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Guirguis AA, Ofir-Rosenfeld Y, Knezevic K, Blackaby W, Hardick D, Chan YC, Motazedian A, Gillespie A, Vassiliadis D, Lam EYN, Tran K, Andrews B, Harbour ME, Vasiliauskaite L, Saunders CJ, Tsagkogeorga G, Azevedo A, Obacz J, Pilka ES, Carkill M, MacPherson L, Wainwright EN, Liddicoat B, Blyth BJ, Albertella MR, Rausch O, Dawson MA. Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity. Cancer Discov 2023; 13:2228-2247. [PMID: 37548590 DOI: 10.1158/2159-8290.cd-23-0007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/06/2023] [Accepted: 08/02/2023] [Indexed: 08/08/2023]
Abstract
Therapies that enhance antitumor immunity have altered the natural history of many cancers. Consequently, leveraging nonoverlapping mechanisms to increase immunogenicity of cancer cells remains a priority. Using a novel enzymatic inhibitor of the RNA methyl-transferase METTL3, we demonstrate a global decrease in N6-methyladenosine (m6A) results in double-stranded RNA (dsRNA) formation and a profound cell-intrinsic interferon response. Through unbiased CRISPR screens, we establish dsRNA-sensing and interferon signaling are primary mediators that potentiate T-cell killing of cancer cells following METTL3 inhibition. We show in a range of immunocompetent mouse models that although METTL3 inhibition is equally efficacious to anti-PD-1 therapy, the combination has far greater preclinical activity. Using SPLINTR barcoding, we demonstrate that anti-PD-1 therapy and METTL3 inhibition target distinct malignant clones, and the combination of these therapies overcomes clones insensitive to the single agents. These data provide the mole-cular and preclinical rationale for employing METTL3 inhibitors to promote antitumor immunity in the clinic. SIGNIFICANCE This work demonstrates that METTL3 inhibition stimulates a cell-intrinsic interferon response through dsRNA formation. This immunomodulatory mechanism is distinct from current immunotherapeutic agents and provides the molecular rationale for combination with anti-PD-1 immune-checkpoint blockade to augment antitumor immunity. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Andrew A Guirguis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - Kathy Knezevic
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | | | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Ali Motazedian
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Andrea Gillespie
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dane Vassiliadis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Kevin Tran
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | | | | | | | | | - Georgia Tsagkogeorga
- Storm Therapeutics Ltd, Cambridge, United Kingdom
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Joanna Obacz
- Storm Therapeutics Ltd, Cambridge, United Kingdom
| | | | - Marie Carkill
- Charles River Laboratories, Portishead, United -Kingdom
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Elanor N Wainwright
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Brian Liddicoat
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Benjamin J Blyth
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | | | | | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, -Victoria, Australia
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2
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Páleníková P, Harbour ME, Prodi F, Minczuk M, Zeviani M, Ghelli A, Fernández-Vizarra E. Duplexing complexome profiling with SILAC to study human respiratory chain assembly defects. Biochim Biophys Acta Bioenerg 2021; 1862:148395. [PMID: 33600785 DOI: 10.1016/j.bbabio.2021.148395] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022]
Abstract
Complexome Profiling (CP) combines size separation, by electrophoresis or other means, of native multimeric complexes with protein identification by mass spectrometry (MS). Peptide MS analysis of the multiple fractions in which the sample is separated, results in the creation of protein abundance profiles in function of molecular size, providing a visual output of the assembly status of a group of proteins of interest. Stable isotope labeling by amino acids in cell culture (SILAC) is an established quantitative proteomics technique that allows duplexing in the MS analysis as well as the comparison of relative protein abundances between the samples, which are processed and analyzed together. Combining SILAC and CP permitted the direct comparison of migration and abundance of the proteins present in the mitochondrial respiratory chain complexes in two different samples. This analysis, however, introduced a level of complexity in data processing for which bioinformatic tools had to be developed in order to generate the normalized protein abundance profiles. The advantages and challenges of using of this type of analysis for the characterization of two cell lines carrying pathological variants in MT-CO3 and MT-CYB is reviewed. An additional unpublished example of SILAC-CP of a cell line with an in-frame 18-bp deletion in MT-CYB is presented. In these cells, in contrast to other MT-CYB deficient models, a small proportion of complex III2 is formed and it is found associated with fully assembled complex I. This analysis also revealed a profuse accumulation of assembly intermediates containing complex III subunits UQCR10 and CYC1, as well as a profound early-stage complex IV assembly defect.
