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Bajda S, Dermauw W, Panteleri R, Sugimoto N, Douris V, Tirry L, Osakabe M, Vontas J, Van Leeuwen T. A mutation in the PSST homologue of complex I (NADH:ubiquinone oxidoreductase) from Tetranychus urticae is associated with resistance to METI acaricides. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 80:79-90. [PMID: 27919778 DOI: 10.1016/j.ibmb.2016.11.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/25/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
The acaricidal compounds pyridaben, tebufenpyrad and fenpyroximate are frequently used in the control of phytophagous mites such as Tetranychus urticae, and are referred to as Mitochondrial Electron Transport Inhibitors, acting at the quinone binding pocket of complex I (METI-I acaricides). Because of their very frequent use, resistance evolved fast more than 20 years ago, and is currently wide-spread. Increased activity of P450 monooxygenases has been often associated with resistance, but target-site based resistance mechanisms were never reported. Here, we report the discovery of a mutation (H92R) in the PSST homologue of complex I in METI-I resistant T. urticae strains. The position of the mutation was studied using the high-resolution crystal structure of Thermus thermophilus, and was located in a stretch of amino acids previously photo-affinity labeled by fenpyroximate. Selection experiments with a strain segregating for the mutant allele, together with marker-assisted back-crossing of the mutation in a susceptible background, confirmed the involvement of the mutation in METI-I resistance. Additionally, an independent genetic mapping approach; QTL analysis identified the genomic region of pyridaben resistance, which included the PSST gene. Last, we used CRISPR-Cas9 genome editing tools to introduce the mutation in the Drosophila PSST homologue.
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Affiliation(s)
- Sabina Bajda
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424, 1090 GE Amsterdam, The Netherlands
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium
| | - Rafaela Panteleri
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece
| | - Naoya Sugimoto
- Kyoto University, Graduate School of Agriculture, Laboratory of Ecological Information, Kyoto 606-8502, Japan
| | - Vassilis Douris
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece; Department of Biology, University of Crete, 71409 Heraklion, Greece
| | - Luc Tirry
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium
| | - Masahiro Osakabe
- Kyoto University, Graduate School of Agriculture, Laboratory of Ecological Information, Kyoto 606-8502, Japan
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece; Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece
| | - Thomas Van Leeuwen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424, 1090 GE Amsterdam, The Netherlands; Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium.
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202
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Structure of Mammalian Respiratory Supercomplex I 1 III 2 IV 1. Cell 2016; 167:1598-1609.e10. [DOI: 10.1016/j.cell.2016.11.012] [Citation(s) in RCA: 251] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 01/14/2023]
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203
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Kahlhöfer F, Kmita K, Wittig I, Zwicker K, Zickermann V. Accessory subunit NUYM (NDUFS4) is required for stability of the electron input module and activity of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:175-181. [PMID: 27871794 DOI: 10.1016/j.bbabio.2016.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 11/18/2022]
Abstract
Mitochondrial complex I is an intricate 1MDa membrane protein complex with a central role in aerobic energy metabolism. The minimal form of complex I consists of fourteen central subunits that are conserved from bacteria to man. In addition, eukaryotic complex I comprises some 30 accessory subunits of largely unknown function. The gene for the accessory NDUFS4 subunit of human complex I is a hot spot for fatal pathogenic mutations in humans. We have deleted the gene for the orthologous NUYM subunit in the aerobic yeast Yarrowia lipolytica, an established model system to study eukaryotic complex I and complex I linked diseases. We observed assembly of complex I which lacked only subunit NUYM and retained weak interaction with assembly factor N7BML (human NDUFAF2). Absence of NUYM caused distortion of iron sulfur clusters of the electron input domain leading to decreased complex I activity and increased release of reactive oxygen species. We conclude that NUYM has an important stabilizing function for the electron input module of complex I and is essential for proper complex I function.
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Affiliation(s)
- Flora Kahlhöfer
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany
| | - Katarzyna Kmita
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Biochemistry I, Medical School, Goethe-University Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University Frankfurt am Main, Germany
| | - Klaus Zwicker
- Institute of Biochemistry I, Medical School, Goethe University Frankfurt am Main, Germany
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University Frankfurt am Main, Germany.
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204
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Bianciardi L, Imperatore V, Fernandez-Vizarra E, Lopomo A, Falabella M, Furini S, Galluzzi P, Grosso S, Zeviani M, Renieri A, Mari F, Frullanti E. Exome sequencing coupled with mRNA analysis identifies NDUFAF6 as a Leigh gene. Mol Genet Metab 2016; 119:214-222. [PMID: 27623250 DOI: 10.1016/j.ymgme.2016.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 01/30/2023]
Abstract
We report here the case of a young male who started to show verbal fluency disturbance, clumsiness and gait anomalies at the age of 3.5years and presented bilateral striatal necrosis. Clinically, the diagnosis was compatible with Leigh syndrome but the underlying molecular defect remained elusive even after exome analysis using autosomal/X-linked recessive or de novo models. Dosage of respiratory chain activity on fibroblasts, but not in muscle, underlined a deficit in complex I. Re-analysis of heterozygous probably pathogenic variants, inherited from one healthy parent, identified the p.Ala178Pro in NDUFAF6, a complex I assembly factor. RNA analysis showed an almost mono-allelic expression of the mutated allele in blood and fibroblasts and puromycin treatment on cultured fibroblasts did not lead to the rescue of the maternal allele expression, not supporting the involvement of nonsense-mediated RNA decay mechanism. Complementation assay underlined a recovery of complex I activity after transduction of the wild-type gene. Since the second mutation was not detected and promoter methylation analysis resulted normal, we hypothesized a non-exonic event in the maternal allele affecting a regulatory element that, in conjunction with the paternal mutation, leads to the autosomal recessive disorder and the different allele expression in various tissues. This paper confirms NDUFAF6 as a genuine morbid gene and proposes the coupling of exome sequencing with mRNA analysis as a method useful for enhancing the exome sequencing detection rate when the simple application of classical inheritance models fails.
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Affiliation(s)
| | | | | | - Angela Lopomo
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Micol Falabella
- Mitochondrial Biology Unit, Medical Research Council Cambridge, Cambridge, UK; Department of Biochemical Sciences, Sapienza University, Rome, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Paolo Galluzzi
- Unit of Diagnostic and Therapeutic Neuroradiology, Department of Neurosciences, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Massimo Zeviani
- Mitochondrial Biology Unit, Medical Research Council Cambridge, Cambridge, UK
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
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205
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Li L, Wang Z, He P, Ma S, Du J, Jiang R. Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:314-324. [PMID: 27746285 PMCID: PMC5093780 DOI: 10.1016/j.gpb.2016.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 02/24/2016] [Indexed: 01/14/2023]
Abstract
Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network are in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, including KEGG orthologous groups and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network. We devised two statistical methods to infer pairwise relationships between microbial functional units based on a deep sequencing dataset of gut microbiome from type 2 diabetes (T2D) patients as well as healthy controls. Networks containing such functional units and their significant interactions were constructed subsequently. We conducted a variety of analyses of global properties, local properties, and functional modules in the resulting functional networks. Our data indicate that besides the observations consistent with the current knowledge, this study provides novel biological insights into the gut microbiome associated with T2D.
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Affiliation(s)
- Lianshuo Li
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Zicheng Wang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Peng He
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shining Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jie Du
- Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing 100029, China
| | - Rui Jiang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
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206
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Transcriptome analysis of Cronobacter sakazakii ATCC BAA-894 after interaction with human intestinal epithelial cell line HCT-8. Appl Microbiol Biotechnol 2016; 100:311-22. [PMID: 26481623 DOI: 10.1007/s00253-015-7053-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/20/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
Cronobacter spp. are opportunistic pathogens that are responsible for infections including severe meningitis, septicemia, and necrotizing enterocolitis in neonates and infants. To date, questions still remain regarding the mechanisms of pathogenicity and virulence determinants for each bacterial strain. In this study, we established an in vitro model for Cronobacter sakazakii ATCC BAA-894 infection of HCT-8 human colorectal epithelial cells. The transcriptome profile of C. sakazakii ATCC BAA-894 after interaction with HCT-8 cells was determined using high-throughput whole-transcriptome sequencing (RNA sequencing (RNA-seq)). Gene expression profiles indicated that 139 genes were upregulated and 72 genes were downregulated in the adherent C. sakazakii ATCC BAA-894 strain on HCT-8 cells compared to the cultured bacteria in the cell-free medium. Expressions of some flagella genes and virulence factors involved in adherence were upregulated. High osmolarity and osmotic stress-associated genes were highly upregulated, as well as genes responsible for the synthesis of lipopolysaccharides and outer membrane proteins, iron acquisition systems, and glycerol and glycerophospholipid metabolism. In sum, our study provides further insight into the mechanisms underlying C. sakazakii pathogenesis in the human gastrointestinal tract.
