1
|
Tian R, Guo H, Jin Z, Zhang F, Zhao J, Seim I. Molecular evolution of vision-related genes may contribute to marsupial photic niche adaptations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.982073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Vision plays an essential role in the life of many animals. While most mammals are night-active (nocturnal), many have adapted to novel light environments. This includes diurnal (day-active) and crepuscular (twilight-active) species. Here, we used integrative approaches to investigate the molecular evolution of 112 vision-related genes across 19 genomes representing most marsupial orders. We found that four genes (GUCA1B, GUCY2F, RGR, and SWS2) involved in retinal phototransduction likely became functionally redundant in the ancestor of marsupials, a group of largely obligate nocturnal mammals. We also show evidence of rapid evolution and positive selection of bright-light vision genes in the common ancestor of Macropus (kangaroos, wallaroos, and wallabies). Macropus-specific amino acid substitutions in opsin genes (LWS and SWS1), in particular, may be an adaptation for crepuscular vision in this genus via opsin spectral sensitivity tuning. Our study set the stage for functional genetics studies and provides a stepping stone to future research efforts that fully capture the visual repertoire of marsupials.
Collapse
|
2
|
Padavannil A, Ayala-Hernandez MG, Castellanos-Silva EA, Letts JA. The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I. Front Mol Biosci 2022; 8:798353. [PMID: 35047558 PMCID: PMC8762328 DOI: 10.3389/fmolb.2021.798353] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023] Open
Abstract
Complex I (CI) is the largest protein complex in the mitochondrial oxidative phosphorylation electron transport chain of the inner mitochondrial membrane and plays a key role in the transport of electrons from reduced substrates to molecular oxygen. CI is composed of 14 core subunits that are conserved across species and an increasing number of accessory subunits from bacteria to mammals. The fact that adding accessory subunits incurs costs of protein production and import suggests that these subunits play important physiological roles. Accordingly, knockout studies have demonstrated that accessory subunits are essential for CI assembly and function. Furthermore, clinical studies have shown that amino acid substitutions in accessory subunits lead to several debilitating and fatal CI deficiencies. Nevertheless, the specific roles of CI’s accessory subunits have remained mysterious. In this review, we explore the possible roles of each of mammalian CI’s 31 accessory subunits by integrating recent high-resolution CI structures with knockout, assembly, and clinical studies. Thus, we develop a framework of experimentally testable hypotheses for the function of the accessory subunits. We believe that this framework will provide inroads towards the complete understanding of mitochondrial CI physiology and help to develop strategies for the treatment of CI deficiencies.
Collapse
Affiliation(s)
- Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Maria G Ayala-Hernandez
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Eimy A Castellanos-Silva
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| |
Collapse
|
3
|
Adav SS, Park JE, Sze SK. Quantitative profiling brain proteomes revealed mitochondrial dysfunction in Alzheimer's disease. Mol Brain 2019; 12:8. [PMID: 30691479 PMCID: PMC6350377 DOI: 10.1186/s13041-019-0430-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/22/2019] [Indexed: 11/10/2022] Open
Abstract
Mitochondrial dysfunction is a key feature in both aging and neurodegenerative diseases including Alzheimer’s disease (AD), but the molecular signature that distinguishes pathological changes in the AD from healthy aging in the brain mitochondria remain poorly understood. In order to unveil AD specific mitochondrial dysfunctions, this study adopted a discovery-driven approach with isobaric tag for relative and absolute quantitation (iTRAQ) and label-free quantitative proteomics, and profiled the mitochondrial proteomes in human brain tissues of healthy and AD individuals. LC-MS/MS-based iTRAQ quantitative proteomics approach revealed differentially altered mitochondriomes that distinguished the AD’s pathophysiology-induced from aging-associated changes. Our results showed that dysregulated mitochondrial complexes including electron transport chain (ETC) and ATP-synthase are the potential driver for pathology of the AD. The iTRAQ results were cross-validated with independent label-free quantitative proteomics experiments to confirm that the subunit of electron transport chain complex I, particularly NDUFA4 and NDUFA9 were altered in AD patients, suggesting destabilization of the junction between membrane and matrix arms of mitochondrial complex I impacted the mitochondrial functions in the AD. iTRAQ quantitative proteomics of brain mitochondriomes revealed disparity in healthy aging and age-dependent AD.
