201
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Casaletti L, Lima PS, Oliveira LN, Borges CL, Báo SN, Bailão AM, Soares CMA. Analysis of Paracoccidioides lutzii mitochondria: a proteomic approach. Yeast 2017; 34:179-188. [PMID: 27886402 DOI: 10.1002/yea.3225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 01/21/2023] Open
Abstract
The genus Paracoccidioides is composed of thermal dimorphic fungi, causative agents of paracoccidioidomycosis, one of the most frequent systemic mycoses in Latin America. Mitochondria have sophisticated machinery for ATP production, which involves metabolic pathways such as citric acid and glyoxylate cycles, electron transport chain and oxidative phosphorylation. In addition, this organelle performs a variety of functions in the cell, working as an exceptional metabolic signalling centre that contributes to cellular stress responses, as autophagy and apoptosis in eukaryotic organisms. The aim of this work was to perform a descriptive proteomic analysis of mitochondria in Paracoccidioides lutzii yeast cells. After mitochondria fractionation, samples enriched in mitochondrial proteins were digested with trypsin and analysed using a NanoUPLC-MSE system (Waters Corporation, Manchester, UK). Ours results revealed that the established protocol for purification of mitochondria was very effective for P. lutzii, and 298 proteins were identified as primarily mitochondrial, in our analysis. To our knowledge, this is the first compilation of mitochondrial proteins from P. lutzii, to date. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- L Casaletti
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil.,Escola de Engenharia, Pontifícia Universidade Católica de Goiás, 74605-010, Goiânia, Goiás, Brazil
| | - P S Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - L N Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil.,Programa de Pós-graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, 70910-900, Brasília, Distrito Federal, Brazil
| | - C L Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - S N Báo
- Laboratório de Microscopia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900, Brasília, Distrito Federal, Brazil
| | - A M Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - C M A Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
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202
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Calvo SE, Julien O, Clauser KR, Shen H, Kamer KJ, Wells JA, Mootha VK. Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. Mol Cell Proteomics 2017; 16:512-523. [PMID: 28122942 DOI: 10.1074/mcp.m116.063818] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/06/2017] [Indexed: 01/08/2023] Open
Abstract
The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by an N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here, we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that whereas presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved, including a length of ∼20-60 amino acids, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-terminus of mature proteins that follow the N-end rule from bacteria. As in yeast, ∼80% of mouse presequence cleavage sites match canonical motifs for three mitochondrial peptidases (MPP, Icp55, and Oct1), whereas the remainder do not match any known peptidase motifs. We show that mature mitochondrial proteins often exist with a spectrum of N-termini, consistent with a model of multiple cleavage events by MPP and Icp55. In addition to analysis of canonical targeting presequences, our N-terminal dataset allows the exploration of other cleavage events and provides support for polypeptide cleavage into two distinct enzymes (Hsd17b4), protein cleavages key for signaling (Oma1, Opa1, Htra2, Mavs, and Bcs2l13), and in several cases suggests novel protein isoforms (Scp2, Acadm, Adck3, Hsdl2, Dlst, and Ogdh). We present an integrated catalog of mammalian mitochondrial N-termini that can be used as a community resource to investigate individual proteins, to elucidate mechanisms of mammalian mitochondrial processing, and to allow researchers to engineer tags distally to the presequence cleavage.
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Affiliation(s)
- Sarah E Calvo
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114; .,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115.,¶Broad Institute, Cambridge, Massachusetts 02141
| | | | | | - Hongying Shen
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Kimberli J Kamer
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - James A Wells
- **Departments of Pharmaceutical Chemistry and.,§§Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143
| | - Vamsi K Mootha
- From the ‡Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,§Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
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203
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Burén S, Jiang X, López-Torrejón G, Echavarri-Erasun C, Rubio LM. Purification and In Vitro Activity of Mitochondria Targeted Nitrogenase Cofactor Maturase NifB. FRONTIERS IN PLANT SCIENCE 2017; 8:1567. [PMID: 28955359 PMCID: PMC5601070 DOI: 10.3389/fpls.2017.01567] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/28/2017] [Indexed: 05/13/2023]
Abstract
Active NifB is a milestone in the process of engineering nitrogen fixing plants. NifB is an extremely O2-sensitive S-adenosyl methionine (SAM)-radical enzyme that provides the key metal cluster intermediate (NifB-co) for the biosyntheses of the active-site cofactors of all three types of nitrogenases. NifB and NifB-co are unique to diazotrophic organisms. In this work, we have expressed synthetic codon-optimized versions of NifB from the γ-proteobacterium Azotobacter vinelandii and the thermophilic methanogen Methanocaldococcus infernus in Saccharomyces cerevisiae and in Nicotiana benthamiana. NifB proteins were targeted to the mitochondria, where O2 consumption is high and bacterial-like [Fe-S] cluster assembly operates. In yeast, NifB proteins were co-expressed with NifU, NifS, and FdxN proteins that are involved in NifB [Fe-S] cluster assembly and activity. The synthetic version of thermophilic NifB accumulated in soluble form within the yeast cell, while the A. vinelandii version appeared to form aggregates. Similarly, NifB from M. infernus was expressed at higher levels in leaves of Nicotiana benthamiana and accumulated as a soluble protein while A. vinelandii NifB was mainly associated with the non-soluble cell fraction. Soluble M. infernus NifB was purified from aerobically grown yeast and biochemically characterized. The purified protein was functional in the in vitro FeMo-co synthesis assay. This work presents the first active NifB protein purified from a eukaryotic cell, and highlights the importance of screening nif genes from different organisms in order to sort the best candidates to assemble a functional plant nitrogenase.
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204
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Migdal I, Skibior-Blaszczyk R, Heidorn-Czarna M, Kolodziejczak M, Garbiec A, Janska H. AtOMA1 Affects the OXPHOS System and Plant Growth in Contrast to Other Newly Identified ATP-Independent Proteases in Arabidopsis Mitochondria. FRONTIERS IN PLANT SCIENCE 2017; 8:1543. [PMID: 28936218 PMCID: PMC5594102 DOI: 10.3389/fpls.2017.01543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/23/2017] [Indexed: 05/17/2023]
Abstract
Compared with yeast, our knowledge on members of the ATP-independent plant mitochondrial proteolytic machinery is rather poor. In the present study, using confocal microscopy and immunoblotting, we proved that homologs of yeast Oma1, Atp23, Imp1, Imp2, and Oct1 proteases are localized in Arabidopsis mitochondria. We characterized these components of the ATP-independent proteolytic system as well as the earlier identified protease, AtICP55, with an emphasis on their significance in plant growth and functionality in the OXPHOS system. A functional complementation assay demonstrated that out of all the analyzed proteases, only AtOMA1 and AtICP55 could substitute for a lack of their yeast counterparts. We did not observe any significant developmental or morphological changes in plants lacking the studied proteases, either under optimal growth conditions or after exposure to stress, with the only exception being retarded root growth in oma1-1, thus implying that the absence of a single mitochondrial ATP-independent protease is not critical for Arabidopsis growth and development. We did not find any evidence indicating a clear functional complementation of the missing protease by any other protease at the transcript or protein level. Studies on the impact of the analyzed proteases on mitochondrial bioenergetic function revealed that out of all the studied mutants, only oma1-1 showed differences in activities and amounts of OXPHOS proteins. Among all the OXPHOS disorders found in oma1-1, the complex V deficiency is distinctive because it is mainly associated with decreased catalytic activity and not correlated with complex abundance, which has been observed in the case of supercomplex I + III2 and complex I deficiencies. Altogether, our study indicates that despite the presence of highly conservative homologs, the mitochondrial ATP-independent proteolytic system is not functionally conserved in plants as compared with yeast. Our findings also highlight the importance of AtOMA1 in maintenance of proper function of the OXPHOS system as well as in growth and development of Arabidopsis thaliana.
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Affiliation(s)
- Iwona Migdal
- Institute of Experimental Biology, Faculty of Biological Sciences, University of WroclawWroclaw, Poland
| | - Renata Skibior-Blaszczyk
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of WroclawWroclaw, Poland
| | - Malgorzata Heidorn-Czarna
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of WroclawWroclaw, Poland
| | - Marta Kolodziejczak
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of WroclawWroclaw, Poland
| | - Arnold Garbiec
- Institute of Experimental Biology, Faculty of Biological Sciences, University of WroclawWroclaw, Poland
| | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of WroclawWroclaw, Poland
- *Correspondence: Hanna Janska,
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205
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Westermann B, Jacome ASV, Rompais M, Carapito C, Schaeffer-Reiss C. Doublet N-Terminal Oriented Proteomics for N-Terminomics and Proteolytic Processing Identification. Methods Mol Biol 2017; 1574:77-90. [PMID: 28315244 DOI: 10.1007/978-1-4939-6850-3_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The study of the N-terminome and the precise identification of proteolytic processing events are key in biology. Dedicated methodologies have been developed as the comprehensive characterization of the N-terminome can hardly be achieved by standard proteomics methods. In this context, we have set up a trimethoxyphenyl phosphonium (TMPP) labeling approach that allows the characterization of both N-terminal and internal digestion peptides in a single experiment. This latter point is a major advantage of our strategy as most N-terminomics methods rely on the enrichment of N-terminal peptides and thus exclude internal peptides.We have implemented a double heavy/light TMPP labeling and an automated data validation workflow that make our doublet N-terminal oriented proteomics (dN-TOP) strategy efficient for high-throughput N-terminome analysis.
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Affiliation(s)
- Benoit Westermann
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France
| | - Alvaro Sebastian Vaca Jacome
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France
| | - Magali Rompais
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France
| | - Christine Carapito
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France
| | - Christine Schaeffer-Reiss
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, CNRS-UdS, UMR 7178, University of Strasbourg, 25, rue Becquerel, 67087, Strasbourg, France.
