates the import of mitochondrial proteins. In addition, folding of the newly synthesized proteins takes place in a busy environment. A system of folding helper proteins, molecular chaperones and co-chaperones, are present to maintain proper conformation and thus avoid protein aggregation and premature damage. The components of the import machinery are well characterised, but the targeting signals and how they are recognised and decoded remains in some cases unclear. Here we provide some detail on the types of targeting signals involved in the protein import process. Furthermore, we discuss the very elaborate chaperone systems of the intermembrane space that are needed to overcome the particular challenges for the folding process in this compartment. The mechanisms that sustain productive folding in the face of aggregation and damage in mitochondria are critical components of the stress response and play an important role in cell homeostasis.
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Affiliation(s)
- Anna-Roza Dimogkioka
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow University Avenue Glasgow G12 8QQ Scotland UK
| | - Jamie Lees
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow University Avenue Glasgow G12 8QQ Scotland UK
| | - Erik Lacko
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow University Avenue Glasgow G12 8QQ Scotland UK
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow University Avenue Glasgow G12 8QQ Scotland UK
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14
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Wikramanayake TC, Nicu C, Chéret J, Czyzyk TA, Paus R. Mitochondrially localized MPZL3 emerges as a signaling hub of mammalian physiology. Bioessays 2021; 43:e2100126. [PMID: 34486148 DOI: 10.1002/bies.202100126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 12/23/2022]
Abstract
MPZL3 is a nuclear-encoded, mitochondrially localized, immunoglobulin-like V-type protein that functions as a key regulator of epithelial cell differentiation, lipid metabolism, ROS production, glycemic control, and energy expenditure. Recently, MPZL3 has surfaced as an important modulator of sebaceous gland function and of hair follicle cycling, an organ transformation process that is also governed by peripheral clock gene activity and PPARγ. Given the phenotype similarities and differences between Mpzl3 and Pparγ knockout mice, we propose that MPZL3 serves as a signaling hub that is regulated by core clock gene products and/or PPARγ to translate signals from these nuclear transcription factors to the mitochondria to modulate circadian and metabolic regulation. Conservation between murine and human MPZL3 suggests that human MPZL3 may have similarly complex functions in health and disease. We summarize current knowledge and discuss future directions to elucidate the full spectrum of MPZL3 functions in mammalian physiology.
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Affiliation(s)
- Tongyu C Wikramanayake
- Dr Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA.,Molecular Cell and Developmental Biology Program, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Carina Nicu
- Dr Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA.,Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Jérémy Chéret
- Dr Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Traci A Czyzyk
- Department of Anesthesiology & Perioperative Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA.,Metabolic Health Program, Mayo Clinic in Arizona, Scottsdale, Arizona, USA.,Discovery Biology-CMD, Merck & Co., Inc., South San Francisco, California, USA
| | - Ralf Paus
- Dr Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA.,Monasterium Laboratory, Münster, Germany.,Centre for Dermatology Research, University of Manchester and NIHR Manchester Biomedical Research Centre, Manchester, UK
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15
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Sensing, signaling and surviving mitochondrial stress. Cell Mol Life Sci 2021; 78:5925-5951. [PMID: 34228161 PMCID: PMC8316193 DOI: 10.1007/s00018-021-03887-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/11/2022]
Abstract
Mitochondrial fidelity is a key determinant of longevity and was found to be perturbed in a multitude of disease contexts ranging from neurodegeneration to heart failure. Tight homeostatic control of the mitochondrial proteome is a crucial aspect of mitochondrial function, which is severely complicated by the evolutionary origin and resulting peculiarities of the organelle. This is, on one hand, reflected by a range of basal quality control factors such as mitochondria-resident chaperones and proteases, that assist in import and folding of precursors as well as removal of aggregated proteins. On the other hand, stress causes the activation of several additional mechanisms that counteract any damage that may threaten mitochondrial function. Countermeasures depend on the location and intensity of the stress and on a range of factors that are equipped to sense and signal the nature of the encountered perturbation. Defective mitochondrial import activates mechanisms that combat the accumulation of precursors in the cytosol and the import pore. To resolve proteotoxic stress in the organelle interior, mitochondria depend on nuclear transcriptional programs, such as the mitochondrial unfolded protein response and the integrated stress response. If organelle damage is too severe, mitochondria signal for their own destruction in a process termed mitophagy, thereby preventing further harm to the mitochondrial network and allowing the cell to salvage their biological building blocks. Here, we provide an overview of how different types and intensities of stress activate distinct pathways aimed at preserving mitochondrial fidelity.