Collapse
Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
| | - Jung Eun Park
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
4
|
McManus MJ, Picard M, Chen HW, De Haas HJ, Potluri P, Leipzig J, Towheed A, Angelin A, Sengupta P, Morrow RM, Kauffman BA, Vermulst M, Narula J, Wallace DC. Mitochondrial DNA Variation Dictates Expressivity and Progression of Nuclear DNA Mutations Causing Cardiomyopathy. Cell Metab 2019; 29:78-90.e5. [PMID: 30174309 PMCID: PMC6717513 DOI: 10.1016/j.cmet.2018.08.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 02/01/2018] [Accepted: 08/01/2018] [Indexed: 02/03/2023]
Abstract
Nuclear-encoded mutations causing metabolic and degenerative diseases have highly variable expressivity. Patients sharing the homozygous mutation (c.523delC) in the adenine nucleotide translocator 1 gene (SLC25A4, ANT1) develop cardiomyopathy that varies from slowly progressive to fulminant. This variability correlates with the mitochondrial DNA (mtDNA) lineage. To confirm that mtDNA variants can modulate the expressivity of nuclear DNA (nDNA)-encoded diseases, we combined in mice the nDNA Slc25a4-/- null mutation with a homoplasmic mtDNA ND6P25L or COIV421A variant. The ND6P25L variant significantly increased the severity of cardiomyopathy while the COIV421A variant was phenotypically neutral. The adverse Slc25a4-/- and ND6P25L combination was associated with impaired mitochondrial complex I activity, increased oxidative damage, decreased l-Opa1, altered mitochondrial morphology, sensitization of the mitochondrial permeability transition pore, augmented somatic mtDNA mutation levels, and shortened lifespan. The strikingly different phenotypic effects of these mild mtDNA variants demonstrate that mtDNA can be an important modulator of autosomal disease.
Collapse
Affiliation(s)
- Meagan J McManus
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Martin Picard
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA; Departments of Psychiatry and Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Hsiao-Wen Chen
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Hans J De Haas
- Department of Medicine, Mount Sinai Hospital, New York, NY 10029, USA
| | - Prasanth Potluri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Jeremy Leipzig
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Atif Towheed
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Partho Sengupta
- Department of Medicine, Mount Sinai Hospital, New York, NY 10029, USA
| | - Ryan M Morrow
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Brett A Kauffman
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Marc Vermulst
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Jagat Narula
- Department of Medicine, Mount Sinai Hospital, New York, NY 10029, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
5
|
Ratcliffe LE, Vázquez Villaseñor I, Jennings L, Heath PR, Mortiboys H, Schwartzentruber A, Karyka E, Simpson JE, Ince PG, Garwood CJ, Wharton SB. Loss of IGF1R in Human Astrocytes Alters Complex I Activity and Support for Neurons. Neuroscience 2018; 390:46-59. [PMID: 30056117 PMCID: PMC6372003 DOI: 10.1016/j.neuroscience.2018.07.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 11/15/2022]
Abstract
We have established a novel human astrocyte-neuron co-culture system. Astrocytes provided contact-mediated support for neurite outgrowth. IGF1R-impaired astrocytes are less able to protect neurons under stress conditions. Microarray analysis of these astrocytes identified changes in energy metabolism.
The insulin/insulin-like growth factor 1 (IGF1) signaling pathways are implicated in longevity and in progression of Alzheimer’s disease. Previously, we showed that insulin-like growth factor 1 receptor (IGF1R) and downstream signaling transcripts are reduced in astrocytes in human brain with progression of Alzheimer’s neuropathology and developed a model of IGF1 signaling impairment in human astrocytes using an IGF1R-specific monoclonal antibody, MAB391. Here, we have established a novel human astrocyte-neuron co-culture system to determine whether loss of astrocytic IGF1R affects their support for neurons. Astrocyte-neuron co-cultures were developed using human primary astrocytes and differentiated Lund Human Mesencephalic Cells (LUHMES). Neurite outgrowth assays, performed to measure astrocytic support for neurons, showed astrocytes provided contact-mediated support for neurite outgrowth. Loss of IGF1R did not affect neurite outgrowth under control conditions but when challenged with hydrogen peroxide IGF1R-impaired astrocytes were less able to protect LUHMES. To determine how loss of IGF1R affects neuronal support MAB391-treated astrocytes were FACS sorted from GFP-LUHMES and their transcriptomic profile was investigated using microarrays. Changes in transcripts involved in astrocyte energy metabolism were identified, particularly NDUFA2 and NDUFB6, which are related to complex I assembly. Loss of complex I activity in MAB391-treated astrocytes validated these findings. In conclusion, reduced IGF1 signaling in astrocytes impairs their support for neurons under conditions of stress and this is associated with defects in the mitochondrial respiratory chain in astrocytes.
