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Chen J, Chen Y, He W, Liang H, Hong T, Li T, Du H. Transcriptome analysis reveals the molecular mechanism of differences in growth between photoautotrophy and heterotrophy in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2024; 15:1407915. [PMID: 38962244 PMCID: PMC11219824 DOI: 10.3389/fpls.2024.1407915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/20/2024] [Indexed: 07/05/2024]
Abstract
Background The green alga Chlamydomonas reinhardtii can grow photoautotrophically utilizing light and CO2, and heterotrophically utilizing acetate. The physiological and biochemical responses of autotrophy and heterotrophy are different in C. reinhardtii. However, there is no complete understanding of the molecular physiology between autotrophy and heterotrophy. Therefore, we performed biochemical, molecular and transcriptome analysis of C. reinhardtii between autotrophy and heterotrophy. Results The cell growth characterization demonstrated that heterotrophic cell had enhanced growth rates, and autotrophic cell accumulated more chlorophyll. The transcriptome data showed that a total of 2,970 differentially expressed genes (DEGs) were identified from photoautotrophy 12h (P12h) to heterotrophy 12h (H12h). The DEGs were involved in photosynthesis, the tricarboxylic acid cycle (TCA), pyruvate and oxidative phosphorylation metabolisms. Moreover, the results of qRT-PCR revealed that the relative expression levels of malate dehydrogenase (MDH), succinate dehydrogenase (SDH), ATP synthase (ATPase), and starch synthase (SSS) were increased significantly from P12h and H12h. The protein activity of NAD-malate dehydrogenase (NAD-MDH) and succinate dehydrogenase (SDH) were significantly higher in the H12h group. Conclusion The above results indicated that the high growth rate observed in heterotrophic cell may be the effects of environmental or genetic regulation of photosynthesis. Therefore, the identification of novel candidate genes in heterotrophy will contribute to the development of microalga strains with higher growth capacity and better performance for biomass production.
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Affiliation(s)
- Jing Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Yuanhao Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Weiling He
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Honghao Liang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Ting Hong
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Tangcheng Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
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Torraco A, Bianchi M, Verrigni D, Gelmetti V, Riley L, Niceta M, Martinelli D, Montanari A, Guo Y, Rizza T, Diodato D, Di Nottia M, Lucarelli B, Sorrentino F, Piemonte F, Francisci S, Tartaglia M, Valente E, Dionisi‐Vici C, Christodoulou J, Bertini E, Carrozzo R. A novel mutation in
NDUFB11
unveils a new clinical phenotype associated with lactic acidosis and sideroblastic anemia. Clin Genet 2016; 91:441-447. [DOI: 10.1111/cge.12790] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 01/06/2023]
Affiliation(s)
- A. Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - M. Bianchi
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - D. Verrigni
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - V. Gelmetti
- Neurogenetics Unit, CSS‐Mendel LaboratoryIRCCS Casa Sollievo della Sofferenza San Giovanni Rotondo Italy
| | - L. Riley
- Genetic Metabolic Disorders Research UnitChildren's Hospital at Westmead Sydney Australia
- Discipline of Paediatrics & Child HealthUniversity of Sydney Sydney Australia
| | - M. Niceta
- Division of Genetic Disorders and Rare DiseasesBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - D. Martinelli
- Division of MetabolismBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - A. Montanari
- Pasteur Institute – Cenci Bolognetti FoundationSapienza University of Rome Rome Italy
| | - Y. Guo
- Genetic Metabolic Disorders Research UnitChildren's Hospital at Westmead Sydney Australia
| | - T. Rizza
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - D. Diodato
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - M. Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - B. Lucarelli
- Stem Cell Transplant Unit, Department of Hematology and OncologyBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - F. Sorrentino
- UO Talassemici ‐Anemie Rare del Globulo Rosso, Ospedale S Eugenio Rome Italy
| | - F. Piemonte
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - S. Francisci
- Department of Biology and Biotechnologies “C. Darwin”Sapienza University of Rome Rome Italy