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16
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Increased mitochondrial protein import and cardiolipin remodelling upon early mtUPR. PLoS Genet 2021; 17:e1009664. [PMID: 34214073 PMCID: PMC8282050 DOI: 10.1371/journal.pgen.1009664] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/15/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial defects can cause a variety of human diseases and protective mechanisms exist to maintain mitochondrial functionality. Imbalances in mitochondrial proteostasis trigger a transcriptional program, termed mitochondrial unfolded protein response (mtUPR). However, the temporal sequence of events in mtUPR is unclear and the consequences on mitochondrial protein import are controversial. Here, we have quantitatively analyzed all main import pathways into mitochondria after different time spans of mtUPR induction. Kinetic analyses reveal that protein import into all mitochondrial subcompartments strongly increases early upon mtUPR and that this is accompanied by rapid remodelling of the mitochondrial signature lipid cardiolipin. Genetic inactivation of cardiolipin synthesis precluded stimulation of protein import and compromised cellular fitness. At late stages of mtUPR upon sustained stress, mitochondrial protein import efficiency declined. Our work clarifies the enigma of protein import upon mtUPR and identifies sequential mtUPR stages, in which an early increase in protein biogenesis to restore mitochondrial proteostasis is followed by late stages characterized by a decrease in import capacity upon prolonged stress induction. Mitochondria are essential organelles and involved in numerous important functions like ATP production, biosynthesis of metabolites and co-factors or regulation of programmed cell death. To fulfill this plethora of different tasks, mitochondria require an extensive proteome, which is build by import of nuclear-encoded precursor proteins from the cytosol. Mitochondrial defects can cause a variety of severe human disorders that often affect tissues with high energy demand e.g. heart, muscle or brain. However, protective mechanisms exist that are triggered upon mitochondrial dysfunction: Imbalances in mitochondrial proteostasis are sensed by the cell and elicit a nuclear transcriptional response, termed mitochondrial unfolded protein response (mtUPR). Transcription of mitochondrial chaperones and proteases is increased to counteract mitochondrial dysfunctions. In this study, we investigated if mtUPR progresses in different temporal stages and how protein import is affected upon mtUPR. We discover that mtUPR is subdivided into an early phase, in which protein import increases and a late phase, in which it declines. Stimulation of protein import is accompanied by an increase and remodelling of the mitochondrial signature lipid cardiolipin. Our work establishes a novel model how cells respond to dysfunctional mitochondria, in which cardiolipin and protein import are modulated as first protective measures.
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17
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Transmembrane Coordination of Preprotein Recognition and Motor Coupling by the Mitochondrial Presequence Receptor Tim50. Cell Rep 2021; 30:3092-3104.e4. [PMID: 32130909 DOI: 10.1016/j.celrep.2020.02.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/13/2019] [Accepted: 02/07/2020] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial preproteins contain amino-terminal presequences directing them to the presequence translocase of the mitochondrial inner membrane (TIM23 complex). Depending on additional downstream import signals, TIM23 either inserts preproteins into the inner membrane or translocates them into the matrix. Matrix import requires the coupling of the presequence translocase-associated motor (PAM) to TIM23. The molecular mechanisms coordinating preprotein recognition by TIM23 in the intermembrane space (IMS) with PAM activation in the matrix are unknown. Here we show that subsequent to presequence recognition in the IMS, the Tim50 matrix domain facilitates the recruitment of the coupling factor Pam17. Next, the IMS domain of Tim50 promotes PAM recruitment to TIM23. Finally, the Tim50 transmembrane segment stimulates the matrix-directed import-driving force exerted by PAM. We propose that recognition of preprotein segments in the IMS and transfer of signal information across the inner membrane by Tim50 determine import motor activation.
