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Jung SJ, Sridhara S, Ott M. Early steps in the biogenesis of mitochondrially encoded oxidative phosphorylation subunits. IUBMB Life 2024; 76:125-139. [PMID: 37712772 DOI: 10.1002/iub.2784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
The complexes mediating oxidative phosphorylation (OXPHOS) in the inner mitochondrial membrane consist of proteins encoded in the nuclear or the mitochondrial DNA. The mitochondrially encoded membrane proteins (mito-MPs) represent the catalytic core of these complexes and follow complicated pathways for biogenesis. Owing to their overall hydrophobicity, mito-MPs are co-translationally inserted into the inner membrane by the Oxa1 insertase. After insertion, OXPHOS biogenesis factors mediate the assembly of mito-MPs into complexes and participate in the regulation of mitochondrial translation, while protein quality control factors recognize and degrade faulty or excess proteins. This review summarizes the current understanding of these early steps occurring during the assembly of mito-MPs by concentrating on results obtained in the model organism baker's yeast.
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Affiliation(s)
- Sung-Jun Jung
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Martin Ott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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2
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Li P, Wang Z, Wang X, Liu F, Wang H. Changes in Phytohormones and Transcriptomic Reprogramming in Strawberry Leaves under Different Light Qualities. Int J Mol Sci 2024; 25:2765. [PMID: 38474012 DOI: 10.3390/ijms25052765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the phytohormones and transcriptomic reprogramming in strawberry leaves under different light qualities are still unclear. In this study, we treated strawberry plants with sunlight, sunlight covered with a 50% sunshade net, no light, blue light (460 nm), red light (660 nm), and a 50% red/50% blue LED light combination for 3 days and 7 days. Our results revealed that the light quality has an effect on the contents of Chl a and Chl b, the minimal fluorescence (F0), and the Pn of strawberry plants. The light quality also affected the contents of abscisic acid (ABA), auxin (IAA), trans-zeatin-riboside (tZ), jasmonic acid (JA), and salicylic acid (SA). RNA sequencing (RNA-seq) revealed that differentially expressed genes (DEGs) are significantly enriched in photosynthesis antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolisms, carotenoid biosynthesis, tryptophan metabolism, phenylalanine metabolism, zeatin biosynthesis, and linolenic acid metabolism. We then selected the key DEGs based on the results of a weighted gene co-expression network analysis (WGCNA) and drew nine metabolic heatmaps and protein-protein interaction networks to map light regulation.
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Affiliation(s)
- Peng Li
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Zhiqiang Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Xiaodi Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Fengzhi Liu
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Haibo Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
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3
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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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Dreishpoon MB, Bick NR, Petrova B, Warui DM, Cameron A, Booker SJ, Kanarek N, Golub TR, Tsvetkov P. FDX1 regulates cellular protein lipoylation through direct binding to LIAS. J Biol Chem 2023; 299:105046. [PMID: 37453661 PMCID: PMC10462841 DOI: 10.1016/j.jbc.2023.105046] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D, and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore-induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post-translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 directly regulates protein lipoylation by binding the lipoyl synthase (LIAS) enzyme promoting its functional binding to the lipoyl carrier protein GCSH and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss of function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling established that FDX1 loss-of-function results in the induction of both compensatory metabolism-related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-function is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting its role in cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.
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Affiliation(s)
| | - Nolan R Bick
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Boryana Petrova
- Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Douglas M Warui
- Department of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes Medical Institute, The Pennsylvania State University, State College, Pennsylvania, USA
| | | | - Squire J Booker
- Department of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes Medical Institute, The Pennsylvania State University, State College, Pennsylvania, USA
| | - Naama Kanarek
- Broad Institute of Harvard and MIT, Cambridge, USA; Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Todd R Golub
- Broad Institute of Harvard and MIT, Cambridge, USA; Harvard Medical School, Boston, Massachusetts, USA; Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
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5
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Rivett ED, Addis HG, Dietz JV, Carroll-Deaton JA, Gupta S, Foreman KL, Dang MA, Fox JL, Khalimonchuk O, Hegg EL. Evidence that the catalytic mechanism of heme a synthase involves the formation of a carbocation stabilized by a conserved glutamate. Arch Biochem Biophys 2023; 744:109665. [PMID: 37348627 PMCID: PMC10529832 DOI: 10.1016/j.abb.2023.109665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
In eukaryotes and many aerobic prokaryotes, the final step of aerobic respiration is catalyzed by an aa3-type cytochrome c oxidase, which requires a modified heme cofactor, heme a. The conversion of heme b, the prototypical cellular heme, to heme o and ultimately to heme a requires two modifications, the latter of which is conversion of a methyl group to an aldehyde, catalyzed by heme a synthase (HAS). The N- and C-terminal halves of HAS share homology, and each half contains a heme-binding site. Previous reports indicate that the C-terminal site is occupied by a heme b cofactor. The N-terminal site may function as the substrate (heme o) binding site, although this has not been confirmed experimentally. Here, we assess the role of conserved residues from the N- and C-terminal heme-binding sites in HAS from prokaryotic (Shewanella oneidensis) and eukaryotic (Saccharomyces cerevisiae) species - SoHAS/CtaA and ScHAS/Cox15, respectively. A glutamate within the N-terminal site is found to be critical for activity in both types of HAS, consistent with the hypothesis that a carbocation forms transiently during catalysis. In contrast, the residue occupying the analogous C-terminal position is dispensable for enzyme activity. In SoHAS, the C-terminal heme ligands are critical for stability, while in ScHAS, substitutions in either heme-binding site have little effect on global structure. In both species, in vivo accumulation of heme o requires the presence of an inactive HAS variant, highlighting a potential regulatory role for HAS in heme o biosynthesis.
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Affiliation(s)
- Elise D Rivett
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Hannah G Addis
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Jonathan V Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA
| | - Jayda A Carroll-Deaton
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Shipra Gupta
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Koji L Foreman
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Minh Anh Dang
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jennifer L Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA.
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA; Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, USA; Fred & Pamela Buffett Cancer Center, Omaha, NE, 68198, USA.
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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6
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Dreishpoon MB, Bick NR, Petrova B, Warui DM, Cameron A, Booker SJ, Kanarek N, Golub TR, Tsvetkov P. FDX1 regulates cellular protein lipoylation through direct binding to LIAS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.526472. [PMID: 36778498 PMCID: PMC9915701 DOI: 10.1101/2023.02.03.526472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 regulates protein lipoylation by directly binding to the lipoyl synthase (LIAS) enzyme and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss-of-function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling of cells growing in either normal or low glucose conditions established that FDX1 loss-of-function results in the induction of both compensatory metabolism related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-functions is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.
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Affiliation(s)
| | | | - Boryana Petrova
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children’s Hospital, Boston, MA USA
| | - Douglas M. Warui
- Department of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes Medical Institute, The Pennsylvania State University, PA, United States
| | | | - Squire J. Booker
- Department of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes Medical Institute, The Pennsylvania State University, PA, United States
| | - Naama Kanarek
- Broad Institute of Harvard and MIT, Cambridge, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children’s Hospital, Boston, MA USA
| | - Todd R. Golub
- Broad Institute of Harvard and MIT, Cambridge, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
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7
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Schulz V, Basu S, Freibert SA, Webert H, Boss L, Mühlenhoff U, Pierrel F, Essen LO, Warui DM, Booker SJ, Stehling O, Lill R. Functional spectrum and specificity of mitochondrial ferredoxins FDX1 and FDX2. Nat Chem Biol 2023; 19:206-217. [PMID: 36280795 PMCID: PMC10873809 DOI: 10.1038/s41589-022-01159-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/01/2022] [Indexed: 02/04/2023]
Abstract
Ferredoxins comprise a large family of iron-sulfur (Fe-S) proteins that shuttle electrons in diverse biological processes. Human mitochondria contain two isoforms of [2Fe-2S] ferredoxins, FDX1 (aka adrenodoxin) and FDX2, with known functions in cytochrome P450-dependent steroid transformations and Fe-S protein biogenesis. Here, we show that only FDX2, but not FDX1, is involved in Fe-S protein maturation. Vice versa, FDX1 is specific not only for steroidogenesis, but also for heme a and lipoyl cofactor biosyntheses. In the latter pathway, FDX1 provides electrons to kickstart the radical chain reaction catalyzed by lipoyl synthase. We also identified lipoylation as a target of the toxic antitumor copper ionophore elesclomol. Finally, the striking target specificity of each ferredoxin was assigned to small conserved sequence motifs. Swapping these motifs changed the target specificity of these electron donors. Together, our findings identify new biochemical tasks of mitochondrial ferredoxins and provide structural insights into their functional specificity.
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Affiliation(s)
- Vinzent Schulz
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Somsuvro Basu
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
- Freelance Medical Communications Consultant, Brno, Czech Republic
| | - Sven-A Freibert
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Holger Webert
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Linda Boss
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Fabien Pierrel
- Univ. of Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble, France
| | - Lars-O Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Douglas M Warui
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, USA
| | - Oliver Stehling
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany.
- Centre for Synthetic Microbiology, Synmikro, Marburg, Germany.
| | - Roland Lill
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany.
- Centre for Synthetic Microbiology, Synmikro, Marburg, Germany.
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8
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Coordination of metal center biogenesis in human cytochrome c oxidase. Nat Commun 2022; 13:3615. [PMID: 35750769 PMCID: PMC9232578 DOI: 10.1038/s41467-022-31413-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/16/2022] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial cytochrome c oxidase (CcO) or respiratory chain complex IV is a heme aa3-copper oxygen reductase containing metal centers essential for holo-complex biogenesis and enzymatic function that are assembled by subunit-specific metallochaperones. The enzyme has two copper sites located in the catalytic core subunits. The COX1 subunit harbors the CuB site that tightly associates with heme a3 while the COX2 subunit contains the binuclear CuA site. Here, we report that in human cells the CcO copper chaperones form macromolecular assemblies and cooperate with several twin CX9C proteins to control heme a biosynthesis and coordinate copper transfer sequentially to the CuA and CuB sites. These data on CcO illustrate a mechanism that regulates the biogenesis of macromolecular enzymatic assemblies with several catalytic metal redox centers and prevents the accumulation of cytotoxic reactive assembly intermediates.