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206
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Two proteomic methodologies for defining N-termini of mature human mitochondrial aminoacyl-tRNA synthetases. Methods 2017; 113:111-119. [DOI: 10.1016/j.ymeth.2016.10.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 11/21/2022] Open
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207
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Schendzielorz AB, Schulz C, Lytovchenko O, Clancy A, Guiard B, Ieva R, van der Laan M, Rehling P. Two distinct membrane potential-dependent steps drive mitochondrial matrix protein translocation. J Cell Biol 2016; 216:83-92. [PMID: 28011846 PMCID: PMC5223606 DOI: 10.1083/jcb.201607066] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/30/2016] [Accepted: 11/28/2016] [Indexed: 12/03/2022] Open
Abstract
Schendzielorz et al. report that mitochondrial precursors display different dependencies on the membrane potential (Δψ) for translocation. Two distinct Δψ-dependent steps promote precursor translocation, the first driving presequence translocation and the second acting on the mature portion of the polypeptide chain. Two driving forces energize precursor translocation across the inner mitochondrial membrane. Although the membrane potential (Δψ) is considered to drive translocation of positively charged presequences through the TIM23 complex (presequence translocase), the activity of the Hsp70-powered import motor is crucial for the translocation of the mature protein portion into the matrix. In this study, we show that mitochondrial matrix proteins display surprisingly different dependencies on the Δψ. However, a precursor’s hypersensitivity to a reduction of the Δψ is not linked to the respective presequence, but rather to the mature portion of the polypeptide chain. The presequence translocase constituent Pam17 is specifically recruited by the receptor Tim50 to promote the transport of hypersensitive precursors into the matrix. Our analyses show that two distinct Δψ-driven translocation steps energize precursor passage across the inner mitochondrial membrane. The Δψ- and Pam17-dependent import step identified in this study is positioned between the two known energy-dependent steps: Δψ-driven presequence translocation and adenosine triphosphate–driven import motor activity.
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Affiliation(s)
- Alexander Benjamin Schendzielorz
- Department of Cellular Biochemistry, University Medical Center Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Christian Schulz
- Department of Cellular Biochemistry, University Medical Center Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Oleksandr Lytovchenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Anne Clancy
- Department of Molecular Biology, University Medical Center Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Raffaele Ieva
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre de Biologie Intégrative, Université de Toulouse, Centre National de la Recherche Scientifique, Unité Propre de Service, 31062 Toulouse, France.,Institute of Biochemistry and Molecular Biology, Center for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Martin van der Laan
- Institute of Biochemistry and Molecular Biology, Center for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany .,Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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208
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Harsman A, Oeljeklaus S, Wenger C, Huot JL, Warscheid B, Schneider A. The non-canonical mitochondrial inner membrane presequence translocase of trypanosomatids contains two essential rhomboid-like proteins. Nat Commun 2016; 7:13707. [PMID: 27991487 PMCID: PMC5187411 DOI: 10.1038/ncomms13707] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/24/2016] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial protein import is essential for all eukaryotes. Here we show that the early diverging eukaryote Trypanosoma brucei has a non-canonical inner membrane (IM) protein translocation machinery. Besides TbTim17, the single member of the Tim17/22/23 family in trypanosomes, the presequence translocase contains nine subunits that co-purify in reciprocal immunoprecipitations and with a presequence-containing substrate that is trapped in the translocation channel. Two of the newly discovered subunits are rhomboid-like proteins, which are essential for growth and mitochondrial protein import. Rhomboid-like proteins were proposed to form the protein translocation pore of the ER-associated degradation system, suggesting that they may contribute to pore formation in the presequence translocase of T. brucei. Pulldown of import-arrested mitochondrial carrier protein shows that the carrier translocase shares eight subunits with the presequence translocase. This indicates that T. brucei may have a single IM translocase that with compositional variations mediates import of presequence-containing and carrier proteins.
The mitochondrial protein import machinery is crucial for eukaryotes but little is known about its evolutionary origin. Here, the authors characterize the translocase of the inner membrane (TIM) in trypanosomes, showing that it contains two rhomboid-like proteins essential for protein import.
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Affiliation(s)
- Anke Harsman
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany
| | - Christoph Wenger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Jonathan L Huot
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
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209
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A cell-free organelle-based in vitro system for studying the peroxisomal protein import machinery. Nat Protoc 2016; 11:2454-2469. [PMID: 27831570 DOI: 10.1038/nprot.2016.147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Here we describe a protocol to dissect the peroxisomal matrix protein import pathway using a cell-free in vitro system. The system relies on a postnuclear supernatant (PNS), which is prepared from rat/mouse liver, to act as a source of peroxisomes and cytosolic components. A typical in vitro assay comprises the following steps: (i) incubation of the PNS with an in vitro-synthesized 35S-labeled reporter protein; (ii) treatment of the organelle suspension with a protease that degrades reporter proteins that have not associated with peroxisomes; and (iii) SDS-PAGE/autoradiography analysis. To study transport of proteins into peroxisomes, it is possible to use organelle-resident proteins that contain a peroxisomal targeting signal (PTS) as reporters in the assay. In addition, a receptor (PEX5L/S or PEX5L.PEX7) can be used to report the dynamics of shuttling proteins that mediate the import process. Thus, different but complementary perspectives on the mechanism of this pathway can be obtained. We also describe strategies to fortify the system with recombinant proteins to increase import yields and block specific parts of the machinery at a number of steps. The system recapitulates all the steps of the pathway, including mono-ubiquitination of PEX5L/S at the peroxisome membrane and its ATP-dependent export back into the cytosol by PEX1/PEX6. An in vitro import(/export) experiment can be completed in 24 h.
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210
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Eldomery MK, Akdemir ZC, Vögtle FN, Charng WL, Mulica P, Rosenfeld JA, Gambin T, Gu S, Burrage LC, Al Shamsi A, Penney S, Jhangiani SN, Zimmerman HH, Muzny DM, Wang X, Tang J, Medikonda R, Ramachandran PV, Wong LJ, Boerwinkle E, Gibbs RA, Eng CM, Lalani SR, Hertecant J, Rodenburg RJ, Abdul-Rahman OA, Yang Y, Xia F, Wang MC, Lupski JR, Meisinger C, Sutton VR. MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death. Genome Med 2016; 8:106. [PMID: 27799064 PMCID: PMC5088683 DOI: 10.1186/s13073-016-0360-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease. METHODS Whole exome sequencing was performed on four unrelated probands with left ventricular non-compaction (LVNC), developmental delay (DD), seizures, and severe hypotonia. Proposed pathogenic variants were confirmed by Sanger sequencing or array comparative genomic hybridization. Functional analysis of the identified MIP variants was performed using the model organism Saccharomyces cerevisiae as the protein and its functions are highly conserved from yeast to human. RESULTS Biallelic single nucleotide variants (SNVs) or copy number variants (CNVs) in MIPEP, which encodes MIP, were present in all four probands, three of whom had infantile/childhood death. Two patients had compound heterozygous SNVs (p.L582R/p.L71Q and p.E602*/p.L306F) and one patient from a consanguineous family had a homozygous SNV (p.K343E). The fourth patient, identified through the GeneMatcher tool, a part of the Matchmaker Exchange Project, was found to have inherited a paternal SNV (p.H512D) and a maternal CNV (1.4-Mb deletion of 13q12.12) that includes MIPEP. All amino acids affected in the patients' missense variants are highly conserved from yeast to human and therefore S. cerevisiae was employed for functional analysis (for p.L71Q, p.L306F, and p.K343E). The mutations p.L339F (human p.L306F) and p.K376E (human p.K343E) resulted in a severe decrease of Oct1 protease activity and accumulation of non-processed Oct1 substrates and consequently impaired viability under respiratory growth conditions. The p.L83Q (human p.L71Q) failed to localize to the mitochondria. CONCLUSIONS Our findings reveal for the first time the role of the mitochondrial intermediate peptidase in human disease. Loss of MIP function results in a syndrome which consists of LVNC, DD, seizures, hypotonia, and cataracts. Our approach highlights the power of data exchange and the importance of an interrelationship between clinical and research efforts for disease gene discovery.
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Affiliation(s)
- Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Patrycja Mulica
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Aisha Al Shamsi
- Department of Pediatrics, Tawam Hospital, Al Ain, 15258, United Arab Emirates
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Holly H Zimmerman
- Department of Pediatrics, University of Mississippi Medical Center, 2500N State St, Jackson, MS, 39216, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jia Tang
- Medical Genetics Center, Jiang Men Maternity and Childhealth Care Hospital, Jiang Men, 529000, China
| | - Ravi Medikonda
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Prasanna V Ramachandran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Jozef Hertecant
- Department of Pediatrics, Tawam Hospital, Al Ain, 15258, United Arab Emirates
| | - Richard J Rodenburg
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, RadboudUMC, 6500HB, Nijmegen, Netherlands
| | - Omar A Abdul-Rahman
- Department of Pediatrics, University of Mississippi Medical Center, 2500N State St, Jackson, MS, 39216, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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211
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Wasilewski M, Chojnacka K, Chacinska A. Protein trafficking at the crossroads to mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:125-137. [PMID: 27810356 DOI: 10.1016/j.bbamcr.2016.10.019] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/14/2022]
Abstract
Mitochondria are central power stations in the cell, which additionally serve as metabolic hubs for a plethora of anabolic and catabolic processes. The sustained function of mitochondria requires the precisely controlled biogenesis and expression coordination of proteins that originate from the nuclear and mitochondrial genomes. Accuracy of targeting, transport and assembly of mitochondrial proteins is also needed to avoid deleterious effects on protein homeostasis in the cell. Checkpoints of mitochondrial protein transport can serve as signals that provide information about the functional status of the organelles. In this review, we summarize recent advances in our understanding of mitochondrial protein transport and discuss examples that involve communication with the nucleus and cytosol.
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Affiliation(s)
- Michal Wasilewski
- International Institute of Molecular and Cell Biology in Warsaw, Poland.
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212
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Woellhaf MW, Sommer F, Schroda M, Herrmann JM. Proteomic profiling of the mitochondrial ribosome identifies Atp25 as a composite mitochondrial precursor protein. Mol Biol Cell 2016; 27:3031-3039. [PMID: 27582385 PMCID: PMC5063612 DOI: 10.1091/mbc.e16-07-0513] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 11/15/2022] Open
Abstract
Whereas the structure and function of cytosolic ribosomes are well characterized, we only have a limited understanding of the mitochondrial translation apparatus. Using SILAC-based proteomic profiling, we identified 13 proteins that cofractionated with the mitochondrial ribosome, most of which play a role in translation or ribosomal biogenesis. One of these proteins is a homologue of the bacterial ribosome-silencing factor (Rsf). This protein is generated from the composite precursor protein Atp25 upon internal cleavage by the matrix processing peptidase MPP, and in this respect, it differs from all other characterized mitochondrial proteins of baker's yeast. We observed that cytosolic expression of Rsf, but not of noncleaved Atp25 protein, is toxic. Our results suggest that eukaryotic cells face the challenge of avoiding negative interference from the biogenesis of their two distinct translation machineries.