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18
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Benincá C, Zanette V, Brischigliaro M, Johnson M, Reyes A, Valle DAD, J Robinson A, Degiorgi A, Yeates A, Telles BA, Prudent J, Baruffini E, S F Santos ML, R de Souza RL, Fernandez-Vizarra E, Whitworth AJ, Zeviani M. Mutation in the MICOS subunit gene APOO (MIC26) associated with an X-linked recessive mitochondrial myopathy, lactic acidosis, cognitive impairment and autistic features. J Med Genet 2021; 58:155-167. [PMID: 32439808 PMCID: PMC7116790 DOI: 10.1136/jmedgenet-2020-106861] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/13/2020] [Accepted: 04/12/2020] [Indexed: 02/02/2023]
Abstract
BACKGROUND Mitochondria provide ATP through the process of oxidative phosphorylation, physically located in the inner mitochondrial membrane (IMM). The mitochondrial contact site and organising system (MICOS) complex is known as the 'mitoskeleton' due to its role in maintaining IMM architecture. APOO encodes MIC26, a component of MICOS, whose exact function in its maintenance or assembly has still not been completely elucidated. METHODS We have studied a family in which the most affected subject presented progressive developmental delay, lactic acidosis, muscle weakness, hypotonia, weight loss, gastrointestinal and body temperature dysautonomia, repetitive infections, cognitive impairment and autistic behaviour. Other family members showed variable phenotype presentation. Whole exome sequencing was used to screen for pathological variants. Patient-derived skin fibroblasts were used to confirm the pathogenicity of the variant found in APOO. Knockout models in Drosophila melanogaster and Saccharomyces cerevisiae were employed to validate MIC26 involvement in MICOS assembly and mitochondrial function. RESULTS A likely pathogenic c.350T>C transition was found in APOO predicting an I117T substitution in MIC26. The mutation caused impaired processing of the protein during import and faulty insertion into the IMM. This was associated with altered MICOS assembly and cristae junction disruption. The corresponding mutation in MIC26 or complete loss was associated with mitochondrial structural and functional deficiencies in yeast and D. melanogaster models. CONCLUSION This is the first case of pathogenic mutation in APOO, causing altered MICOS assembly and neuromuscular impairment. MIC26 is involved in the assembly or stability of MICOS in humans, yeast and flies.
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Affiliation(s)
- Cristiane Benincá
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, Cambridgeshire, UK
- Department of Genetics, Federal University of Parana, Curitiba, Paraná, Brazil
| | - Vanessa Zanette
- Department of Genetics, Federal University of Parana, Curitiba, Paraná, Brazil
| | | | - Mark Johnson
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, Cambridgeshire, UK
| | - Aurelio Reyes
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, Cambridgeshire, UK
| | | | - Alan J Robinson
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, Cambridgeshire, UK
| | - Andrea Degiorgi
- Department of Chemistry, University of Parma, Parma, Emilia-Romagna, Italy
| | - Anna Yeates
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire, UK
| | | | - Julien Prudent
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, Cambridgeshire, UK
| | - Enrico Baruffini
- Department of Chemistry, University of Parma, Parma, Emilia-Romagna, Italy
| | | | | | | | | | - Massimo Zeviani
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, Cambridgeshire, UK
- Department of Neurosciences, University of Padova, Padova, Veneto, Italy
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19
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Gomez-Fabra Gala M, Vögtle FN. Mitochondrial proteases in human diseases. FEBS Lett 2021; 595:1205-1222. [PMID: 33453058 DOI: 10.1002/1873-3468.14039] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022]
Abstract
Mitochondria contain more than 1000 different proteins, including several proteolytic enzymes. These mitochondrial proteases form a complex system that performs limited and terminal proteolysis to build the mitochondrial proteome, maintain, and control its functions or degrade mitochondrial proteins and peptides. During protein biogenesis, presequence proteases cleave and degrade mitochondrial targeting signals to obtain mature functional proteins. Processing by proteases also exerts a regulatory role in modulation of mitochondrial functions and quality control enzymes degrade misfolded, aged, or superfluous proteins. Depending on their different functions and substrates, defects in mitochondrial proteases can affect the majority of the mitochondrial proteome or only a single protein. Consequently, mutations in mitochondrial proteases have been linked to several human diseases. This review gives an overview of the components and functions of the mitochondrial proteolytic machinery and highlights the pathological consequences of dysfunctional mitochondrial protein processing and turnover.
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Affiliation(s)
- Maria Gomez-Fabra Gala
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany.,Faculty of Biology, University of Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Germany
| | - Friederike-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany.,CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
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20
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Palmer CS, Anderson AJ, Stojanovski D. Mitochondrial protein import dysfunction: mitochondrial disease, neurodegenerative disease and cancer. FEBS Lett 2021; 595:1107-1131. [PMID: 33314127 DOI: 10.1002/1873-3468.14022] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/12/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022]
Abstract
The majority of proteins localised to mitochondria are encoded by the nuclear genome, with approximately 1500 proteins imported into mammalian mitochondria. Dysfunction in this fundamental cellular process is linked to a variety of pathologies including neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancer, demonstrating the importance of mitochondrial protein import machinery for cellular function. Correct import of proteins into mitochondria requires the co-ordinated activity of multimeric protein translocation and sorting machineries located in both the outer and inner mitochondrial membranes, directing the imported proteins to the destined mitochondrial compartment. This dynamic process maintains cellular homeostasis, and its dysregulation significantly affects cellular signalling pathways and metabolism. This review summarises current knowledge of the mammalian mitochondrial import machinery and the pathological consequences of mutation of its components. In addition, we will discuss the role of mitochondrial import in cancer, and our current understanding of the role of mitochondrial import in neurodegenerative diseases including Alzheimer's disease, Huntington's disease and Parkinson's disease.