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207
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Cryo-EM structure of respiratory complex I reveals a link to mitochondrial sulfur metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1935-1942. [PMID: 27693469 DOI: 10.1016/j.bbabio.2016.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/22/2016] [Accepted: 09/29/2016] [Indexed: 12/17/2022]
Abstract
Mitochondrial complex I is a 1MDa membrane protein complex with a central role in aerobic energy metabolism. The bioenergetic core functions are executed by 14 central subunits that are conserved from bacteria to man. Despite recent progress in structure determination, our understanding of the function of the ~30 accessory subunits associated with the mitochondrial complex is still limited. We have investigated the structure of complex I from the aerobic yeast Yarrowia lipolytica by cryo-electron microscopy. Our density map at 7.9Å resolution closely matches the 3.6-3.9Å X-ray structure of the Yarrowia lipolytica complex. However, the cryo-EM map indicated an additional subunit on the side of the matrix arm above the membrane surface, pointing away from the membrane arm. The density, which is not present in any previously described complex I structure and occurs in about 20 % of the particles, was identified as the accessory sulfur transferase subunit ST1. The Yarrowia lipolytica complex I preparation is active in generating H2S from the cysteine derivative 3-mercaptopyruvate, catalyzed by ST1. We thus provide evidence for a link between respiratory complex I and mitochondrial sulfur metabolism.
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208
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Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. Purification of Ovine Respiratory Complex I Results in a Highly Active and Stable Preparation. J Biol Chem 2016; 291:24657-24675. [PMID: 27672209 DOI: 10.1074/jbc.m116.735142] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/15/2016] [Indexed: 01/06/2023] Open
Abstract
NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies.
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Affiliation(s)
- James A Letts
- From the Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Gianluca Degliesposti
- the Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Karol Fiedorczuk
- From the Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria,; the Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
| | - Mark Skehel
- the Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Leonid A Sazanov
- From the Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria,.
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209
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Gawryluk RMR, Kamikawa R, Stairs CW, Silberman JD, Brown MW, Roger AJ. The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian. Curr Biol 2016; 26:2729-2738. [PMID: 27666965 DOI: 10.1016/j.cub.2016.08.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/21/2016] [Accepted: 08/09/2016] [Indexed: 12/26/2022]
Abstract
Mitochondria exist on a functional and evolutionary continuum that includes anaerobic mitochondrion-related organelles (MROs), such as hydrogenosomes. Hydrogenosomes lack many classical mitochondrial features, including conspicuous cristae, mtDNA, the tricarboxylic acid (TCA) cycle, and ATP synthesis powered by an electron transport chain (ETC); instead, they produce ATP anaerobically, liberating H2 and CO2 gas in the process. However, our understanding of the evolutionary transformation from aerobic mitochondria to various MRO types remains incomplete. Here we describe a novel MRO from a cercomonad (Brevimastigomonas motovehiculus n. sp.; Rhizaria). We have sequenced its 30,608-bp mtDNA and characterized organelle function through a combination of transcriptomic, genomic, and cell biological approaches. B. motovehiculus MROs are metabolically versatile, retaining mitochondrial metabolic pathways, such as a TCA cycle and ETC-driven ATP synthesis, but also possessing hydrogenosomal-type pyruvate metabolism and substrate-level phosphorylation. Notably, the B. motovehiculus ETC is degenerate and appears to be losing cytochrome-based electron transport (complexes III and IV). Furthermore, the F1Fo ATP synthase (complex V) is unique, with the highly conserved Atpα subunit fragmented into four separate pieces. The B. motovehiculus MRO appears to be in the process of losing aerobic metabolic capacities. Our findings shed light on the transition between organelle types, specifically the early stages of mitochondrial adaptation to anaerobiosis.
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Affiliation(s)
- Ryan M R Gawryluk
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan; Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Halifax, NS B3H 4R2, Canada.
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210
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Siebels I, Dröse S. Charge translocation by mitochondrial NADH:ubiquinone oxidoreductase (complex I) from Yarrowia lipolytica measured on solid-supported membranes. Biochem Biophys Res Commun 2016; 479:277-282. [PMID: 27639643 DOI: 10.1016/j.bbrc.2016.09.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 11/17/2022]
Abstract
The charge translocation by purified reconstituted mitochondrial complex I from the obligate aerobic yeast Yarrowia lipolytica was investigated after adsorption of proteoliposomes to solid-supported membranes. In presence of n-decylubiquinone (DBQ), pulses of NADH provided by rapid solution exchange induced charge transfer reflecting steady-state pumping activity of the reconstituted enzyme. The signal amplitude increased with time, indicating 'deactive→active' transition of the Yarrowia complex I. Furthermore, an increase of the membrane-conductivity after addition of 5-(N-ethyl-N-isopropyl)amiloride (EIPA) was detected which questiones the use of EIPA as an inhibitor of the Na+/H+-antiporter-like subunits of complex I. This investigation shows that electrical measurements on solid-supported membranes are a suitable method to analyze transport events and 'active/deactive' transition of mitochondrial complex I.
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Affiliation(s)
- Ilka Siebels
- Molecular Bioenergetics Group, Medical School, Johann Wolfgang Goethe-University, 60590, Frankfurt am Main, Germany; Goethe University Frankfurt, Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Protein Reaction Control Group, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Stefan Dröse
- Molecular Bioenergetics Group, Medical School, Johann Wolfgang Goethe-University, 60590, Frankfurt am Main, Germany; Department of Anesthesiology, Intensive-Care Medicine and Pain Therapy, University Hospital Frankfurt, 60590, Frankfurt am Main, Germany.
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211
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Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA. Atomic structure of the entire mammalian mitochondrial complex I. Nature 2016; 538:406-410. [PMID: 27595392 DOI: 10.1038/nature19794] [Citation(s) in RCA: 359] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 12/15/2022]
Abstract
Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations.
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Affiliation(s)
- Karol Fiedorczuk
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, UK
| | - James A Letts
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | | | - Karol Kaszuba
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, UK
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
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212
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Wu XM, Yang CQ, Mao YB, Wang LJ, Shangguan XX, Chen XY. Targeting insect mitochondrial complex I for plant protection. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1925-1935. [PMID: 26914579 PMCID: PMC5069633 DOI: 10.1111/pbi.12553] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 02/14/2016] [Accepted: 02/16/2016] [Indexed: 05/29/2023]
Abstract
Plant engineered to express double-stranded RNA (dsRNA) can target the herbivorous insect gene for silencing. Although mounting evidence has emerged to support feasibility of this new pest control technology, field application is slow largely due to lack of potent targets. Here, we show that suppression of the gene encoding NDUFV2, a subunit of mitochondrial complex I that catalyses NADH dehydrogenation in respiratory chain, was highly lethal to insects. Feeding cotton bollworm (Helicoverpa armigera) larvae with transgenic cotton tissues expressing NDUFV2 dsRNA led to mortality up to 80% within 5 days, and almost no larvae survived after 7 days of feeding, due to the altered mitochondrial structure and activity. Transcriptome comparisons showed a drastic repression of dopa decarboxylase genes. Reciprocal assays with Asian corn borer (Ostrinia furnacalis), another lepidopteran species, revealed the sequence-specific effect of NDUFV2 suppression. Furthermore, the hemipteran lugus Apolygus lucorum was also liable to NDUFV2 repression. These data demonstrate that the mitochondrial complex I is a promising target with both sequence specificity and wide applicability for the development of new-generation insect-proof crops.
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Affiliation(s)
- Xiu-Ming Wu
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center (Shanghai), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chang-Qing Yang
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center (Shanghai), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying-Bo Mao
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center (Shanghai), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Jian Wang
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center (Shanghai), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Xia Shangguan
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center (Shanghai), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics and National Plant Gene Research Center (Shanghai), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
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213
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Holt PJ, Efremov RG, Nakamaru-Ogiso E, Sazanov LA. Reversible FMN dissociation from Escherichia coli respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1777-1785. [PMID: 27555334 DOI: 10.1016/j.bbabio.2016.08.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/04/2016] [Accepted: 08/17/2016] [Indexed: 12/13/2022]
Abstract
Respiratory complex I transfers electrons from NADH to quinone, utilizing the reaction energy to translocate protons across the membrane. It is a key enzyme of the respiratory chain of many prokaryotic and most eukaryotic organisms. The reversible NADH oxidation reaction is facilitated in complex I by non-covalently bound flavin mononucleotide (FMN). Here we report that the catalytic activity of E. coli complex I with artificial electron acceptors potassium ferricyanide (FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar range in oxidized complex I to the nanomolar range in the NADH reduced enzyme, with an FMN dissociation time constant of ~5s. The oxidation state of complex I, rather than that of FMN, proved critical to the dissociation. Such dissociation is not observed with the T. thermophilus enzyme and our analysis suggests that the difference may be due to the unusually high redox potential of Fe-S cluster N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo by releasing FMN under highly reducing conditions.
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Affiliation(s)
- Peter J Holt
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Rouslan G Efremov
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, United States
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria.