| | - M. Tartaglia
- Division of Genetic Disorders and Rare DiseasesBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - E.M. Valente
- Section of Neurosciences, Department of Medicine and SurgeryUniversity of Salerno Salerno Italy
| | - C. Dionisi‐Vici
- Division of MetabolismBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - J. Christodoulou
- Genetic Metabolic Disorders Research UnitChildren's Hospital at Westmead Sydney Australia
- Discipline of Paediatrics & Child HealthUniversity of Sydney Sydney Australia
- Discipline of Genetic MedicineUniversity of Sydney Sydney Australia
| | - E. Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
| | - R. Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesù Children's Hospital, IRCCS Rome Italy
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3
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Scheffler IE. Mitochondrial disease associated with complex I (NADH-CoQ oxidoreductase) deficiency. J Inherit Metab Dis 2015; 38:405-15. [PMID: 25224827 DOI: 10.1007/s10545-014-9768-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/27/2014] [Accepted: 09/02/2014] [Indexed: 01/09/2023]
Abstract
Mitochondrial diseases due to a reduced capacity for oxidative phosphorylation were first identified more than 20 years ago, and their incidence is now recognized to be quite significant. In a large proportion of cases the problem can be traced to a complex I (NADH-CoQ oxidoreductase) deficiency (Phenotype MIM #252010). Because the complex consists of 44 subunits, there are many potential targets for pathogenic mutations, both on the nuclear and mitochondrial genomes. Surprisingly, however, almost half of the complex I deficiencies are due to defects in as yet unidentified genes that encode proteins other than the structural proteins of the complex. This review attempts to summarize what we know about the molecular basis of complex I deficiencies: mutations in the known structural genes, and mutations in an increasing number of genes encoding "assembly factors", that is, proteins required for the biogenesis of a functional complex I that are not found in the final complex I. More such genes must be identified before definitive genetic counselling can be applied in all cases of affected families.
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Affiliation(s)
- Immo E Scheffler
- Division of Biology (Molecular Biology Section), University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093-0322, USA,
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4
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Chen Q, Moghaddas S, Hoppel CL, Lesnefsky EJ. Ischemic defects in the electron transport chain increase the production of reactive oxygen species from isolated rat heart mitochondria. Am J Physiol Cell Physiol 2008; 294:C460-6. [DOI: 10.1152/ajpcell.00211.2007] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cardiac ischemia decreases complex III activity, cytochrome c content, and respiration through cytochrome oxidase in subsarcolemmal mitochondria (SSM) and interfibrillar mitochondria (IFM). The reversible blockade of electron transport with amobarbital during ischemia protects mitochondrial respiration and decreases myocardial injury during reperfusion. These findings support that mitochondrial damage occurs during ischemia and contributes to myocardial injury during reperfusion. The current study addressed whether ischemic damage to the electron transport chain (ETC) increased the net production of reactive oxygen species (ROS) from mitochondria. SSM and IFM were isolated from 6-mo-old Fisher 344 rat hearts following 25 min global ischemia or following 40 min of perfusion alone as controls. H2O2release from SSM and IFM was measured using the amplex red assay. With glutamate as a complex I substrate, the net production of H2O2was increased by 178 ± 14% and 179 ± 17% in SSM and IFM ( n = 9), respectively, following ischemia compared with controls ( n = 8). With succinate as substrate in the presence of rotenone, H2O2increased by 272 ± 22% and 171 ± 21% in SSM and IFM, respectively, after ischemia. Inhibitors of electron transport were used to assess maximal ROS production. Inhibition of complex I with rotenone increased H2O2production by 179 ± 24% and 155 ± 14% in SSM and IFM, respectively, following ischemia. Ischemia also increased the antimycin A-stimulated production of H2O2from complex III. Thus ischemic damage to the ETC increased both the capacity and the net production of H2O2from complex I and complex III and sets the stage for an increase in ROS production during reperfusion as a mechanism of cardiac injury.