Collapse
Affiliation(s)
- Laura E Ratcliffe
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Irina Vázquez Villaseñor
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Luke Jennings
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Aurelie Schwartzentruber
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Evangelia Karyka
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Paul G Ince
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK.
| | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| |
Collapse
|
6
|
Cueto R, Zhang L, Shan HM, Huang X, Li X, Li YF, Lopez J, Yang WY, Lavallee M, Yu C, Ji Y, Yang X, Wang H. Identification of homocysteine-suppressive mitochondrial ETC complex genes and tissue expression profile - Novel hypothesis establishment. Redox Biol 2018; 17:70-88. [PMID: 29679893 PMCID: PMC6006524 DOI: 10.1016/j.redox.2018.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/22/2018] [Indexed: 12/13/2022] Open
Abstract
Hyperhomocysteinemia (HHcy) is an independent risk factor for cardiovascular disease (CVD) which has been implicated in matochondrial (Mt) function impairment. In this study, we characterized Hcy metabolism in mouse tissues by using LC-ESI-MS/MS analysis, established tissue expression profiles for 84 nuclear-encoded Mt electron transport chain complex (nMt-ETC-Com) genes in 20 human and 19 mouse tissues by database mining, and modeled the effect of HHcy on Mt-ETC function. Hcy levels were high in mouse kidney/lung/spleen/liver (24-14 nmol/g tissue) but low in brain/heart (~5 nmol/g). S-adenosylhomocysteine (SAH) levels were high in the liver/kidney (59-33 nmol/g), moderate in lung/heart/brain (7-4 nmol/g) and low in spleen (1 nmol/g). S-adenosylmethionine (SAM) was comparable in all tissues (42-18 nmol/g). SAM/SAH ratio was as high as 25.6 in the spleen but much lower in the heart/lung/brain/kidney/liver (7-0.6). The nMt-ETC-Com genes were highly expressed in muscle/pituitary gland/heart/BM in humans and in lymph node/heart/pancreas/brain in mice. We identified 15 Hcy-suppressive nMt-ETC-Com genes whose mRNA levels were negatively correlated with tissue Hcy levels, including 11 complex-I, one complex-IV and two complex-V genes. Among the 11 Hcy-suppressive complex-I genes, 4 are complex-I core subunits. Based on the pattern of tissue expression of these genes, we classified tissues into three tiers (high/mid/low-Hcy responsive), and defined heart/eye/pancreas/brain/kidney/liver/testis/embryonic tissues as tier 1 (high-Hcy responsive) tissues in both human and mice. Furthermore, through extensive literature mining, we found that most of the Hcy-suppressive nMt-ETC-Com genes were suppressed in HHcy conditions and related with Mt complex assembly/activity impairment in human disease and experimental models. We hypothesize that HHcy inhibits Mt complex I gene expression leading to Mt dysfunction.
Collapse
Affiliation(s)
- Ramon Cueto
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Lixiao Zhang
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Hui Min Shan
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Xiao Huang
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Xinyuan Li
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Ya-Feng Li
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Jahaira Lopez
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - William Y Yang
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Muriel Lavallee
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Catherine Yu
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA; The Geisinger Commonwealth School of Medicine, Scranton, PA, USA
| | - Yong Ji
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing 210029, China.