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214
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Wang Y, Song X, Zhang Y, Wang B, Zou X. Effects of nitrogen availability on polymalic acid biosynthesis in the yeast-like fungus Aureobasidium pullulans. Microb Cell Fact 2016; 15:146. [PMID: 27549441 PMCID: PMC4994417 DOI: 10.1186/s12934-016-0547-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 08/15/2016] [Indexed: 12/03/2022] Open
Abstract
Background Polymalic acid (PMA) is a novel polyester polymer that has been broadly used in the medical and food industries. Its monomer, L-malic acid, is also a potential C4 platform chemical. However, little is known about the mechanism of PMA biosynthesis in the yeast-like fungus, Aureobasidium pullulans. In this study, the effects of different nitrogen concentration on cell growth and PMA biosynthesis were investigated via comparative transcriptomics and proteomics analyses, and a related signaling pathway was also evaluated. Results A high final PMA titer of 44.00 ± 3.65 g/L (49.9 ± 4.14 g/L of malic acid after hydrolysis) was achieved in a 5-L fermentor under low nitrogen concentration (2 g/L of NH4NO3), which was 18.3 % higher yield than that obtained under high nitrogen concentration (10 g/L of NH4NO3). Comparative transcriptomics profiling revealed that a set of genes, related to the ribosome, ribosome biogenesis, proteasome, and nitrogen metabolism, were significantly up- or down-regulated under nitrogen sufficient conditions, which could be regulated by the TOR signaling pathway. Fourteen protein spots were identified via proteomics analysis, and were found to be associated with cell division and growth, energy metabolism, and the glycolytic pathway. qRT-PCR further confirmed that the expression levels of key genes involved in the PMA biosynthetic pathway (GLK, CS, FUM, DAT, and MCL) and the TOR signaling pathway (GS, TOR1, Tap42, and Gat1) were upregulated due to nitrogen limitation. Under rapamycin stress, PMA biosynthesis was obviously inhibited in a dose-dependent manner, and the transcription levels of TOR1, MCL, and DAT were also downregulated. Conclusions The level of nitrogen could regulate cell growth and PMA biosynthesis. Low concentration of nitrogen was beneficial for PMA biosynthesis, which could upregulate the expression of key genes involved in the PMA biosynthesis pathway. Cell growth and PMA biosynthesis might be mediated by the TOR signaling pathway in response to nitrogen. This study will help us to deeply understand the molecular mechanisms of PMA biosynthesis, and to develop an effective process for the production of PMA and malic acid chemicals. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0547-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongkang Wang
- College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, 2 Tian Sheng Road, Beibei, Chongqing, 400715, People's Republic of China
| | - Xiaodan Song
- College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, 2 Tian Sheng Road, Beibei, Chongqing, 400715, People's Republic of China
| | - Yongjun Zhang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, People's Republic of China
| | - Bochu Wang
- Ministry of Education, Key Laboratory of Biorheological Science and Technology (Chongqing University), Chongqing, 400044, People's Republic of China
| | - Xiang Zou
- College of Pharmaceutical Sciences, Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Southwest University, 2 Tian Sheng Road, Beibei, Chongqing, 400715, People's Republic of China. .,Ministry of Education, Key Laboratory of Biorheological Science and Technology (Chongqing University), Chongqing, 400044, People's Republic of China.
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215
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Role of mitochondrial complex I and protective effect of CoQ10 supplementation in propofol induced cytotoxicity. J Bioenerg Biomembr 2016; 48:413-23. [DOI: 10.1007/s10863-016-9673-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/02/2016] [Indexed: 10/21/2022]
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216
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Suenobu T, Shibata S, Fukuzumi S. Catalytic Formation of Hydrogen Peroxide from Coenzyme NADH and Dioxygen with a Water-Soluble Iridium Complex and a Ubiquinone Coenzyme Analogue. Inorg Chem 2016; 55:7747-54. [PMID: 27403568 DOI: 10.1021/acs.inorgchem.6b01220] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A ubiquinone coenzyme analogue (Q0: 2,3-dimethoxy-5-methyl-1,4-benzoquinone) was reduced by coenzyme NADH to yield the corresponding reduced form of Q0 (Q0H2) in the presence of a catalytic amount of a [C,N] cyclometalated organoiridium complex (1: [Ir(III)(Cp*)(4-(1H-pyrazol-1-yl-κN(2))benzoic acid-κC(3))(H2O)]2SO4) in water at ambient temperature as observed in the respiratory chain complex I (Complex I). In the catalytic cycle, the reduction of 1 by NADH produces the corresponding iridium hydride complex that in turn reduces Q0 to produce Q0H2. Q0H2 reduced dioxygen to yield hydrogen peroxide (H2O2) under slightly basic conditions. Catalytic generation of H2O2 was made possible in the reaction of O2 with NADH as the functional expression of NADH oxidase in white blood cells utilizing the redox cycle of Q0 as well as 1 for the first time in a nonenzymatic homogeneous reaction system.
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Affiliation(s)
- Tomoyoshi Suenobu
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, ALCA and SENTAN, Japan Science and Technology , Suita, Osaka 565-0871, Japan
| | - Satoshi Shibata
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, ALCA and SENTAN, Japan Science and Technology , Suita, Osaka 565-0871, Japan
| | - Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, ALCA and SENTAN, Japan Science and Technology , Suita, Osaka 565-0871, Japan.,Department of Chemistry and Nano Science, Ewha Womans University , Seoul 120-750, Korea.,Faculty of Science and Engineering, Meijo University, ALCA and SENTAN, Japan Science and Technology Agency , Nagoya, Aichi 468-0073, Japan
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217
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Sperling E, Górecki K, Drakenberg T, Hägerhäll C. Functional Differentiation of Antiporter-Like Polypeptides in Complex I; a Site-Directed Mutagenesis Study of Residues Conserved in MrpA and NuoL but Not in MrpD, NuoM, and NuoN. PLoS One 2016; 11:e0158972. [PMID: 27391676 PMCID: PMC4938563 DOI: 10.1371/journal.pone.0158972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/26/2016] [Indexed: 01/29/2023] Open
Abstract
It has long been known that the three largest subunits in the membrane domain (NuoL, NuoM and NuoN) of complex I are homologous to each other, as well as to two subunits (MrpA and MrpD) from a Na+/H+ antiporter, Mrp. MrpA and NuoL are more similar to each other and the same is true for MrpD and NuoN. This suggests a functional differentiation which was proven experimentally in a deletion strain model system, where NuoL could restore the loss of MrpA, but not that of MrpD and vice versa. The simplest explanation for these observations was that the MrpA and MrpD proteins are not antiporters, but rather single subunit ion channels that together form an antiporter. In this work our focus was on a set of amino acid residues in helix VIII, which are only conserved in NuoL and MrpA (but not in any of the other antiporter-like subunits.) and to compare their effect on the function of these two proteins. By combining complementation studies in B. subtilis and 23Na-NMR, response of mutants to high sodium levels were tested. All of the mutants were able to cope with high salt levels; however, all but one mutation (M258I/M225I) showed differences in the efficiency of cell growth and sodium efflux. Our findings showed that, although very similar in sequence, NuoL and MrpA seem to differ on the functional level. Nonetheless the studied mutations gave rise to interesting phenotypes which are of interest in complex I research.
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Affiliation(s)
- Eva Sperling
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
- * E-mail:
| | - Kamil Górecki
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Torbjörn Drakenberg
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Cecilia Hägerhäll
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
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218
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Sánchez-Caballero L, Ruzzenente B, Bianchi L, Assouline Z, Barcia G, Metodiev M, Rio M, Funalot B, van den Brand M, Guerrero-Castillo S, Molenaar J, Koolen D, Brandt U, Rodenburg R, Nijtmans L, Rötig A. Mutations in Complex I Assembly Factor TMEM126B Result in Muscle Weakness and Isolated Complex I Deficiency. Am J Hum Genet 2016; 99:208-16. [PMID: 27374773 DOI: 10.1016/j.ajhg.2016.05.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/17/2016] [Indexed: 11/26/2022] Open
Abstract
Mitochondrial complex I deficiency results in a plethora of often severe clinical phenotypes manifesting in early childhood. Here, we report on three complex-I-deficient adult subjects with relatively mild clinical symptoms, including isolated, progressive exercise-induced myalgia and exercise intolerance but with normal later development. Exome sequencing and targeted exome sequencing revealed compound-heterozygous mutations in TMEM126B, encoding a complex I assembly factor. Further biochemical analysis of subject fibroblasts revealed a severe complex I deficiency caused by defective assembly. Lentiviral complementation with the wild-type cDNA restored the complex I deficiency, demonstrating the pathogenic nature of these mutations. Further complexome analysis of one subject indicated that the complex I assembly defect occurred during assembly of its membrane module. Our results show that TMEM126B defects can lead to complex I deficiencies and, interestingly, that symptoms can occur only after exercise.
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219
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Zhang Y, Gong XG, Wang ZZ, Sun HM, Guo ZY, Gai C, Hu JH, Ma L, Li P, Chen NH. Protective effects of DJ-1 medicated Akt phosphorylation on mitochondrial function are promoted by Da-Bu-Yin-Wan in 1-methyl-4-phenylpyridinium-treated human neuroblastoma SH-SY5Y cells. JOURNAL OF ETHNOPHARMACOLOGY 2016; 187:83-93. [PMID: 27114059 DOI: 10.1016/j.jep.2016.04.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 11/11/2015] [Accepted: 04/20/2016] [Indexed: 06/05/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Da-Bu-Yin-Wan (DBYW), a historically traditional Chinese medicine formula, was originally defined over 600 years ago. In recent decades, DBYW was clinically employed to treat Parkinson's disease (PD). AIM OF THE STUDY To explore the underlying mechanism of DBYW on mitochondrial function, we investigated the effect of DBYW on mitochondrial function from the perspectives of DJ-1 and Akt signaling. MATERIALS AND METHODS Human derived neuroblastoma SH-SY5Y cells were transiently transfected with the plasmid pcDNA3-Flag-DJ-1 aimed to overexpress the DJ-1 protein. Transfected cells were treated with 1-methyl-4-phenylpyridinium (MPP(+)), a PD-related mitochondrial complex I inhibitor, in the absence and presence of DBYW. The cell viability was assessed by Cell Counting Kit-8 assay. The protein expressions of DJ-1 and Akt signaling were examined by western blotting. The mitochondrial mass was evaluated by confocal fluorescence microscopy. The mitochondrial complex I activity and cellular ATP content were measured by commercial kits. RESULTS Transfection with pcDNA3-Flag-DJ-1 decreased the MPP(+)-induced toxicity and overexpressed the DJ-1. In DJ-1 overexpressed cells, the mitochondrial mass was raised, mitochondrial complex I activity was improved, and cellular ATP content was increased. In addition, overexpression of DJ-1 augmented the Akt phosphorylation on threonine 308 and serine 473. Moreover, DBYW promoted the above effects in DJ-1 expressed cells. CONCLUSIONS These data suggest that DJ-1 protects the mitochondrial function by medicating Akt phosphorylation in MPP(+)-treated SH-SY5Y cells. Moreover, DBYW enhances the protective effect of DJ-1 medicated Akt phosphorylation on mitochondrial function.