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Affiliation(s)
- Michael W Woellhaf
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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213
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Chatterjee A, Seyfferth J, Lucci J, Gilsbach R, Preissl S, Böttinger L, Mårtensson CU, Panhale A, Stehle T, Kretz O, Sahyoun AH, Avilov S, Eimer S, Hein L, Pfanner N, Becker T, Akhtar A. MOF Acetyl Transferase Regulates Transcription and Respiration in Mitochondria. Cell 2016; 167:722-738.e23. [DOI: 10.1016/j.cell.2016.09.052] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/22/2016] [Accepted: 09/27/2016] [Indexed: 11/29/2022]
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214
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The versatility of the mitochondrial presequence processing machinery: cleavage, quality control and turnover. Cell Tissue Res 2016; 367:73-81. [DOI: 10.1007/s00441-016-2492-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/06/2016] [Accepted: 08/10/2016] [Indexed: 12/12/2022]
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215
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Curcumin, mitochondrial biogenesis, and mitophagy: Exploring recent data and indicating future needs. Biotechnol Adv 2016; 34:813-826. [DOI: 10.1016/j.biotechadv.2016.04.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/11/2016] [Accepted: 04/28/2016] [Indexed: 11/23/2022]
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216
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Chen L, Shan Y, Weng Y, Sui Z, Zhang X, Liang Z, Zhang L, Zhang Y. Hydrophobic Tagging-Assisted N-Termini Enrichment for In-Depth N-Terminome Analysis. Anal Chem 2016; 88:8390-5. [DOI: 10.1021/acs.analchem.6b02453] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Lingfan Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yichu Shan
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yejing Weng
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Xiaodan Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhen Liang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
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217
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Garg SG, Gould SB. The Role of Charge in Protein Targeting Evolution. Trends Cell Biol 2016; 26:894-905. [PMID: 27524662 DOI: 10.1016/j.tcb.2016.07.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/28/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022]
Abstract
Two eukaryotic compartments are of endosymbiotic origin, the mitochondrion and plastid. These organelles need to import hundreds of proteins from the cytosol. The import machineries of both are of independent origin, but function in a similar fashion and recognize N-terminal targeting sequences that also share similarities. Targeting, however, is generally specific, even though plastid targeting evolved in the presence of established mitochondrial targeting. Here we review current advances on protein import into mitochondria and plastids from diverse eukaryotic lineages and highlight the impact of charged amino acids in targeting. Their presence or absence alone can determine localization, and comparisons across diverse eukaryotes, and their different types of mitochondria and plastids, uncover unexplored avenues of protein import research.
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Affiliation(s)
- Sriram G Garg
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.
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218
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Towards the development of an enzyme replacement therapy for the metabolic disorder propionic acidemia. Mol Genet Metab Rep 2016; 8:51-60. [PMID: 27504265 PMCID: PMC4968140 DOI: 10.1016/j.ymgmr.2016.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 12/11/2022] Open
Abstract
Propionic acidemia (PA) is a life-threatening disease caused by the deficiency of a mitochondrial biotin-dependent enzyme known as propionyl coenzyme-A carboxylase (PCC). This enzyme is responsible for degrading the metabolic intermediate, propionyl coenzyme-A (PP-CoA), derived from multiple metabolic pathways. Currently, except for drastic surgical and dietary intervention that can only provide partial symptomatic relief, no other form of therapeutic option is available for this genetic disorder. Here, we examine a novel approach in protein delivery by specifically targeting and localizing our protein candidate of interest into the mitochondrial matrix of the cells. In order to test this concept of delivery, we have utilized cell penetrating peptides (CPPs) and mitochondria targeting sequences (MTS) to form specific fusion PCC protein, capable of translocating and localizing across cell membranes. In vitro delivery of our candidate fusion proteins, evaluated by confocal images and enzymatic activity assay, indicated effectiveness of this strategy. Therefore, it holds immense potential in creating a new paradigm in site-specific protein delivery and enzyme replacement therapeutic for PA.
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Key Words
- CPPs, cell penetrating peptides
- CoA, coenzyme-A
- ERT, enzyme replacement therapy
- Enzyme replacement therapy
- His-tag, six histidines tag
- LAD, lipoamine dehydrogenase
- MPP, mitochondrial processing peptidase
- MTS, mitochondria targeting sequences
- Mitochondrial targeting sequences
- PA, propionic acidemia
- PCC, propionyl coenzyme-A carboxylase
- PCCA, PCCα subunit
- PCCB, PCCβ subunit
- PP-CoA, propionyl coenzyme-A
- Propionic acidemia
- Propionyl coenzyme-A carboxylase
- Protein transduction domains
- UPLC-MS/MS, ultra performance liquid chromatography tandem mass spectrometry
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219
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Import of a major mitochondrial enzyme depends on synergy between two distinct helices of its presequence. Biochem J 2016; 473:2813-29. [PMID: 27422783 PMCID: PMC5095901 DOI: 10.1042/bcj20160535] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/15/2016] [Indexed: 12/13/2022]
Abstract
Mammalian glutamate dehydrogenase (GDH), a nuclear-encoded enzyme central to cellular metabolism, is among the most abundant mitochondrial proteins (constituting up to 10% of matrix proteins). To attain such high levels, GDH depends on very efficient mitochondrial targeting that, for human isoenzymes hGDH1 and hGDH2, is mediated by an unusually long cleavable presequence (N53). Here, we studied the mitochondrial transport of these proteins using isolated yeast mitochondria and human cell lines. We found that both hGDHs were very rapidly imported and processed in isolated mitochondria, with their presequences (N53) alone being capable of directing non-mitochondrial proteins into mitochondria. These presequences were predicted to form two α helices (α1: N 1–10; α2: N 16–32) separated by loops. Selective deletion of the α1 helix abolished the mitochondrial import of hGDHs. While the α1 helix alone had a very weak hGDH mitochondrial import capacity, it could direct efficiently non-mitochondrial proteins into mitochondria. In contrast, the α2 helix had no autonomous mitochondrial-targeting capacity. A peptide consisting of α1 and α2 helices without intervening sequences had GDH transport efficiency comparable with that of N53. Mutagenesis of the cleavage site blocked the intra-mitochondrial processing of hGDHs, but did not affect their mitochondrial import. Replacement of all three positively charged N-terminal residues (Arg3, Lys7 and Arg13) by Ala abolished import. We conclude that the synergistic interaction of helices α1 and α2 is crucial for the highly efficient import of hGDHs into mitochondria.
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220
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Peleh V, Cordat E, Herrmann JM. Mia40 is a trans-site receptor that drives protein import into the mitochondrial intermembrane space by hydrophobic substrate binding. eLife 2016; 5. [PMID: 27343349 PMCID: PMC4951193 DOI: 10.7554/elife.16177] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/24/2016] [Indexed: 11/13/2022] Open
Abstract
Many proteins of the mitochondrial IMS contain conserved cysteines that are oxidized to disulfide bonds during their import. The conserved IMS protein Mia40 is essential for the oxidation and import of these proteins. Mia40 consists of two functional elements: an N-terminal cysteine-proline-cysteine motif conferring substrate oxidation, and a C-terminal hydrophobic pocket for substrate binding. In this study, we generated yeast mutants to dissect both Mia40 activities genetically and biochemically. Thereby we show that the substrate-binding domain of Mia40 is both necessary and sufficient to promote protein import, indicating that trapping by Mia40 drives protein translocation. An oxidase-deficient Mia40 mutant is inviable, but can be partially rescued by the addition of the chemical oxidant diamide. Our results indicate that Mia40 predominantly serves as a trans-site receptor of mitochondria that binds incoming proteins via hydrophobic interactions thereby mediating protein translocation across the outer membrane by a ‘holding trap’ rather than a ‘folding trap’ mechanism. DOI:http://dx.doi.org/10.7554/eLife.16177.001 Human, yeast and other eukaryotic cells contain compartments called mitochondria that perform several vital tasks, including supplying the cell with energy. Each mitochondrion is surrounded by an inner and an outer membrane, which are separated by an intermembrane space that contains a host of molecules, including proteins. Intermembrane space proteins are made in the cytosol before being transported into the intermembrane space through pores in the mitochondrion’s outer membrane. Many of these proteins have the ability to form disulfide bonds within their structures, which help the proteins to fold and assemble correctly, but they only acquire these bonds once they have entered the intermembrane space. An enzyme called Mia40 sits inside the intermembrane space and helps other proteins to fold correctly. This Mia40-induced folding had been suggested to help proteins to move into the intermembrane space. Mia40 contains two important regions: one region acts as an enzyme and adds disulfide bonds to other proteins, and the other region binds to the intermembrane space proteins. Peleh et al. have now generated versions of Mia40 that lack one or the other of these regions in yeast cells, and then tested to see if these mutants could drive proteins across the outer membrane of mitochondria. The results show that it is the ability of Mia40 to bind proteins – and not its enzyme activity – that is essential for importing proteins into the intermembrane space. As disulfide bond formation is not critical for importing proteins into the intermembrane space, future studies could test whether Mia40 also helps to transport proteins that cannot form disulfide bonds. Presumably, Mia40 has a much broader relevance for importing mitochondrial proteins than was previously thought. DOI:http://dx.doi.org/10.7554/eLife.16177.002
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Affiliation(s)
- Valentina Peleh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
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221
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Dasari S, Kölling R. Role of mitochondrial processing peptidase and AAA proteases in processing of the yeast acetohydroxyacid synthase precursor. FEBS Open Bio 2016; 6:765-73. [PMID: 27398316 PMCID: PMC4932456 DOI: 10.1002/2211-5463.12088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 11/16/2022] Open
Abstract
We studied presequence processing of the mitochondrial‐matrix targeted acetohydroxyacid synthase (Ilv2). C‐terminal 3HA‐tagging altered the cleavage pattern from a single step to sequential two‐step cleavage, giving rise to two Ilv2‐3HA forms (A and B). Both cleavage events were dependent on the mitochondrial processing peptidase (MPP). We present evidence for the involvement of three AAA ATPases, m‐ and i‐AAA proteases, and Mcx1, in Ilv2‐3HA processing. Both, precursor to A‐form and A‐form to B‐form cleavage were strongly affected in a ∆yme1 mutant. These defects could be suppressed by overexpression of MPP, suggesting that MPP activity is limiting in the ∆yme1 mutant. Our data suggest that for some substrates AAA ATPases could play an active role in the translocation of matrix‐targeted proteins.