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Affiliation(s)
- Catherine S Palmer
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Alexander J Anderson
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
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21
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Kücükköse C, Taskin AA, Marada A, Brummer T, Dennerlein S, Vögtle FN. Functional coupling of presequence processing and degradation in human mitochondria. FEBS J 2021; 288:600-613. [PMID: 32491259 DOI: 10.1111/febs.15358] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/31/2020] [Accepted: 05/04/2020] [Indexed: 12/31/2022]
Abstract
The mitochondrial proteome is built and maintained mainly by import of nuclear-encoded precursor proteins. Most of these precursors use N-terminal presequences as targeting signals that are removed by mitochondrial matrix proteases. The essential mitochondrial processing protease MPP cleaves presequences after import into the organelle thereby enabling protein folding and functionality. The cleaved presequences are subsequently degraded by peptidases. While most of these processes have been discovered in yeast, characterization of the human enzymes is still scarce. As the matrix presequence peptidase PreP has been reported to play a role in Alzheimer's disease, analysis of impaired peptide turnover in human cells is of huge interest. Here, we report the characterization of HEK293T PreP knockout cells. Loss of PreP causes severe defects in oxidative phosphorylation and changes in nuclear expression of stress response marker genes. The mitochondrial defects upon lack of PreP result from the accumulation of presequence peptides that trigger feedback inhibition of MPP and accumulation of nonprocessed precursor proteins. Also, the mitochondrial intermediate peptidase MIP that cleaves eight residues from a subset of precursors after MPP processing is compromised upon loss of PreP suggesting that PreP also degrades MIP generated octapeptides. Investigation of the PrePR183Q patient mutation associated with neurological disorders revealed that the mutation destabilizes the protein making it susceptible to enhanced degradation and aggregation upon heat shock. Taken together, our data reveal a functional coupling between precursor processing by MPP and MIP and presequence degradation by PreP in human mitochondria that is crucial to maintain a functional organellar proteome.
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Affiliation(s)
- Cansu Kücükköse
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Germany
- Faculty of Biology, University of Freiburg, Germany
| | - Asli Aras Taskin
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
| | - Adinarayana Marada
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Germany
| | - Tilman Brummer
- Faculty of Medicine, Institute of Molecular Medicine and Cell Research, University of Freiburg, Germany
- Centre for Biological Signalling Studies BIOSS, University of Freiburg, Germany
- Comprehensive Cancer Centre Freiburg, University of Freiburg, Germany
- DKTK Partner Site Freiburg and DKFZ, Heidelberg, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | - Friederike-Nora Vögtle
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
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22
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Friedl J, Knopp MR, Groh C, Paz E, Gould SB, Herrmann JM, Boos F. More than just a ticket canceller: the mitochondrial processing peptidase tailors complex precursor proteins at internal cleavage sites. Mol Biol Cell 2020; 31:2657-2668. [PMID: 32997570 PMCID: PMC8734313 DOI: 10.1091/mbc.e20-08-0524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 11/11/2022] Open
Abstract
Most mitochondrial proteins are synthesized as precursors that carry N-terminal presequences. After they are imported into mitochondria, these targeting signals are cleaved off by the mitochondrial processing peptidase (MPP). Using the mitochondrial tandem protein Arg5,6 as a model substrate, we demonstrate that MPP has an additional role in preprotein maturation, beyond the removal of presequences. Arg5,6 is synthesized as a polyprotein precursor that is imported into mitochondria and subsequently separated into two distinct enzymes. This internal processing is performed by MPP, which cleaves the Arg5,6 precursor at its N-terminus and at an internal site. The peculiar organization of Arg5,6 is conserved across fungi and reflects the polycistronic arginine operon in prokaryotes. MPP cleavage sites are also present in other mitochondrial fusion proteins from fungi, plants, and animals. Hence, besides its role as a "ticket canceller" for removal of presequences, MPP exhibits a second conserved activity as an internal processing peptidase for complex mitochondrial precursor proteins.