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Affiliation(s)
- Yi Zhang
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China; Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Xiao-Gang Gong
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China; College of Special Education, Beijing Union University, Beijing 100075, China
| | - Zhen-Zhen Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hong-Mei Sun
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
| | - Zhen-Yu Guo
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Cong Gai
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jing-Hong Hu
- Center for Scientific Research, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ling Ma
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ping Li
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Science, China-Japan Friendship Hospital, Beijing 100029, China
| | - Nai-Hong Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
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220
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Pinske C, Sargent F. Exploring the directionality of Escherichia coli formate hydrogenlyase: a membrane-bound enzyme capable of fixing carbon dioxide to organic acid. Microbiologyopen 2016; 5:721-737. [PMID: 27139710 PMCID: PMC5061711 DOI: 10.1002/mbo3.365] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/14/2016] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
During mixed‐acid fermentation Escherichia coli produces formate, which is initially excreted out the cell. Accumulation of formate, and dropping extracellular pH, leads to biosynthesis of the formate hydrogenlyase (FHL) complex. FHL consists of membrane and soluble domains anchored within the inner membrane. The soluble domain comprises a [NiFe] hydrogenase and a formate dehydrogenase that link formate oxidation directly to proton reduction with the release of CO2 and H2. Thus, the function of FHL is to oxidize excess formate at low pH. FHL subunits share identity with subunits of the respiratory Complex I. In particular, the FHL membrane domain contains subunits (HycC and HycD) that are homologs of NuoL/M/N and NuoH, respectively, which have been implicated in proton translocation. In this work, strain engineering and new assays demonstrate unequivocally the nonphysiological reverse activity of FHL in vivo and in vitro. Harnessing FHL to reduce CO2 to formate is biotechnologically important. Moreover, assays for both possible FHL reactions provide opportunities to explore the bioenergetics using biochemical and genetic approaches. Comprehensive mutagenesis of hycC did not identify any single amino acid residues essential for FHL operation. However, the HycD E199, E201, and E203 residues were found to be critically important for FHL function.
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Affiliation(s)
- Constanze Pinske
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, United Kingdom
| | - Frank Sargent
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, United Kingdom.
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221
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Fromm S, Senkler J, Eubel H, Peterhänsel C, Braun HP. Life without complex I: proteome analyses of an Arabidopsis mutant lacking the mitochondrial NADH dehydrogenase complex. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3079-93. [PMID: 27122571 PMCID: PMC4867900 DOI: 10.1093/jxb/erw165] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The mitochondrial NADH dehydrogenase complex (complex I) is of particular importance for the respiratory chain in mitochondria. It is the major electron entry site for the mitochondrial electron transport chain (mETC) and therefore of great significance for mitochondrial ATP generation. We recently described an Arabidopsis thaliana double-mutant lacking the genes encoding the carbonic anhydrases CA1 and CA2, which both form part of a plant-specific 'carbonic anhydrase domain' of mitochondrial complex I. The mutant lacks complex I completely. Here we report extended analyses for systematically characterizing the proteome of the ca1ca2 mutant. Using various proteomic tools, we show that lack of complex I causes reorganization of the cellular respiration system. Reduced electron entry into the respiratory chain at the first segment of the mETC leads to induction of complexes II and IV as well as alternative oxidase. Increased electron entry at later segments of the mETC requires an increase in oxidation of organic substrates. This is reflected by higher abundance of proteins involved in glycolysis, the tricarboxylic acid cycle and branched-chain amino acid catabolism. Proteins involved in the light reaction of photosynthesis, the Calvin cycle, tetrapyrrole biosynthesis, and photorespiration are clearly reduced, contributing to the significant delay in growth and development of the double-mutant. Finally, enzymes involved in defense against reactive oxygen species and stress symptoms are much induced. These together with previously reported insights into the function of plant complex I, which were obtained by analysing other complex I mutants, are integrated in order to comprehensively describe 'life without complex I'.
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Affiliation(s)
- Steffanie Fromm
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany Institut für Botanik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Christoph Peterhänsel
- Institut für Botanik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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Narayanan M, Sakyiama JA, Elguindy MM, Nakamaru-Ogiso E. Roles of subunit NuoL in the proton pumping coupling mechanism of NADH:ubiquinone oxidoreductase (complex I) from Escherichia coli. J Biochem 2016; 160:205-215. [PMID: 27118783 DOI: 10.1093/jb/mvw027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/09/2016] [Indexed: 01/13/2023] Open
Abstract
Respiratory complex I has an L-shaped structure formed by the hydrophilic arm responsible for electron transfer and the membrane arm that contains protons pumping machinery. Here, to gain mechanistic insights into the role of subunit NuoL, we investigated the effects of Mg2+, Zn2+ and the Na+/H+ antiporter inhibitor 5-(N-ethyl-N-isopropyl)-amiloride (EIPA) on proton pumping activities of various isolated NuoL mutant complex I after reconstitution into Escherichia coli double knockout (DKO) membrane vesicles lacking complex I and the NADH dehydrogenase type 2. We found that Mg2+ was critical for proton pumping activity of complex I. At 2 µM Zn2+, proton pumping of the wild-type was selectively inhibited without affecting electron transfer; no inhibition in proton pumping of D178N and D400A was observed, suggesting the involvement of these residues in Zn2+ binding. Fifteen micromolar of EIPA caused up to ∼40% decrease in the proton pumping activity of the wild-type, D303A and D400A/E, whereas no significant change was detected in D178N, indicating its possible involvement in the EIPA binding. Furthermore, when menaquinone-rich DKO membranes were used, the proton pumping efficiency in the wild-type was decreased significantly (∼50%) compared with NuoL mutants strongly suggesting that NuoL is involved in the high efficiency pumping mechanism in complex I.
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Affiliation(s)
- Madhavan Narayanan
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Joseph A Sakyiama
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Mahmoud M Elguindy
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA 19104, USA
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Sánchez-Caballero L, Guerrero-Castillo S, Nijtmans L. Unraveling the complexity of mitochondrial complex I assembly: A dynamic process. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:980-90. [PMID: 27040506 DOI: 10.1016/j.bbabio.2016.03.031] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
Mammalian complex I is composed of 44 different subunits and its assembly requires at least 13 specific assembly factors. Proper function of the mitochondrial respiratory chain enzyme is of crucial importance for cell survival due to its major participation in energy production and cell signaling. Complex I assembly depends on the coordination of several crucial processes that need to be tightly interconnected and orchestrated by a number of assembly factors. The understanding of complex I assembly evolved from simple sequential concept to the more sophisticated modular assembly model describing a convoluted process. According to this model, the different modules assemble independently and associate afterwards with each other to form the final enzyme. In this review, we aim to unravel the complexity of complex I assembly and provide the latest insights in this fundamental and fascinating process. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Laura Sánchez-Caballero
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Sergio Guerrero-Castillo
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo Nijtmans
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
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Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes. J Bacteriol 2016; 198:1268-80. [PMID: 26833419 PMCID: PMC4859585 DOI: 10.1128/jb.01025-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED NADH:quinone oxidoreductase (complex I) is a bioenergetic enzyme that transfers electrons from NADH to quinone, conserving the energy of this reaction by contributing to the proton motive force. While the importance of NADH oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex I to bacterial electron transport chains has been tested in only a few species. Here, we analyze the function of two phylogenetically distinct complex I isozymes in Rhodobacter sphaeroides, an alphaproteobacterium that contains well-characterized electron transport chains. We found that R. sphaeroides complex I activity is important for aerobic respiration and required for anaerobic dimethyl sulfoxide (DMSO) respiration (in the absence of light), photoautotrophic growth, and photoheterotrophic growth (in the absence of an external electron acceptor). Our data also provide insight into the functions of the phylogenetically distinct R. sphaeroidescomplex I enzymes (complex IA and complex IE) in maintaining a cellular redox state during photoheterotrophic growth. We propose that the function of each isozyme during photoheterotrophic growth is either NADH synthesis (complex IA) or NADH oxidation (complex IE). The canonical alphaproteobacterial complex I isozyme (complex IA) was also shown to be important for routing electrons to nitrogenase-mediated H2 production, while the horizontally acquired enzyme (complex IE) was dispensable in this process. Unlike the singular role of complex I in mitochondria, we predict that the phylogenetically distinct complex I enzymes found across bacterial species have evolved to enhance the functions of their respective electron transport chains. IMPORTANCE Cells use a proton motive force (PMF), NADH, and ATP to support numerous processes. In mitochondria, complex I uses NADH oxidation to generate a PMF, which can drive ATP synthesis. This study analyzed the function of complex I in bacteria, which contain more-diverse and more-flexible electron transport chains than mitochondria. We tested complex I function in Rhodobacter sphaeroides, a bacterium predicted to encode two phylogenetically distinct complex I isozymes. R. sphaeroides cells lacking both isozymes had growth defects during all tested modes of growth, illustrating the important function of this enzyme under diverse conditions. We conclude that the two isozymes are not functionally redundant and predict that phylogenetically distinct complex I enzymes have evolved to support the diverse lifestyles of bacteria.