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Affiliation(s)
- Suvarna Dasari
- Institut für Lebensmittelwissenschaft und Biotechnologie Fg. Hefegenetik und Gärungstechnologie (150f) Universität Hohenheim Stuttgart Germany
| | - Ralf Kölling
- Institut für Lebensmittelwissenschaft und Biotechnologie Fg. Hefegenetik und Gärungstechnologie (150f) Universität Hohenheim Stuttgart Germany
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222
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Couto N, Wood J, Barber J. The role of glutathione reductase and related enzymes on cellular redox homoeostasis network. Free Radic Biol Med 2016; 95:27-42. [PMID: 26923386 DOI: 10.1016/j.freeradbiomed.2016.02.028] [Citation(s) in RCA: 474] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 02/19/2016] [Accepted: 02/24/2016] [Indexed: 02/07/2023]
Abstract
In this review article we examine the role of glutathione reductase in the regulation, modulation and maintenance of cellular redox homoeostasis. Glutathione reductase is responsible for maintaining the supply of reduced glutathione; one of the most abundant reducing thiols in the majority of cells. In its reduced form, glutathione plays key roles in the cellular control of reactive oxygen species. Reactive oxygen species act as intracellular and extracellular signalling molecules and complex cross talk between levels of reactive oxygen species, levels of oxidised and reduced glutathione and other thiols, and antioxidant enzymes such as glutathione reductase determine the most suitable conditions for redox control within a cell or for activation of programmed cell death. Additionally, we discuss the translation and expression of glutathione reductase in a number of organisms including yeast and humans. In yeast and human cells, a single gene expresses more than one form of glutathione reductase, destined for residence in the cytoplasm or for translocation to different organelles; in plants, however, two genes encoding this protein have been described. In general, insects and kinetoplastids (a group of protozoa, including Plasmodia and Trypanosoma) do not express glutathione reductase or glutathione biosynthetic enzymes. Instead, they express either the thioredoxin system or the trypanothione system. The thioredoxin system is also present in organisms that have the glutathione system and there may be overlapping functions with cross-talk between the two systems. Finally we evaluate therapeutic targets to overcome oxidative stress associated cellular disorders.
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Affiliation(s)
- Narciso Couto
- Michael Barber Centre for Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Road, Manchester M1 7DN, UK; ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK.
| | - Jennifer Wood
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jill Barber
- Michael Barber Centre for Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Road, Manchester M1 7DN, UK; Manchester Pharmacy School, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
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223
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Sinzel M, Tan T, Wendling P, Kalbacher H, Özbalci C, Chelius X, Westermann B, Brügger B, Rapaport D, Dimmer KS. Mcp3 is a novel mitochondrial outer membrane protein that follows a unique IMP-dependent biogenesis pathway. EMBO Rep 2016; 17:965-81. [PMID: 27226123 DOI: 10.15252/embr.201541273] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 04/26/2016] [Indexed: 11/09/2022] Open
Abstract
Mitochondria are separated from the remainder of the eukaryotic cell by the mitochondrial outer membrane (MOM). The MOM plays an important role in different transport processes like lipid trafficking and protein import. In yeast, the ER-mitochondria encounter structure (ERMES) has a central, but poorly defined role in both activities. To understand the functions of the ERMES, we searched for suppressors of the deficiency of one of its components, Mdm10, and identified a novel mitochondrial protein that we named Mdm10 complementing protein 3 (Mcp3). Mcp3 partially rescues a variety of ERMES-related phenotypes. We further demonstrate that Mcp3 is an integral protein of the MOM that follows a unique import pathway. It is recognized initially by the import receptor Tom70 and then crosses the MOM via the translocase of the outer membrane. Mcp3 is next relayed to the TIM23 translocase at the inner membrane, gets processed by the inner membrane peptidase (IMP) and finally integrates into the MOM. Hence, Mcp3 follows a novel biogenesis route where a MOM protein is processed by a peptidase of the inner membrane.
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Affiliation(s)
- Monika Sinzel
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Tao Tan
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Philipp Wendling
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Cagakan Özbalci
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Xenia Chelius
- Cell Biology, University of Bayreuth, Bayreuth, Germany
| | | | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Kai Stefan Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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224
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Kardon JR, Yien YY, Huston NC, Branco DS, Hildick-Smith GJ, Rhee KY, Paw BH, Baker TA. Mitochondrial ClpX Activates a Key Enzyme for Heme Biosynthesis and Erythropoiesis. Cell 2016; 161:858-67. [PMID: 25957689 DOI: 10.1016/j.cell.2015.04.017] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 01/15/2015] [Accepted: 03/13/2015] [Indexed: 12/21/2022]
Abstract
The mitochondrion maintains and regulates its proteome with chaperones primarily inherited from its bacterial endosymbiont ancestor. Among these chaperones is the AAA+ unfoldase ClpX, an important regulator of prokaryotic physiology with poorly defined function in the eukaryotic mitochondrion. We observed phenotypic similarity in S. cerevisiae genetic interaction data between mitochondrial ClpX (mtClpX) and genes contributing to heme biosynthesis, an essential mitochondrial function. Metabolomic analysis revealed that 5-aminolevulinic acid (ALA), the first heme precursor, is 5-fold reduced in yeast lacking mtClpX activity and that total heme is reduced by half. mtClpX directly stimulates ALA synthase in vitro by catalyzing incorporation of its cofactor, pyridoxal phosphate. This activity is conserved in mammalian homologs; additionally, mtClpX depletion impairs vertebrate erythropoiesis, which requires massive upregulation of heme biosynthesis to supply hemoglobin. mtClpX, therefore, is a widely conserved stimulator of an essential biosynthetic pathway and uses a previously unrecognized mechanism for AAA+ unfoldases.
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Affiliation(s)
- Julia R Kardon
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yvette Y Yien
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas C Huston
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Diana S Branco
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gordon J Hildick-Smith
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Barry H Paw
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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225
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Venne AS, Solari FA, Faden F, Paretti T, Dissmeyer N, Zahedi RP. An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events in Arabidopsis thaliana. Proteomics 2016; 15:2458-69. [PMID: 26010716 DOI: 10.1002/pmic.201500014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/28/2015] [Accepted: 05/20/2015] [Indexed: 11/11/2022]
Abstract
We applied an extended charge-based fractional diagonal chromatography (ChaFRADIC) workflow to analyze the N-terminal proteome of Arabidopsis thaliana seedlings. Using iTRAQ protein labeling and a multi-enzyme digestion approach including trypsin, GluC, and subtilisin, a total of 200 μg per enzyme, and measuring only one third of each ChaFRADIC-enriched fraction by LC-MS, we quantified a total of 2791 unique N-terminal peptides corresponding to 2249 different unique N-termini from 1270 Arabidopsis proteins. Our data indicate the power, reproducibility, and sensitivity of the applied strategy that might be applicable to quantify proteolytic events from as little as 20 μg of protein per condition across up to eight different samples. Furthermore, our data clearly reflect the methionine excision dogma as well as the N-end rule degradation pathway (NERP) discriminating into a stabilizing or destabilizing function of N-terminal amino acid residues. We found bona fide NERP destabilizing residues underrepresented, and the list of neo N-termini from wild type samples may represent a helpful resource during the evaluation of NERP substrate candidates. All MS data have been deposited in the ProteomeXchange with identifier PXD001855 (http://proteomecentral.proteomexchange.org/dataset/PXD001855).
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Affiliation(s)
- A Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Frederik Faden
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Tomasso Paretti
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany.,Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, Italy
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
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226
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Sánchez-Caballero L, Guerrero-Castillo S, Nijtmans L. Unraveling the complexity of mitochondrial complex I assembly: A dynamic process. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:980-90. [PMID: 27040506 DOI: 10.1016/j.bbabio.2016.03.031] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
Mammalian complex I is composed of 44 different subunits and its assembly requires at least 13 specific assembly factors. Proper function of the mitochondrial respiratory chain enzyme is of crucial importance for cell survival due to its major participation in energy production and cell signaling. Complex I assembly depends on the coordination of several crucial processes that need to be tightly interconnected and orchestrated by a number of assembly factors. The understanding of complex I assembly evolved from simple sequential concept to the more sophisticated modular assembly model describing a convoluted process. According to this model, the different modules assemble independently and associate afterwards with each other to form the final enzyme. In this review, we aim to unravel the complexity of complex I assembly and provide the latest insights in this fundamental and fascinating process. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Laura Sánchez-Caballero
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Sergio Guerrero-Castillo
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo Nijtmans
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
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227
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Turakhiya U, von der Malsburg K, Gold VAM, Guiard B, Chacinska A, van der Laan M, Ieva R. Protein Import by the Mitochondrial Presequence Translocase in the Absence of a Membrane Potential. J Mol Biol 2016; 428:1041-1052. [PMID: 26827728 DOI: 10.1016/j.jmb.2016.01.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/15/2015] [Accepted: 01/01/2016] [Indexed: 11/17/2022]
Abstract
The highly organized mitochondrial inner membrane harbors enzymes that produce the bulk of cellular ATP via oxidative phosphorylation. The majority of inner membrane protein precursors are synthesized in the cytosol. Precursors with a cleavable presequence are imported by the presequence translocase (TIM23 complex), while other precursors containing internal targeting signals are imported by the carrier translocase (TIM22 complex). Both TIM23 and TIM22 are activated by the transmembrane electrochemical potential. Many small inner membrane proteins, however, do not resemble canonical TIM23 or TIM22 substrates and their mechanism of import is unknown. We report that subunit e of the F1Fo-ATP synthase, a small single-spanning inner membrane protein that is critical for inner membrane organization, is imported by TIM23 in a process that does not require activation by the membrane potential. Absence of positively charged residues at the matrix-facing amino-terminus of subunit e facilitates membrane potential-independent import. Instead, engineered positive charges establish a dependence of the import reaction on the electrochemical potential. Our results have two major implications. First, they reveal an unprecedented pathway of protein import into the mitochondrial inner membrane, which is mediated by TIM23. Second, they directly demonstrate the role of the membrane potential in driving the electrophoretic transport of positively charged protein segments across the inner membrane.
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Affiliation(s)
- Uma Turakhiya
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School for Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Karina von der Malsburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Vicki A M Gold
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Agnieszka Chacinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Martin van der Laan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Raffaele Ieva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, 31077 Toulouse, France.