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Affiliation(s)
- Petra Páleníková
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michael E Harbour
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Federica Prodi
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | - Michal Minczuk
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Massimo Zeviani
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Anna Ghelli
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | - Erika Fernández-Vizarra
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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3
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Páleníková P, Harbour ME, Ding S, Fearnley IM, Van Haute L, Rorbach J, Scavetta R, Minczuk M, Rebelo-Guiomar P. Quantitative density gradient analysis by mass spectrometry (qDGMS) and complexome profiling analysis (ComPrAn) R package for the study of macromolecular complexes. Biochim Biophys Acta Bioenerg 2021; 1862:148399. [PMID: 33592209 PMCID: PMC8047798 DOI: 10.1016/j.bbabio.2021.148399] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 11/28/2022]
Abstract
Many cellular processes involve the participation of large macromolecular assemblies. Understanding their function requires methods allowing to study their dynamic and mechanistic properties. Here we present a method for quantitative analysis of native protein or ribonucleoprotein complexes by mass spectrometry following their separation by density – qDGMS. Mass spectrometric quantitation is enabled through stable isotope labelling with amino acids in cell culture (SILAC). We provide a complete guide, from experimental design to preparation of publication-ready figures, using a purposely-developed R package – ComPrAn. As specific examples, we present the use of sucrose density gradients to inspect the assembly and dynamics of the human mitochondrial ribosome (mitoribosome), its interacting proteins, the small subunit of the cytoplasmic ribosome, cytoplasmic aminoacyl-tRNA synthetase complex and the mitochondrial PDH complex. ComPrAn provides tools for analysis of peptide-level data as well as normalization and clustering tools for protein-level data, dedicated visualization functions and graphical user interface. Although, it has been developed for the analysis of qDGMS samples, it can also be used for other proteomics experiments that involve 2-state labelled samples separated into fractions. We show that qDGMS and ComPrAn can be used to study macromolecular complexes in their native state, accounting for the dynamics inherent to biological systems and benefiting from its proteome-wide quantitative and qualitative capability. qDGMS is a novel method to study macromolecular complex composition and assembly. Complexes are separated in near-native form by density gradient ultracentrifugation. SILAC enables simultaneous quantitative proteomic analysis of two biological samples. R package ComPrAn allows analysis of SILAC complexome profiling and qDGMS data sets.
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Affiliation(s)
- Petra Páleníková
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Michael E Harbour
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Shujing Ding
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Ian M Fearnley
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Joanna Rorbach
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | | | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom.
| | - Pedro Rebelo-Guiomar
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom.
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4
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Bundgaard A, James AM, Harbour ME, Murphy MP, Fago A. Stable mitochondrial CICIII 2 supercomplex interactions in reptiles versus homeothermic vertebrates. J Exp Biol 2020; 223:jeb223776. [PMID: 32393546 PMCID: PMC7328143 DOI: 10.1242/jeb.223776] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022]
Abstract
The association of complex I (CI), complex III (CIII) and complex IV (CIV) of the mitochondrial electron transport chain into stable high molecular weight supercomplexes (SCs) has been observed in several prokaryotes and eukaryotes, but among vertebrates it has only been examined in mammals. The biological role of these SCs is unclear but suggestions so far include enhanced electron transfer between complexes, decreased production of the reactive oxygen species (ROS) O2- and H2O2, or enhanced structural stability. Here, we provide the first overview on the stability, composition and activity of mitochondrial SCs in representative species of several vertebrate classes to determine patterns of SC variation across endotherms and ectotherms. We found that the stability of the CICIII2 SC and the inclusion of CIV within the SC varied considerably. Specifically, when solubilized by the detergent DDM, mitochondrial CICIII2 SCs were unstable in endotherms (birds and mammals) and highly stable in reptiles. Using mass-spectrometric complexomics, we confirmed that the CICIII2 is the major SC in the turtle, and that 90% of CI is found in this highly stable SC. Interestingly, the presence of stable SCs did not prevent mitochondrial H2O2 production and was not associated with elevated respiration rates of mitochondria isolated from the examined species. Together, these data show that SC stability varies among vertebrates and is greatest in poikilothermic reptiles and weakest in endotherms. This pattern suggests an adaptive role of SCs to varying body temperature, but not necessarily a direct effect on electron transfer or in the prevention of ROS production.
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Affiliation(s)
| | - Andrew M James
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Michael E Harbour
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Angela Fago
- Department of Biology, Aarhus University, 8000 Aarhus, Denmark
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5
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Protasoni M, Pérez‐Pérez R, Lobo‐Jarne T, Harbour ME, Ding S, Peñas A, Diaz F, Moraes CT, Fearnley IM, Zeviani M, Ugalde C, Fernández‐Vizarra E. Respiratory supercomplexes act as a platform for complex III-mediated maturation of human mitochondrial complexes I and IV. EMBO J 2020; 39:e102817. [PMID: 31912925 PMCID: PMC6996572 DOI: 10.15252/embj.2019102817] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/02/2019] [Accepted: 11/26/2019] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial respiratory chain (MRC) enzymes associate in supercomplexes (SCs) that are structurally interdependent. This may explain why defects in a single component often produce combined enzyme deficiencies in patients. A case in point is the alleged destabilization of complex I in the absence of complex III. To clarify the structural and functional relationships between complexes, we have used comprehensive proteomic, functional, and biogenetical approaches to analyze a MT-CYB-deficient human cell line. We show that the absence of complex III blocks complex I biogenesis by preventing the incorporation of the NADH module rather than decreasing its stability. In addition, complex IV subunits appeared sequestered within complex III subassemblies, leading to defective complex IV assembly as well. Therefore, we propose that complex III is central for MRC maturation and SC formation. Our results challenge the notion that SC biogenesis requires the pre-formation of fully assembled individual complexes. In contrast, they support a cooperative-assembly model in which the main role of complex III in SCs is to provide a structural and functional platform for the completion of overall MRC biogenesis.