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9
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Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. Nat Ecol Evol 2022; 6:630-643. [PMID: 35332281 PMCID: PMC9090980 DOI: 10.1038/s41559-022-01703-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/15/2022] [Indexed: 01/31/2023]
Abstract
Primates have adapted to numerous environments and lifestyles, but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of hematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers between populations. Compared to baboons at low altitude, we found that high-altitude geladas exhibit significantly expanded chest circumferences, potentially allowing for greater lung surface area for increased oxygen diffusion. We identified gelada-specific amino acid substitutions in the alpha-chain subunit of adult hemoglobin but found that gelada hemoglobin does not exhibit markedly altered oxygenation properties compared to lowland primates. We also found that geladas at high altitude do not exhibit elevated blood hemoglobin concentrations, in contrast to the normal acclimatization response to hypoxia in lowland primates. The absence of altitude-related polycythemia suggests that geladas are able to sustain adequate tissue-oxygen delivery despite environmental hypoxia. Finally, we identified numerous genes and genomic regions exhibiting accelerated rates of evolution, as well as gene families exhibiting expansions in the gelada lineage, potentially reflecting altitude-related selection. Our findings lend insight into putative mechanisms of high-altitude adaptation while suggesting promising avenues for functional hypoxia research.
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10
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Diversity of Cytochrome c Oxidase Assembly Proteins in Bacteria. Microorganisms 2022; 10:microorganisms10050926. [PMID: 35630371 PMCID: PMC9145763 DOI: 10.3390/microorganisms10050926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/10/2022] Open
Abstract
Cytochrome c oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form water in a reaction coupled to energy conservation. The three-subunit core of the enzyme is conserved, whereas several proteins identified to function in the biosynthesis of the common family A1 cytochrome c oxidase show diversity in bacteria. Using the model organisms Bacillus subtilis, Corynebacterium glutamicum, Paracoccus denitrificans, and Rhodobacter sphaeroides, the present review focuses on proteins for assembly of the heme a, heme a3, CuB, and CuA metal centers. The known biosynthesis proteins are, in most cases, discovered through the analysis of mutants. All proteins directly involved in cytochrome c oxidase assembly have likely not been identified in any organism. Limitations in the use of mutants to identify and functionally analyze biosynthesis proteins are discussed in the review. Comparative biochemistry helps to determine the role of assembly factors. This information can, for example, explain the cause of some human mitochondrion-based diseases and be used to find targets for new antimicrobial drugs. It also provides information regarding the evolution of aerobic bacteria.
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11
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Wikramanayake TC, Chéret J, Sevilla A, Birch-Machin M, Paus R. Targeting mitochondria in dermatological therapy: Beyond oxidative damage and skin aging. Expert Opin Ther Targets 2022; 26:233-259. [PMID: 35249436 DOI: 10.1080/14728222.2022.2049756] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The analysis of the role of the mitochondria in oxidative damage and skin aging is a significant aspect of dermatological research. Mitochondria generate most reactive oxygen species (ROS); however, excessive ROS are cytotoxic and DNA-damaging and promote (photo-)aging. ROS also possesses key physiological and regulatory functions and mitochondrial dysfunction is prominent in several skin diseases including skin cancers. Although many standard dermatotherapeutics modulate mitochondrial function, dermatological therapy rarely targets the mitochondria. Accordingly, there is a rationale for "mitochondrial dermatology"-based approaches to be applied to therapeutic research. AREAS COVERED This paper examines the functions of mitochondria in cutaneous physiology beyond energy (ATP) and ROS production. Keratinocyte differentiation and epidermal barrier maintenance, appendage morphogenesis and homeostasis, photoaging and skin cancer are considered. Based on related PubMed search results, the paper evaluates thyroid hormones, glucocorticoids, Vitamin D3 derivatives, retinoids, cannabinoid receptor agonists, PPARγ agonists, thyrotropin, and thyrotropin-releasing hormone as instructive lead compounds. Moreover, the mitochondrial protein MPZL3 as a promising new drug target for future "mitochondrial dermatology" is highlighted. EXPERT OPINION Future dermatological therapeutic research should have a mitochondrial medicine emphasis. Focusing on selected lead agents, protein targets, in silico drug design, and model diseases will fertilize a mito-centric approach.
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Affiliation(s)
- Tongyu C Wikramanayake
- Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, U.S.A.,Molecular Cell and Developmental Biology Program, University of Miami Miller School of Medicine, Miami, FL, U.S.A
| | - Jérémy Chéret
- Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, U.S.A
| | - Alec Sevilla
- Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, U.S.A
| | - Mark Birch-Machin
- Dermatological Sciences, Translational and Clinical Research Institute, and The UK National Innovation Centre for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Ralf Paus
- Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, U.S.A.,Monasterium Laboratory, Münster, Germany.,Centre for Dermatology Research, University of Manchester, and NIHR Manchester Biomedical Research Centre, Manchester, UK
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12
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Niemuth NJ, Curtis BJ, Laudadio ED, Sostare E, Bennett EA, Neureuther NJ, Mohaimani AA, Schmoldt A, Ostovich ED, Viant MR, Hamers RJ, Klaper RD. Energy Starvation in Daphnia magna from Exposure to a Lithium Cobalt Oxide Nanomaterial. Chem Res Toxicol 2021; 34:2287-2297. [PMID: 34724609 DOI: 10.1021/acs.chemrestox.1c00189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Growing evidence across organisms points to altered energy metabolism as an adverse outcome of metal oxide nanomaterial toxicity, with a mechanism of toxicity potentially related to the redox chemistry of processes involved in energy production. Despite this evidence, the significance of this mechanism has gone unrecognized in nanotoxicology due to the field's focus on oxidative stress as a universal─but nonspecific─nanotoxicity mechanism. To further explore metabolic impacts, we determined lithium cobalt oxide's (LCO's) effects on these pathways in the model organism Daphnia magna through global gene-expression analysis using RNA-Seq and untargeted metabolomics by direct-injection mass spectrometry. Our results show that a sublethal 1 mg/L 48 h exposure of D. magna to LCO nanosheets causes significant impacts on metabolic pathways versus untreated controls, while exposure to ions released over 48 h does not. Specifically, transcriptomic analysis using DAVID indicated significant enrichment (Benjamini-adjusted p ≤0.0.5) in LCO-exposed animals for changes in pathways involved in the cellular response to starvation (25 genes), mitochondrial function (70 genes), ATP-binding (70 genes), oxidative phosphorylation (53 genes), NADH dehydrogenase activity (12 genes), and protein biosynthesis (40 genes). Metabolomic analysis using MetaboAnalyst indicated significant enrichment (γ-adjusted p <0.1) for changes in amino acid metabolism (19 metabolites) and starch, sucrose, and galactose metabolism (7 metabolites). Overlap of significantly impacted pathways by RNA-Seq and metabolomics suggests amino acid breakdown and increased sugar import for energy production. Results indicate that LCO-exposed Daphnia respond to energy starvation by altering metabolic pathways, both at the gene expression and metabolite levels. These results support altered energy production as a sensitive nanotoxicity adverse outcome for LCO exposure and suggest negative impacts on energy metabolism as an important avenue for future studies of nanotoxicity, including for other biological systems and for metal oxide nanomaterials more broadly.
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Affiliation(s)
- Nicholas J Niemuth
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, Wisconsin 53204, United States
| | - Becky J Curtis
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, Wisconsin 53204, United States
| | - Elizabeth D Laudadio
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Elena Sostare
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Evan A Bennett
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, Wisconsin 53204, United States
| | - Nicklaus J Neureuther
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, Wisconsin 53204, United States
| | - Aurash A Mohaimani
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, Wisconsin 53204, United States
| | - Angela Schmoldt
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, Wisconsin 53204, United States
| | - Eric D Ostovich
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, Wisconsin 53204, United States
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Robert J Hamers
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Rebecca D Klaper
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, Wisconsin 53204, United States
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13
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Rivett ED, Heo L, Feig M, Hegg EL. Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer. Crit Rev Biochem Mol Biol 2021; 56:640-668. [PMID: 34428995 DOI: 10.1080/10409238.2021.1957668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Aerobic respiration is a key energy-producing pathway in many prokaryotes and virtually all eukaryotes. The final step of aerobic respiration is most commonly catalyzed by heme-copper oxidases embedded in the cytoplasmic or mitochondrial membrane. The majority of these terminal oxidases contain a prenylated heme (typically heme a or occasionally heme o) in the active site. In addition, many heme-copper oxidases, including mitochondrial cytochrome c oxidases, possess a second heme a cofactor. Despite the critical role of heme a in the electron transport chain, the details of the mechanism by which heme b, the prototypical cellular heme, is converted to heme o and then to heme a remain poorly understood. Recent structural investigations, however, have helped clarify some elements of heme a biosynthesis. In this review, we discuss the insight gained from these advances. In particular, we present a new structural model of heme o synthase (HOS) based on distance restraints from inferred coevolutionary relationships and refined by molecular dynamics simulations that are in good agreement with the experimentally determined structures of HOS homologs. We also analyze the two structures of heme a synthase (HAS) that have recently been solved by other groups. For both HOS and HAS, we discuss the proposed catalytic mechanisms and highlight how new insights into the heme-binding site locations shed light on previously obtained biochemical data. Finally, we explore the implications of the new structural data in the broader context of heme trafficking in the heme a biosynthetic pathway and heme-copper oxidase assembly.