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228
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Pedrajas JR, McDonagh B, Hernández-Torres F, Miranda-Vizuete A, González-Ojeda R, Martínez-Galisteo E, Padilla CA, Bárcena JA. Glutathione Is the Resolving Thiol for Thioredoxin Peroxidase Activity of 1-Cys Peroxiredoxin Without Being Consumed During the Catalytic Cycle. Antioxid Redox Signal 2016; 24:115-28. [PMID: 26159064 DOI: 10.1089/ars.2015.6366] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIMS A three-step catalytic cycle is common to all peroxiredoxins (Prxs), despite structural and kinetic differences. The second step in 1-Cys type Prxs is a matter of debate since they lack an additional cysteine to play the resolving role, as happens with the 2-Cys Prxs. The aim of this study was to elucidate the role of glutathione (GSH) in the thioredoxin-dependent peroxidase activity of Saccharomyces cerevisiae mitochondrial Prx1p, a 1-Cys type Prx. RESULTS The peroxidatic Cys91 residue of two Prx1p peptides can be linked by a disulfide, which can be reduced by thioredoxin and by GSH (Km=6.1 μM). GSH forms a mixed disulfide with the peroxidatic cysteine spontaneously in vitro and in vivo. Mitochondrial Trx3p deglutathionylates Prx1p without formation of GSSG so that GSH is not consumed in the process. The structural unit of native Prx1p is a dimer whose subunits are not covalently linked, but a hexameric assembly of three disulfide-bound dimers can also be formed. INNOVATION GSH is presented as a protective cofactor of Prx1p, which is not consumed during the peroxidase reaction, but provides a robust mechanism as the resolving cysteine and efficiently prevents Prx1p overoxidation. GSH exerts these roles at concentrations well below those commonly considered necessary for its antioxidant and redox buffering functions. CONCLUSION A 1-Cys peroxide scavenging mechanism operates in yeast mitochondria involving an autonomous glutathione molecule and the thioredoxin system, which could have universal validity. Prx1p is fairly well protected from overoxidation, questioning its role in a floodgate mechanism for H2O2 signaling.
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Affiliation(s)
- José Rafael Pedrajas
- 1 Biochemistry and Cellular Signaling Group, Department of Experimental Biology, University of Jaén , Jaén, Spain
| | - Brian McDonagh
- 2 MRC-Arthritis Research UK Centre for Integrated Research into Musculoskeletal Aging (CIMA), Skeletal Muscle Pathophysiology Group, Institute of Ageing and Chronic Disease, University of Liverpool , Liverpool, United Kingdom
| | | | - Antonio Miranda-Vizuete
- 4 Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla , Sevilla, Spain
| | - Raúl González-Ojeda
- 5 Department of Biochemistry and Molecular Biology, University of Córdoba , Córdoba, Spain .,6 Córdoba Maimónides Institute for Biomedical Research , IMIBIC, Córdoba, Spain
| | - Emilia Martínez-Galisteo
- 5 Department of Biochemistry and Molecular Biology, University of Córdoba , Córdoba, Spain .,6 Córdoba Maimónides Institute for Biomedical Research , IMIBIC, Córdoba, Spain
| | - C Alicia Padilla
- 5 Department of Biochemistry and Molecular Biology, University of Córdoba , Córdoba, Spain .,6 Córdoba Maimónides Institute for Biomedical Research , IMIBIC, Córdoba, Spain
| | - José Antonio Bárcena
- 5 Department of Biochemistry and Molecular Biology, University of Córdoba , Córdoba, Spain .,6 Córdoba Maimónides Institute for Biomedical Research , IMIBIC, Córdoba, Spain
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229
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Walton A, Tsiatsiani L, Jacques S, Stes E, Messens J, Van Breusegem F, Goormachtig S, Gevaert K. Diagonal chromatography to study plant protein modifications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:945-51. [PMID: 26772901 DOI: 10.1016/j.bbapap.2016.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/01/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
An interesting asset of diagonal chromatography, which we have introduced for contemporary proteome research, is its high versatility concerning proteomic applications. Indeed, the peptide modification or sorting step that is required between consecutive peptide separations can easily be altered and thereby allows for the enrichment of specific, though different types of peptides. Here, we focus on the application of diagonal chromatography for the study of modifications of plant proteins. In particular, we show how diagonal chromatography allows for studying proteins processed by proteases, protein ubiquitination, and the oxidation of protein-bound methionines. We discuss the actual sorting steps needed for each of these applications and the obtained results. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Alan Walton
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liana Tsiatsiani
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Silke Jacques
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Elisabeth Stes
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.
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230
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Nouws J, Goswami AV, Bestwick M, McCann BJ, Surovtseva YV, Shadel GS. Mitochondrial Ribosomal Protein L12 Is Required for POLRMT Stability and Exists as Two Forms Generated by Alternative Proteolysis during Import. J Biol Chem 2015; 291:989-97. [PMID: 26586915 DOI: 10.1074/jbc.m115.689299] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/21/2023] Open
Abstract
To translate the 13 mtDNA-encoded mRNAs involved in oxidative phosphorylation (OXPHOS), mammalian mitochondria contain a dedicated set of ribosomes comprising rRNAs encoded by the mitochondrial genome and mitochondrial ribosomal proteins (MRPs) that are encoded by nuclear genes and imported into the matrix. In addition to their role in the ribosome, several MRPs have auxiliary functions or have been implicated in other cellular processes like cell cycle regulation and apoptosis. For example, we have shown that human MRPL12 binds and activates mitochondrial RNA polymerase (POLRMT), and hence has distinct functions in the ribosome and mtDNA transcription. Here we provide concrete evidence that there are two mature forms of mammalian MRPL12 that are generated by a two-step cleavage during import, involving efficient cleavage by mitochondrial processing protease and a second inefficient or regulated cleavage by mitochondrial intermediate protease. We also show that knock-down of MRPL12 by RNAi results in instability of POLRMT, but not other primary mitochondrial transcription components, and a corresponding decrease in mitochondrial transcription rates. Knock-down of MRPL10, the binding partner of MRPL12 in the ribosome, results in selective degradation of the mature long form of MRPL12, but has no effect on POLRMT. We propose that the two forms of MRPL12 are involved in homeostatic regulation of mitochondrial transcription and ribosome biogenesis that likely contribute to cell cycle, growth regulation, and longevity pathways to which MRPL12 has been linked.
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Affiliation(s)
| | | | - Megan Bestwick
- From the Departments of Pathology and the Department of Chemistry, Linfield College, McMinnville, Oregon 97128, and
| | - Beverly Jo McCann
- From the Departments of Pathology and the Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | | | - Gerald S Shadel
- From the Departments of Pathology and Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8023,
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231
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Burkhart JM, Taskin AA, Zahedi RP, Vögtle FN. Quantitative Profiling for Substrates of the Mitochondrial Presequence Processing Protease Reveals a Set of Nonsubstrate Proteins Increased upon Proteotoxic Stress. J Proteome Res 2015; 14:4550-63. [PMID: 26446170 DOI: 10.1021/acs.jproteome.5b00327] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The majority of mitochondrial preproteins are targeted via N-terminal presequences that are cleaved upon import into the organelle. The essential mitochondrial processing protease (MPP) is assumed to cleave the majority of incoming precursors; however, only a small fraction of mitochondrial precursors have been experimentally analyzed limiting the information on MPP recognition and substrate specificity. Here we present the first systematic approach for identification of authentic MPP substrate proteins using a temperature-sensitive mutant of the MPP subunit Mas1. Inactivation of MPP at nonpermissive temperature leads to accumulation of immature precursors in mitochondria, which were measured by quantitative N-terminal ChaFRADIC. This led to the identification of 66 novel MPP substrates. Deduction of the cleaved presequences determines arginine in position -2 of the cleavage site as a main factor for MPP recognition. Interestingly, a set of nonprocessed proteins was also increased in mas1 mutant mitochondria. Additionally, mas1 mitochondria respond to temperature elevation with an increase in membrane potential and oxygen consumption. These changes might indicate that mas1 cells exert a response to balance the proteotoxic stress induced by MPP dysfunction.
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Affiliation(s)
- Julia M Burkhart
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Asli A Taskin
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg , Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Faculty of Biology, Universität Freiburg , Schänzlestrasse 1, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg , Albertstrasse 19A, 79104 Freiburg, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - F-Nora Vögtle
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg , Stefan-Meier-Str. 17, 79104 Freiburg, Germany
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232
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N-Terminal Presequence-Independent Import of Phosphofructokinase into Hydrogenosomes of Trichomonas vaginalis. EUKARYOTIC CELL 2015; 14:1264-75. [PMID: 26475173 DOI: 10.1128/ec.00104-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 10/08/2015] [Indexed: 12/27/2022]
Abstract
Mitochondrial evolution entailed the origin of protein import machinery that allows nuclear-encoded proteins to be targeted to the organelle, as well as the origin of cleavable N-terminal targeting sequences (NTS) that allow efficient sorting and import of matrix proteins. In hydrogenosomes and mitosomes, reduced forms of mitochondria with reduced proteomes, NTS-independent targeting of matrix proteins is known. Here, we studied the cellular localization of two glycolytic enzymes in the anaerobic pathogen Trichomonas vaginalis: PPi-dependent phosphofructokinase (TvPPi-PFK), which is the main glycolytic PFK activity of the protist, and ATP-dependent PFK (TvATP-PFK), the function of which is less clear. TvPPi-PFK was detected predominantly in the cytosol, as expected, while all four TvATP-PFK paralogues were imported into T. vaginalis hydrogenosomes, although none of them possesses an NTS. The heterologous expression of TvATP-PFK in Saccharomyces cerevisiae revealed an intrinsic capability of the protein to be recognized and imported into yeast mitochondria, whereas yeast ATP-PFK resides in the cytosol. TvATP-PFK consists of only a catalytic domain, similarly to "short" bacterial enzymes, while ScATP-PFK includes an N-terminal extension, a catalytic domain, and a C-terminal regulatory domain. Expression of the catalytic domain of ScATP-PFK and short Escherichia coli ATP-PFK in T. vaginalis resulted in their partial delivery to hydrogenosomes. These results indicate that TvATP-PFK and the homologous ATP-PFKs possess internal structural targeting information that is recognized by the hydrogenosomal import machinery. From an evolutionary perspective, the predisposition of ancient ATP-PFK to be recognized and imported into hydrogenosomes might be a relict from the early phases of organelle evolution.