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Affiliation(s)
- Jana Friedl
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Michael R. Knopp
- Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Carina Groh
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Eyal Paz
- Departments of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sven B. Gould
- Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Johannes M. Herrmann
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
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Skeletal Phenotypes Due to Abnormalities in Mitochondrial Protein Homeostasis and Import. Int J Mol Sci 2020; 21:ijms21218327. [PMID: 33171986 PMCID: PMC7664180 DOI: 10.3390/ijms21218327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial disease represents a collection of rare genetic disorders caused by mitochondrial dysfunction. These disorders can be quite complex and heterogeneous, and it is recognized that mitochondrial disease can affect any tissue at any age. The reasons for this variability are not well understood. In this review, we develop and expand a subset of mitochondrial diseases including predominantly skeletal phenotypes. Understanding how impairment ofdiverse mitochondrial functions leads to a skeletal phenotype will help diagnose and treat patients with mitochondrial disease and provide additional insight into the growing list of human pathologies associated with mitochondrial dysfunction. The underlying disease genes encode factors involved in various aspects of mitochondrial protein homeostasis, including proteases and chaperones, mitochondrial protein import machinery, mediators of inner mitochondrial membrane lipid homeostasis, and aminoacylation of mitochondrial tRNAs required for translation. We further discuss a complex of frequently associated phenotypes (short stature, cataracts, and cardiomyopathy) potentially explained by alterations to steroidogenesis, a process regulated by mitochondria. Together, these observations provide novel insight into the consequences of impaired mitochondrial protein homeostasis.
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24
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The ubiquitin-proteasome system and its crosstalk with mitochondria as therapeutic targets in medicine. Pharmacol Res 2020; 163:105248. [PMID: 33065283 DOI: 10.1016/j.phrs.2020.105248] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
The ubiquitin-proteasome system constitutes a major pathway for protein degradation in the cell. Therefore the crosstalk of this pathway with mitochondria is a major topic with direct relevance to many mitochondrial diseases. Proteasome dysfunction triggers not only protein toxicity, but also mitochondrial dysfunction. The involvement of proteasomes in the regulation of protein transport into mitochondria contributes to an increase in mitochondrial function defects. On the other hand, mitochondrial impairment stimulates reactive oxygen species production, which increases protein damage, and protein misfolding and aggregation leading to proteasome overload. Concurrently, mitochondrial dysfunction compromises cellular ATP production leading to reduced protein ubiquitination and proteasome activity. In this review we discuss the complex relationship and interdependence of the ubiquitin-proteasome system and mitochondria. Furthermore, we describe pharmacological inhibition of proteasome activity as a novel strategy to treat a group of mitochondrial diseases.
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25
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Vögtle F. Open questions on the mitochondrial unfolded protein response. FEBS J 2020; 288:2856-2869. [DOI: 10.1111/febs.15569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/28/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Friederike‐Nora Vögtle
- Institute of Biochemistry and Molecular Biology ZBMZ Faculty of Medicine University of Freiburg Germany
- CIBSS ‐ Centre for Integrative Biological Signalling Studies University of Freiburg Germany
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26
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Savojardo C, Bruciaferri N, Tartari G, Martelli PL, Casadio R. DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks. Bioinformatics 2020; 36:56-64. [PMID: 31218353 PMCID: PMC6956790 DOI: 10.1093/bioinformatics/btz512] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/31/2019] [Accepted: 06/17/2019] [Indexed: 11/18/2022] Open
Abstract
Motivation The correct localization of proteins in cell compartments is a key issue for their function. Particularly, mitochondrial proteins are physiologically active in different compartments and their aberrant localization contributes to the pathogenesis of human mitochondrial pathologies. Many computational methods exist to assign protein sequences to subcellular compartments such as nucleus, cytoplasm and organelles. However, a substantial lack of experimental evidence in public sequence databases hampered so far a finer grain discrimination, including also intra-organelle compartments. Results We describe DeepMito, a novel method for predicting protein sub-mitochondrial cellular localization. Taking advantage of powerful deep-learning approaches, such as convolutional neural networks, our method is able to achieve very high prediction performances when discriminating among four different mitochondrial compartments (matrix, outer, inner and intermembrane regions). The method is trained and tested in cross-validation on a newly generated, high-quality dataset comprising 424 mitochondrial proteins with experimental evidence for sub-organelle localizations. We benchmark DeepMito towards the only one recent approach developed for the same task. Results indicate that DeepMito performances are superior. Finally, genomic-scale prediction on a highly-curated dataset of human mitochondrial proteins further confirms the effectiveness of our approach and suggests that DeepMito is a good candidate for genome-scale annotation of mitochondrial protein subcellular localization. Availability and implementation The DeepMito web server as well as all datasets used in this study are available at http://busca.biocomp.unibo.it/deepmito. A standalone version of DeepMito is available on DockerHub at https://hub.docker.com/r/bolognabiocomp/deepmito. DeepMito source code is available on GitHub at https://github.com/BolognaBiocomp/deepmito Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Niccolò Bruciaferri
- Biocomputing Group, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Giacomo Tartari
- Biocomputing Group, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Italian National Research Council (CNR), Bari, Italy
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Italian National Research Council (CNR), Bari, Italy
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Regulation of mitochondrial plasticity by the i-AAA protease YME1L. Biol Chem 2020; 401:877-890. [DOI: 10.1515/hsz-2020-0120] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022]
Abstract
AbstractMitochondria are multifaceted metabolic organelles and adapt dynamically to various developmental transitions and environmental challenges. The metabolic flexibility of mitochondria is provided by alterations in the mitochondrial proteome and is tightly coupled to changes in the shape of mitochondria. Mitochondrial proteases are emerging as important posttranslational regulators of mitochondrial plasticity. The i-AAA protease YME1L, an ATP-dependent proteolytic complex in the mitochondrial inner membrane, coordinates mitochondrial biogenesis and dynamics with the metabolic output of mitochondria. mTORC1-dependent lipid signaling drives proteolytic rewiring of mitochondria by YME1L. While the tissue-specific loss of YME1L in mice is associated with heart failure, disturbed eye development, and axonal degeneration in the spinal cord, YME1L activity supports growth of pancreatic ductal adenocarcinoma cells. YME1L thus represents a key regulatory protease determining mitochondrial plasticity and metabolic reprogramming and is emerging as a promising therapeutic target.