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5
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Quinol type compound in cytochrome c preparations leads to non-enzymatic reduction of cytochrome c during the measurement of complex III activity. Mitochondrion 2007; 8:155-63. [PMID: 18272433 DOI: 10.1016/j.mito.2007.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2007] [Revised: 11/30/2007] [Accepted: 12/11/2007] [Indexed: 10/22/2022]
Abstract
Measurement of complex III activity is critical to the diagnosis of human mitochondrial disease and the study of mitochondrial pathobiology. Activity is measured as the maximal rate of antimycin A-sensitive reduction of exogenous cytochrome c by detergent-solubilized mitochondria. Complex III activity exhibited an unexpected variation based upon the commercial source of cytochrome c owing to an increase in the antimycin A-insensitive background reduction of cytochrome c and variable increases in total activity. Analysis of cytochrome c (producing a high-background) by fast protein liquid chromatography yielded a contaminant peak containing a lipid extractable component with redox spectra and mass spectroscopy fragmentation suggestive of a quinol. Measurement of inhibitor-sensitive rates are critical for the accurate and reproducible measurement of complex III activity and serve as a key quality control to screen for non-enzymatic reactions that obscure complex III activity.
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6
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Cardol P, González-Halphen D, Reyes-Prieto A, Baurain D, Matagne RF, Remacle C. The mitochondrial oxidative phosphorylation proteome of Chlamydomonas reinhardtii deduced from the Genome Sequencing Project. PLANT PHYSIOLOGY 2005; 137:447-59. [PMID: 15710684 PMCID: PMC1065347 DOI: 10.1104/pp.104.054148] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Revised: 11/25/2004] [Accepted: 11/25/2004] [Indexed: 05/20/2023]
Affiliation(s)
- Pierre Cardol
- Genetics of Microorganisms , Institute of Plant Biology B22, University of Liege, B-4000 Liege, Belgium
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7
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Lam E, Richard M. In vitro reconstitution of the electron pathway from water to cytochrome f
of spinach thylakoids. FEBS Lett 2001. [DOI: 10.1016/0014-5793(82)80635-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Chomyn A. Mitochondrial genetic control of assembly and function of complex I in mammalian cells. J Bioenerg Biomembr 2001; 33:251-7. [PMID: 11695835 DOI: 10.1023/a:1010791204961] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Sixteen years ago, we demonstrated, by immunological and biochemical approaches, that seven subunits of complex I are encoded in mitochondrial DNA (mtDNA) and synthesized on mitochondrial ribosomes in mammalian cells. More recently, we carried out a biochemical, molecular, and cellular analysis of a mutation in the gene for one of these subunits, ND4, that causes Leber's hereditary optic neuropathy (LHON). We demonstrated that, in cells carrying this mutation, the mtDNA-encoded subunits of complex I are assembled into a complex, but the rate of complex I-dependent respiration is decreased. Subsequently, we isolated several mutants affected in one or another of the mtDNA-encoded subunits of complex I by exposing established cell lines to high concentrations of rotenone. Our analyses of these mtDNA mutations affecting subunits of complex I have shown that at least two of these subunits, ND4 and ND6, are essential for the assembly of the enzyme. ND5 appears to be located at the periphery of the enzyme and, while it is not essential for assembly of the other mtDNA-encoded subunits into a complex, it is essential for complex I activity. In fact, the synthesis of the ND5 polypeptide is rate limiting for the activity of the enzyme.
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MESH Headings
- Animals
- DNA, Mitochondrial/genetics
- Electron Transport Complex I
- Gene Expression Regulation, Enzymologic
- Humans
- Mitochondria/enzymology
- Mutation
- NADH, NADPH Oxidoreductases/biosynthesis
- NADH, NADPH Oxidoreductases/chemistry
- NADH, NADPH Oxidoreductases/genetics
- Optic Atrophy, Hereditary, Leber/enzymology
- Optic Atrophy, Hereditary, Leber/genetics
- Protein Subunits
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- A Chomyn
- California Institute of Technology, Division of Biology, Pasadena 91125, USA.