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Affiliation(s)
- Elise D Rivett
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Eric L Hegg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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14
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Dietz JV, Fox JL, Khalimonchuk O. Down the Iron Path: Mitochondrial Iron Homeostasis and Beyond. Cells 2021; 10:cells10092198. [PMID: 34571846 PMCID: PMC8468894 DOI: 10.3390/cells10092198] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Cellular iron homeostasis and mitochondrial iron homeostasis are interdependent. Mitochondria must import iron to form iron–sulfur clusters and heme, and to incorporate these cofactors along with iron ions into mitochondrial proteins that support essential functions, including cellular respiration. In turn, mitochondria supply the cell with heme and enable the biogenesis of cytosolic and nuclear proteins containing iron–sulfur clusters. Impairment in cellular or mitochondrial iron homeostasis is deleterious and can result in numerous human diseases. Due to its reactivity, iron is stored and trafficked through the body, intracellularly, and within mitochondria via carefully orchestrated processes. Here, we focus on describing the processes of and components involved in mitochondrial iron trafficking and storage, as well as mitochondrial iron–sulfur cluster biogenesis and heme biosynthesis. Recent findings and the most pressing topics for future research are highlighted.
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Affiliation(s)
- Jonathan V. Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
| | - Jennifer L. Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA;
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
- Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE 68198, USA
- Correspondence:
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15
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Lee AY. Skin Pigmentation Abnormalities and Their Possible Relationship with Skin Aging. Int J Mol Sci 2021; 22:ijms22073727. [PMID: 33918445 PMCID: PMC8038212 DOI: 10.3390/ijms22073727] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Skin disorders showing abnormal pigmentation are often difficult to manage because of their uncertain etiology or pathogenesis. Abnormal pigmentation is a common symptom accompanying aging skin. The association between skin aging and skin pigmentation abnormalities can be attributed to certain inherited disorders characterized by premature aging and abnormal pigmentation in the skin and some therapeutic modalities effective for both. Several molecular mechanisms, including oxidative stress, mitochondrial DNA mutations, DNA damage, telomere shortening, hormonal changes, and autophagy impairment, have been identified as involved in skin aging. Although each of these skin aging-related mechanisms are interconnected, this review examined the role of each mechanism in skin hyperpigmentation or hypopigmentation to propose the possible association between skin aging and pigmentation abnormalities.
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Affiliation(s)
- Ai-Young Lee
- Department of Dermatology, College of Medicine, Dongguk University Ilsan Hospital, 814 Siksa-dong, Ilsandong-gu, Goyang-si 410-773, Gyeonggi-do, Korea
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16
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Functions of Cytochrome c oxidase Assembly Factors. Int J Mol Sci 2020; 21:ijms21197254. [PMID: 33008142 PMCID: PMC7582755 DOI: 10.3390/ijms21197254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022] Open
Abstract
Cytochrome c oxidase is the terminal complex of eukaryotic oxidative phosphorylation in mitochondria. This process couples the reduction of electron carriers during metabolism to the reduction of molecular oxygen to water and translocation of protons from the internal mitochondrial matrix to the inter-membrane space. The electrochemical gradient formed is used to generate chemical energy in the form of adenosine triphosphate to power vital cellular processes. Cytochrome c oxidase and most oxidative phosphorylation complexes are the product of the nuclear and mitochondrial genomes. This poses a series of topological and temporal steps that must be completed to ensure efficient assembly of the functional enzyme. Many assembly factors have evolved to perform these steps for insertion of protein into the inner mitochondrial membrane, maturation of the polypeptide, incorporation of co-factors and prosthetic groups and to regulate this process. Much of the information about each of these assembly factors has been gleaned from use of the single cell eukaryote Saccharomyces cerevisiae and also mutations responsible for human disease. This review will focus on the assembly factors of cytochrome c oxidase to highlight some of the outstanding questions in the assembly of this vital enzyme complex.
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17
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Singh AP, Salvatori R, Aftab W, Kohler A, Carlström A, Forne I, Imhof A, Ott M. Molecular Connectivity of Mitochondrial Gene Expression and OXPHOS Biogenesis. Mol Cell 2020; 79:1051-1065.e10. [PMID: 32877643 DOI: 10.1016/j.molcel.2020.07.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 01/05/2023]
Abstract
Mitochondria contain their own gene expression systems, including membrane-bound ribosomes dedicated to synthesizing a few hydrophobic subunits of the oxidative phosphorylation (OXPHOS) complexes. We used a proximity-dependent biotinylation technique, BioID, coupled with mass spectrometry to delineate in baker's yeast a comprehensive network of factors involved in biogenesis of mitochondrial encoded proteins. This mitochondrial gene expression network (MiGENet) encompasses proteins involved in transcription, RNA processing, translation, or protein biogenesis. Our analyses indicate the spatial organization of these processes, thereby revealing basic mechanistic principles and the proteins populating strategically important sites. For example, newly synthesized proteins are directly handed over to ribosomal tunnel exit-bound factors that mediate membrane insertion, co-factor acquisition, or their mounting into OXPHOS complexes in a special early assembly hub. Collectively, the data reveal the connectivity of mitochondrial gene expression, reflecting a unique tailoring of the mitochondrial gene expression system.
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Affiliation(s)
- Abeer Prakash Singh
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Roger Salvatori
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Wasim Aftab
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany; Graduate School for Quantitative Biosciences (QBM), Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Andreas Kohler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ignasi Forne
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden.
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18
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Abstract
The integral membrane protein heme A synthase (HAS) catalyzes the biosynthesis of heme A, which is a prerequisite for cellular respiration in a wide range of aerobic organisms. Previous studies have revealed that HAS can form homo-oligomeric complexes, and this oligomerization appears to be evolutionarily conserved among prokaryotes and eukaryotes and is shown to be essential for the biological function of eukaryotic HAS. Despite its importance, little is known about the detailed structural properties of HAS oligomers. Here, we aimed to address this critical issue by analyzing the oligomeric state of HAS from Aquifex aeolicus (AaHAS) using a combination of techniques, including size exclusion chromatography coupled with multiangle light scattering (SEC-MALS), cross-linking, laser-induced liquid bead ion desorption mass spectrometry (LILBID-MS), and single-particle electron cryomicroscopy (cryo-EM). Our results show that HAS forms a thermostable trimeric complex. A cryo-EM density map provides information on the oligomerization interface of the AaHAS trimer. These results provide structural insights into HAS multimerization and expand our knowledge of this important enzyme.IMPORTANCE Heme A is a vital redox cofactor unique for the terminal cytochrome c oxidase in mitochondria and many microorganisms. It plays a key role in oxygen reduction by serving as an electron carrier and as the oxygen-binding site. Heme A is synthesized from heme O by an integral membrane protein, heme A synthase (HAS). Defects in HAS impair cellular respiration and have been linked to various human diseases, e.g., fatal infantile hypertrophic cardiomyopathy and Leigh syndrome. HAS exists as a stable oligomeric complex, and studies have shown that oligomerization of eukaryotic HAS is necessary for its proper function. However, the molecular architecture of the HAS oligomeric complex has remained uncharacterized. The present study shows that HAS forms trimers and reveals how the oligomeric arrangement contributes to the complex stability and flexibility, enabling HAS to perform its catalytic function effectively. This work provides the basic understanding for future studies on heme A biosynthesis.
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19
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Sreedhar A, Aguilera-Aguirre L, Singh KK. Mitochondria in skin health, aging, and disease. Cell Death Dis 2020; 11:444. [PMID: 32518230 PMCID: PMC7283348 DOI: 10.1038/s41419-020-2649-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 02/08/2023]
Abstract
The skin is a high turnover organ, and its constant renewal depends on the rapid proliferation of its progenitor cells. The energy requirement for these metabolically active cells is met by mitochondrial respiration, an ATP generating process driven by a series of protein complexes collectively known as the electron transport chain (ETC) that is located on the inner membrane of the mitochondria. However, reactive oxygen species (ROS) like superoxide, singlet oxygen, peroxides are inevitably produced during respiration and disrupt macromolecular and cellular structures if not quenched by the antioxidant system. The oxidative damage caused by mitochondrial ROS production has been established as the molecular basis of multiple pathophysiological conditions, including aging and cancer. Not surprisingly, the mitochondria are the primary organelle affected during chronological and UV-induced skin aging, the phenotypic manifestations of which are the direct consequence of mitochondrial dysfunction. Also, deletions and other aberrations in the mitochondrial DNA (mtDNA) are frequent in photo-aged skin and skin cancer lesions. Recent studies have revealed a more innate role of the mitochondria in maintaining skin homeostasis and pigmentation, which are affected when the essential mitochondrial functions are impaired. Some common and rare skin disorders have a mitochondrial involvement and include dermal manifestations of primary mitochondrial diseases as well as congenital skin diseases caused by damaged mitochondria. With studies increasingly supporting the close association between mitochondria and skin health, its therapeutic targeting in the skin-either via an ATP production boost or free radical scavenging-has gained attention from clinicians and aestheticians alike. Numerous bioactive compounds have been identified that improve mitochondrial functions and have proved effective against aged and diseased skin. In this review, we discuss the essential role of mitochondria in regulating normal and abnormal skin physiology and the possibility of targeting this organelle in various skin disorders.
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Affiliation(s)
| | | | - Keshav K Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
- Integartive Center For Aging Research and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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20
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From Synthesis to Utilization: The Ins and Outs of Mitochondrial Heme. Cells 2020; 9:cells9030579. [PMID: 32121449 PMCID: PMC7140478 DOI: 10.3390/cells9030579] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 12/14/2022] Open
Abstract
Heme is a ubiquitous and essential iron containing metallo-organic cofactor required for virtually all aerobic life. Heme synthesis is initiated and completed in mitochondria, followed by certain covalent modifications and/or its delivery to apo-hemoproteins residing throughout the cell. While the biochemical aspects of heme biosynthetic reactions are well understood, the trafficking of newly synthesized heme—a highly reactive and inherently toxic compound—and its subsequent delivery to target proteins remain far from clear. In this review, we summarize current knowledge about heme biosynthesis and trafficking within and outside of the mitochondria.