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28
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Deshwal S, Fiedler KU, Langer T. Mitochondrial Proteases: Multifaceted Regulators of Mitochondrial Plasticity. Annu Rev Biochem 2020; 89:501-528. [PMID: 32075415 DOI: 10.1146/annurev-biochem-062917-012739] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria are essential metabolic hubs that dynamically adapt to physiological demands. More than 40 proteases residing in different compartments of mitochondria, termed mitoproteases, preserve mitochondrial proteostasis and are emerging as central regulators of mitochondrial plasticity. These multifaceted enzymes limit the accumulation of short-lived, regulatory proteins within mitochondria, modulate the activity of mitochondrial proteins by protein processing, and mediate the degradation of damaged proteins. Various signaling cascades coordinate the activity of mitoproteases to preserve mitochondrial homeostasis and ensure cell survival. Loss of mitoproteases severely impairs the functional integrity of mitochondria, is associated with aging, and causes pleiotropic diseases. Understanding the dual function of mitoproteases as regulatory and quality control enzymes will help unravel the role of mitochondrial plasticity in aging and disease.
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Affiliation(s)
- Soni Deshwal
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany;
| | - Kai Uwe Fiedler
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany;
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
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29
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Vazquez-Calvo C, Suhm T, Büttner S, Ott M. The basic machineries for mitochondrial protein quality control. Mitochondrion 2019; 50:121-131. [PMID: 31669238 DOI: 10.1016/j.mito.2019.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/10/2019] [Accepted: 10/02/2019] [Indexed: 11/16/2022]
Abstract
Mitochondria play pivotal roles in cellular energy metabolism, the synthesis of essential biomolecules and the regulation of cell death and aging. The proper folding, unfolding and degradation of the many proteins active within mitochondria is surveyed by the mitochondrial quality control machineries. Here, we describe the principal components of the mitochondrial quality control system and recent developments in the elucidation of the molecular mechanisms maintaining a functional mitochondrial proteome.
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Affiliation(s)
- Carmela Vazquez-Calvo
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusväg 16, Stockholm 106 91, Sweden; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm 106 91, Sweden
| | - Tamara Suhm
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusväg 16, Stockholm 106 91, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm 106 91, Sweden; Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria.
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusväg 16, Stockholm 106 91, Sweden.
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Affiliation(s)
- Michael Bader
- From the Max-Delbrück-Center for Molecular Medicine, Berlin, Germany (M.B., N.A.).,Charité-University Medicine, Berlin, Germany (M.B.).,German Center for Cardiovascular Research, Berlin Partner Site (M.B., N.A.).,Berlin Institute of Health, Germany (M.B.).,Institute for Biology, University of Lübeck, Germany (M.B.)
| | - Natalia Alenina
- From the Max-Delbrück-Center for Molecular Medicine, Berlin, Germany (M.B., N.A.).,German Center for Cardiovascular Research, Berlin Partner Site (M.B., N.A.)
| | - Dallan Young
- Biochemistry and Molecular Biology, University of Calgary, Canada (D.Y.)
| | - Robson A S Santos
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil (R.A.S.S.)
| | - Rhian M Touyz
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, United Kingdom (R.M.T.)