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Affiliation(s)
- Margherita Protasoni
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | | | | | - Michael E Harbour
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Shujing Ding
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Ana Peñas
- Instituto de Investigación Hospital 12 de Octubre (i+12)MadridSpain
| | - Francisca Diaz
- Department of NeurologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Carlos T Moraes
- Department of NeurologyMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Ian M Fearnley
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Massimo Zeviani
- Medical Research Council‐Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Department of NeurosciencesUniversity of PadovaPadovaItaly
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i+12)MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723MadridSpain
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6
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Van Haute L, Hendrick AG, D'Souza AR, Powell CA, Rebelo-Guiomar P, Harbour ME, Ding S, Fearnley IM, Andrews B, Minczuk M. METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis. Nucleic Acids Res 2019; 47:10267-10281. [PMID: 31665743 PMCID: PMC6821322 DOI: 10.1093/nar/gkz735] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/03/2019] [Indexed: 01/08/2023] Open
Abstract
Post-transcriptional RNA modifications, the epitranscriptome, play important roles in modulating the functions of RNA species. Modifications of rRNA are key for ribosome production and function. Identification and characterization of enzymes involved in epitranscriptome shaping is instrumental for the elucidation of the functional roles of specific RNA modifications. Ten modified sites have been thus far identified in the mammalian mitochondrial rRNA. Enzymes responsible for two of these modifications have not been characterized. Here, we identify METTL15, show that it is the main N4-methylcytidine (m4C) methyltransferase in human cells and demonstrate that it is responsible for the methylation of position C839 in mitochondrial 12S rRNA. We show that the lack of METTL15 results in a reduction of the mitochondrial de novo protein synthesis and decreased steady-state levels of protein components of the oxidative phosphorylation system. Without functional METTL15, the assembly of the mitochondrial ribosome is decreased, with the late assembly components being unable to be incorporated efficiently into the small subunit. We speculate that m4C839 is involved in the stabilization of 12S rRNA folding, therefore facilitating the assembly of the mitochondrial small ribosomal subunits. Taken together our data show that METTL15 is a novel protein necessary for efficient translation in human mitochondria.
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Affiliation(s)
- Lindsey Van Haute
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Alan G Hendrick
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Aaron R D'Souza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.,Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Rua Alfredo Allen 208, Porto 4200-135, Portugal
| | - Michael E Harbour
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.,STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Shujing Ding
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Ian M Fearnley
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Byron Andrews
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
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7
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Tavoulari S, Thangaratnarajah C, Mavridou V, Harbour ME, Martinou JC, Kunji ER. The yeast mitochondrial pyruvate carrier is a hetero-dimer in its functional state. EMBO J 2019; 38:e100785. [PMID: 30979775 PMCID: PMC6517818 DOI: 10.15252/embj.2018100785] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 02/02/2023] Open
Abstract
The mitochondrial pyruvate carrier (MPC) is critical for cellular homeostasis, as it is required in central metabolism for transporting pyruvate from the cytosol into the mitochondrial matrix. MPC has been implicated in many diseases and is being investigated as a drug target. A few years ago, small membrane proteins, called MPC1 and MPC2 in mammals and Mpc1, Mpc2 and Mpc3 in yeast, were proposed to form large protein complexes responsible for this function. However, the MPC complexes have never been isolated and their composition, oligomeric state and functional properties have not been defined. Here, we identify the functional unit of MPC from Saccharomyces cerevisiae In contrast to earlier hypotheses, we demonstrate that MPC is a hetero-dimer, not a multimeric complex. When not engaged in hetero-dimers, the yeast Mpc proteins can also form homo-dimers that are, however, inactive. We show that the earlier described substrate transport properties and inhibitor profiles are embodied by the hetero-dimer. This work provides a foundation for elucidating the structure of the functional complex and the mechanism of substrate transport and inhibition.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Vasiliki Mavridou
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michael E Harbour
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Edmund Rs Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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8
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Gahura O, Šubrtová K, Váchová H, Panicucci B, Fearnley IM, Harbour ME, Walker JE, Zíková A. The F 1 -ATPase from Trypanosoma brucei is elaborated by three copies of an additional p18-subunit. FEBS J 2017; 285:614-628. [PMID: 29247468 DOI: 10.1111/febs.14364] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/16/2017] [Accepted: 12/08/2017] [Indexed: 01/09/2023]
Abstract
The F-ATPases (also called the F1 Fo -ATPases or ATP synthases) are multi-subunit membrane-bound molecular machines that produce ATP in bacteria and in eukaryotic mitochondria and chloroplasts. The structures and enzymic mechanisms of their F1 -catalytic domains are highly conserved in all species investigated hitherto. However, there is evidence that the F-ATPases from the group of protozoa known as Euglenozoa have novel features. Therefore, we have isolated pure and active F1 -ATPase from the euglenozoan parasite, Trypanosoma brucei, and characterized it. All of the usual eukaryotic subunits (α, β, γ, δ, and ε) were present in the enzyme, and, in addition, two unique features were detected. First, each of the three α-subunits in the F1 -domain has been cleaved by proteolysis in vivo at two sites eight residues apart, producing two assembled fragments. Second, the T. brucei F1 -ATPase has an additional subunit, called p18, present in three copies per complex. Suppression of expression of p18 affected in vitro growth of both the insect and infectious mammalian forms of T. brucei. It also reduced the levels of monomeric and multimeric F-ATPase complexes and diminished the in vivo hydrolytic activity of the enzyme significantly. These observations imply that p18 plays a role in the assembly of the F1 domain. These unique features of the F1 -ATPase extend the list of special characteristics of the F-ATPase from T. brucei, and also, demonstrate that the architecture of the F1 -ATPase complex is not strictly conserved in eukaryotes.