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21
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Mitochondrial dysfunctions trigger the calcium signaling-dependent fungal multidrug resistance. Proc Natl Acad Sci U S A 2019; 117:1711-1721. [PMID: 31811023 DOI: 10.1073/pnas.1911560116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Drug resistance in fungal pathogens has risen steadily over the past decades due to long-term azole therapy or triazole usage in agriculture. Modification of the drug target protein to prevent drug binding is a major recognized route to induce drug resistance. However, mechanisms for nondrug target-induced resistance remain only loosely defined. Here, we explore the molecular mechanisms of multidrug resistance resulted from an efficient adaptation strategy for survival in drug environments in the human pathogen Aspergillus fumigatus We show that mutants conferring multidrug resistance are linked with mitochondrial dysfunction induced by defects in heme A biosynthesis. Comparison of the gene expression profiles between the drug-resistant mutants and the parental wild-type strain shows that multidrug-resistant transporters, chitin synthases, and calcium-signaling-related genes are significantly up-regulated, while scavenging mitochondrial reactive oxygen species (ROS)-related genes are significantly down-regulated. The up-regulated-expression genes share consensus calcium-dependent serine threonine phosphatase-dependent response elements (the binding sites of calcium-signaling transcription factor CrzA). Accordingly, drug-resistant mutants show enhanced cytosolic Ca2+ transients and persistent nuclear localization of CrzA. In comparison, calcium chelators significantly restore drug susceptibility and increase azole efficacy either in laboratory-derived or in clinic-isolated A. fumigatus strains. Thus, the mitochondrial dysfunction as a fitness cost can trigger calcium signaling and, therefore, globally up-regulate a series of embedding calcineurin-dependent-response-element genes, leading to antifungal resistance. These findings illuminate how fitness cost affects drug resistance and suggest that disruption of calcium signaling might be a promising therapeutic strategy to fight against nondrug target-induced drug resistance.
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22
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Responses of unicellular predators to cope with the phototoxicity of photosynthetic prey. Nat Commun 2019; 10:5606. [PMID: 31811209 PMCID: PMC6898599 DOI: 10.1038/s41467-019-13568-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/14/2019] [Indexed: 12/22/2022] Open
Abstract
Feeding on unicellular photosynthetic organisms by unicellular eukaryotes is the base of the aquatic food chain and evolutionarily led to the establishment of photosynthetic endosymbionts/organelles. Photosynthesis generates reactive oxygen species and damages cells; thus, photosynthetic organisms possess several mechanisms to cope with the stress. Here, we demonstrate that photosynthetic prey also exposes unicellular amoebozoan and excavates predators to photosynthetic oxidative stress. Upon illumination, there is a commonality in transcriptomic changes among evolutionarily distant organisms feeding on photosynthetic prey. One of the genes commonly upregulated is a horizontally transferred homolog of algal and plant genes for chlorophyll degradation/detoxification. In addition, the predators reduce their phagocytic uptake while accelerating digestion of photosynthetic prey upon illumination, reducing the number of photosynthetic cells inside the predator cells, as this also occurs in facultative endosymbiotic associations upon certain stresses. Thus, some mechanisms in predators observed here probably have been necessary for evolution of endosymbiotic associations. Photosynthesis generates reactive oxygen species that can damage cells. Here, the authors show that unicellular predators of photosynthetic prey have shared responses to photosynthetic oxidative stress and these may also have been important for the evolution of endosymbiosis.
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23
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Franco LVR, Su CH, McStay GP, Yu GJ, Tzagoloff A. Cox2p of yeast cytochrome oxidase assembles as a stand-alone subunit with the Cox1p and Cox3p modules. J Biol Chem 2018; 293:16899-16911. [PMID: 30224355 DOI: 10.1074/jbc.ra118.004138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/11/2018] [Indexed: 11/06/2022] Open
Abstract
Cytochrome oxidase (COX) is a hetero-oligomeric complex of the mitochondrial inner membrane that reduces molecular oxygen to water, a reaction coupled to proton transfer from the mitochondrial matrix to the intermembrane space. In the yeast Saccharomyces cerevisiae, COX is composed of 11-13 different polypeptide subunits. Here, using pulse labeling of mitochondrial gene products in isolated yeast mitochondria, combined with purification of tagged COX subunits and ancillary factors, we studied the Cox2p assembly intermediates. Analysis of radiolabeled Cox2p obtained in pulldown assays by native gel electrophoresis revealed the existence of several assembly intermediates, the largest of which had an estimated mass of 450-550 kDa. None of the other known subunits of COX were present in these Cox2p intermediates. This was also true for the several ancillary factors having still undefined functions in COX assembly. In agreement with earlier evidence, Cox18p and Cox20p, previously shown to be involved in processing and in membrane insertion of the Cox2p precursor, were found to be associated with the two largest Cox2p intermediates. A small fraction of the Cox2p module contained Sco1p and Coa6p, which have been implicated in metalation of the binuclear copper site on this subunit. Our results indicate that following its insertion into the mitochondrial inner membrane, Cox2p assembles as a stand-alone protein with the compositionally more complex Cox1p and Cox3p modules.
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Affiliation(s)
- Leticia Veloso R Franco
- From the Department of Biological Sciences, Columbia University, New York, New York 10027 and
| | - Chen-Hsien Su
- From the Department of Biological Sciences, Columbia University, New York, New York 10027 and
| | - Gavin P McStay
- Department of Biological Sciences, Staffordshire University, Stoke-on-Trent, ST4 2DF, United Kingdom
| | - George J Yu
- From the Department of Biological Sciences, Columbia University, New York, New York 10027 and
| | - Alexander Tzagoloff
- From the Department of Biological Sciences, Columbia University, New York, New York 10027 and
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24
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Herwaldt EJ, Rivett ED, White AJ, Hegg EL. Cox15 interacts with the cytochrome bc 1 dimer within respiratory supercomplexes as well as in the absence of cytochrome c oxidase. J Biol Chem 2018; 293:16426-16439. [PMID: 30181213 DOI: 10.1074/jbc.ra118.002496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 08/15/2018] [Indexed: 11/06/2022] Open
Abstract
The heme a molecule is an obligatory cofactor in the terminal enzyme complex of the electron transport chain, cytochrome c oxidase. Heme a is synthesized from heme o by a multi-spanning inner membrane protein, heme a synthase (Cox15 in the yeast Saccharomyces cerevisiae). The insertion of heme a is critical for cytochrome c oxidase function and assembly, but this process has not been fully elucidated. To improve our understanding of heme a insertion into cytochrome c oxidase, here we investigated the protein-protein interactions that involve Cox15 in S. cerevisiae In addition to observing Cox15 in homooligomeric complexes, we found that a portion of Cox15 also associates with the mitochondrial respiratory supercomplexes. When supercomplex formation was abolished, as in the case of stalled cytochrome bc 1 or cytochrome c oxidase assembly, Cox15 maintained an interaction with select proteins from both respiratory complexes. In the case of stalled cytochrome bc 1 assembly, Cox15 interacted with the late-assembling cytochrome c oxidase subunit, Cox13. When cytochrome c oxidase assembly was stalled, Cox15 unexpectedly maintained its interaction with the cytochrome bc 1 protein, Cor1. Our results indicate that Cox15 and Cor1 continue to interact in the cytochrome bc 1 dimer even in the absence of supercomplexes or when the supercomplexes are destabilized. These findings reveal that Cox15 not only associates with respiratory supercomplexes, but also interacts with the cytochrome bc 1 dimer even in the absence of cytochrome c oxidase.
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Affiliation(s)
- Emily J Herwaldt
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Elise D Rivett
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Antoineen J White
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Eric L Hegg
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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25
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From B to A: making an essential cofactor in a human parasite. Biochem J 2017; 474:3089-3092. [PMID: 28860337 DOI: 10.1042/bcj20170446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/17/2022]
Abstract
Trypanosomatids are parasitic eukaryotic organisms that cause human disease. These organisms have complex lifestyles; cycling between vertebrate and insect hosts and alternating between two morphologies; a replicating form and an infective, nonreplicating one. Because trypanosomatids are one of the few organisms that do not synthesize the essential cofactor, heme, these parasites sequester the most common form, heme B, from their hosts. Once acquired, the parasites derivatize heme B to heme A by two sequential enzyme reactions. Although heme C is found in many cytochrome c and c1 proteins, heme A is the cofactor of only one known protein, cytochrome c oxidase (CcO). In a recent issue of the Biochemical Journal, Merli et al. [Biochem. J. (2017) 474, 2315-2332] demonstrate that the final step in the synthesis of heme A by heme A synthase (TcCox15) and the subsequent activity of CcO are essential for infectivity and replication of Trypanosoma cruzi.
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26
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Su CH, Tzagoloff A. Cox16 protein is physically associated with Cox1p assembly intermediates and with cytochrome oxidase. J Biol Chem 2017; 292:16277-16283. [PMID: 28821616 DOI: 10.1074/jbc.m117.801811] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/16/2017] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial cytochrome oxidase (COX) catalyzes the last step in the respiratory pathway. In the yeast Saccharomyces cerevisiae, this inner membrane complex is composed of 11 protein subunits. Expression of COX is assisted by some two dozen ancillary proteins that intercede at different stages of the assembly pathway. One such protein, Cox16p, encoded by COX16, was shown to be essential for the activity and assembly of COX. The function of Cox16p, however, has not been determined. We present evidence that Cox16p is present in Cox1p assembly intermediates and in COX. This is based on the finding that Cox16p, tagged with a dual polyhistidine and protein C tag, co-immunopurified with Cox1p assembly intermediates. The pulldown assays also indicated the presence of Cox16p in mature COX and in supercomplexes consisting of COX and the bc1 complex. From the Western signal strengths, Cox16p appears to be substoichiometric with Cox1p and Cox4p, which could indicate that Cox16p is only present in a fraction of COX. In conclusion, our results indicate that Cox16p is a constituent of several Cox1p assembly intermediates and of COX.