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31
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Demir F, Niedermaier S, Villamor JG, Huesgen PF. Quantitative proteomics in plant protease substrate identification. THE NEW PHYTOLOGIST 2018; 218:936-943. [PMID: 28493421 DOI: 10.1111/nph.14587] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/07/2017] [Indexed: 05/17/2023]
Abstract
Contents Summary 936 I. Introduction 936 II. The quest for plant protease substrates - proteomics to the rescue? 937 III. Quantitative proteome comparison reveals candidate substrates 938 IV. Dynamic metabolic stable isotope labeling to measure protein turnover in vivo 938 V. Terminomics - large-scale identification of protease cleavage sites 939 VI. Substrate or not substrate, that is the question 940 VII. Concluding remarks 941 Acknowledgements 941 References 941 SUMMARY: Proteolysis is a central regulatory mechanism of protein homeostasis and protein function that affects all aspects of plant life. Higher plants encode for hundreds of proteases, but their physiological substrates and hence their molecular functions remain mostly unknown. Current quantitative mass spectrometry-based proteomics enables unbiased large-scale interrogation of the proteome and its modifications. Here we provide an overview of proteomics techniques that allow profiling of changes in protein abundance, measurement of proteome turnover rates, identification of protease cleavage sites in vivo and in vitro and determination of protease sequence specificity. We discuss how these techniques can help to reveal protease substrates and determine plant protease function, illustrated by recent studies on selected plant proteases.
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Affiliation(s)
- Fatih Demir
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Stefan Niedermaier
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Joji Grace Villamor
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Pitter Florian Huesgen
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
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32
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Vögtle FN, Brändl B, Larson A, Pendziwiat M, Friederich MW, White SM, Basinger A, Kücükköse C, Muhle H, Jähn JA, Keminer O, Helbig KL, Delto CF, Myketin L, Mossmann D, Burger N, Miyake N, Burnett A, van Baalen A, Lovell MA, Matsumoto N, Walsh M, Yu HC, Shinde DN, Stephani U, Van Hove JLK, Müller FJ, Helbig I. Mutations in PMPCB Encoding the Catalytic Subunit of the Mitochondrial Presequence Protease Cause Neurodegeneration in Early Childhood. Am J Hum Genet 2018; 102:557-573. [PMID: 29576218 PMCID: PMC5985287 DOI: 10.1016/j.ajhg.2018.02.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial disorders causing neurodegeneration in childhood are genetically heterogeneous, and the underlying genetic etiology remains unknown in many affected individuals. We identified biallelic variants in PMPCB in individuals of four families including one family with two affected siblings with neurodegeneration and cerebellar atrophy. PMPCB encodes the catalytic subunit of the essential mitochondrial processing protease (MPP), which is required for maturation of the majority of mitochondrial precursor proteins. Mitochondria isolated from two fibroblast cell lines and induced pluripotent stem cells derived from one affected individual and differentiated neuroepithelial stem cells showed reduced PMPCB levels and accumulation of the processing intermediate of frataxin, a sensitive substrate for MPP dysfunction. Introduction of the identified PMPCB variants into the homologous S. cerevisiae Mas1 protein resulted in a severe growth and MPP processing defect leading to the accumulation of mitochondrial precursor proteins and early impairment of the biogenesis of iron-sulfur clusters, which are indispensable for a broad range of crucial cellular functions. Analysis of biopsy materials of an affected individual revealed changes and decreased activity in iron-sulfur cluster-containing respiratory chain complexes and dysfunction of mitochondrial and cytosolic Fe-S cluster-dependent enzymes. We conclude that biallelic mutations in PMPCB cause defects in MPP proteolytic activity leading to dysregulation of iron-sulfur cluster biogenesis and triggering a complex neurological phenotype of neurodegeneration in early childhood.
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Affiliation(s)
- F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany.