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233
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Mani J, Meisinger C, Schneider A. Peeping at TOMs-Diverse Entry Gates to Mitochondria Provide Insights into the Evolution of Eukaryotes. Mol Biol Evol 2015; 33:337-51. [PMID: 26474847 DOI: 10.1093/molbev/msv219] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are essential for eukaryotic life and more than 95% of their proteins are imported as precursors from the cytosol. The targeting signals for this posttranslational import are conserved in all eukaryotes. However, this conservation does not hold true for the protein translocase of the mitochondrial outer membrane that serves as entry gate for essentially all precursor proteins. Only two of its subunits, Tom40 and Tom22, are conserved and thus likely were present in the last eukaryotic common ancestor. Tom7 is found in representatives of all supergroups except the Excavates. This suggests that it was added to the core of the translocase after the Excavates segregated from all other eukaryotes. A comparative analysis of the biochemically and functionally characterized outer membrane translocases of yeast, plants, and trypanosomes, which represent three eukaryotic supergroups, shows that the receptors that recognize the conserved import signals differ strongly between the different systems. They present a remarkable example of convergent evolution at the molecular level. The structural diversity of the functionally conserved import receptors therefore provides insight into the early evolutionary history of mitochondria.
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Affiliation(s)
- Jan Mani
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Chris Meisinger
- Institut für Biochemie und Molekularbiologie, ZBMZ and BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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234
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Lee JH, Jiang Y, Kwon YT, Lee MJ. Pharmacological Modulation of the N-End Rule Pathway and Its Therapeutic Implications. Trends Pharmacol Sci 2015; 36:782-797. [PMID: 26434644 DOI: 10.1016/j.tips.2015.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/13/2015] [Accepted: 07/16/2015] [Indexed: 11/26/2022]
Abstract
The N-end rule pathway is a proteolytic system in which single N-terminal amino acids of short-lived substrates determine their metabolic half-lives. Substrates of this pathway have been implicated in the pathogenesis of many diseases, including malignancies, neurodegeneration, and cardiovascular disorders. This review provides a comprehensive overview of current knowledge about the mechanism and functions of the N-end rule pathway. Pharmacological strategies for the modulation of target substrate degradation are also reviewed, with emphasis on their in vivo implications. Given the rapid advances in structural and biochemical understanding of the recognition components (N-recognins) of the N-end rule pathway, small-molecule inhibitors and activating ligands of N-recognins emerge as therapeutic agents with novel mechanisms of action.
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Affiliation(s)
- Jung Hoon Lee
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yanxialei Jiang
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Protein Metabolism Medical Research Center, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Neuroscience Research Institute, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
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235
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Garg S, Stölting J, Zimorski V, Rada P, Tachezy J, Martin WF, Gould SB. Conservation of Transit Peptide-Independent Protein Import into the Mitochondrial and Hydrogenosomal Matrix. Genome Biol Evol 2015; 7:2716-26. [PMID: 26338186 PMCID: PMC4607531 DOI: 10.1093/gbe/evv175] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The origin of protein import was a key step in the endosymbiotic acquisition of mitochondria. Though the main translocon of the mitochondrial outer membrane, TOM40, is ubiquitous among organelles of mitochondrial ancestry, the transit peptides, or N-terminal targeting sequences (NTSs), recognised by the TOM complex, are not. To better understand the nature of evolutionary conservation in mitochondrial protein import, we investigated the targeting behavior of Trichomonas vaginalis hydrogenosomal proteins in Saccharomyces cerevisiae and vice versa. Hydrogenosomes import yeast mitochondrial proteins even in the absence of their native NTSs, but do not import yeast cytosolic proteins. Conversely, yeast mitochondria import hydrogenosomal proteins with and without their short NTSs. Conservation of an NTS-independent mitochondrial import route from excavates to opisthokonts indicates its presence in the eukaryote common ancestor. Mitochondrial protein import is known to entail electrophoresis of positively charged NTSs across the electrochemical gradient of the inner mitochondrial membrane. Our present findings indicate that mitochondrial transit peptides, which readily arise from random sequences, were initially selected as a signal for charge-dependent protein targeting specifically to the mitochondrial matrix. Evolutionary loss of the electron transport chain in hydrogenosomes and mitosomes lifted the selective constraints that maintain positive charge in NTSs, allowing first the NTS charge, and subsequently the NTS itself, to be lost. This resulted in NTS-independent matrix targeting, which is conserved across the evolutionary divide separating trichomonads and yeast, and which we propose is the ancestral state of mitochondrial protein import.
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Affiliation(s)
- Sriram Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Stölting
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Verena Zimorski
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Petr Rada
- Department of Parasitology, Charles University in Prague, Faculty of Science, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Charles University in Prague, Faculty of Science, Czech Republic
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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236
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Bauer NC, Doetsch PW, Corbett AH. Mechanisms Regulating Protein Localization. Traffic 2015; 16:1039-61. [PMID: 26172624 DOI: 10.1111/tra.12310] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 07/08/2015] [Accepted: 07/08/2015] [Indexed: 12/23/2022]
Abstract
Cellular functions are dictated by protein content and activity. There are numerous strategies to regulate proteins varying from modulating gene expression to post-translational modifications. One commonly used mode of regulation in eukaryotes is targeted localization. By specifically redirecting the localization of a pool of existing protein, cells can achieve rapid changes in local protein function. Eukaryotic cells have evolved elegant targeting pathways to direct proteins to the appropriate cellular location or locations. Here, we provide a general overview of these localization pathways, with a focus on nuclear and mitochondrial transport, and present a survey of the evolutionarily conserved regulatory strategies identified thus far. We end with a description of several specific examples of proteins that exploit localization as an important mode of regulation.
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Affiliation(s)
- Nicholas C Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Current address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
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237
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Li J, Sha B. The structure of Tim50(164-361) suggests the mechanism by which Tim50 receives mitochondrial presequences. Acta Crystallogr F Struct Biol Commun 2015; 71:1146-51. [PMID: 26323300 PMCID: PMC4555921 DOI: 10.1107/s2053230x15013102] [Citation(s) in RCA: 9] [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: 10/01/2014] [Accepted: 07/07/2015] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial preproteins are transported through the translocase of the outer membrane (TOM) complex. Tim50 and Tim23 then transfer preproteins with N-terminal targeting presequences through the intermembrane space (IMS) across the inner membrane. The crystal structure of the IMS domain of Tim50 [Tim50(164-361)] has previously been determined to 1.83 Å resolution. Here, the crystal structure of Tim50(164-361) at 2.67 Å resolution that was crystallized using a different condition is reported. Compared with the previously determined Tim50(164-361) structure, significant conformational changes occur within the protruding β-hairpin of Tim50 and the nearby helix A2. These findings indicate that the IMS domain of Tim50 exhibits significant structural plasticity within the putative presequence-binding groove, which may play important roles in the function of Tim50 as a receptor protein in the TIM complex that interacts with the presequence and multiple other proteins. More interestingly, the crystal packing indicates that helix A1 from the neighboring monomer docks into the putative presequence-binding groove of Tim50(164-361), which may mimic the scenario of Tim50 and the presequence complex. Tim50 may recognize and bind the presequence helix by utilizing the inner side of the protruding β-hairpin through hydrophobic interactions. Therefore, the protruding β-hairpin of Tim50 may play critical roles in receiving the presequence and recruiting Tim23 for subsequent protein translocations.
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Affiliation(s)
- Jingzhi Li
- Department of Cell, Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Bingdong Sha
- Department of Cell, Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, Birmingham, AL 35294, USA
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238
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Marino G, Eckhard U, Overall CM. Protein Termini and Their Modifications Revealed by Positional Proteomics. ACS Chem Biol 2015; 10:1754-64. [PMID: 26042555 DOI: 10.1021/acschembio.5b00189] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A myriad of co- and post-translational modifications occur at protein N- and C-termini, resulting in an extra layer of proteome complexity and an additional source of protein regulation. Here, we review N- and C-terminal modifications and the contemporary positional proteomics techniques used to isolate protein terminal peptides from complex protein mixtures and characterize their diversity and occurrence in biological systems. Furthermore, these degradomics strategies--often referred to as N- and C-terminomics--represent dedicated high-throughput techniques to study proteolysis in dynamic living systems. Over the past decade, terminomics studies have provided indispensable information on the functional states of individual proteins, cell types, tissues, and biological processes and delivered fundamental new data for the Human Proteome Project, including high confidence identifications of many so-called "missing proteins", which had not been identified by traditional proteomics analyses.
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Affiliation(s)
- Giada Marino
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ulrich Eckhard
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M. Overall
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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239
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Mayr JA, Haack TB, Freisinger P, Karall D, Makowski C, Koch J, Feichtinger RG, Zimmermann FA, Rolinski B, Ahting U, Meitinger T, Prokisch H, Sperl W. Spectrum of combined respiratory chain defects. J Inherit Metab Dis 2015; 38:629-40. [PMID: 25778941 PMCID: PMC4493854 DOI: 10.1007/s10545-015-9831-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 01/22/2023]
Abstract
Inherited disorders of mitochondrial energy metabolism form a large and heterogeneous group of metabolic diseases. More than 250 gene defects have been reported to date and this number continues to grow. Mitochondrial diseases can be grouped into (1) disorders of oxidative phosphorylation (OXPHOS) subunits and their assembly factors, (2) defects of mitochondrial DNA, RNA and protein synthesis, (3) defects in the substrate-generating upstream reactions of OXPHOS, (4) defects in relevant cofactors and (5) defects in mitochondrial homeostasis. Deficiency of more than one respiratory chain enzyme is a common finding. Combined defects are found in 49 % of the known disease-causing genes of mitochondrial energy metabolism and in 57 % of patients with OXPHOS defects identified in our diagnostic centre. Combined defects of complexes I, III, IV and V are typically due to deficiency of mitochondrial DNA replication, RNA metabolism or translation. Defects in cofactors can result in combined defects of various combinations, and defects of mitochondrial homeostasis can result in a generalised decrease of all OXPHOS enzymes. Noteworthy, identification of combined defects can be complicated by different degrees of severity of each affected enzyme. Furthermore, even defects of single respiratory chain enzymes can result in combined defects due to aberrant formation of respiratory chain supercomplexes. Combined OXPHOS defects have a great variety of clinical manifestations in terms of onset, course severity and tissue involvement. They can present as classical encephalomyopathy but also with hepatopathy, nephropathy, haematologic findings and Perrault syndrome in a subset of disorders.