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Affiliation(s)
- Chen-Hsien Su
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Alexander Tzagoloff
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
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27
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Singhal RK, Kruse C, Heidler J, Strecker V, Zwicker K, Düsterwald L, Westermann B, Herrmann JM, Wittig I, Rapaport D. Coi1 is a novel assembly factor of the yeast complex III-complex IV supercomplex. Mol Biol Cell 2017; 28:mbc.E17-02-0093. [PMID: 28794267 PMCID: PMC5620370 DOI: 10.1091/mbc.e17-02-0093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 01/30/2023] Open
Abstract
The yeast bc1 complex (complex III) and cytochrome oxidase (complex IV) are mosaics of core subunits encoded by the mitochondrial genome and additional nuclear-encoded proteins imported from the cytosol. Both complexes build in the mitochondrial inner membrane various supramolecular assemblies. The formation of the individual complexes and their supercomplexes depends on the activity of dedicated assembly factors. We identified a so far uncharacterized mitochondrial protein (open reading frame YDR381C-A) as an important assembly factor for complex III, complex IV, and their supercomplexes. Therefore, we named this protein Cox interacting (Coi) 1. Deletion of COI1 results in decreased respiratory growth, reduced membrane potential, and hampered respiration, as well as slow fermentative growth at low temperature. In addition, coi1Δ cells harbour reduced steady-state levels of subunits of complexes III and IV as well as of the assembled complexes and supercomplexes. Interaction of Coi1 with respiratory chain subunits seems transient, as it appears to be a stoichiometric subunit neither of complex III nor of complex IV. Collectively, this work identifies a novel protein that plays a role in the assembly of the mitochondrial respiratory chain.
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Affiliation(s)
- Ravi K Singhal
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Christine Kruse
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Valentina Strecker
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
| | - Klaus Zwicker
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Lea Düsterwald
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | | | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University, Frankfurt am Main, Germany
- Cluster of Excellence "Macromolecular Complexes", Goethe University, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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28
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Abstract
The ATP production (oxidative phosphorylation) involves five complexes embedded in the inner membrane of mitochondria. The yeast Saccharomyces cerevisiae is mainly used as a model for the study of oxidative phosphorylation; mutants are easy to produce and are still viable due to their ability to grow using the fermentation pathway. Here, we present a process for analyzing mitochondrial respiratory complexes using native electrophoresis (BN-PAGE) coupled to LC-MS/MS. BN-PAGE (1) permits the separation of functional respiratory complexes, thus allowing in-gel activity detection of most of the respiratory complexes and (2) provides convenient samples for bottom-up proteomics. Combining BN-PAGE and LC-MS/MS leads to the identification of the subunit composition of membrane complexes and offers the possibility of highlighting potential interacting proteins.
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Heme A synthesis and CcO activity are essential for Trypanosoma cruzi infectivity and replication. Biochem J 2017; 474:2315-2332. [DOI: 10.1042/bcj20170084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 11/17/2022]
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, presents a complex life cycle and adapts its metabolism to nutrients’ availability. Although T. cruzi is an aerobic organism, it does not produce heme. This cofactor is acquired from the host and is distributed and inserted into different heme-proteins such as respiratory complexes in the parasite's mitochondrion. It has been proposed that T. cruzi's energy metabolism relies on a branched respiratory chain with a cytochrome c oxidase-type aa3 (CcO) as the main terminal oxidase. Heme A, the cofactor for all eukaryotic CcO, is synthesized via two sequential enzymatic reactions catalyzed by heme O synthase (HOS) and heme A synthase (HAS). Previously, TcCox10 and TcCox15 (Trypanosoma cruzi Cox10 and Cox15 proteins) were identified in T. cruzi. They presented HOS and HAS activity, respectively, when they were expressed in yeast. Here, we present the first characterization of TcCox15 in T. cruzi, confirming its role as HAS. It was differentially detected in the different T. cruzi stages, being more abundant in the replicative forms. This regulation could reflect the necessity of more heme A synthesis, and therefore more CcO activity at the replicative stages. Overexpression of a non-functional mutant caused a reduction in heme A content. Moreover, our results clearly showed that this hindrance in the heme A synthesis provoked a reduction on CcO activity and, in consequence, an impairment on T. cruzi survival, proliferation and infectivity. This evidence supports that T. cruzi depends on the respiratory chain activity along its life cycle, being CcO an essential terminal oxidase.
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30
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Tissue- and Condition-Specific Isoforms of Mammalian Cytochrome c Oxidase Subunits: From Function to Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1534056. [PMID: 28593021 PMCID: PMC5448071 DOI: 10.1155/2017/1534056] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/29/2017] [Indexed: 01/05/2023]
Abstract
Cytochrome c oxidase (COX) is the terminal enzyme of the electron transport chain and catalyzes the transfer of electrons from cytochrome c to oxygen. COX consists of 14 subunits, three and eleven encoded, respectively, by the mitochondrial and nuclear DNA. Tissue- and condition-specific isoforms have only been reported for COX but not for the other oxidative phosphorylation complexes, suggesting a fundamental requirement to fine-tune and regulate the essentially irreversible reaction catalyzed by COX. This article briefly discusses the assembly of COX in mammals and then reviews the functions of the six nuclear-encoded COX subunits that are expressed as isoforms in specialized tissues including those of the liver, heart and skeletal muscle, lung, and testes: COX IV-1, COX IV-2, NDUFA4, NDUFA4L2, COX VIaL, COX VIaH, COX VIb-1, COX VIb-2, COX VIIaH, COX VIIaL, COX VIIaR, COX VIIIH/L, and COX VIII-3. We propose a model in which the isoforms mediate the interconnected regulation of COX by (1) adjusting basal enzyme activity to mitochondrial capacity of a given tissue; (2) allosteric regulation to adjust energy production to need; (3) altering proton pumping efficiency under certain conditions, contributing to thermogenesis; (4) providing a platform for tissue-specific signaling; (5) stabilizing the COX dimer; and (6) modulating supercomplex formation.
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31
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García-Villegas R, Camacho-Villasana Y, Shingú-Vázquez MÁ, Cabrera-Orefice A, Uribe-Carvajal S, Fox TD, Pérez-Martínez X. The Cox1 C-terminal domain is a central regulator of cytochrome c oxidase biogenesis in yeast mitochondria. J Biol Chem 2017; 292:10912-10925. [PMID: 28490636 DOI: 10.1074/jbc.m116.773077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
Cytochrome c oxidase (CcO) is the last electron acceptor in the respiratory chain. The CcO core is formed by mitochondrial DNA-encoded Cox1, Cox2, and Cox3 subunits. Cox1 synthesis is highly regulated; for example, if CcO assembly is blocked, Cox1 synthesis decreases. Mss51 activates translation of COX1 mRNA and interacts with Cox1 protein in high-molecular-weight complexes (COA complexes) to form the Cox1 intermediary assembly module. Thus, Mss51 coordinates both Cox1 synthesis and assembly. We previously reported that the last 15 residues of the Cox1 C terminus regulate Cox1 synthesis by modulating an interaction of Mss51 with Cox14, another component of the COA complexes. Here, using site-directed mutagenesis of the mitochondrial COX1 gene from Saccharomyces cerevisiae, we demonstrate that mutations P521A/P522A and V524E disrupt the regulatory role of the Cox1 C terminus. These mutations, as well as C terminus deletion (Cox1ΔC15), reduced binding of Mss51 and Cox14 to COA complexes. Mss51 was enriched in a translationally active form that maintains full Cox1 synthesis even if CcO assembly is blocked in these mutants. Moreover, Cox1ΔC15, but not Cox1-P521A/P522A and Cox1-V524E, promoted formation of aberrant supercomplexes in CcO assembly mutants lacking Cox2 or Cox4 subunits. The aberrant supercomplex formation depended on the presence of cytochrome b and Cox3, supporting the idea that supercomplex assembly factors associate with Cox3 and demonstrating that supercomplexes can be formed even if CcO is inactive and not fully assembled. Our results indicate that the Cox1 C-terminal end is a key regulator of CcO biogenesis and that it is important for supercomplex formation/stability.
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Affiliation(s)
- Rodolfo García-Villegas
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Yolanda Camacho-Villasana
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Miguel Ángel Shingú-Vázquez
- the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Alfredo Cabrera-Orefice
- the Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands, and
| | - Salvador Uribe-Carvajal
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Thomas D Fox
- the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Xochitl Pérez-Martínez
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico,
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32
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Mutated PET117 causes complex IV deficiency and is associated with neurodevelopmental regression and medulla oblongata lesions. Hum Genet 2017; 136:759-769. [PMID: 28386624 PMCID: PMC5429353 DOI: 10.1007/s00439-017-1794-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/31/2017] [Indexed: 10/30/2022]
Abstract
The genetic basis of the many progressive, multi systemic, mitochondrial diseases that cause a lack of cellular ATP production is heterogeneous, with defects found both in the mitochondrial genome as well as in the nuclear genome. Many different mutations have been found in the genes encoding subunits of the enzyme complexes of the oxidative phosphorylation system. In addition, mutations in genes encoding proteins involved in the assembly of these complexes are known to cause mitochondrial disorders. Here we describe two sisters with a mitochondrial disease characterized by lesions in the medulla oblongata, as demonstrated by brain magnetic resonance imaging, and an isolated complex IV deficiency and reduced levels of individual complex IV subunits. Whole exome sequencing revealed a homozygous nonsense mutation resulting in a premature stop codon in the gene encoding Pet117, a small protein that has previously been predicted to be a complex IV assembly factor. PET117 has not been identified as a mitochondrial disease gene before. Lentiviral complementation of patient fibroblasts with wild-type PET117 restored the complex IV deficiency, proving that the gene defect is responsible for the complex IV deficiency in the patients, and indicating a pivotal role of this protein in the proper functioning of complex IV. Although previous studies had suggested a possible role of this protein in the insertion of copper into complex IV, studies in patient fibroblasts could not confirm this. This case presentation thus implicates mutations in PET117 as a novel cause of mitochondrial disease.