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Affiliation(s)
- Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Karolína Šubrtová
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic
| | - Hana Váchová
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic
| | - Brian Panicucci
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic
| | - Ian M Fearnley
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Michael E Harbour
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - John E Walker
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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9
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Bottani E, Cerutti R, Harbour ME, Ravaglia S, Dogan SA, Giordano C, Fearnley IM, D'Amati G, Viscomi C, Fernandez-Vizarra E, Zeviani M. TTC19 Plays a Husbandry Role on UQCRFS1 Turnover in the Biogenesis of Mitochondrial Respiratory Complex III. Mol Cell 2017; 67:96-105.e4. [PMID: 28673544 DOI: 10.1016/j.molcel.2017.06.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/03/2017] [Accepted: 06/01/2017] [Indexed: 12/29/2022]
Abstract
Loss-of-function mutations in TTC19 (tetra-tricopeptide repeat domain 19) have been associated with severe neurological phenotypes and mitochondrial respiratory chain complex III deficiency. We previously demonstrated the mitochondrial localization of TTC19 and its link with complex III biogenesis. Here we provide detailed insight into the mechanistic role of TTC19, by investigating a Ttc19?/? mouse model that shows progressive neurological and metabolic decline, decreased complex III activity, and increased production of reactive oxygen species. By using both the Ttc19?/? mouse model and a range of human cell lines, we demonstrate that TTC19 binds to the fully assembled complex III dimer, i.e., after the incorporation of the iron-sulfur Rieske protein (UQCRFS1). The in situ maturation of UQCRFS1 produces N-terminal polypeptides, which remain bound to holocomplex III. We show that, in normal conditions, these UQCRFS1 fragments are rapidly removed, but when TTC19 is absent they accumulate within complex III, causing its structural and functional impairment.
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Affiliation(s)
- Emanuela Bottani
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Raffaele Cerutti
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Michael E Harbour
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Sabrina Ravaglia
- Istituto Neurologico "Casimiro Mondino," via Mondino 2, Pavia 27100, Italy
| | - Sukru Anil Dogan
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Carla Giordano
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Ian M Fearnley
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Giulia D'Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Carlo Viscomi
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK
| | - Erika Fernandez-Vizarra
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK.
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building Hills Road, Cambridge CB2 0XY, UK.
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10
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Bridges HR, Mohammed K, Harbour ME, Hirst J. Subunit NDUFV3 is present in two distinct isoforms in mammalian complex I. Biochim Biophys Acta Bioenerg 2017; 1858:197-207. [PMID: 27940020 PMCID: PMC5293009 DOI: 10.1016/j.bbabio.2016.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 01/10/2023]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the electron transport chain in mammalian mitochondria. Extensive proteomic and structural analyses of complex I from Bos taurus heart mitochondria have shown it comprises 45 subunits encoded on both the nuclear and mitochondrial genomes; 44 of them are different and one is present in two copies. The bovine heart enzyme has provided a model for studying the composition of complex I in other mammalian species, including humans, but the possibility of additional subunits or isoforms in other species or tissues has not been explored. Here, we describe characterization of the complexes I purified from five rat tissues and from a rat hepatoma cell line. We identify a~50kDa isoform of subunit NDUFV3, for which the canonical isoform is only ~10kDa in size. We combine LC-MS and MALDI-TOF mass spectrometry data from two different purification methods (chromatography and immuno-purification) with information from blue native PAGE analyses to show the long isoform is present in the mature complex, but at substoichiometric levels. It is also present in complex I in cultured human cells. We describe evidence that the long isoform is more abundant in both the mitochondria and purified complexes from brain (relative to in heart, liver, kidney and skeletal muscle) and more abundant still in complex I in cultured cells. We propose that the long 50kDa isoform competes with its canonical 10kDa counterpart for a common binding site on the flavoprotein domain of complex I.
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Affiliation(s)
- Hannah R Bridges
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Khairunnisa Mohammed
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Michael E Harbour
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K..
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11
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Menger KE, James AM, Cochemé HM, Harbour ME, Chouchani ET, Ding S, Fearnley IM, Partridge L, Murphy MP. Fasting, but Not Aging, Dramatically Alters the Redox Status of Cysteine Residues on Proteins in Drosophila melanogaster. Cell Rep 2015; 13:1285. [PMID: 28873344 PMCID: PMC5643521 DOI: 10.1016/j.celrep.2015.10.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Menger KE, James AM, Cochemé HM, Harbour ME, Chouchani ET, Ding S, Fearnley IM, Partridge L, Murphy MP. Fasting, but Not Aging, Dramatically Alters the Redox Status of Cysteine Residues on Proteins in Drosophila melanogaster. Cell Rep 2015; 11:1856-65. [PMID: 26095360 PMCID: PMC4508341 DOI: 10.1016/j.celrep.2015.05.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/26/2015] [Accepted: 05/19/2015] [Indexed: 12/26/2022] Open
Abstract
Altering the redox state of cysteine residues on protein surfaces is an important response to environmental challenges. Although aging and fasting alter many redox processes, the role of cysteine residues is uncertain. To address this, we used a redox proteomic technique, oxidative isotope-coded affinity tags (OxICAT), to assess cysteine-residue redox changes in Drosophila melanogaster during aging and fasting. This approach enabled us to simultaneously identify and quantify the redox state of several hundred cysteine residues in vivo. Cysteine residues within young flies had a bimodal distribution with peaks at ∼10% and ∼85% reversibly oxidized. Surprisingly, these cysteine residues did not become more oxidized with age. In contrast, 24 hr of fasting dramatically oxidized cysteine residues that were reduced under fed conditions while also reducing cysteine residues that were initially oxidized. We conclude that fasting, but not aging, dramatically alters cysteine-residue redox status in D. melanogaster. The redox state and identity of cysteine residues in flies can be determined by OxICAT Overall cysteine-residue redox state does not change with age H2O2 and paraquat have surprisingly distinct effects on cysteine-residue redox state Fasting for 24 hr dramatically alters the redox state of cysteine residues
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Affiliation(s)
- Katja E Menger
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | | | - Helena M Cochemé