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Affiliation(s)
- Johannes A Mayr
- Department of Paediatrics, Paracelsus Medical University, SALK Salzburg, Salzburg, 5020, Austria,
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240
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Vaca Jacome AS, Rabilloud T, Schaeffer-Reiss C, Rompais M, Ayoub D, Lane L, Bairoch A, Van Dorsselaer A, Carapito C. N-terminome analysis of the human mitochondrial proteome. Proteomics 2015; 15:2519-24. [DOI: 10.1002/pmic.201400617] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/10/2015] [Accepted: 04/30/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Alvaro Sebastian Vaca Jacome
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Thierry Rabilloud
- Laboratoire de Chimie et Biologie des Métaux; UMR CNRS-CEA-UGA 5249; iRTSV/LCBM, CEA Grenoble Grenoble France
| | - Christine Schaeffer-Reiss
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Magali Rompais
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Daniel Ayoub
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Lydie Lane
- CALIPHO Group; SIB-Swiss Institute of Bioinformatics; Geneva Switzerland
- Department of Human Protein Sciences; Faculty of Medicine; Geneva Switzerland
| | - Amos Bairoch
- CALIPHO Group; SIB-Swiss Institute of Bioinformatics; Geneva Switzerland
- Department of Human Protein Sciences; Faculty of Medicine; Geneva Switzerland
| | - Alain Van Dorsselaer
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
| | - Christine Carapito
- BioOrganic Mass Spectrometry Laboratory (LSMBO); Université de Strasbourg; IPHC; Strasbourg France
- IPHC, CNRS; UMR7178; Strasbourg France
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241
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Rana A, Kumar D, Rub A, Akhter Y. Proteome-scale identification and characterization of mitochondria targeting proteins of Mycobacterium avium subspecies paratuberculosis: Potential virulence factors modulating host mitochondrial function. Mitochondrion 2015; 23:42-54. [PMID: 26048556 DOI: 10.1016/j.mito.2015.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/21/2015] [Accepted: 05/04/2015] [Indexed: 02/03/2023]
Abstract
Mycobacterium avium subsp. paratuberculosis is the etiological agent of Johne's Disease among ruminants. During the course of infection, it expresses a number of proteins for its successful persistence inside the host that cause variety of physiological abnormalities in the host. Mitochondrion is one of the attractive targets for pathogenic bacteria. Employing a proteome-wide sequence and structural signature based approach we have identified 46 M. avium subsp. paratuberculosis proteins as potential targets for the host mitochondrial targeting. These may act as virulence factors modulating mitochondrial physiology for bacterial survival and immune evasion inside the host cells.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, 176206 Himachal Pradesh, India
| | - Devender Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, 176206 Himachal Pradesh, India
| | - Abdur Rub
- Infection and Immunity Lab, Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Yusuf Akhter
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, 176206 Himachal Pradesh, India.
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242
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Pagel O, Loroch S, Sickmann A, Zahedi RP. Current strategies and findings in clinically relevant post-translational modification-specific proteomics. Expert Rev Proteomics 2015; 12:235-53. [PMID: 25955281 PMCID: PMC4487610 DOI: 10.1586/14789450.2015.1042867] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical samples, often limited in sample amount. Thus, quantitative proteomics holds a great potential to discover, validate and accurately quantify biomarkers in body fluids and primary tissues. A major effort will be to improve the complete integration of robust but sensitive proteomics technology to clinical environments. Here, we discuss PTMs that are relevant for clinical research, with a focus on phosphorylation, glycosylation and proteolytic cleavage; furthermore, we give an overview on the current developments and novel findings in mass spectrometry-based PTM research.
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Affiliation(s)
- Oliver Pagel
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | | | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
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243
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Jobling RK, Assoum M, Gakh O, Blaser S, Raiman JA, Mignot C, Roze E, Dürr A, Brice A, Lévy N, Prasad C, Paton T, Paterson AD, Roslin NM, Marshall CR, Desvignes JP, Roëckel-Trevisiol N, Scherer SW, Rouleau GA, Mégarbané A, Isaya G, Delague V, Yoon G. PMPCA mutations cause abnormal mitochondrial protein processing in patients with non-progressive cerebellar ataxia. Brain 2015; 138:1505-17. [PMID: 25808372 PMCID: PMC4542620 DOI: 10.1093/brain/awv057] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/09/2014] [Accepted: 01/06/2015] [Indexed: 11/13/2022] Open
Abstract
Non-progressive cerebellar ataxias are a rare group of disorders that comprise approximately 10% of static infantile encephalopathies. We report the identification of mutations in PMPCA in 17 patients from four families affected with cerebellar ataxia, including the large Lebanese family previously described with autosomal recessive cerebellar ataxia and short stature of Norman type and localized to chromosome 9q34 (OMIM #213200). All patients present with non-progressive cerebellar ataxia, and the majority have intellectual disability of variable severity. PMPCA encodes α-MPP, the alpha subunit of mitochondrial processing peptidase, the primary enzyme responsible for the maturation of the vast majority of nuclear-encoded mitochondrial proteins, which is necessary for life at the cellular level. Analysis of lymphoblastoid cells and fibroblasts from patients homozygous for the PMPCA p.Ala377Thr mutation and carriers demonstrate that the mutation impacts both the level of the alpha subunit encoded by PMPCA and the function of mitochondrial processing peptidase. In particular, this mutation impacts the maturation process of frataxin, the protein which is depleted in Friedreich ataxia. This study represents the first time that defects in PMPCA and mitochondrial processing peptidase have been described in association with a disease phenotype in humans.
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Affiliation(s)
- Rebekah K Jobling
- 1 Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Mirna Assoum
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France
| | - Oleksandr Gakh
- 4 Department of Paediatric and Adolescent Medicine and Mayo Clinic Children's Centre, Mayo Clinic, Rochester, MN, USA
| | - Susan Blaser
- 5 Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Julian A Raiman
- 1 Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Cyril Mignot
- 6 Département de Génétique, Unité de Génétique Clinique, APHP, Groupe Hospitalier Pitié-Salpêtrière; Centre de Référence Maladies Rares 'Déficiences Intellectuelles de Causes Rares'; Groupe de Recherche Clinique UPMC Univ Paris 06; Paris, France
| | - Emmanuel Roze
- 7 Sorbonne Université, UPMC Univ Paris 06, UM 75, ICM, F-75013 Paris, France 8 Inserm, U 1127, ICM, F-75013 Paris, France 9 Cnrs, UMR 7225, ICM, F-75013 Paris, France 10 ICM, Paris, F-75013 Paris, France 11 AP-HP, Hôpital de la Salpêtrière, Département de Neurologie, F-75013, Paris, France
| | - Alexandra Dürr
- 7 Sorbonne Université, UPMC Univ Paris 06, UM 75, ICM, F-75013 Paris, France 8 Inserm, U 1127, ICM, F-75013 Paris, France 9 Cnrs, UMR 7225, ICM, F-75013 Paris, France 10 ICM, Paris, F-75013 Paris, France 12 AP-HP, Hôpital de la Salpêtrière, Département de Génétique et Cytogénétique, F-75013, Paris, France
| | - Alexis Brice
- 7 Sorbonne Université, UPMC Univ Paris 06, UM 75, ICM, F-75013 Paris, France 8 Inserm, U 1127, ICM, F-75013 Paris, France 9 Cnrs, UMR 7225, ICM, F-75013 Paris, France 10 ICM, Paris, F-75013 Paris, France 12 AP-HP, Hôpital de la Salpêtrière, Département de Génétique et Cytogénétique, F-75013, Paris, France
| | - Nicolas Lévy
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France 13 Département de Génétique Médicale, Hôpital d'Enfants de la Timone, AP-HM, Marseille, France
| | - Chitra Prasad
- 14 Medical Genetics Program, Department of Pediatrics, London Health Sciences Centre, London, Ontario, Canada
| | - Tara Paton
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Andrew D Paterson
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nicole M Roslin
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jean-Pierre Desvignes
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France
| | - Nathalie Roëckel-Trevisiol
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France
| | - Stephen W Scherer
- 15 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada 16 McLaughlin Centre and Department of Molecular Genetics, University of Toronto
| | - Guy A Rouleau
- 17 Montreal Neurological Institute and Hospital and Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - André Mégarbané
- 18 Unité de Génétique Médicale and Laboratoire Associé Inserm UMR S_910, Faculté de Médecine, Université Saint Joseph, Beirut, Lebanon 19 Institut Jérôme Lejeune, Paris, France
| | - Grazia Isaya
- 4 Department of Paediatric and Adolescent Medicine and Mayo Clinic Children's Centre, Mayo Clinic, Rochester, MN, USA
| | - Valérie Delague
- 2 Inserm, UMR_S 910, 13385, Marseille, France 3 Aix Marseille Université, GMGF, 13385, Marseille, France
| | - Grace Yoon
- 1 Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada 20 Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
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244
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Marcondes M, Alves F, Assis D, Hirata I, Juliano L, Oliveira V, Juliano M. Substrate specificity of mitochondrial intermediate peptidase analysed by a support-bound peptide library. FEBS Open Bio 2015; 5:429-36. [PMID: 26082885 PMCID: PMC4459094 DOI: 10.1016/j.fob.2015.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/20/2015] [Accepted: 05/07/2015] [Indexed: 11/26/2022] Open
Abstract
A synthetic support-bound FRET peptide library was constructed. This was used to investigate the substrate specificity of recombinant human mitochondrial intermediate peptidase (hMIP). Polar uncharged residues at P1 and P1′ are preferred by this enzyme. hMIP can hydrolyse peptides shorter than 8 residues. The importance of F/L/I at P8 and T/S/G at P5, in natural substrates of hMIP was not seen with this peptide library.