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33
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Cytochrome c Oxidase Biogenesis and Metallochaperone Interactions: Steps in the Assembly Pathway of a Bacterial Complex. PLoS One 2017; 12:e0170037. [PMID: 28107462 PMCID: PMC5249081 DOI: 10.1371/journal.pone.0170037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/27/2016] [Indexed: 12/31/2022] Open
Abstract
Biogenesis of mitochondrial cytochrome c oxidase (COX) is a complex process involving the coordinate expression and assembly of numerous subunits (SU) of dual genetic origin. Moreover, several auxiliary factors are required to recruit and insert the redox-active metal compounds, which in most cases are buried in their protein scaffold deep inside the membrane. Here we used a combination of gel electrophoresis and pull-down assay techniques in conjunction with immunostaining as well as complexome profiling to identify and analyze the composition of assembly intermediates in solubilized membranes of the bacterium Paracoccus denitrificans. Our results show that the central SUI passes through at least three intermediate complexes with distinct subunit and cofactor composition before formation of the holoenzyme and its subsequent integration into supercomplexes. We propose a model for COX biogenesis in which maturation of newly translated COX SUI is initially assisted by CtaG, a chaperone implicated in CuB site metallation, followed by the interaction with the heme chaperone Surf1c to populate the redox-active metal-heme centers in SUI. Only then the remaining smaller subunits are recruited to form the mature enzyme which ultimately associates with respiratory complexes I and III into supercomplexes.
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34
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Taylor NG, Swenson S, Harris NJ, Germany EM, Fox JL, Khalimonchuk O. The Assembly Factor Pet117 Couples Heme a Synthase Activity to Cytochrome Oxidase Assembly. J Biol Chem 2016; 292:1815-1825. [PMID: 27998984 DOI: 10.1074/jbc.m116.766980] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/13/2016] [Indexed: 11/06/2022] Open
Abstract
Heme a is an essential metalloporphyrin cofactor of the mitochondrial respiratory enzyme cytochrome c oxidase (CcO). Its synthesis from heme b requires several enzymes, including the evolutionarily conserved heme a synthase (Cox15). Oligomerization of Cox15 appears to be important for the process of heme a biosynthesis and transfer to maturing CcO. However, the details of this process remain elusive, and the roles of any additional CcO assembly factors that may be involved remain unclear. Here we report the systematic analysis of one such uncharacterized assembly factor, Pet117, and demonstrate in Saccharomyces cerevisiae that this evolutionarily conserved protein is necessary for Cox15 oligomerization and function. Pet117 is shown to reside in the mitochondrial matrix, where it is associated with the inner membrane. Pet117 functions at the later maturation stages of the core CcO subunit Cox1 that precede Cox1 hemylation. Pet117 also physically interacts with Cox15 and specifically mediates the stability of Cox15 oligomeric complexes. This Cox15-Pet117 interaction observed by co-immunoprecipitation persists in the absence of heme a synthase activity, is dependent upon Cox1 synthesis and early maturation steps, and is further dependent upon the presence of the matrix-exposed, unstructured linker region of Cox15 needed for Cox15 oligomerization, suggesting that this region mediates the interaction or that the interaction is lost when Cox15 is unable to oligomerize. Based on these findings, it was concluded that Pet117 mediates coupling of heme a synthesis to the CcO assembly process in eukaryotes.
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Affiliation(s)
- Nicholas G Taylor
- From the Department of Chemistry and Biochemistry, College of Charleston, Charleston, South Carolina 29424
| | - Samantha Swenson
- the Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | - Nicholas J Harris
- From the Department of Chemistry and Biochemistry, College of Charleston, Charleston, South Carolina 29424
| | - Edward M Germany
- the Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | - Jennifer L Fox
- From the Department of Chemistry and Biochemistry, College of Charleston, Charleston, South Carolina 29424.
| | - Oleh Khalimonchuk
- the Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588.
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35
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Ribosome-Associated Mba1 Escorts Cox2 from Insertion Machinery to Maturing Assembly Intermediates. Mol Cell Biol 2016; 36:2782-2793. [PMID: 27550809 PMCID: PMC5086520 DOI: 10.1128/mcb.00361-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/08/2016] [Accepted: 08/17/2016] [Indexed: 01/25/2023] Open
Abstract
The three conserved core subunits of the cytochrome c oxidase are encoded by mitochondria in close to all eukaryotes. The Cox2 subunit spans the inner membrane twice, exposing the N and C termini to the intermembrane space. For this, the N terminus is exported cotranslationally by Oxa1 and subsequently undergoes proteolytic maturation in Saccharomyces cerevisiae. Little is known about the translocation of the C terminus, but Cox18 has been identified to be a critical protein in this process. Here we find that the scaffold protein Cox20, which promotes processing of Cox2, is in complex with the ribosome receptor Mba1 and translating mitochondrial ribosomes in a Cox2-dependent manner. The Mba1-Cox20 complex accumulates when export of the C terminus of Cox2 is blocked by the loss of the Cox18 protein. While Cox20 engages with Cox18, Mba1 is no longer present at this stage. Our analyses indicate that Cox20 associates with nascent Cox2 and Mba1 to promote Cox2 maturation cotranslationally. We suggest that Mba1 stabilizes the Cox20-ribosome complex and supports the handover of Cox2 to the Cox18 tail export machinery.
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36
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Callegari S, Richter F, Chojnacka K, Jans DC, Lorenzi I, Pacheu-Grau D, Jakobs S, Lenz C, Urlaub H, Dudek J, Chacinska A, Rehling P. TIM29 is a subunit of the human carrier translocase required for protein transport. FEBS Lett 2016; 590:4147-4158. [PMID: 27718247 PMCID: PMC5215392 DOI: 10.1002/1873-3468.12450] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 09/21/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022]
Abstract
Hydrophobic inner mitochondrial membrane proteins with internal targeting signals, such as the metabolite carriers, use the carrier translocase (TIM22 complex) for transport into the inner membrane. Defects in this transport pathway have been associated with neurodegenerative disorders. While the TIM22 complex is well studied in baker's yeast, very little is known about the mammalian TIM22 complex. Using immunoprecipitation, we purified the human carrier translocase and identified a mitochondrial inner membrane protein TIM29 as a novel component, specific to metazoa. We show that TIM29 is a constituent of the 440 kDa TIM22 complex and interacts with oxidized TIM22. Our analyses demonstrate that TIM29 is required for the structural integrity of the TIM22 complex and for import of substrate proteins by the carrier translocase.
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Affiliation(s)
- Sylvie Callegari
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | - Frank Richter
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | | | - Daniel C Jans
- Department of NanoBiophotonics, Mitochondrial Structure and Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, Germany
| | - Isotta Lorenzi
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | - David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Mitochondrial Structure and Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Germany
| | - Jan Dudek
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | | | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany.,MaxPlanck Institute for Biophysical Chemistry, Göttingen, Germany
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37
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Richter-Dennerlein R, Oeljeklaus S, Lorenzi I, Ronsör C, Bareth B, Schendzielorz AB, Wang C, Warscheid B, Rehling P, Dennerlein S. Mitochondrial Protein Synthesis Adapts to Influx of Nuclear-Encoded Protein. Cell 2016; 167:471-483.e10. [PMID: 27693358 PMCID: PMC5055049 DOI: 10.1016/j.cell.2016.09.003] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/01/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022]
Abstract
Mitochondrial ribosomes translate membrane integral core subunits of the oxidative phosphorylation system encoded by mtDNA. These translation products associate with nuclear-encoded, imported proteins to form enzyme complexes that produce ATP. Here, we show that human mitochondrial ribosomes display translational plasticity to cope with the supply of imported nuclear-encoded subunits. Ribosomes expressing mitochondrial-encoded COX1 mRNA selectively engage with cytochrome c oxidase assembly factors in the inner membrane. Assembly defects of the cytochrome c oxidase arrest mitochondrial translation in a ribosome nascent chain complex with a partially membrane-inserted COX1 translation product. This complex represents a primed state of the translation product that can be retrieved for assembly. These findings establish a mammalian translational plasticity pathway in mitochondria that enables adaptation of mitochondrial protein synthesis to the influx of nuclear-encoded subunits. Mitochondrial ribosomes display translational plasticity COX1 translation in mitochondria is stalled in the absence of nuclear-encoded COX4 A ribosome nascent chain complex of COX1 is a primed state for complex IV assembly MITRAC regulates translation via COX1 ribosome nascent chain complexes interaction
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Affiliation(s)
- Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Faculty of Biology, University Freiburg, 79104 Freiburg, Germany
| | - Isotta Lorenzi
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | - Christin Ronsör
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | - Bettina Bareth
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | | | - Cong Wang
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty of Biology, University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Centre Göttingen, GZMB, 37073 Göttingen, Germany
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38
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Römpler K, Müller T, Juris L, Wissel M, Vukotic M, Hofmann K, Deckers M. Overlapping Role of Respiratory Supercomplex Factor Rcf2 and Its N-terminal Homolog Rcf3 in Saccharomyces cerevisiae. J Biol Chem 2016; 291:23769-23778. [PMID: 27662906 DOI: 10.1074/jbc.m116.734665] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial electron transport chain consists of individual protein complexes arranged into large macromolecular structures, termed respiratory chain supercomplexes or respirasomes. In the yeast Saccharomyces cerevisiae, respiratory chain supercomplexes form by association of the bc1 complex with the cytochrome c oxidase. Formation and maintenance of these assemblies are promoted by specific respiratory supercomplex factors, the Rcf proteins. For these proteins a regulatory function in bridging the electron transfer within supercomplexes has been proposed. Here we report on the maturation of Rcf2 into an N- and C-terminal peptide. We show that the previously uncharacterized Rcf3 (YBR255c-A) is a homolog of the N-terminal Rcf2 peptide, whereas Rcf1 is homologous to the C-terminal portion. Both Rcf3 and the C-terminal fragment of Rcf2 associate with monomeric cytochrome c oxidase and respiratory chain supercomplexes. A lack of Rcf2 and Rcf3 increases oxygen flux through the respiratory chain by up-regulation of the cytochrome c oxidase activity. A double gene deletion of RCF2 and RCF3 affects cellular survival under non-fermentable growth conditions, suggesting an overlapping role for both proteins in the regulation of the OXPHOS activity. Furthermore, our data suggest an association of all three Rcf proteins with the bc1 complex in the absence of a functional cytochrome c oxidase and identify a supercomplex independent interaction network of the Rcf proteins.