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9
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Jung C, Higgins CM, Xu Z. Measuring the quantity and activity of mitochondrial electron transport chain complexes in tissues of central nervous system using blue native polyacrylamide gel electrophoresis. Anal Biochem 2000; 286:214-23. [PMID: 11067743 DOI: 10.1006/abio.2000.4813] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondrial dysfunction and degeneration are associated with many neurodegenerative disorders. A dysfunctional mitochondrial electron transport chain (ETC) impairs ATP production and accelerates the generation of free radicals. To evaluate mitochondrial function, reliable methods are needed. Conventional spectrophotometric assays may not eliminate interference from nonspecific enzyme activities and do not measure quantities of specific ETC complexes. Blue native polyacrylamide gel electrophoresis (BN-PAGE) has been used to resolve mitochondrial ETC complexes. Combined with histochemical staining, it has also been applied to measure ETC enzyme activities in muscles. The current study is to determine (1) whether BN-PAGE can be used to detect ETC complexes from different regions of the central nervous system (CNS) and (2) the quantitative range of BN-PAGE in measuring the amounts and activities of different ETC complexes. By systematically varying the protein amount and the time of histochemical reactions, we have found linear ranges comparable to spectrophotometric assays for measuring enzyme activities of several ETC complexes. In addition, we found linear ranges for measuring protein quantities in several ETC complexes. These results demonstrate that BN-PAGE can be used to measure the amount and activity of the ETC enzymes from the nerve tissues and, thus, can be applied to evaluate the functional changes of mitochondria in neurodegenerative disorders.
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Affiliation(s)
- C Jung
- Department of Biochemistry and Molecular Pharmacology, Department of Cell Biology, Neuroscience Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA
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10
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Glinka Y, Tipton KF, Youdim MB. Mechanism of inhibition of mitochondrial respiratory complex I by 6-hydroxydopamine and its prevention by desferrioxamine. Eur J Pharmacol 1998; 351:121-9. [PMID: 9698213 DOI: 10.1016/s0014-2999(98)00279-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Inhibition of mitochondrial complex I by 6-hydroxydopamine was studied in brain and liver preparations. NADH-quinone reductase activity of this complex from rat brain was inhibited by 6-hydroxydopamine partially uncompetitively with respect to NADH with a value of Ki 0.051 +/- 0.014 mM. The inhibition patterns for liver NADH-quinone reductase were more complicated than those obtained with the brain enzyme. Desferrioxamine behaved as a 'competitive' activator of complex I from both liver and brain (Ka = 2 mM and 0.02 mM, respectively). It also protected brain complex I against the inhibition by increasing Ki value about 10-fold. Furthermore, in the presence of desferrioxamine the residual activity of enzyme-substrate-inhibitor complex was increased. The data suggest that desferrioxamine does not compete directly with 6-hydroxydopamine for binding to the inhibitory site, but induces a conformation which is unfavorable for the binding of the inhibitor to the protein. The qualitative and quantitative differences between the behavior of the liver and brain enzyme complexes indicate that the assumption that the behavior of liver mitochondria can be used as a model for the situation in brain should be reconsidered.
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Affiliation(s)
- Y Glinka
- Department of Pharmacology, Rappaport Family Research Institute, NPF, Faculty of Medicine, Technion, Haifa, Israel
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11
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Scheffler IE. Molecular genetics of succinate:quinone oxidoreductase in eukaryotes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1998; 60:267-315. [PMID: 9594577 DOI: 10.1016/s0079-6603(08)60895-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Succinate:quinone oxidoreductase is a membrane-associated complex in mitochondria, often referred to as complex II, based on the fractionation scheme developed by Y. Hatefi and colleagues. It consists of four peptides, two of which are integral membrane proteins (15 and 12-13 kDa, respectively) and two others that are peripheral membrane proteins, i.e., a flavoprotein (Fp, 70 kDa) and an iron-protein (Ip, 27 kDa). The mature, functional complex contains a cytochrome in association with the membrane proteins, a flavin linked covalently to the largest peptide, and three iron-sulfur clusters in the 27-kDa subunit. The present review touches only briefly on the biochemical and biophysical properties of this complex. Instead, the focus is on the molecular-genetic studies that have become possible since the first genes from eukaryotes were cloned in 1989. The evolutionary conservation of the amino acid sequence of both the Fp and the Ip peptides has facilitated the cloning of these genes from a large variety of eukaryotic organisms by PCR-based methods. The review addresses questions related to the regulation of the expression of these genes, with an emphasis on mammals and yeast, for which most of the information is available. Four different genes have to be co-ordinately regulated. Transcriptional as well as posttranscriptional regulatory mechanisms have been observed in diverse organisms. Intriguing observations have been made in studies of this enzyme during the life cycle of organisms existing alternately under aerobic and anaerobic conditions. Naturally occurring or induced mutations in these genes have shed light on several questions related to the assembly of this complex, and on the relationship between structure and function. Four different peptides are imported into the mitochondria. They have to be modified, folded, and assembled. The stage is set for the exploration of highly specific changes introduced by site-directed mutagenesis. Until recently the genes were believed to be exclusively nuclear in all eukaryotes, but exceptions have since been found. This finding has relevance in the discussion of the evolution of mitochondria from prokaryotes. A highly conserved set of genes is found in prokaryotes, and some informative comparisons on gene organization and expression in prokaryotes and eukaryotes have been included.