The substrate specificity of recombinant human mitochondrial intermediate peptidase (hMIP) using a synthetic support-bound FRET peptide library is presented. The collected fluorescent beads, which contained the hydrolysed peptides generated by hMIP, were sequenced by Edman degradation. The results showed that this peptidase presents a remarkable preference for polar uncharged residues at P1 and P1′ substrate positions: Ser = Gln > Thr at P1 and Ser > Thr at P1′. Non-polar residues were frequent at the substrate P3, P2, P2′ and P3′ positions. Analysis of the predicted MIP processing sites in imported mitochondrial matrix proteins shows these cleavages indeed occur between polar uncharged residues. Previous analysis of these processing sites indicated the importance of positions far from the MIP cleavage site, namely the presence of a hydrophobic residue (Phe or Leu) at P8 and a polar uncharged residue (Ser or Thr) at P5. To evaluate this, additional kinetic analyses were carried out, using fluorogenic substrates synthesized based on the processing sites attributed to MIP. The results described here underscore the importance of the P1 and P1′ substrate positions for the hydrolytic activity of hMIP. The information presented in this work will help in the design of new substrate-based inhibitors for this peptidase.
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Key Words
- Abz, ortho-aminobenzoic acid
- DCM, dichloromethane
- DIPEA, N,N-diisopropylethylamine
- DMF, dimethylformamide
- EDDnp, N-(2,4-dinitrophenyl)-ethylenediamine
- FRET libraries
- FRET, fluorescence resonance energy transfer
- HOBt, hydroxybenzotriazole
- Mitochondria
- NMM, N-methylmorpholine
- Octapeptidyl amino peptidase 1
- Peptidase
- Substrate specificity
- TBTU, O-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium tetrafluoroborate
- hMIP, human mitochondrial intermediate peptidase
- oct1
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Affiliation(s)
| | | | | | | | | | - V. Oliveira
- Corresponding authors at: Universidade Federal de São Paulo (UNIFESP), Department of Biophysics, Rua Pedro de Toledo, 669, Enzymology Laboratory – 7th Floor, São Paulo, Brazil. Tel./fax: +55 11 55764450x1966 (V. Oliveira). Universidade Federal de São Paulo (UNIFESP), Department of Biophysics, Rua 3 de maio, 100, Ed INFAR 2nd Floor, São Paulo, Brazil. Tel./fax: +55 11 55764450x1960 (M.A. Juliano).
| | - M.A. Juliano
- Corresponding authors at: Universidade Federal de São Paulo (UNIFESP), Department of Biophysics, Rua Pedro de Toledo, 669, Enzymology Laboratory – 7th Floor, São Paulo, Brazil. Tel./fax: +55 11 55764450x1966 (V. Oliveira). Universidade Federal de São Paulo (UNIFESP), Department of Biophysics, Rua 3 de maio, 100, Ed INFAR 2nd Floor, São Paulo, Brazil. Tel./fax: +55 11 55764450x1960 (M.A. Juliano).
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Abstract
Recent advances in mitochondrial biology have revealed the high diversity and complexity of proteolytic enzymes that regulate mitochondrial function. We have classified mitochondrial proteases, or mitoproteases, on the basis of their function and location, and defined the human mitochondrial degradome as the complete set of mitoproteases that are encoded by the human genome. In addition to their nonspecific degradative functions, mitoproteases perform highly regulated proteolytic reactions that are important in mitochondrial function, integrity and homeostasis. These include protein synthesis, quality control, mitochondrial biogenesis and dynamics, mitophagy and apoptosis. Impaired or dysregulated function of mitoproteases is associated with ageing and with many pathological conditions such as neurodegenerative disorders, metabolic syndromes and cancer. A better understanding of the mitochondrial proteolytic landscape and its modulation may contribute to improving human lifespan and 'healthspan'.
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246
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Schulz C, Schendzielorz A, Rehling P. Unlocking the presequence import pathway. Trends Cell Biol 2015; 25:265-75. [DOI: 10.1016/j.tcb.2014.12.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
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247
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Carrie C, Venne AS, Zahedi RP, Soll J. Identification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2691-708. [PMID: 25732537 PMCID: PMC4986872 DOI: 10.1093/jxb/erv064] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Most mitochondrial proteins contain an N-terminal targeting signal that is removed by specific proteases following import. In plant mitochondria, only mitochondrial processing peptidase (MPP) has been characterized to date. Therefore, we sought to determine the substrates and cleavage sites of the Arabidopsis thaliana homologues to the yeast Icp55 and Oct1 proteins, using the newly developed ChaFRADIC method for N-terminal protein sequencing. We identified 88 and seven putative substrates for Arabidopsis ICP55 and OCT1, respectively. It was determined that the Arabidopsis ICP55 contains an almost identical cleavage site to that of Icp55 from yeast. However, it can also remove a far greater range of amino acids. The OCT1 substrates from Arabidopsis displayed no consensus cleavage motif, and do not contain the classical -10R motif identified in other eukaryotes. Arabidopsis OCT1 can also cleave presequences independently, without the prior cleavage of MPP. It was concluded that while both OCT1 and ICP55 were probably acquired early on in the evolution of mitochondria, their substrate profiles and cleavage sites have either remained very similar or diverged completely.
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Affiliation(s)
- Chris Carrie
- Department of Biology I, Botany, Ludwig-Maximilians Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany
| | - A Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 11, D-44139 Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 11, D-44139 Dortmund, Germany
| | - Jürgen Soll
- Department of Biology I, Botany, Ludwig-Maximilians Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany Munich Centre for Integrated Protein Science, CiPSM, Ludwig-Maximilians Universität München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany
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248
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Bode M, Woellhaf MW, Bohnert M, van der Laan M, Sommer F, Jung M, Zimmermann R, Schroda M, Herrmann JM. Redox-regulated dynamic interplay between Cox19 and the copper-binding protein Cox11 in the intermembrane space of mitochondria facilitates biogenesis of cytochrome c oxidase. Mol Biol Cell 2015; 26:2385-401. [PMID: 25926683 PMCID: PMC4571295 DOI: 10.1091/mbc.e14-11-1526] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 04/24/2015] [Indexed: 01/02/2023] Open
Abstract
Members of the twin Cx9C protein family constitute the largest group of proteins in the intermembrane space (IMS) of mitochondria. Despite their conserved nature and their essential role in the biogenesis of the respiratory chain, the molecular function of twin Cx9C proteins is largely unknown. We performed a SILAC-based quantitative proteomic analysis to identify interaction partners of the conserved twin Cx9C protein Cox19. We found that Cox19 interacts in a dynamic manner with Cox11, a copper transfer protein that facilitates metalation of the Cu(B) center of subunit 1 of cytochrome c oxidase. The interaction with Cox11 is critical for the stable accumulation of Cox19 in mitochondria. Cox19 consists of a helical hairpin structure that forms a hydrophobic surface characterized by two highly conserved tyrosine-leucine dipeptides. These residues are essential for Cox19 function and its specific binding to a cysteine-containing sequence in Cox11. Our observations suggest that an oxidative modification of this cysteine residue of Cox11 stimulates Cox19 binding, pointing to a redox-regulated interplay of Cox19 and Cox11 that is critical for copper transfer in the IMS and thus for biogenesis of cytochrome c oxidase.
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Affiliation(s)
- Manuela Bode
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Michael W Woellhaf
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Maria Bohnert
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany
| | - Martin van der Laan
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104 Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, 66424 Homburg, Germany
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66424 Homburg, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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249
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A Heterologous Reporter Defines the Role of the Tetanus Toxin Interchain Disulfide in Light-Chain Translocation. Infect Immun 2015; 83:2714-24. [PMID: 25895970 DOI: 10.1128/iai.00477-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 11/20/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) and tetanus toxin (TeNT) are the most potent toxins for humans and elicit unique pathologies due to their ability to traffic within motor neurons. BoNTs act locally within motor neurons to elicit flaccid paralysis, while retrograde TeNT traffics to inhibitory neurons within the central nervous system (CNS) to elicit spastic paralysis. BoNT and TeNT are dichain proteins linked by an interchain disulfide bond comprised of an N-terminal catalytic light chain (LC) and a C-terminal heavy chain (HC) that encodes an LC translocation domain (HCT) and a receptor-binding domain (HCR). LC translocation is the least understood property of toxin action, but it involves low pH, proteolysis, and an intact interchain disulfide bridge. Recently, Pirazzini et al. (FEBS Lett 587:150-155, 2013, http://dx.doi.org/10.1016/j.febslet.2012.11.007) observed that inhibitors of thioredoxin reductase (TrxR) blocked TeNT and BoNT action in cerebellar granular neurons. In the current study, an atoxic TeNT LC translocation reporter was engineered by fusing β-lactamase to the N terminus of TeNT [βlac-TeNT(RY)] to investigate LC translocation in primary cortical neurons and Neuro-2a cells. βlac-TeNT(RY) retained the interchain disulfide bond, showed ganglioside-dependent binding to neurons, required acidification to promote βlac translocation, and was sensitive to auranofin, an inhibitor of thioredoxin reductase. Mutation of βlac-TeNT(RY) at C439S and C467S eliminated the interchain disulfide bond and inhibited βlac translocation. These data support the requirement of an intact interchain disulfide for LC translocation and imply that disulfide reduction is a prerequisite for LC delivery into the host cytosol. The data also support a model that LC translocation proceeds from the C to the N terminus. βlac-TeNT(RY) is the first reporter system to measure translocation by an AB single-chain toxin in intact cells.
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Bohovych I, Chan SS, Khalimonchuk O. Mitochondrial protein quality control: the mechanisms guarding mitochondrial health. Antioxid Redox Signal 2015; 22:977-94. [PMID: 25546710 PMCID: PMC4390190 DOI: 10.1089/ars.2014.6199] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/20/2014] [Indexed: 12/20/2022]
Abstract
SIGNIFICANCE Mitochondria are complex dynamic organelles pivotal for cellular physiology and human health. Failure to maintain mitochondrial health leads to numerous maladies that include late-onset neurodegenerative diseases and cardiovascular disorders. Furthermore, a decline in mitochondrial health is prevalent with aging. A set of evolutionary conserved mechanisms known as mitochondrial quality control (MQC) is involved in recognition and correction of the mitochondrial proteome. RECENT ADVANCES Here, we review current knowledge and latest developments in MQC. We particularly focus on the proteolytic aspect of MQC and its impact on health and aging. CRITICAL ISSUES While our knowledge about MQC is steadily growing, critical gaps remain in the mechanistic understanding of how MQC modules sense damage and preserve mitochondrial welfare, particularly in higher organisms. FUTURE DIRECTIONS Delineating how coordinated action of the MQC modules orchestrates physiological responses on both organellar and cellular levels will further elucidate the current picture of MQC's role and function in health, cellular stress, and degenerative diseases.
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Affiliation(s)
- Iryna Bohovych
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
- Nebraska Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Sherine S.L. Chan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
- Nebraska Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska
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