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Zhang Y, Gong XG, Wang ZZ, Sun HM, Guo ZY, Hu JH, Ma L, Li P, Chen NH. Overexpression of DJ-1/PARK7, the Parkinson's disease-related protein, improves mitochondrial function via Akt phosphorylation on threonine 308 in dopaminergic neuron-like cells. Eur J Neurosci 2016; 43:1379-88. [PMID: 26913805 DOI: 10.1111/ejn.13216] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/29/2016] [Accepted: 02/18/2016] [Indexed: 12/27/2022]
Abstract
DJ-1/PARK7, the Parkinson's disease-related protein, plays an important role in mitochondrial function. However, the mechanisms by which DJ-1 affects mitochondrial function are not fully understood. Akt is a promoter of neuron survival and is partly involved in the neurodegenerative process. This research aimed at investigating a possible relationship between DJ-1 and Akt signalling in regulating mitochondrial function in the dopaminergic neuron-like cells SH-SY5Y and PC-12. Overexpression of DJ-1 was firstly validated at both the transcriptional and translational levels after transit transfection with plasmid pcDNA3-Flag-DJ-1. Confocal fluorescence microscopy demonstrated that overexpression of DJ-1 increased the mitochondrial mass, but did not disrupt the mitochondrial morphology. In addition, mitochondrial complex I activity was raised in DJ-1-overexpressing cells, and this rise occurred with an increase in cellular adenosine 5'-triphosphate content. Moreover, immunoblotting demonstrated that the levels of phosphoinositide 3-kinase and the total Akt were not altered in DJ-1-overexpressing cells, and nor was the Akt phosphorylation on serine 473 changed. By contrast, Akt phosphorylation on threonine 308 was significantly augmented by overexpression of DJ-1, and the expression of glycogen synthase kinase-3beta, a downstream effector of Akt, was suppressed. In summary, these results suggest that overexpression of DJ-1 improves the mitochondrial function, at least in part, through a mechanism involving Akt phosphorylation on threonine 308.
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Affiliation(s)
- Yi Zhang
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 North 3rd Ring Eastern Road, Beijing, 100029, China.,Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiao-Gang Gong
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 North 3rd Ring Eastern Road, Beijing, 100029, China
| | - Zhen-Zhen Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong-Mei Sun
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 North 3rd Ring Eastern Road, Beijing, 100029, China
| | - Zhen-Yu Guo
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 North 3rd Ring Eastern Road, Beijing, 100029, China
| | - Jing-Hong Hu
- Center for Scientific Research, School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Ling Ma
- Department of Anatomy, School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 North 3rd Ring Eastern Road, Beijing, 100029, China
| | - Ping Li
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Science, China-Japan Friendship Hospital, Beijing, China
| | - Nai-Hong Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
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226
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Pereira RJ, Barreto FS, Pierce NT, Carneiro M, Burton RS. Transcriptome-wide patterns of divergence during allopatric evolution. Mol Ecol 2016; 25:1478-93. [DOI: 10.1111/mec.13579] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/03/2015] [Accepted: 01/06/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Ricardo J. Pereira
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Felipe S. Barreto
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331 USA
| | - N. Tessa Pierce
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
| | - Miguel Carneiro
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Ronald S. Burton
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
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227
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Ezraty B, Barras F. The ‘liaisons dangereuses’ between iron and antibiotics. FEMS Microbiol Rev 2016; 40:418-35. [DOI: 10.1093/femsre/fuw004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 12/15/2022] Open
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228
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Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. Sci Rep 2016; 6:22583. [PMID: 26935041 PMCID: PMC4776286 DOI: 10.1038/srep22583] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/18/2016] [Indexed: 12/20/2022] Open
Abstract
To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70-84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress.
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229
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Gnandt E, Dörner K, Strampraad MFJ, de Vries S, Friedrich T. The multitude of iron-sulfur clusters in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1068-1072. [PMID: 26944855 DOI: 10.1016/j.bbabio.2016.02.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/19/2016] [Accepted: 02/26/2016] [Indexed: 12/13/2022]
Abstract
Respiratory complex I couples the electron transfer from NADH to ubiquinone with the translocation of protons across the membrane. Complex I contains one non-covalently bound flavin mononucleotide and, depending on the species, up to ten iron-sulfur (Fe/S) clusters as cofactors. The reason for the presence of the multitude of Fe/S clusters in complex I remained enigmatic for a long time. The question was partly answered by investigations on the evolution of the complex revealing the stepwise construction of the electron transfer domain from several modules. Extension of the ancestral to the modern electron input domain was associated with the acquisition of several Fe/S-proteins. The X-ray structure of the complex showed that the NADH oxidation-site is connected with the quinone-reduction site by a chain of seven Fe/S-clusters. Fast enzyme kinetics revealed that this chain of Fe/S-clusters is used to regulate electron-tunneling rates within the complex. A possible function of the off-pathway cluster N1a is discussed. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Emmanuel Gnandt
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, 79104 Freiburg i. Br., Germany
| | - Katerina Dörner
- Deutsches Elektronen-Synchrotron DESY, CFEL, Notkestr. 85, Hamburg, Germany
| | - Marc F J Strampraad
- Delft University of Technology, Department of Biotechnology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Simon de Vries
- Delft University of Technology, Department of Biotechnology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, 79104 Freiburg i. Br., Germany.
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230
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Lim SC, Hroudová J, Van Bergen NJ, Lopez Sanchez MIG, Trounce IA, McKenzie M. Loss of mitochondrial DNA-encoded protein ND1 results in disruption of complex I biogenesis during early stages of assembly. FASEB J 2016; 30:2236-48. [PMID: 26929434 DOI: 10.1096/fj.201500137r] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/12/2016] [Indexed: 12/20/2022]
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase) must be assembled precisely from 45 protein subunits for it to function correctly. One of its mitochondrial DNA (mtDNA) encoded subunits, ND1, is incorporated during the early stages of complex I assembly. However, little is known about how mutations in ND1 affect this assembly process. We found that in human 143B cybrid cells carrying a homoplasmic MT-ND1 mutation, ND1 protein could not be translated. As a result, the early stages of complex I assembly were disrupted, with mature complex I undetectable and complex I-linked respiration severely reduced to 2.0% of control levels. Interestingly, complex IV (ferrocytochrome c:oxygen oxidoreductase) steady-state levels were also reduced to 40.3%, possibly due to its diminished stability in the absence of respiratory supercomplex formation. This was in comparison with 143B cybrid controls (that contained wild-type mtDNA on the same nuclear background), which exhibited normal complex I, complex IV, and supercomplex assembly. We conclude that the loss of ND1 stalls complex I assembly during the early stages of its biogenesis, which not only results in the loss of mature complex I but also disrupts the stability of complex IV and the respiratory supercomplex to cause mitochondrial dysfunction.-Lim, S. C., Hroudová, J., Van Bergen, N. J., Lopez Sanchez, M. I. G., Trounce, I. A., McKenzie, M. Loss of mitochondrial DNA-encoded protein ND1 results in disruption of complex I biogenesis during early stages of assembly.
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Affiliation(s)
- Sze Chern Lim
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Melbourne, Victoria, Australia
| | - Jana Hroudová
- Department of Psychiatry, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Nicole J Van Bergen
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia; and
| | - M Isabel G Lopez Sanchez
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia; and
| | - Ian A Trounce
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia; and
| | - Matthew McKenzie
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Melbourne, Victoria, Australia; Monash University, Clayton, Melbourne, Victoria, Australia
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231
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Candas D, Qin L, Fan M, Li JJ. Experimental Approaches to Study Mitochondrial Localization and Function of a Nuclear Cell Cycle Kinase, Cdk1. J Vis Exp 2016:53417. [PMID: 26967001 DOI: 10.3791/53417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Although mitochondria possess their own transcriptional machinery, merely 1% of mitochondrial proteins are synthesized inside the organelle. The nuclear-encoded proteins are transported into mitochondria guided by their mitochondria targeting sequences (MTS); however, a majority of mitochondrial localized proteins lack an identifiable MTS. Nevertheless, the fact that MTS can instruct proteins to go into the mitochondria provides a valuable tool for studying mitochondrial functions of normally nuclear and/or cytoplasmic proteins. We have recently identified the cell cycle kinase CyclinB1/Cdk1 complex in the mitochondria. To specifically study the mitochondrial functions of this complex, mitochondrial overexpression and knock-down of this complex without interfering with its nuclear or cytoplasmic functions were essential. By tagging CyclinB1/Cdk1 with MTS, we were able to achieve mitochondrial overexpression of this complex to study its mitochondrial targets as well as functions. Via tagging dominant-negative Cdk1 with MTS, inhibition of Cdk1 activity was accomplished particularly in the mitochondria. Potential mitochondrial targets of CyclinB1/Cdk1 complex were identified using a gel-based proteomics approach. Unlike traditional 2D gel analysis, we employed 2-dimensional difference gel electrophoresis (2D-DIGE) technology followed by phosphoprotein staining to fluorescently label differentially phosphorylated proteins in mitochondrial Cdk1 expressing cells. Identification of phosphoprotein spots that were altered in wild type versus dominant negative Cdk1 bearing mitochondria revealed the identity of mitochondrial targets of Cdk1. Finally, to determine the effect of CyclinB1/Cdk1 mitochondrial localization in cell cycle progression, a cell proliferation assay using a synthetic thymidine analogue EdU (5-ethynyl-2'-deoxyuridine) was used to monitor the cells as they go through the cell cycle and replicate their DNA. Altogether, we demonstrated a variety of approaches available to study mitochondrial localization and activity of a cell cycle kinase. These are advanced, yet easy to follow methods that will be beneficial to many cell biology researchers.