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Affiliation(s)
- I E Scheffler
- Department of Biology, University of California, San Diego 92093, USA
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12
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Haass-Männle H, Zimmermann HW. Selective photoaffinity labelling of one mitochondrial protein in living cells of Saccharomyces cerevisiae with the fluorescent probe APMC. Identification of the target protein as subunit I of cytochrome c oxidase. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1997; 41:90-102. [PMID: 9440317 DOI: 10.1016/s1011-1344(97)00088-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The lipophilic, cationic fluorochrome azopentylmethylindocarbocyanine (APMC) specifically stains the mitochondria in living yeast cells (Saccharomyces cerevisiae WT X 2180). It contains a photosensitive diazirine ring and is suitable for photoaffinity labelling. By combining photoaffinity labelling, micro-gel electrophoresis (SDS-PAGE), and detection of the APMC fluorescence with a microfluorimeter, we established a highly sensitive procedure for determining the apparent molecular weight of the APMC-labelled proteins in yeast cells. On vital staining at 0.1 microM APMC for 30 min, only one mitochondrial protein with an apparent molecular weight of 40 kDa is labelled with high intensity. At increased dye concentrations proteins of 47 and 49 kDa are labelled too, however not until all binding sites of the 40 kDa protein are occupied. Obviously, the APMC cations have a pronounced affinity for this protein. It was shown by fractional centrifugation that the labelled 40 kDa protein is a constituent of the inner mitochondrial membrane. One driving force for the accumulation of the APMC cations is the trans-membrane potential (TMP) across the inner mitochondrial membrane. Consequently, uncouplers like dinitrophenol (DNP) and carbonylcyanidechlorophenyl-hydrazone (CCCP), ionophores (valinomycin, gramicidin), and inhibitors of the respiratory chain (myxothiazol, KCN), which decrease the TMP, also diminish the APMC accumulation and labelling. And conversely, drugs, which hyperpolarize the inner membrane (nigericin, atractyloside), favour APMC labelling. Another driving force of APMC accumulation is the dye's lipophilicity, which facilitates dye accumulation by hydrophobic interaction with the very lipophilic proteins of the inner mitochondrial membranes. This was shown by competitive double staining experiments. Thiamine strongly inhibits APMC labelling. Obviously, the transport of the APMC cations is facilitated by the thiamine carrier, and thiamine competes for the same binding sites, which are occupied by the dye cations. Chloramphenicol is an inhibitor of the mitochondrial protein synthesis without affecting the TMP. On preincubation, chloramphenicol completely quenches the signal of the 40 kDa protein. Therefore, this protein must be encoded on the mtDNA. The only 40 kDa protein with adequate properties is the subunit I of cytochrome c oxidase. Obviously, it is the preferred target of the APMC cations on photoaffinity labelling. This assignment agrees with the strong hydrophobicity of the labelled 40 kDa protein, which was tested with various detergents. It also agrees with the solvatochromism of the protein-bound APMC label, and finally with the paralellism of the labelled protein with cytochrome c oxidase on fractional ammonium sulfate precipitation.