- Institute of Healthy Ageing and GEE, University College London, London WC1E 6BT, UK; Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | | | - Edward T Chouchani
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115-5730, USA
| | - Shujing Ding
- MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, UK
| | | | - Linda Partridge
- Institute of Healthy Ageing and GEE, University College London, London WC1E 6BT, UK; Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
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Harbour ME, Seaman MNJ. Evolutionary variations of VPS29, and their implications for the heteropentameric model of retromer. Commun Integr Biol 2014. [DOI: 10.4161/cib.16855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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14
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Hesketh GG, Pérez-Dorado I, Jackson LP, Wartosch L, Schäfer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MNJ, Luzio JP, Owen DJ. VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface. Dev Cell 2014; 29:591-606. [PMID: 24856514 PMCID: PMC4059916 DOI: 10.1016/j.devcel.2014.04.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 02/03/2014] [Accepted: 04/09/2014] [Indexed: 11/18/2022]
Abstract
VARP is a Rab32/38 effector that also binds to the endosomal/lysosomal R-SNARE VAMP7. VARP binding regulates VAMP7 participation in SNARE complex formation and can therefore influence VAMP7-mediated membrane fusion events. Mutant versions of VARP that cannot bind Rab32:GTP, designed on the basis of the VARP ankyrin repeat/Rab32:GTP complex structure described here, unexpectedly retain endosomal localization, showing that VARP recruitment is not dependent on Rab32 binding. We show that recruitment of VARP to the endosomal membrane is mediated by its direct interaction with VPS29, a subunit of the retromer complex, which is involved in trafficking from endosomes to the TGN and the cell surface. Transport of GLUT1 from endosomes to the cell surface requires VARP, VPS29, and VAMP7 and depends on the direct interaction between VPS29 and VARP. Finally, we propose that endocytic cycling of VAMP7 depends on its interaction with VARP and, consequently, also on retromer.
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Affiliation(s)
- Geoffrey G Hesketh
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Inmaculada Pérez-Dorado
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Lauren P Jackson
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Lena Wartosch
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ingmar B Schäfer
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Sally R Gray
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Airlie J McCoy
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Oliver B Zeldin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Michael E Harbour
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Philip R Evans
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Matthew N J Seaman
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
| | - J Paul Luzio
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
| | - David J Owen
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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Zavodszky E, Seaman MN, Moreau K, Jimenez-Sanchez M, Breusegem SY, Harbour ME, Rubinsztein DC. Mutation in VPS35 associated with Parkinson's disease impairs WASH complex association and inhibits autophagy. Nat Commun 2014; 5:3828. [PMID: 24819384 PMCID: PMC4024763 DOI: 10.1038/ncomms4828] [Citation(s) in RCA: 317] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 04/07/2014] [Indexed: 12/13/2022] Open
Abstract
Endosomal protein sorting controls the localization of many physiologically important proteins and is linked to several neurodegenerative diseases. VPS35 is a component of the retromer complex, which mediates endosome-to-Golgi retrieval of membrane proteins such as the cation-independent mannose 6-phosphate receptor. Furthermore, retromer is also required for the endosomal recruitment of the actin nucleation promoting WASH complex. The VPS35 D620N mutation causes a rare form of autosomal-dominant Parkinson's disease (PD). Here we show that this mutant associates poorly with the WASH complex and impairs WASH recruitment to endosomes. Autophagy is impaired in cells expressing PD-mutant VPS35 or lacking WASH. The autophagy defects can be explained, at least in part, by abnormal trafficking of the autophagy protein ATG9A. Thus, the PD-causing D620N mutation in VPS35 restricts WASH complex recruitment to endosomes, and reveals a novel role for the WASH complex in autophagosome formation.
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Affiliation(s)
- Eszter Zavodszky
- Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
- These authors contributed equally to this work
| | - Matthew N.J. Seaman
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
- These authors contributed equally to this work
| | - Kevin Moreau
- Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Maria Jimenez-Sanchez
- Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Sophia Y. Breusegem
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
| | - Michael E. Harbour
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
| | - David C. Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
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16
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Helfer E, Harbour ME, Henriot V, Lakisic G, Sousa-Blin C, Volceanov L, Seaman MNJ, Gautreau A. Endosomal recruitment of the WASH complex: active sequences and mutations impairing interaction with the retromer. Biol Cell 2013; 105:191-207. [PMID: 23331060 DOI: 10.1111/boc.201200038] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 01/11/2013] [Indexed: 12/27/2022]
Abstract
BACKGROUND INFORMATION The Wiskott-Aldrich syndrome protein and scar homolog (WASH) complex is the major Arp2/3 activator at the surface of endosomes. The branched actin network, that the WASH complex induces, contributes to cargo sorting and scission of transport intermediates destined for most endosomal routes. A major challenge is to understand how the WASH molecular machine is recruited to the surface of endosomes. The retromer endosomal machinery has been proposed by us and others to play a role in this process. RESULTS In this work, we used an unbiased approach to identify the endosomal receptor of the WASH complex. We have delineated a short fragment of the FAM21 subunit that is able to displace the endogenous WASH complex from endosomes. Using a proteomic approach, we have identified the retromer cargo selective complex (CSC) as a partner of the active FAM21 sequence displacing the endogenous WASH complex. A point mutation in FAM21 that abolishes CSC interaction also impairs WASH complex displacement activity. The CSC is composed of three subunits, VPS35, VPS29 and VPS26. FAM21 directly binds the VPS35 subunit of the retromer CSC. Additionally, we show that a point mutant of VPS35 that blocks binding to VPS29 also prevents association with FAM21 and the WASH complex revealing a novel role for the VPS35-VPS29 interaction in regulating retromer association with the WASH complex. CONCLUSIONS This novel approach of endogenous WASH displacement confirms previous suggestions that the retromer is the receptor of the WASH complex at the surface of endosomes and identify key residues that mediate this interaction. The interaction between these two endosomal machineries, the WASH complex and the retromer, is likely to play a critical role in forming platforms at the surface of endosomes for efficient sorting of cargoes.