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Affiliation(s)
- Demet Candas
- Radiation Oncology, University of California, Davis;
| | - Lili Qin
- Radiation Oncology, University of California, Davis
| | - Ming Fan
- Radiation Oncology, University of California, Davis
| | - Jian-Jian Li
- Radiation Oncology, University of California, Davis
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232
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Wirth C, Brandt U, Hunte C, Zickermann V. Structure and function of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:902-14. [PMID: 26921811 DOI: 10.1016/j.bbabio.2016.02.013] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 12/13/2022]
Abstract
Proton-pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and most complicated enzyme of the respiratory chain. Fourteen central subunits represent the minimal form of complex I and can be assigned to functional modules for NADH oxidation, ubiquinone reduction, and proton pumping. In addition, the mitochondrial enzyme comprises some 30 accessory subunits surrounding the central subunits that are not directly associated with energy conservation. Complex I is known to release deleterious oxygen radicals (ROS) and its dysfunction has been linked to a number of hereditary and degenerative diseases. We here review recent progress in structure determination, and in understanding the role of accessory subunits and functional analysis of mitochondrial complex I. For the central subunits, structures provide insight into the arrangement of functional modules including the substrate binding sites, redox-centers and putative proton channels and pump sites. Only for two of the accessory subunits, detailed structures are available. Nevertheless, many of them could be localized in the overall structure of complex I, but most of these assignments have to be considered tentative. Strikingly, redox reactions and proton pumping machinery are spatially completely separated and the site of reduction for the hydrophobic substrate ubiquinone is found deeply buried in the hydrophilic domain of the complex. The X-ray structure of complex I from Yarrowia lipolytica provides clues supporting the previously proposed two-state stabilization change mechanism, in which ubiquinone redox chemistry induces conformational states and thereby drives proton pumping. The same structural rearrangements may explain the active/deactive transition of complex I implying an integrated mechanistic model for energy conversion and regulation. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Christophe Wirth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Ulrich Brandt
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany.
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233
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Bageshwar UK, VerPlank L, Baker D, Dong W, Hamsanathan S, Whitaker N, Sacchettini JC, Musser SM. High Throughput Screen for Escherichia coli Twin Arginine Translocation (Tat) Inhibitors. PLoS One 2016; 11:e0149659. [PMID: 26901445 PMCID: PMC4764201 DOI: 10.1371/journal.pone.0149659] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/03/2016] [Indexed: 01/29/2023] Open
Abstract
The twin arginine translocation (Tat) pathway transports fully-folded and assembled proteins in bacteria, archaea and plant thylakoids. The Tat pathway contributes to the virulence of numerous bacterial pathogens that cause disease in humans, cattle and poultry. Thus, the Tat pathway has the potential to be a novel therapeutic target. Deciphering the Tat protein transport mechanism has been challenging since the active translocon only assembles transiently in the presence of substrate and a proton motive force. To identify inhibitors of Tat transport that could be used as biochemical tools and possibly as drug development leads, we developed a high throughput screen (HTS) to assay the effects of compounds in chemical libraries against protein export by the Escherichia coli Tat pathway. The primary screen is a live cell assay based on a fluorescent Tat substrate that becomes degraded in the cytoplasm when Tat transport is inhibited. Consequently, low fluorescence in the presence of a putative Tat inhibitor was scored as a hit. Two diverse chemical libraries were screened, yielding average Z'-factors of 0.74 and 0.44, and hit rates of ~0.5% and 0.04%, respectively. Hits were evaluated by a series of secondary screens. Electric field gradient (Δψ) measurements were particularly important since the bacterial Tat transport requires a Δψ. Seven low IC50 hits were eliminated by Δψ assays, suggesting ionophore activity. As Δψ collapse is generally toxic to animal cells and efficient membrane permeability is generally favored during the selection of library compounds, these results suggest that secondary screening of hits against electrochemical effects should be done early during hit validation. Though none of the short-listed compounds inhibited Tat transport directly, the screening and follow-up assays developed provide a roadmap to pursue Tat transport inhibitors.
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Affiliation(s)
- Umesh K. Bageshwar
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX, United States of America
| | - Lynn VerPlank
- Broad Institute, Cambridge, MA, United States of America
| | - Dwight Baker
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States of America
| | - Wen Dong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States of America
| | - Shruthi Hamsanathan
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX, United States of America
| | - Neal Whitaker
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX, United States of America
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States of America
| | - Siegfried M. Musser
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX, United States of America
- * E-mail:
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234
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Berrisford JM, Baradaran R, Sazanov LA. Structure of bacterial respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:892-901. [PMID: 26807915 DOI: 10.1016/j.bbabio.2016.01.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 12/23/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. It is the largest protein assembly of respiratory chains and one of the most elaborate redox membrane proteins known. Bacterial enzyme is about half the size of mitochondrial and thus provides its important "minimal" model. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The L-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. We have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus, the membrane domain from Escherichia coli and recently of the intact, entire complex I from T. thermophilus (536 kDa, 16 subunits, 9 iron-sulphur clusters, 64 transmembrane helices). The 95Å long electron transfer pathway through the enzyme proceeds from the primary electron acceptor flavin mononucleotide through seven conserved Fe-S clusters to the unusual elongated quinone-binding site at the interface with the membrane domain. Four putative proton translocation channels are found in the membrane domain, all linked by the central flexible axis containing charged residues. The redox energy of electron transfer is coupled to proton translocation by the as yet undefined mechanism proposed to involve long-range conformational changes. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
| | - Rozbeh Baradaran
- Memorial Sloan-Kettering Cancer Center, 430 E 67th Street, NY 10065, USA
| | - Leonid A Sazanov
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.
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235
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Subrahmanian N, Remacle C, Hamel PP. Plant mitochondrial Complex I composition and assembly: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1001-14. [PMID: 26801215 DOI: 10.1016/j.bbabio.2016.01.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
In the mitochondrial inner membrane, oxidative phosphorylation generates ATP via the operation of several multimeric enzymes. The proton-pumping Complex I (NADH:ubiquinone oxidoreductase) is the first and most complicated enzyme required in this process. Complex I is an L-shaped enzyme consisting of more than 40 subunits, one FMN molecule and eight Fe-S clusters. In recent years, genetic and proteomic analyses of Complex I mutants in various model systems, including plants, have provided valuable insights into the assembly of this multimeric enzyme. Assisted by a number of key players, referred to as "assembly factors", the assembly of Complex I takes place in a sequential and modular manner. Although a number of factors have been identified, their precise function in mediating Complex I assembly still remains to be elucidated. This review summarizes our current knowledge of plant Complex I composition and assembly derived from studies in plant model systems such as Arabidopsis thaliana and Chlamydomonas reinhardtii. Plant Complex I is highly conserved and comprises a significant number of subunits also present in mammalian and fungal Complexes I. Plant Complex I also contains additional subunits absent from the mammalian and fungal counterpart, whose function in enzyme activity and assembly is not clearly understood. While 14 assembly factors have been identified for human Complex I, only two proteins, namely GLDH and INDH, have been established as bona fide assembly factors for plant Complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Nitya Subrahmanian
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Claire Remacle
- Institute of Botany, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
| | - Patrice Paul Hamel
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA; The Ohio State University, Department of Biological Chemistry and Pharmacology, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA.