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Affiliation(s)
- Katharina Römpler
- From the Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany and
| | - Tobias Müller
- From the Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany and
| | - Lisa Juris
- From the Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany and
| | - Mirjam Wissel
- From the Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany and
| | - Milena Vukotic
- From the Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany and
| | - Kay Hofmann
- the Institute for Genetics, University of Cologne, D-50674 Cologne, Germany
| | - Markus Deckers
- From the Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany and
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39
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Bareth B, Nikolov M, Lorenzi I, Hildenbeutel M, Mick DU, Helbig C, Urlaub H, Ott M, Rehling P, Dennerlein S. Oms1 associates with cytochrome c oxidase assembly intermediates to stabilize newly synthesized Cox1. Mol Biol Cell 2016; 27:1570-80. [PMID: 27030670 PMCID: PMC4865315 DOI: 10.1091/mbc.e15-12-0811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial cytochrome c oxidase assembles in the inner membrane from subunits of dual genetic origin. The assembly process of the enzyme is initiated by membrane insertion of the mitochondria-encoded Cox1 subunit. During complex maturation, transient assembly intermediates, consisting of structural subunits and specialized chaperone-like assembly factors, are formed. In addition, cofactors such as heme and copper have to be inserted into the nascent complex. To regulate the assembly process, the availability of Cox1 is under control of a regulatory feedback cycle in which translation of COX1 mRNA is stalled when assembly intermediates of Cox1 accumulate through inactivation of the translational activator Mss51. Here we isolate a cytochrome c oxidase assembly intermediate in preparatory scale from coa1Δ mutant cells, using Mss51 as bait. We demonstrate that at this stage of assembly, the complex has not yet incorporated the heme a cofactors. Using quantitative mass spectrometry, we define the protein composition of the assembly intermediate and unexpectedly identify the putative methyltransferase Oms1 as a constituent. Our analyses show that Oms1 participates in cytochrome c oxidase assembly by stabilizing newly synthesized Cox1.
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Affiliation(s)
- Bettina Bareth
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Miroslav Nikolov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Isotta Lorenzi
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Markus Hildenbeutel
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - David U Mick
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Christin Helbig
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany Bioanalytik Group, Department of Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Martin Ott
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
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Swenson S, Cannon A, Harris NJ, Taylor NG, Fox JL, Khalimonchuk O. Analysis of Oligomerization Properties of Heme a Synthase Provides Insights into Its Function in Eukaryotes. J Biol Chem 2016; 291:10411-25. [PMID: 26940873 DOI: 10.1074/jbc.m115.707539] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/06/2022] Open
Abstract
Heme a is an essential cofactor for function of cytochrome c oxidase in the mitochondrial electron transport chain. Several evolutionarily conserved enzymes have been implicated in the biosynthesis of heme a, including the heme a synthase Cox15. However, the structure of Cox15 is unknown, its enzymatic mechanism and the role of active site residues remain debated, and recent discoveries suggest additional chaperone-like roles for this enzyme. Here, we investigated Cox15 in the model eukaryote Saccharomyces cerevisiae via several approaches to examine its oligomeric states and determine the effects of active site and human pathogenic mutations. Our results indicate that Cox15 exhibits homotypic interactions, forming highly stable complexes dependent upon hydrophobic interactions. This multimerization is evolutionarily conserved and independent of heme levels and heme a synthase catalytic activity. Four conserved histidine residues are demonstrated to be critical for eukaryotic heme a synthase activity and cannot be substituted with other heme-ligating amino acids. The 20-residue linker region connecting the two conserved domains of Cox15 is also important; removal of this linker impairs both Cox15 multimerization and enzymatic activity. Mutations of COX15 causing single amino acid conversions associated with fatal infantile hypertrophic cardiomyopathy and the neurological disorder Leigh syndrome result in impaired stability (S344P) or catalytic function (R217W), and the latter mutation affects oligomeric properties of the enzyme. Structural modeling of Cox15 suggests these two mutations affect protein folding and heme binding, respectively. We conclude that Cox15 multimerization is important for heme a biosynthesis and/or transfer to maturing cytochrome c oxidase.
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Affiliation(s)
- Samantha Swenson
- From the Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588 and
| | - Andrew Cannon
- From the Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588 and
| | - Nicholas J Harris
- the Department of Chemistry and Biochemistry, College of Charleston, Charleston, South Carolina 29424
| | - Nicholas G Taylor
- the Department of Chemistry and Biochemistry, College of Charleston, Charleston, South Carolina 29424
| | - Jennifer L Fox
- the Department of Chemistry and Biochemistry, College of Charleston, Charleston, South Carolina 29424
| | - Oleh Khalimonchuk
- From the Department of Biochemistry and Nebraska Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588 and
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Mayorga JP, Camacho-Villasana Y, Shingú-Vázquez M, García-Villegas R, Zamudio-Ochoa A, García-Guerrero AE, Hernández G, Pérez-Martínez X. A Novel Function of Pet54 in Regulation of Cox1 Synthesis in Saccharomyces cerevisiae Mitochondria. J Biol Chem 2016; 291:9343-55. [PMID: 26929411 DOI: 10.1074/jbc.m116.721985] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 12/21/2022] Open
Abstract
Cytochrome c oxidase assembly requires the synthesis of the mitochondria-encoded core subunits, Cox1, Cox2, and Cox3. In yeast, Pet54 protein is required to activate translation of the COX3 mRNA and to process the aI5β intron on the COX1 transcript. Here we report a third, novel function of Pet54 on Cox1 synthesis. We observed that Pet54 is necessary to achieve an efficient Cox1 synthesis. Translation of the COX1 mRNA is coupled to the assembly of cytochrome c oxidase by a mechanism that involves Mss51. This protein activates translation of the COX1 mRNA by acting on the COX1 5'-UTR, and, in addition, it interacts with the newly synthesized Cox1 protein in high molecular weight complexes that include the factors Coa3 and Cox14. Deletion of Pet54 decreased Cox1 synthesis, and, in contrast to what is commonly observed for other assembly mutants, double deletion of cox14 or coa3 did not recover Cox1 synthesis. Our results show that Pet54 is a positive regulator of Cox1 synthesis that renders Mss51 competent as a translational activator of the COX1 mRNA and that this role is independent of the assembly feedback regulatory loop of Cox1 synthesis. Pet54 may play a role in Mss51 hemylation/conformational change necessary for translational activity. Moreover, Pet54 physically interacts with the COX1 mRNA, and this binding was independent of the presence of Mss51.
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Affiliation(s)
- Juan Pablo Mayorga
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Yolanda Camacho-Villasana
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Miguel Shingú-Vázquez
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences Monash University, Clayton, Victoria 3800, Australia, and
| | - Rodolfo García-Villegas
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Angélica Zamudio-Ochoa
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Aldo E García-Guerrero
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Greco Hernández
- the Division of Basic Research, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Xochitl Pérez-Martínez
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico,
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Kovářová N, Pecina P, Nůsková H, Vrbacký M, Zeviani M, Mráček T, Viscomi C, Houštěk J. Tissue- and species-specific differences in cytochrome c oxidase assembly induced by SURF1 defects. Biochim Biophys Acta Mol Basis Dis 2016; 1862:705-715. [PMID: 26804654 PMCID: PMC4793088 DOI: 10.1016/j.bbadis.2016.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/08/2015] [Accepted: 01/08/2016] [Indexed: 12/17/2022]
Abstract
Mitochondrial protein SURF1 is a specific assembly factor of cytochrome c oxidase (COX), but its function is poorly understood. SURF1 gene mutations cause a severe COX deficiency manifesting as the Leigh syndrome in humans, whereas in mice SURF1−/− knockout leads only to a mild COX defect. We used SURF1−/− mouse model for detailed analysis of disturbed COX assembly and COX ability to incorporate into respiratory supercomplexes (SCs) in different tissues and fibroblasts. Furthermore, we compared fibroblasts from SURF1−/− mouse and SURF1 patients to reveal interspecies differences in kinetics of COX biogenesis using 2D electrophoresis, immunodetection, arrest of mitochondrial proteosynthesis and pulse-chase metabolic labeling. The crucial differences observed are an accumulation of abundant COX1 assembly intermediates, low content of COX monomer and preferential recruitment of COX into I–III2–IVn SCs in SURF1 patient fibroblasts, whereas SURF1−/− mouse fibroblasts were characterized by low content of COX1 assembly intermediates and milder decrease in COX monomer, which appeared more stable. This pattern was even less pronounced in SURF1−/− mouse liver and brain. Both the control and SURF1−/− mice revealed only negligible formation of the I–III2–IVn SCs and marked tissue differences in the contents of COX dimer and III2–IV SCs, also less noticeable in liver and brain than in heart and muscle. Our studies support the view that COX assembly is much more dependent on SURF1 in humans than in mice. We also demonstrate markedly lower ability of mouse COX to form I–III2–IVn supercomplexes, pointing to tissue-specific and species-specific differences in COX biogenesis. In SURF1 −/− mouse the decrease of COX amount and activity was tissue/cell specific. Assembly kinetics proceeded to the level of stable COX monomer in SURF1 −/− mouse. COX assembly intermediates were faster degraded/depleted in time in SURF1 −/− mouse. COX was preferentially recruited in supercomplex I–III2–IV1 in SURF1 patient cells. Newly synthesized COX monomer was unstable and rapidly degraded in SURF1 patient.