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Affiliation(s)
- Emmanuèle Helfer
- Centre de Recherche de Gif, Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, Avenue de la Terrasse, Gif-sur-Yvette Cedex 91198, France
| | - Michael E Harbour
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0XY, UK
| | - Véronique Henriot
- Centre de Recherche de Gif, Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, Avenue de la Terrasse, Gif-sur-Yvette Cedex 91198, France
| | - Goran Lakisic
- Centre de Recherche de Gif, Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, Avenue de la Terrasse, Gif-sur-Yvette Cedex 91198, France
| | - Carla Sousa-Blin
- Centre de Recherche de Gif, Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, Avenue de la Terrasse, Gif-sur-Yvette Cedex 91198, France
| | - Larisa Volceanov
- Centre de Recherche de Gif, Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, Avenue de la Terrasse, Gif-sur-Yvette Cedex 91198, France
| | - Matthew N J Seaman
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0XY, UK
| | - Alexis Gautreau
- Centre de Recherche de Gif, Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, Avenue de la Terrasse, Gif-sur-Yvette Cedex 91198, France
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17
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Vardarajan BN, Bruesegem SY, Harbour ME, St. George-Hyslop P, Seaman MN, Farrer LA, Seaman MNJ, Farrer LA. Identification of Alzheimer disease-associated variants in genes that regulate retromer function. Neurobiol Aging 2012; 33:2231.e15-2231.e30. [PMID: 22673115 PMCID: PMC3391348 DOI: 10.1016/j.neurobiolaging.2012.04.020] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 03/13/2012] [Accepted: 04/30/2012] [Indexed: 12/18/2022]
Abstract
The proteolytic processing of amyloid precursor protein (APP) to generate the neurotoxic amyloid β (Aβ) peptide is central to the pathogenesis of Alzheimer disease (AD). The endocytic system mediates the processing of APP by controlling its access to secretases that cleave APP. A key mediator of APP localization is SorL1-a membrane protein that has been genetically linked to AD. The retromer complex is a conserved protein complex required for endosome-to-Golgi retrieval of a number of physiologically important membrane proteins including SorL1. Based on the prior suggestion that endocytosis and retromer sorting pathways might be involved, we hypothesized that variants in other genes in this pathway might also modulate AD risk. Genetic association of AD with 451 polymorphisms in 15 genes encoding retromer or retromer-associated proteins was tested in a Caucasian sample of 8309 AD cases and 7366 cognitively normal elders using individual single nucleotide polymorphism (SNP)- and gene-based tests. We obtained significant evidence of association with KIAA1033 (VEGAS p = 0.025), SNX1 (VEGAS p = 0.035), SNX3 (p = 0.0057), and RAB7A (VEGAS p = 0.018). Ten KIAA1033 SNPs were also significantly associated with AD in a group of African Americans (513 AD cases, 504 control subjects). Findings with four significant SNX3 SNPs in the discovery sample were replicated in a community-based sample of Israeli-Arabs (124 AD cases, 142 control subjects). We show that Snx3 and Rab7A proteins interact with the cargo-selective retromer complex through independent mechanisms to regulate the membrane association of retromer and thereby are key mediators of retromer function. These data implicate additional AD risk genes in the retromer pathway and formally demonstrate a direct link between the activity of the retromer complex and the pathogenesis of AD.
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Affiliation(s)
- Badri N. Vardarajan
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118
| | - Sophia Y. Bruesegem
- University of Cambridge, Departments of Clinical Biochemistry and Clinical Neurosciences, Cambridge Institute for Medical Research, Addenbrookes Hospital, Cambridge, CB2 0XY, UK
| | - Michael E. Harbour
- University of Cambridge, Departments of Clinical Biochemistry and Clinical Neurosciences, Cambridge Institute for Medical Research, Addenbrookes Hospital, Cambridge, CB2 0XY, UK
| | - Peter St. George-Hyslop
- University of Cambridge, Departments of Clinical Biochemistry and Clinical Neurosciences, Cambridge Institute for Medical Research, Addenbrookes Hospital, Cambridge, CB2 0XY, UK,Tanz Centre for Research in Neurodegenerative Diseases, Department of Medicine, University of Toronto, 1 King’s College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Matthew N.J. Seaman
- University of Cambridge, Departments of Clinical Biochemistry and Clinical Neurosciences, Cambridge Institute for Medical Research, Addenbrookes Hospital, Cambridge, CB2 0XY, UK,Address Correspondence to: Dr. Lindsay Farrer, Genetics Program L320, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118 USA, telephone: (617) 638-5393, fax: (617) 638-4275, , Dr. Matthew Seaman, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrookes Hospital, Cambridge, CB2 0XY, U.K., telephone: 44-1223-763225, fax: 44-1223-762640,
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118,Departments of Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health, 72 East Concord Street, Boston, MA 02118,Address Correspondence to: Dr. Lindsay Farrer, Genetics Program L320, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118 USA, telephone: (617) 638-5393, fax: (617) 638-4275, , Dr. Matthew Seaman, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrookes Hospital, Cambridge, CB2 0XY, U.K., telephone: 44-1223-763225, fax: 44-1223-762640,
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Harbour ME, Seaman MNJ. Evolutionary variations of VPS29, and their implications for the heteropentameric model of retromer. Commun Integr Biol 2011; 4:619-22. [PMID: 22046480 DOI: 10.4161/cib.4.5.16855] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 06/09/2011] [Indexed: 11/19/2022] Open
Abstract
The retromer complex is conserved across all eukaryotic species and functions in physiologically important sorting processes at the endosomal membrane. A key component of retromer is the VPS29 protein that, although structurally similar to phospho-diesterases, has been convincingly shown in the recent study by Swarbrick et al. (PLoS One 6:e20420, 2011) to be a rigid scaffold that interacts with various proteins that function with retromer in endosomal protein sorting. A widely held view, based on initial observations in Saccharomyces cerevisiae, is that retromer functions as a stable heteropentamer. This is, however, contrary to experimental data presented in Swarbrick et al. (and in other studies) that indicate that retromer in higher eukaryotes is a looser association of two subcomplexes that respectively mediate cargo-selection and membrane tubulation. Here we present an analysis of evolutionary variation of the VPS29 protein and discuss why the retromer complex as first characterized in S. cerevisiae is not representative of retromer in other eukaryotic taxa.