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Affiliation(s)
- H Haass-Männle
- Institut für Physikalische Chemie der Universität Freiburg, Freiburg, Germany
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13
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Burger G, Lang BF, Reith M, Gray MW. Genes encoding the same three subunits of respiratory complex II are present in the mitochondrial DNA of two phylogenetically distant eukaryotes. Proc Natl Acad Sci U S A 1996; 93:2328-32. [PMID: 8637872 PMCID: PMC39795 DOI: 10.1073/pnas.93.6.2328] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Although mitochondrial DNA is known to encode a limited number (<20) of the polypeptide components of respiratory complexes I, III, IV, and V, genes for components of complex II [succinate dehydrogenase (ubiquinone); succinate:ubiquinone oxidoreductase, EC 1.3.5.1] are conspicuously lacking in mitochondrial genomes so far characterized. Here we show that the same three subunits of complex II are encoded in the mitochondrial DNA of two phylogenetically distant eukaryotes, Porphyra purpurea (a photosynthetic red alga) and Reclinomonas americana (a heterotrophic zooflagellate). These complex II genes, sdh2, sdh3, and sdh4, are homologs, respectively, of Escherichia coli sdhB, sdhC, and sdhD. In E. coli, sdhB encodes the iron-sulfur subunit of succinate dehydrogenase (SDH), whereas sdhC and sdhD specify, respectively, apocytochrome b558 and a hydrophobic 13-kDa polypeptide, which together anchor SDH to the inner mitochondrial membrane. Amino acid sequence similarities indicate that sdh2, sdh3, and sdh4 were originally encoded in the protomitochondrial genome and have subsequently been transferred to the nuclear genome in most eukaryotes. The data presented here are consistent with the view that mitochondria constitute a monophyletic lineage.
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Affiliation(s)
- G Burger
- Program in Evolutionary Biology, Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Quebec, Canada
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14
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Oostveen FG, Au HC, Meijer PJ, Scheffler IE. A Chinese hamster mutant cell line with a defect in the integral membrane protein CII-3 of complex II of the mitochondrial electron transport chain. J Biol Chem 1995; 270:26104-8. [PMID: 7592812 DOI: 10.1074/jbc.270.44.26104] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In this study, a respiration-deficient Chinese hamster cell line with a defect in succinate dehydrogenase activity is shown to result from a single base change in a codon in the coding sequence for the membrane anchor protein CII-3 (also referred to as QPs-1). A premature translation stop results in the truncation of 33 amino acids from the C terminus. Bovine cDNA encoding this peptide complements the mutation. There is about 82% identity between these two mammalian proteins. The gene for CII-3 was mapped on human chromosome 1, and because it is also found on minichromosomes characterized by our laboratory, we can localize it on the short arm within 1-2 megabases from the centromere.
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Affiliation(s)
- F G Oostveen
- Department of Biology, University of California, San Diego, La Jolla 92093-0322, USA
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15
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Leckschat S, Ream-Robinson D, Scheffler IE. The gene for the iron sulfur protein of succinate dehydrogenase (SDH-IP) maps to human chromosome 1p35-36.1. SOMATIC CELL AND MOLECULAR GENETICS 1993; 19:505-11. [PMID: 8291026 DOI: 10.1007/bf01233256] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A partial human cDNA clone for the iron-protein (IP) subunit of succinate dehydrogenase (EC 1.3.99.1) was used in Southern analyses of restriction enzyme digests of genomic human and hamster DNA as well as hamster-human hybrids containing a limited number of human chromosomes. The gene for this protein was mapped to human chromosome 1. Digestion of genomic DNA with several restriction enzymes yielded two fragments detectable on a Southern blot, in contrast to the expectations based on the sequence of the cDNA clone. A preliminary analysis of a genomic clone with most of the IP gene has indicated the presence of several introns containing restriction sites detected by the Southern analysis. This genomic clone was also used for subregional mapping by fluorescence in situ hybridization (FISH) to human metaphase chromosomes. A single locus in the region 1p35-36.1 was identified.