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236
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Molecular simulation and modeling of complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:915-21. [PMID: 26780586 DOI: 10.1016/j.bbabio.2016.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/23/2022]
Abstract
Molecular modeling and molecular dynamics simulations play an important role in the functional characterization of complex I. With its large size and complicated function, linking quinone reduction to proton pumping across a membrane, complex I poses unique modeling challenges. Nonetheless, simulations have already helped in the identification of possible proton transfer pathways. Simulations have also shed light on the coupling between electron and proton transfer, thus pointing the way in the search for the mechanistic principles underlying the proton pump. In addition to reviewing what has already been achieved in complex I modeling, we aim here to identify pressing issues and to provide guidance for future research to harness the power of modeling in the functional characterization of complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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237
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Pi E, Qu L, Hu J, Huang Y, Qiu L, Lu H, Jiang B, Liu C, Peng T, Zhao Y, Wang H, Tsai SN, Ngai S, Du L. Mechanisms of Soybean Roots' Tolerances to Salinity Revealed by Proteomic and Phosphoproteomic Comparisons Between Two Cultivars. Mol Cell Proteomics 2016; 15:266-88. [PMID: 26407991 PMCID: PMC4762511 DOI: 10.1074/mcp.m115.051961] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/15/2015] [Indexed: 12/23/2022] Open
Abstract
Understanding molecular mechanisms underlying plant salinity tolerance provides valuable knowledgebase for effective crop improvement through genetic engineering. Current proteomic technologies, which support reliable and high-throughput analyses, have been broadly used for exploring sophisticated molecular networks in plants. In the current study, we compared phosphoproteomic and proteomic changes in roots of different soybean seedlings of a salt-tolerant cultivar (Wenfeng07) and a salt-sensitive cultivar (Union85140) induced by salt stress. The root samples of Wenfeng07 and Union85140 at three-trifoliate stage were collected at 0 h, 0.5 h, 1 h, 4 h, 12 h, 24 h, and 48 h after been treated with 150 mm NaCl. LC-MS/MS based phosphoproteomic analysis of these samples identified a total of 2692 phosphoproteins and 5509 phosphorylation sites. Of these, 2344 phosphoproteins containing 3744 phosphorylation sites were quantitatively analyzed. Our results showed that 1163 phosphorylation sites were differentially phosphorylated in the two compared cultivars. Among them, 10 MYB/MYB transcription factor like proteins were identified with fluctuating phosphorylation modifications at different time points, indicating that their crucial roles in regulating flavonol accumulation might be mediated by phosphorylated modifications. In addition, the protein expression profiles of these two cultivars were compared using LC MS/MS based shotgun proteomic analysis, and expression pattern of all the 89 differentially expressed proteins were independently confirmed by qRT-PCR. Interestingly, the enzymes involved in chalcone metabolic pathway exhibited positive correlations with salt tolerance. We confirmed the functional relevance of chalcone synthase, chalcone isomerase, and cytochrome P450 monooxygenase genes using soybean composites and Arabidopsis thaliana mutants, and found that their salt tolerance were positively regulated by chalcone synthase, but was negatively regulated by chalcone isomerase and cytochrome P450 monooxygenase. A novel salt tolerance pathway involving chalcone metabolism, mostly mediated by phosphorylated MYB transcription factors, was proposed based on our findings. (The mass spectrometry raw data are available via ProteomeXchange with identifier PXD002856).
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Affiliation(s)
- Erxu Pi
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China;
| | - Liqun Qu
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Jianwen Hu
- §Shanghai Applied Protein Technology Co. Ltd, Shanghai, 200233, PR China
| | - Yingying Huang
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Lijuan Qiu
- ¶The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Hongfei Lu
- ‖College of Life Science, Zhejiang Sci-Tech University, Hangzhou, 310018, PR China
| | - Bo Jiang
- **College of Biology and Food Engineering, Changshu Institute of Technology, Changshu 215500, PR China
| | - Cong Liu
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Tingting Peng
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Ying Zhao
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Huizhong Wang
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Sau-Na Tsai
- ‡‡Centre for Soybean Research of Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Saiming Ngai
- ‡‡Centre for Soybean Research of Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Liqun Du
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China;
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238
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Schimmeyer J, Bock R, Meyer EH. L-Galactono-1,4-lactone dehydrogenase is an assembly factor of the membrane arm of mitochondrial complex I in Arabidopsis. PLANT MOLECULAR BIOLOGY 2016; 90:117-26. [PMID: 26520835 PMCID: PMC4689740 DOI: 10.1007/s11103-015-0400-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/27/2015] [Indexed: 05/19/2023]
Abstract
L-Galactono-1,4-lactone dehydrogenase (GLDH) catalyses the last enzymatic step of the ascorbate biosynthetic pathway in plants. GLDH is localised to mitochondria and several reports have shown that GLDH is associated with complex I of the respiratory chain. In a gldh knock-out mutant, complex I is not detectable, suggesting that GLDH is essential for complex I assembly or stability. GLDH has not been identified as a genuine complex I subunit, instead, it is present in a smaller, lowly abundant version of complex I called complex I*. In addition, GLDH activity has also been detected in smaller protein complexes within mitochondria membranes. Here, we investigated the role of GLDH during complex I assembly. We identified GLDH in complexes co-localising with some complex I assembly intermediates. Using a mutant that accumulates complex I assembly intermediates, we confirmed that GLDH is associated with the complex I assembly intermediates of 400 and 450 kDa. In addition, we detected accumulation of the 200 kDa complex I assembly intermediate in the gldh mutant. Taken together, our data suggest that GLDH is an assembly factor of the membrane arm of complex I. This function appears to be independent of the role of GLDH in ascorbate synthesis, as evidenced by the ascorbate-deficient mutant vtc2-1 accumulating wild-type levels of complex I. Therefore, we propose that GLDH is a dual-function protein that has a second, non-enzymatic function in complex I assembly as a plant-specific assembly factor. We propose an updated model for complex I assembly that includes complex I* as an assembly intermediate.
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Affiliation(s)
- Joram Schimmeyer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Etienne H Meyer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 rue du général Zimmer, 67084, Strasbourg, France.
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239
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Lyons JA, Hilbers F, Caffrey M. Structure and Function of Bacterial Cytochrome c Oxidases. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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240
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Clock genes-dependent acetylation of complex I sets rhythmic activity of mitochondrial OxPhos. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:596-606. [PMID: 26732296 DOI: 10.1016/j.bbamcr.2015.12.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 11/30/2015] [Accepted: 12/23/2015] [Indexed: 11/20/2022]
Abstract
Physiology of living beings show circadian rhythms entrained by a central timekeeper present in the hypothalamic suprachiasmatic nuclei. Nevertheless, virtually all peripheral tissues hold autonomous molecular oscillators constituted essentially by circuits of gene expression that are organized in negative and positive feed-back loops. Accumulating evidence reveals that cell metabolism is rhythmically controlled by cell-intrinsic molecular clocks and the specific pathways involved are being elucidated. Here, we show that in vitro-synchronized cultured cells exhibit BMAL1-dependent oscillation in mitochondrial respiratory activity, which occurs irrespective of the cell type tested, the protocol of synchronization used and the carbon source in the medium. We demonstrate that the rhythmic respiratory activity is associated to oscillation in cellular NAD content and clock-genes-dependent expression of NAMPT and Sirtuins 1/3 and is traceable back to the reversible acetylation of a single subunit of the mitochondrial respiratory chain Complex I. Our findings provide evidence for a new interlocked transcriptional-enzymatic feedback loop controlling the molecular interplay between cellular bioenergetics and the molecular clockwork.
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241
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Castro PJ, Silva AF, Marreiros BC, Batista AP, Pereira MM. Respiratory complex I: A dual relation with H(+) and Na(+)? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:928-37. [PMID: 26711319 DOI: 10.1016/j.bbabio.2015.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 12/10/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
Abstract
Respiratory complex I couples NADH:quinone oxidoreduction to ion translocation across the membrane, contributing to the buildup of the transmembrane difference of electrochemical potential. H(+) is well recognized to be the coupling ion of this system but some studies suggested that this role could be also performed by Na(+). We have previously observed NADH-driven Na(+) transport opposite to H(+) translocation by menaquinone-reducing complexes I, which indicated a Na(+)/H(+) antiporter activity in these systems. Such activity was also observed for the ubiquinone-reducing mitochondrial complex I in its deactive form. The relation of Na(+) with complex I may not be surprising since the enzyme has three subunits structurally homologous to bona fide Na(+)/H(+) antiporters and translocation of H(+) and Na(+) ions has been described for members of most types of ion pumps and transporters. Moreover, no clearly distinguishable motifs for the binding of H(+) or Na(+) have been recognized yet. We noticed that in menaquinone-reducing complexes I, less energy is available for ion translocation, compared to ubiquinone-reducing complexes I. Therefore, we hypothesized that menaquinone-reducing complexes I perform Na(+)/H(+) antiporter activity in order to achieve the stoichiometry of 4H(+)/2e(-). In agreement, the organisms that use ubiquinone, a high potential quinone, would have kept such Na(+)/H(+) antiporter activity, only operative under determined conditions. This would imply a physiological role(s) of complex I besides a simple "coupling" of a redox reaction and ion transport, which could account for the sophistication of this enzyme. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Paulo J Castro
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Andreia F Silva
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal.
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242
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Friedrich T, Dekovic DK, Burschel S. Assembly of the Escherichia coli NADH:ubiquinone oxidoreductase (respiratory complex I). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:214-23. [PMID: 26682761 DOI: 10.1016/j.bbabio.2015.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022]
Abstract
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, couples the electron transfer from NADH to ubiquinone with the translocation of four protons across the membrane. The Escherichia coli complex I is made up of 13 different subunits encoded by the so-called nuo-genes. The electron transfer is catalyzed by nine cofactors, a flavin mononucleotide and eight iron-sulfur (Fe/S)-clusters. The individual subunits and the cofactors have to be assembled together in a coordinated way to guarantee the biogenesis of the active holoenzyme. Only little is known about the assembly of the bacterial complex compared to the mitochondrial one. Due to the presence of so many Fe/S-clusters the assembly of complex I is intimately connected with the systems responsible for the biogenesis of these clusters. In addition, a few other proteins have been reported to be required for an effective assembly of the complex in other bacteria. The proposed role of known bacterial assembly factors is discussed and the information from other bacterial species is used in this review to draw an as complete as possible model of bacterial complex I assembly. In addition, the supramolecular organization of the complex in E. coli is briefly described. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Prof. Conrad Mullineaux.