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Affiliation(s)
- Michael E Harbour
- University of Cambridge; Cambridge Institue for Medical Research; Addenbrookes Hospital; Cambridge, UK
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Reyes A, He J, Mao CC, Bailey LJ, Di Re M, Sembongi H, Kazak L, Dzionek K, Holmes JB, Cluett TJ, Harbour ME, Fearnley IM, Crouch RJ, Conti MA, Adelstein RS, Walker JE, Holt IJ. Actin and myosin contribute to mammalian mitochondrial DNA maintenance. Nucleic Acids Res 2011; 39:5098-108. [PMID: 21398640 PMCID: PMC3130256 DOI: 10.1093/nar/gkr052] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding non-muscle myosin heavy chain IIA), or the closely related MYH10 gene (encoding non-muscle myosin heavy chain IIB), altered the topology and increased the copy number of mitochondrial DNA; and the latter effect was enhanced when both genes were targeted simultaneously. In contrast, genetic ablation of non-muscle myosin IIB was associated with a 60% decrease in mitochondrial DNA copy number in mouse embryonic fibroblasts, compared to control cells. Gene silencing of β-actin also affected mitochondrial DNA copy number and organization. Protease-protection experiments and iodixanol gradient analysis suggest some β-actin and non-muscle myosin heavy chain IIA reside within human mitochondria and confirm that they are associated with mitochondrial DNA. Collectively, these results strongly implicate the actomyosin cytoskeleton in mammalian mitochondrial DNA maintenance.
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Affiliation(s)
- A Reyes
- MRC Mitochondrial Biology Unit, Cambridge, UK
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Yip CY, Harbour ME, Jayawardena K, Fearnley IM, Sazanov LA. Evolution of respiratory complex I: "supernumerary" subunits are present in the alpha-proteobacterial enzyme. J Biol Chem 2010; 286:5023-33. [PMID: 21115482 DOI: 10.1074/jbc.m110.194993] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. Mitochondrial complex I contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. However, the full protein composition of an α-proteobacterial complex I has not been established previously. Here, we report the first purification and characterization of complex I from the α-proteobacterium Paracoccus denitrificans. Single particle electron microscopy shows that the complex has a well defined L-shape. Unexpectedly, in addition to the 14 core subunits, the enzyme also contains homologues of three supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine nomenclature). This finding suggests that evolution of complex I via addition of supernumerary or "accessory" subunits started before the original endosymbiotic event that led to the creation of the eukaryotic cell. It also provides further confirmation that α-proteobacteria are the closest extant relatives of mitochondria.
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Affiliation(s)
- Chui-ying Yip
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom
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21
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Harbour ME, Breusegem SYA, Antrobus R, Freeman C, Reid E, Seaman MNJ. The cargo-selective retromer complex is a recruiting hub for protein complexes that regulate endosomal tubule dynamics. J Cell Sci 2010; 123:3703-17. [PMID: 20923837 DOI: 10.1242/jcs.071472] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The retromer complex is required for the efficient endosome-to-Golgi retrieval of the CIMPR, sortilin, SORL1, wntless and other physiologically important membrane proteins. Retromer comprises two protein complexes that act together in endosome-to-Golgi retrieval; the cargo-selective complex is a trimer of VPS35, VPS29 and VPS26 that sorts cargo into tubules for retrieval to the Golgi. Tubules are produced by the oligomerization of sorting nexin dimers. Here, we report the identification of five endosomally-localised proteins that modulate tubule formation and are recruited to the membrane via interactions with the cargo-selective retromer complex. One of the retromer-interacting proteins, strumpellin, is mutated in hereditary spastic paraplegia, a progressive length-dependent axonopathy. Here, we show that strumpellin regulates endosomal tubules as part of a protein complex with three other proteins that include WASH1, an actin-nucleating promoting factor. Therefore, in addition to a direct role in endosome-to-Golgi retrieval, the cargo-selective retromer complex also acts as a platform for recruiting physiologically important proteins to endosomal membranes that regulate membrane tubule dynamics.