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Affiliation(s)
- S Leckschat
- Department of Biology, University of California, San Diego, La Jolla 92093-0322
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16
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Chapter 7 Progress in succinate:quinone oxidoreductase research. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/s0167-7306(08)60175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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17
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Chapter 6 NADH-ubiquinone oxidoreductase. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/s0167-7306(08)60174-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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18
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Dreyer JL. Plasma membrane dehydrogenases in rat brain synaptic membranes. Multiplicity and subunit composition. J Bioenerg Biomembr 1990; 22:619-33. [PMID: 2249975 DOI: 10.1007/bf00809067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Plasma membrane redox enzymes have been investigated in synaptic membranes from rat brain nerve terminals. UV-Vis spectra of intact synaptic plasma membranes are presented and the presence of a b-type cytochrome, detectable at 77 degrees K and sensitive to NADH or NADPH, is shown. The molecular characterization of rat synaptic NADH-dehydrogenases was further performed on solubilized enzymes using a recently developed nondissociating polyacrylamide gel electrophoresis technique. Synaptic plasma membranes were solubilized with 1% sodium cholate or Triton X-114 and centrifuged. The supernatant retained over 60% of the NADH-dehydrogenase activity, tested with either DCIP2 or ferricyanide as substrates, together with NADH. Both enzyme activities were insensitive toward rotenone. This extraction procedure also solubilized about 50% of the proteins. When submitted to polyacrylamide gel electrophoresis under nondenaturing conditions and stained for NADH-dehydrogenase activity, five bands of different mobilities were detected. The multiple NADH-dehydrogenases of synaptic plasma membranes were investigated by means of band excision and the five excised bands each submitted to amino acid analysis and to 2-D electrophoresis. The subunit composition of each band was then deduced, together with the molecular weight and pI of each respective subunit. NADH-dehydrogenases have also been purified by means of FPLC on Mono-P (chromatofocusing) followed by gel filtration on Superose 12. NADH-Dehydrogenase IV and V could be purified in their active forms by this approach.
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Affiliation(s)
- J L Dreyer
- Department of Biochemistry, University of Fribourg, Switzerland
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19
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Cloning and characterization of the iron-sulfur subunit gene of succinate dehydrogenase from Saccharomyces cerevisiae. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)86962-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Isolation and characterization of a Saccharomyces cerevisiae mutant with a disrupted gene for the IP subunit of succinate dehydrogenase. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)47237-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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21
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Gould SJ, Subramani S, Scheffler IE. Use of the DNA polymerase chain reaction for homology probing: isolation of partial cDNA or genomic clones encoding the iron-sulfur protein of succinate dehydrogenase from several species. Proc Natl Acad Sci U S A 1989; 86:1934-8. [PMID: 2494655 PMCID: PMC286819 DOI: 10.1073/pnas.86.6.1934] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The DNA polymerase chain reaction was developed for in vitro amplification of specific DNA sequences, and it has been used for a wide variety of purposes in several fields. We have developed an application of the polymerase chain reaction that is useful for the isolation of partial cDNA or genomic clones of conserved genes. We used this technique to clone the gene encoding the iron protein subunit (27 kDa) of succinate dehydrogenase (EC 1.3.5.1) from several species, including human, rat, Drosophila melanogaster, Arabidopsis thaliana, Schizosaccharomyces pombe, and Saccharomyces cerevisiae. Mixed oligonucleotide primers corresponding to two conserved regions of the protein were used in conjunction with genomic and cDNA templates in the reaction. The primers contained all possible nucleotide combinations that could encode the corresponding peptide sequences. These oligonucleotide mixtures contained 262,144 (2(18] and 8192 (2(13] unique sequences, respectively. Use of the polymerase chain reaction for homology probing allows one to utilize more complex mixtures of oligonucleotides as probes than is possible with filter hybridization screening techniques. In addition, the polymerase chain reaction offers the advantage of synthesizing the DNA product directly, in some cases obviating the need to construct cDNA or genomic libraries. This application of the polymerase chain reaction should be useful not only for the identification of conserved genes in a variety of species but also for the isolation of previously unknown members of gene families.