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Affiliation(s)
- Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany; Spemann Graduate School of Biology and Medicine, Albertstr. 19A, 79104 Freiburg i. Br., Germany.
| | - Doris Kreuzer Dekovic
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany; Spemann Graduate School of Biology and Medicine, Albertstr. 19A, 79104 Freiburg i. Br., Germany
| | - Sabrina Burschel
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany
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243
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Jacobsen MW, da Fonseca RR, Bernatchez L, Hansen MM. Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.). Mol Phylogenet Evol 2015; 95:161-70. [PMID: 26654959 DOI: 10.1016/j.ympev.2015.11.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/06/2015] [Accepted: 11/13/2015] [Indexed: 11/29/2022]
Abstract
Several studies have recently reported evidence for positive selection acting on the mitochondrial genome (mitogenome), emphasizing its potential role in adaptive divergence and speciation. In this study we searched 107 full mitogenomes of recently diverged species and lineages of whitefish (Coregonus ssp.) for signals of positive selection. These salmonids show several distinct morphological and ecological differences that may be associated with energetics and therefore potentially positive selection at the mitogenome level. We found that purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, the NADH dehydrogenase 2 gene (ND2) showed a highly elevated dN/dS ratio compared to the other mitochondrial genes, which was significantly higher in whitefish compared to other salmonids. We therefore further examined nonsynonymous evolution in ND2 by (i) mapping amino acid changes to a protein model structure which showed that they were located away from key functional residues of the protein, (ii) locating them in the sequences of other species of fish (Salmonidae, Anguillidae, Scombridae and Percidae) only to find pronounced overlap of nonsynonymous regions. We thus conclude that relaxed purifying selection is driving the evolution of ND2 by affecting mostly regions that have lower functional relevance.
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Affiliation(s)
- Magnus W Jacobsen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
| | - Rute R da Fonseca
- Department of Bioinformatics and RNA Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 København N, Denmark
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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244
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Hubenova Y, Mitov M. Mitochondrial origin of extracelullar transferred electrons in yeast-based biofuel cells. Bioelectrochemistry 2015; 106:232-9. [DOI: 10.1016/j.bioelechem.2014.06.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 06/17/2014] [Indexed: 11/24/2022]
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245
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Degli Esposti M. Genome Analysis of Structure-Function Relationships in Respiratory Complex I, an Ancient Bioenergetic Enzyme. Genome Biol Evol 2015; 8:126-47. [PMID: 26615219 PMCID: PMC4758237 DOI: 10.1093/gbe/evv239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase) is a ubiquitous bioenergetic enzyme formed by over 40 subunits in eukaryotes and a minimum of 11 subunits in bacteria. Recently, crystal structures have greatly advanced our knowledge of complex I but have not clarified the details of its reaction with ubiquinone (Q). This reaction is essential for bioenergy production and takes place in a large cavity embedded within a conserved module that is homologous to the catalytic core of Ni-Fe hydrogenases. However, how a hydrogenase core has evolved into the protonmotive Q reductase module of complex I has remained unclear. This work has exploited the abundant genomic information that is currently available to deduce structure-function relationships in complex I that indicate the evolutionary steps of Q reactivity and its adaptation to natural Q substrates. The results provide answers to fundamental questions regarding various aspects of complex I reaction with Q and help re-defining the old concept that this reaction may involve two Q or inhibitor sites. The re-definition leads to a simplified classification of the plethora of complex I inhibitors while throwing a new light on the evolution of the enzyme function.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Genova, Italy Center for Genomic Sciences, UNAM, Cuernavaca, Mexico
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246
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Letts JA, Sazanov LA. Gaining mass: the structure of respiratory complex I-from bacterial towards mitochondrial versions. Curr Opin Struct Biol 2015; 33:135-45. [PMID: 26387075 DOI: 10.1016/j.sbi.2015.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/13/2015] [Accepted: 08/25/2015] [Indexed: 02/04/2023]
Abstract
The 1MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated.
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Affiliation(s)
- James A Letts
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Leonid A Sazanov
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.
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247
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Wu JS, Lin SY, Liao FY, Hsiao WC, Lee LC, Peng YH, Hsieh CL, Wu MH, Song JS, Yueh A, Chen CH, Yeh SH, Liu CY, Lin SY, Yeh TK, Hsu JTA, Shih C, Ueng SH, Hung MS, Wu SY. Identification of Substituted Naphthotriazolediones as Novel Tryptophan 2,3-Dioxygenase (TDO) Inhibitors through Structure-Based Virtual Screening. J Med Chem 2015; 58:7807-19. [PMID: 26348881 DOI: 10.1021/acs.jmedchem.5b00921] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A structure-based virtual screening strategy, comprising homology modeling, ligand-support binding site optimization, virtual screening, and structure clustering analysis, was developed and used to identify novel tryptophan 2,3-dioxygenase (TDO) inhibitors. Compound 1 (IC50 = 711 nM), selected by virtual screening, showed inhibitory activity toward TDO and was subjected to structural modifications and molecular docking studies. This resulted in the identification of a potent TDO selective inhibitor (11e, IC50 = 30 nM), making it a potential compound for further investigation as a cancer therapeutic and other TDO-related targeted therapy.
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Affiliation(s)
- Jian-Sung Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Shu-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Fang-Yu Liao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Wen-Chi Hsiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Lung-Chun Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Yi-Hui Peng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chia-Ling Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Mine-Hsine Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Andrew Yueh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chun-Hwa Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Shiu-Hwa Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chia-Yeh Liu
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Shu-Yi Lin
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - John T-A Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Shau-Hua Ueng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Ming-Shiu Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
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248
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Functional diversity of complex I subunits in Candida albicans mitochondria. Curr Genet 2015; 62:87-95. [PMID: 26373419 DOI: 10.1007/s00294-015-0518-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
Our interest in the mitochondria of Candida albicans has progressed to the identification of several proteins that are critical to complex I (CI) activity. We speculated that there should be major functional differences at the protein level between mammalian and fungal mitochondria CI. In our pursuit of this idea, we were helped by published data of CI subunit proteins from a broad diversity of species that included two subunit proteins that are not found in mammals. These subunit proteins have been designated as Nuo1p and Nuo2p (NADH-ubiquinone oxidoreductases). Since functional assignments of both C. albicans proteins were unknown, other than having a putative NADH-oxidoreductase activity, we constructed knock-out strains that could be compared to parental cells. The relevance of our research relates to the critical roles of both proteins in cell biology and pathogenesis and their absence in mammals. These features suggest they may be exploited in antifungal drug discovery. Initially, we characterized Goa1p that apparently regulates CI activity but is not a CI subunit protein. We have used the goa1∆ for comparisons to Nuo1p and Nuo2p. We have demonstrated the critical role of these proteins in maintaining CI activities, virulence, and prolonging life span. More recently, transcriptional profiling of the three mutants and an ndh51∆ (protein is a highly conserved CI subunit) has revealed that there are overlapping yet also different functional assignments that suggest subunit specificity. The differences and similarities of each are described below along with our hypotheses to explain these data. Our conclusion and perspective is that the C. albicans CI subunit proteins are highly conserved except for two that define non-mammalian functions.
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249
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Abstract
Complex I functions as a redox-linked proton pump in the respiratory chains of mitochondria and bacteria, driven by the reduction of quinone (Q) by NADH. Remarkably, the distance between the Q reduction site and the most distant proton channels extends nearly 200 Å. To elucidate the molecular origin of this long-range coupling, we apply a combination of large-scale molecular simulations and a site-directed mutagenesis experiment of a key residue. In hybrid quantum mechanics/molecular mechanics simulations, we observe that reduction of Q is coupled to its local protonation by the His-38/Asp-139 ion pair and Tyr-87 of subunit Nqo4. Atomistic classical molecular dynamics simulations further suggest that formation of quinol (QH2) triggers rapid dissociation of the anionic Asp-139 toward the membrane domain that couples to conformational changes in a network of conserved charged residues. Site-directed mutagenesis data confirm the importance of Asp-139; upon mutation to asparagine the Q reductase activity is inhibited by 75%. The current results, together with earlier biochemical data, suggest that the proton pumping in complex I is activated by a unique combination of electrostatic and conformational transitions.
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250
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Lin BY, Kao MC. Therapeutic applications of the TAT-mediated protein transduction system for complex I deficiency and other mitochondrial diseases. Ann N Y Acad Sci 2015; 1350:17-28. [PMID: 26273800 DOI: 10.1111/nyas.12858] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Among the five enzyme complexes in the oxidative phosphorylation system, NADH-coenzyme Q oxidoreductase (also called complex I) is the largest, most intricate, and least understood. This enzyme complex spans the inner mitochondrial membrane and catalyzes the first step of electron transfer by the oxidation of NADH, and thereby provides two electrons for the reduction of quinone to quinol. Complex I deficiency is associated with many severe mitochondrial diseases, including Leber hereditary optic neuropathy and Leigh syndrome. However, to date, conventional treatments for the majority of genetic mitochondrial diseases are only palliative. Developing a reliable and convenient therapeutic approach is therefore considered to be an urgent need. Targeted proteins fused with the protein transduction domain of human immunodeficiency virus 1 transactivator of transcription (TAT) have been shown to enter cells by crossing plasma membranes while retaining their biological activities. Recent developments show that, in fusion with mitochondrial targeting sequences (MTSs), TAT-MTS-bound cargo can be correctly transported into mitochondria and restore the missing function of the cargo protein in patients' cells. The available evidence suggests that the TAT-mediated protein transduction system holds great promise as a potential therapeutic approach to treat complex I deficiency, as well as other mitochondrial diseases.
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Affiliation(s)
- Bo-Yu Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Mou-Chieh Kao
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan.,Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
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