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Affiliation(s)
- Michael E Harbour
- Department of Clinical Biochemistry, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrookes Hospital, Cambridge CB2 0XY, UK
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Hirst J, Sahlender DA, Choma M, Sinka R, Harbour ME, Parkinson M, Robinson MS. Spatial and Functional Relationship of GGAs and AP-1 inDrosophilaand HeLa Cells. Traffic 2009; 10:1696-710. [DOI: 10.1111/j.1600-0854.2009.00983.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Seaman MNJ, Harbour ME, Tattersall D, Read E, Bright N. Membrane recruitment of the cargo-selective retromer subcomplex is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5. J Cell Sci 2009; 122:2371-82. [PMID: 19531583 DOI: 10.1242/jcs.048686] [Citation(s) in RCA: 292] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Retromer is a membrane-associated heteropentameric coat complex that functions in the endosome-to-Golgi retrieval of the cation-independent mannose-6-phosphate receptor, the Wntless protein and other membrane proteins of physiological significance. Retromer comprises two functional subcomplexes: the cargo-selective subcomplex is a trimer of the VPS35, VPS29, VPS26 proteins, whereas the sorting nexin proteins, Snx1 and Snx2 function to tubulate the endosomal membrane. Unlike the sorting nexins, which contain PtdIns3P-binding PX domains, the cargo-selective VPS35/29/26 complex has no lipid-binding domains and its recruitment to the endosomal membrane remains mechanistically uncharacterised. In this study we show that the VPS35/29/26 complex interacts with the small GTPase Rab7 and requires Rab7 for its recruitment to the endosome. We show that the Rab7K157N mutant that causes the peripheral neuropathy, Charcot-Marie-Tooth disease, does not interact with the VPS35/29/26 complex, resulting in a weakened association with the membrane. We have also identified a novel retromer-interacting protein, TBC1D5, which is a member of the Rab GAP family of proteins that negatively regulates VPS35/29/26 recruitment and causes Rab7 to dissociate from the membrane. We therefore propose that recruitment of the cargo-selective VPS35/29/26 complex is catalysed by Rab7 and inhibited by the Rab-GAP protein, TBC1D5.
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Affiliation(s)
- Matthew N J Seaman
- University of Cambridge, Cambridge Institute for Medical Research, Department of Clinical Biochemistry, Wellcome Trust/MRC Building, Addenbrookes Hospital, Hills Road, Cambridge CB2 0XY, UK.
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Hurd TR, Prime TA, Harbour ME, Lilley KS, Murphy MP. Detection of Reactive Oxygen Species-sensitive Thiol Proteins by Redox Difference Gel Electrophoresis. J Biol Chem 2007; 282:22040-51. [PMID: 17525152 DOI: 10.1074/jbc.m703591200] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Reactive oxygen species (ROS) produced by the mitochondrial respiratory chain can be a redox signal, but whether they affect mitochondrial function is unclear. Here we show that low levels of ROS from the respiratory chain under physiological conditions reversibly modify the thiol redox state of mitochondrial proteins involved in fatty acid and carbohydrate metabolism. As these thiol modifications were specific and occurred without bulk thiol changes, we first had to develop a sensitive technique to identify the small number of proteins modified by endogenous ROS. In this technique, redox difference gel electrophoresis, control, and redox-challenged samples are labeled with different thiol-reactive fluorescent tags and then separated on the same two-dimensional gel, enabling the sensitive detection of thiol redox modifications by changes in the relative fluorescence of the two tags within a single protein spot, followed by protein identification by mass spectrometry. Thiol redox modification affected enzyme activity, suggesting that the reversible modification of enzyme activity by ROS from the respiratory chain may be an important and unexplored mode of mitochondrial redox signaling.
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Affiliation(s)
- Thomas R Hurd
- Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge, UK
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Monné M, Robinson AJ, Boes C, Harbour ME, Fearnley IM, Kunji ERS. The mimivirus genome encodes a mitochondrial carrier that transports dATP and dTTP. J Virol 2007; 81:3181-6. [PMID: 17229695 PMCID: PMC1866048 DOI: 10.1128/jvi.02386-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the mitochondrial carrier family have been reported in eukaryotes only, where they transport metabolites and cofactors across the mitochondrial inner membrane to link the metabolic pathways of the cytosol and the matrix. The genome of the giant virus Mimiviridae mimivirus encodes a member of the mitochondrial carrier family of transport proteins. This viral protein has been expressed in Lactococcus lactis and is shown to transport dATP and dTTP. As the 1.2-Mb double-stranded DNA mimivirus genome is rich in A and T residues, we speculate that the virus is using this protein to target the host mitochondria as a source of deoxynucleotides for its replication.
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Affiliation(s)
- Magnus Monné
- Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom
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Abstract
Children with inflammatory bowel disease are known to be at risk of osteopenia. The cause of this osteopenia is likely to be multifactorial, but the inflammatory process with its characteristic overproduction of cytokines has been implicated. To investigate this possible contribution of the disease activity to the development of osteopenia, we performed in vitro assays of the proliferation of osteoblast-like cells of differing origins in response to the inflammatory cytokines tumor necrosis factor-alpha and IL-1/beta. Osteoblast-like cells derived from pediatric bone explants, adherent stromal cells derived from bone marrow (osteoprogenitors), MG-63 osteosarcoma cells, and SV-40 virally transformed osteoprogenitor cells (HCC1) were studied. Tumor necrosis factor-alpha stimulated the proliferation of cells in primary cultures (i.e. from explants and marrow samples) in a linear, dose-dependent manner. In contrast, inhibition of proliferation was observed with the established cell lines (MG-63 and HCC1). IL-1beta stimulated proliferation of all cells apart from the immortalized human bone marrow cell line, HCC1, in which case potent inhibition was observed. We conclude that proinflammatory cytokines are potent regulators of osteoblast-like cell proliferation, and that the responses are specific to cell type. The opposite results obtained with established cell lines compared with the primary cultures suggest that careful consideration should be given to choosing the most suitable cell line for in vitro studies relating to in vivo mechanisms predisposing to osteopenia.
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Affiliation(s)
- M E Harbour
- Department of Child Health, University of Wales College of Medicine, Heath Park, Cardiff, United Kingdom
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