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Affiliation(s)
- Nikola Kovářová
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Petr Pecina
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Hana Nůsková
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Marek Vrbacký
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Massimo Zeviani
- Molecular Neurogenetics Unit, Instituto Neurologico "C. Besta", via Temolo 4, 20126 Milan, Italy; MRC-Mitochondrial Biology Unit, Wellcome Trust MRC Bldg, Addenbrookes Hospital Hills Rd, Cambridge CB2 0XY, UK
| | - Tomáš Mráček
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Carlo Viscomi
- MRC-Mitochondrial Biology Unit, Wellcome Trust MRC Bldg, Addenbrookes Hospital Hills Rd, Cambridge CB2 0XY, UK
| | - Josef Houštěk
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic.
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43
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He D, Fu CJ, Baldauf SL. Multiple Origins of Eukaryotic cox15 Suggest Horizontal Gene Transfer from Bacteria to Jakobid Mitochondrial DNA. Mol Biol Evol 2015; 33:122-33. [PMID: 26412445 DOI: 10.1093/molbev/msv201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The most gene-rich and bacterial-like mitochondrial genomes known are those of Jakobida (Excavata). Of these, the most extreme example to date is the Andalucia godoyi mitochondrial DNA (mtDNA), including a cox15 gene encoding the respiratory enzyme heme A synthase (HAS), which is nuclear-encoded in nearly all other mitochondriate eukaryotes. Thus cox15 in eukaryotes appears to be a classic example of mitochondrion-to-nucleus (endosymbiotic) gene transfer, with A. godoyi uniquely retaining the ancestral state. However, our analyses reveal two highly distinct HAS types (encoded by cox15-1 and cox15-2 genes) and identify A. godoyi mitochondrial cox15-encoded HAS as type-1 and all other eukaryotic cox15-encoded HAS as type-2. Molecular phylogeny places the two HAS types in widely separated clades with eukaryotic type-2 HAS clustering with the bulk of α-proteobacteria (>670 sequences), whereas A. godoyi type-1 HAS clusters with an eclectic set of bacteria and archaea including two α-proteobacteria missing from the type-2 clade. This wide phylogenetic separation of the two HAS types is reinforced by unique features of their predicted protein structures. Meanwhile, RNA-sequencing and genomic analyses fail to detect either cox15 type in the nuclear genome of any jakobid including A. godoyi. This suggests that not only is cox15-1 a relatively recent acquisition unique to the Andalucia lineage but also the jakobid last common ancestor probably lacked both cox15 types. These results indicate that uptake of foreign genes by mtDNA is more taxonomically widespread than previously thought. They also caution against the assumption that all α-proteobacterial-like features of eukaryotes are ancient remnants of endosymbiosis.
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Affiliation(s)
- Ding He
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Cheng-Jie Fu
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Sandra L Baldauf
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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Opa1 overexpression ameliorates the phenotype of two mitochondrial disease mouse models. Cell Metab 2015; 21:845-54. [PMID: 26039449 PMCID: PMC4457891 DOI: 10.1016/j.cmet.2015.04.016] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 02/13/2015] [Accepted: 04/12/2015] [Indexed: 02/07/2023]
Abstract
Increased levels of the mitochondria-shaping protein Opa1 improve respiratory chain efficiency and protect from tissue damage, suggesting that it could be an attractive target to counteract mitochondrial dysfunction. Here we show that Opa1 overexpression ameliorates two mouse models of defective mitochondrial bioenergetics. The offspring from crosses of a constitutive knockout for the structural complex I component Ndufs4 (Ndufs4(-/-)), and of a muscle-specific conditional knockout for the complex IV assembly factor Cox15 (Cox15(sm/sm)), with Opa1 transgenic (Opa1(tg)) mice showed improved motor skills and respiratory chain activities compared to the naive, non-Opa1-overexpressing, models. While the amelioration was modest in Ndufs4(-/-)::Opa1(tg) mice, correction of cristae ultrastructure and mitochondrial respiration, improvement of motor performance and prolongation of lifespan were remarkable in Cox15(sm/sm)::Opa1(tg) mice. Mechanistically, respiratory chain supercomplexes were increased in Cox15(sm/sm)::Opa1(tg) mice, and residual monomeric complex IV was stabilized. In conclusion, cristae shape amelioration by controlled Opa1 overexpression improves two mouse models of mitochondrial disease.
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45
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Dennerlein S, Rehling P. Human mitochondrial COX1 assembly into cytochrome c oxidase at a glance. J Cell Sci 2015; 128:833-7. [DOI: 10.1242/jcs.161729] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Mitochondria provide the main portion of cellular energy in form of ATP produced by the F1Fo ATP synthase, which uses the electrochemical gradient, generated by the mitochondrial respiratory chain (MRC). In human mitochondria, the MRC is composed of four multisubunit enzyme complexes, with the cytochrome c oxidase (COX, also known as complex IV) as the terminal enzyme. COX comprises 14 structural subunits, of nuclear or mitochondrial origin. Hence, mitochondria are faced with the predicament of organizing and controlling COX assembly with subunits that are synthesized by different translation machineries and that reach the inner membrane by alternative transport routes. An increasing number of COX assembly factors have been identified in recent years. Interestingly, mutations in several of these factors have been associated with human disorders leading to COX deficiency. Recently, studies have provided mechanistic insights into crosstalk between assembly intermediates, import processes and the synthesis of COX subunits in mitochondria, thus linking conceptually separated functions. This Cell Science at a Glance article and the accompanying poster will focus on COX assembly and discuss recent discoveries in the field, the molecular functions of known factors, as well as new players and control mechanisms. Furthermore, these findings will be discussed in the context of human COX-related disorders.
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46
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Gurumoorthy P, Ludwig B. Deciphering protein-protein interactions during the biogenesis of cytochrome c oxidase from Paracoccus denitrificans. FEBS J 2014; 282:537-49. [PMID: 25420759 DOI: 10.1111/febs.13160] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 02/01/2023]
Abstract
Biogenesis of the mitochondrial cytochrome c oxidase (COX) is a complex process due to its numerous subunits encoded by two genomes, as well as the localization of redox centers deep within the membrane. Here, we have assessed the biogenesis of the homologous aa₃-type oxidase of the soil bacterium Paracoccus denitrificans. First, protein partners were analyzed using various membrane solubilization strategies to show interactions between COX and CtaG, a chaperone implicated in CuB site metallation. Using an unbiased MS approach after immunological pull-down from untreated or cross-linked membranes, we then extend our view towards a hypothetical 'biogenesis complex' by identifying two further metal-inserting chaperones, Surf1c and Sco, together with enzymes catalyzing heme a synthesis. Our study also tentatively supports previous speculation regarding the existence of a predominantly co-translational mechanism for cofactor insertion during COX biogenesis.
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Affiliation(s)
- Priya Gurumoorthy
- Institute of Biochemistry, Molecular Genetics, Goethe University, Frankfurt am Main, Germany
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47
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A truncating PET100 variant causing fatal infantile lactic acidosis and isolated cytochrome c oxidase deficiency. Eur J Hum Genet 2014; 23:935-9. [PMID: 25293719 PMCID: PMC4305338 DOI: 10.1038/ejhg.2014.214] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/23/2014] [Accepted: 08/27/2014] [Indexed: 02/04/2023] Open
Abstract
Isolated mitochondrial complex IV (cytochrome c oxidase) deficiency is an important cause of mitochondrial disease in children and adults. It is genetically heterogeneous, given that both mtDNA-encoded and nuclear-encoded gene products contribute to structural components and assembly factors. Pathogenic variants within these proteins are associated with clinical variability ranging from isolated organ involvement to multisystem disease presentations. Defects in more than 10 complex IV assembly factors have been described including a recent Lebanese founder mutation in PET100 in patients presenting with Leigh syndrome. We report the clinical and molecular investigation of a patient with a fatal, neonatal-onset isolated complex IV deficiency associated with multiorgan involvement born to consanguineous, first-cousin British Asian parents. Exome sequencing revealed a homozygous truncating variant (c.142C>T, p.(Gln48*)) in the PET100 gene that results in a complete loss of enzyme activity and assembly of the holocomplex. Our report confirms PET100 mutation as an important cause of isolated complex IV deficiency outside of the Lebanese population, extending the phenotypic spectrum associated with abnormalities within this gene.
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48
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Feichtinger RG, Sperl W, Bauer JW, Kofler B. Mitochondrial dysfunction: a neglected component of skin diseases. Exp Dermatol 2014; 23:607-14. [PMID: 24980550 DOI: 10.1111/exd.12484] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2014] [Indexed: 12/20/2022]
Abstract
Aberrant mitochondrial structure and function influence tissue homeostasis and thereby contribute to multiple human disorders and ageing. Ten per cent of patients with primary mitochondrial disorders present skin manifestations that can be categorized into hair abnormalities, rashes, pigmentation abnormalities and acrocyanosis. Less attention has been paid to the fact that several disorders of the skin are linked to alterations of mitochondrial energy metabolism. This review article summarizes the contribution of mitochondrial pathology to both common and rare skin diseases. We explore the intriguing observation that a wide array of skin disorders presents with primary or secondary mitochondrial pathology and that a variety of molecular defects can cause dysfunctional mitochondria. Among them are mutations in mitochondrial- and nuclear DNA-encoded subunits and assembly factors of oxidative phosphorylation (OXPHOS) complexes; mutations in intermediate filament proteins involved in linking, moving and shaping of mitochondria; and disorders of mitochondrial DNA metabolism, fatty acid metabolism and heme synthesis. Thus, we assume that mitochondrial involvement is the rule rather than the exception in skin diseases. We conclude the article by discussing how improving mitochondrial function can be beneficial for aged skin and can be used as an adjunct therapy for certain skin disorders. Consideration of mitochondrial energy metabolism in the skin creates a new perspective for both dermatologists and experts in metabolic disease.
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Affiliation(s)
- René G Feichtinger
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
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