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Affiliation(s)
- S J Gould
- Department of Biology, University of California, San Diego, La Jolla 92093
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22
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Breen GA, Miller DL, Holmans PL, Welch G. Mitochondrial DNA of two independent oligomycin-resistant Chinese hamster ovary cell lines contains a single nucleotide change in the ATPase 6 gene. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67297-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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23
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Garnett KE, Simmons WA, Wing MS, Breen GA. DNA-mediated transfer of complex I genes into three different respiration-deficient Chinese hamster mutant cell lines with defects in complex I of electron transport chain. SOMATIC CELL AND MOLECULAR GENETICS 1985; 11:345-52. [PMID: 3927493 DOI: 10.1007/bf01534411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have used genomic DNA from human or mouse cells as a calcium phosphate precipitate to transfect three different respiration-deficient Chinese hamster mutant cell lines with defects in complex I of the electron transport chain. Transformants were selected in DMEM containing galactose, a medium in which respiration-deficient cells do not grow. Evidence for the DNA-mediated transformation of these respiration-deficient cells with a putative complex I gene includes: the clones are respiration-positive and respire at rates comparable to those of wild-type human, hamster, or mouse cells; the clones have rotenone-sensitive NADH oxidase activities, indicating a functional complex I of the electron transport chain; and the clones appear to be true transformants, as demonstrated by hybridization and Southern blot analyses. These experiments provide the basis for the isolation and subsequent characterization of several of the genes involved with complex I of the mammalian electron transport chain.
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Owen P, Condon C. The succinate dehydrogenase ofEscherichia coli: subunit composition of the Triton X-100-solubilized antigen. FEMS Microbiol Lett 1982. [DOI: 10.1111/j.1574-6968.1982.tb00002.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Malczewski RM, Whitfield CD. Respiration-defective Chinese hamster cell mutants containing low levels of NADH-ubiquinone reductase and cytochrome c oxidase. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34307-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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28
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Chen S, Guillory R. Studies on the interaction of arylazido-beta-alanyl NAD+ with the mitochondrial NADH dehydrogenase. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68846-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Kawato S, Sigel E, Carafoli E, Cherry R. Rotation of cytochrome oxidase in phospholipid vesicles. Investigations of interactions between cytochrome oxidases and between cytochrome oxidase and cytochrome bc1 complex. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68993-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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30
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Jaworowski A, Mayo G, Shaw DC, Campbell HD, Young IG. Characterization of the respiratory NADH dehydrogenase of Escherichia coli and reconstitution of NADH oxidase in ndh mutant membrane vesicles. Biochemistry 1981; 20:3621-8. [PMID: 7020757 DOI: 10.1021/bi00515a049] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Highly purified preparations of the cholate-solubilized respiratory NADH dehydrogenase, isolated from genetically amplified Escherichia coli strains [Jaworowski, A., Campbell, H. D., Poulis, M. I., & Young, I. G. (1981) Biochemistry 20, 2041-2047], have been characterized. Enzyme preparations were shown to contain 70% (w/w) lipid, predominantly phosphatidylethanolamine. One mol of noncovalently bound FAD and approximately 1 mol of ubiquinone/mol of enzyme subunit were detected. The purified enzyme was shown to contain only low levels of Fe and acid-labile S, indicating the absence of iron-sulfur clusters. No Cu, Mo, W, or covalently bound P was detected, and no evidence for other chromophores was obtained from visible and ultraviolet absorption spectra of the purified enzyme or of the delipidated polypeptide prepared by gel filtration in sodium dodecyl sulfate. Protein chemical studies verified that the enzyme consists of a single polypeptide species of Mr 47 000, and the N- and C-terminal cyanogen bromide peptides were identified. The pure enzyme was shown to reconstitute membrane-bound, cyanide-sensitive NADH oxidase activity in membrane vesicles prepared from ndh mutant strains.
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Stumpf DA, Parks JK. Human mitochondrial electron transport chain: assay of succinate: cytochrome c reductase in leukocytes, platelets and cultured fibroblasts. BIOCHEMICAL MEDICINE 1981; 25:234-8. [PMID: 6269538 DOI: 10.1016/0006-2944(81)90080-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Isolation of cytochrome b560 from complex II (succinateùbiquinone oxidoreductase) and its reconstitution with succinate dehydrogenase. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70662-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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34
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Schneider H, Lemasters J, Höchli M, Hackenbrock C. Liposome-mitochondrial inner membrane fusion. Lateral diffusion of integral electron transfer components. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)85768-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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