| | - Björn Brändl
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel 24105, Germany
| | - Austin Larson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Marisa W Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alice Basinger
- Cook Children's Physician Network, Department of Genetics, Fort Worth, TX 76102, USA
| | - Cansu Kücükköse
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany; Faculty of Biology, University of Freiburg, Freiburg 79104, Germany
| | - Hiltrud Muhle
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Johanna A Jähn
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Oliver Keminer
- Fraunhofer-Institut für Molekularbiologie und Angewandte Ökologie IME, ScreeningPort, Hamburg 22525, Germany
| | - Katherine L Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carolyn F Delto
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg 97080, Germany
| | - Lisa Myketin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Dirk Mossmann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Nils Burger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Audrey Burnett
- Cook Children's Physician Network, Department of Genetics, Fort Worth, TX 76102, USA
| | - Andreas van Baalen
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Mark A Lovell
- Department of Pathology, University of Colorado, Aurora, CO 80045, USA
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Maie Walsh
- Adult Genetic Medicine, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
| | - Hung-Chun Yu
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Ulrich Stephani
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Franz-Josef Müller
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel 24105, Germany; Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Ingo Helbig
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany; Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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33
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Stutz K, Müller AT, Hiss JA, Schneider P, Blatter M, Pfeiffer B, Posselt G, Kanfer G, Kornmann B, Wrede P, Altmann KH, Wessler S, Schneider G. Peptide-Membrane Interaction between Targeting and Lysis. ACS Chem Biol 2017; 12:2254-2259. [PMID: 28763193 DOI: 10.1021/acschembio.7b00504] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Certain cationic peptides interact with biological membranes. These often-complex interactions can result in peptide targeting to the membrane, or in membrane permeation, rupture, and cell lysis. We investigated the relationship between the structural features of membrane-active peptides and these effects, to better understand these processes. To this end, we employed a computational method for morphing a membranolytic antimicrobial peptide into a nonmembranolytic mitochondrial targeting peptide by "directed simulated evolution." The results obtained demonstrate that superficially subtle sequence modifications can strongly affect the peptides' membranolytic and membrane-targeting abilities. Spectroscopic and computational analyses suggest that N- and C-terminal structural flexibility plays a crucial role in determining the mode of peptide-membrane interaction.
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Affiliation(s)
- Katharina Stutz
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Alex T. Müller
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Jan A. Hiss
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Markus Blatter
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Bernhard Pfeiffer
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Gernot Posselt
- Department
of Molecular Biology, Division of Microbiology, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Gil Kanfer
- Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), Otto-Stern-Weg-3, 8093 Zurich, Switzerland
| | - Benoît Kornmann
- Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), Otto-Stern-Weg-3, 8093 Zurich, Switzerland
| | - Paul Wrede
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Silja Wessler
- Department
of Molecular Biology, Division of Microbiology, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
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34
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Gomes F, Palma FR, Barros MH, Tsuchida ET, Turano HG, Alegria TGP, Demasi M, Netto LES. Proteolytic cleavage by the inner membrane peptidase (IMP) complex or Oct1 peptidase controls the localization of the yeast peroxiredoxin Prx1 to distinct mitochondrial compartments. J Biol Chem 2017; 292:17011-17024. [PMID: 28821623 DOI: 10.1074/jbc.m117.788588] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 08/17/2017] [Indexed: 01/01/2023] Open
Abstract
Yeast Prx1 is a mitochondrial 1-Cys peroxiredoxin that catalyzes the reduction of endogenously generated H2O2 Prx1 is synthesized on cytosolic ribosomes as a preprotein with a cleavable N-terminal presequence that is the mitochondrial targeting signal, but the mechanisms underlying Prx1 distribution to distinct mitochondrial subcompartments are unknown. Here, we provide direct evidence of the following dual mitochondrial localization of Prx1: a soluble form in the intermembrane space and a form in the matrix weakly associated with the inner mitochondrial membrane. We show that Prx1 sorting into the intermembrane space likely involves the release of the protein precursor within the lipid bilayer of the inner membrane, followed by cleavage by the inner membrane peptidase. We also found that during its import into the matrix compartment, Prx1 is sequentially cleaved by mitochondrial processing peptidase and then by octapeptidyl aminopeptidase 1 (Oct1). Oct1 cleaved eight amino acid residues from the N-terminal region of Prx1 inside the matrix, without interfering with its peroxidase activity in vitro Remarkably, the processing of peroxiredoxin (Prx) proteins by Oct1 appears to be an evolutionarily conserved process because yeast Oct1 could cleave the human mitochondrial peroxiredoxin Prx3 when expressed in Saccharomyces cerevisiae Altogether, the processing of peroxiredoxins by Imp2 or Oct1 likely represents systems that control the localization of Prxs into distinct compartments and thereby contribute to various mitochondrial redox processes.
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Affiliation(s)
- Fernando Gomes
- From the Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo,
| | - Flávio Romero Palma
- From the Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo
| | - Mario H Barros
- the Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo, and
| | - Eduardo T Tsuchida
- From the Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo
| | - Helena G Turano
- the Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo, and
| | - Thiago G P Alegria
- From the Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo
| | - Marilene Demasi
- the Laboratório de Bioquímica e Biofísica, Instituto Butantan, 05503-001 São Paulo, Brazil
| | - Luis E S Netto
- From the Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo,
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35
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Recent advances in mitochondrial biology - integrated aspects. Cell Tissue Res 2016; 367:1-3. [PMID: 27858155 DOI: 10.1007/s00441-016-2533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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