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA; Department of Pharmacology, Temple University - Lewis Katz School of Medicine, Philadelphia, PA, USA; Thrombosis Research Center, Temple University - Lewis Katz School of Medicine, Philadelphia, PA, USA; Cardiovascular Research Center, Temple University - Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Temple University - Lewis Katz School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140, USA; Department of Pharmacology, Temple University - Lewis Katz School of Medicine, Philadelphia, PA, USA; Thrombosis Research Center, Temple University - Lewis Katz School of Medicine, Philadelphia, PA, USA; Cardiovascular Research Center, Temple University - Lewis Katz School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
7
|
An X-chromosome linked mouse model (Ndufa1 S55A) for systemic partial Complex I deficiency for studying predisposition to neurodegeneration and other diseases. Neurochem Int 2017; 109:78-93. [PMID: 28506826 DOI: 10.1016/j.neuint.2017.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/07/2017] [Accepted: 05/08/2017] [Indexed: 01/19/2023]
Abstract
The respiratory chain Complex I deficiencies are the most common cause of mitochondrial diseases. Complex I biogenesis is controlled by 58 genes and at least 47 of these cause mitochondrial disease in humans. Two of these are X-chromosome linked nuclear (nDNA) genes (NDUFA1 and NDUFB11), and 7 are mitochondrial (mtDNA, MT-ND1-6, -4L) genes, which may be responsible for sex-dependent variation in the presentation of mitochondrial diseases. In this study, we describe an X-chromosome linked mouse model (Ndufa1S55A) for systemic partial Complex I deficiency. By homologous recombination, a point mutation T > G within 55th codon of the Ndufa1 gene was introduced. The resulting allele Ndufa1S55A introduced systemic serine-55-alanine (S55A) mutation within the MWFE protein, which is essential for Complex I assembly and stability. The S55A mutation caused systemic partial Complex I deficiency of ∼50% in both sexes. The mutant males (Ndufa1S55A/Y) displayed reduced respiratory exchange ratio (RER) and produced less body heat. They were also hypoactive and ate less. They showed age-dependent Purkinje neurons degeneration. Metabolic profiling of brain, liver and serum from males showed reduced heme levels in mutants, which correlated with altered expressions of Fech and Hmox1 mRNAs in tissues. This is the first genuine X-chromosome linked mouse model for systemic partial Complex I deficiency, which shows age-dependent neurodegeneration. The effect of Complex I deficiency on survival patterns of males vs. females was different. We believe this model will be very useful for studying sex-dependent predisposition to both spontaneous and stress-induced neurodegeneration, cancer, diabetes and other diseases.
Collapse
|
8
|
Potluri P, Procaccio V, Scheffler IE, Wallace DC. High throughput gene complementation screening permits identification of a mammalian mitochondrial protein synthesis (ρ(-)) mutant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1336-1343. [PMID: 26946086 DOI: 10.1016/j.bbabio.2016.02.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 12/26/2022]
Abstract
To identify nuclear DNA (nDNA) oxidative phosphorylation (OXPHOS) gene mutations using cultured cells, we have developed a complementation system based on retroviral transduction with a full length cDNA expression library and selection for OXHOS function by growth in galactose. We have used this system to transduce the Chinese hamster V79-G7 OXPHOS mutant cell line with a defect in mitochondrial protein synthesis. The complemented cells were found to have acquired the cDNA for the bS6m polypeptide of the small subunit of the mitochondrial ribosome. bS6m is a 14 kDa polypeptide located on the outside of the mitochondrial 28S ribosomal subunit and interacts with the rRNA. The V79-G7 mutant protein was found to harbor a methionine to threonine missense mutation at codon 13. The hamster bS6m null mutant could also be complemented by its orthologs from either mouse or human. bS6m protein tagged at its C-terminus by HA, His or GFP localized to the mitochondrion and was fully functional. Through site-directed mutagenesis we identified the probable RNA interacting residues of the bS6m peptide and tested the functional significance of mammalian specific C-terminal region. The N-terminus of the bS6m polypeptide functionally corresponds to that of the prokaryotic small ribosomal subunit, but deletion of C-terminal residues along with the zinc ion coordinating cysteine had no functional effect. Since mitochondrial diseases can result from hundreds to thousands of different nDNA gene mutations, this one step viral complementation cloning may facilitate the molecular diagnosis of a range of nDNA mitochondrial disease mutations. 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.
Collapse
Affiliation(s)
- Prasanth Potluri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Vincent Procaccio
- Dépt. de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Immo E Scheffler
- Division of Biological Sciences, University of California - San Diego, La Jolla, CA, United States
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
9
|
Yadav N, Kumar S, Kumar R, Srivastava P, Sun L, Rapali P, Marlowe T, Schneider A, Inigo JR, O'Malley J, Londonkar R, Gogada R, Chaudhary AK, Yadava N, Chandra D. Mechanism of neem limonoids-induced cell death in cancer: Role of oxidative phosphorylation. Free Radic Biol Med 2016; 90:261-71. [PMID: 26627937 PMCID: PMC4734361 DOI: 10.1016/j.freeradbiomed.2015.11.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/01/2015] [Accepted: 11/23/2015] [Indexed: 12/17/2022]
Abstract
We have previously reported that neem limonoids (neem) induce multiple cancer cell death pathways. Here we dissect the underlying mechanisms of neem-induced apoptotic cell death in cancer. We observed that neem-induced caspase activation does not require Bax/Bak channel-mediated mitochondrial outer membrane permeabilization, permeability transition pore, and mitochondrial fragmentation. Neem enhanced mitochondrial DNA and mitochondrial biomass. While oxidative phosphorylation (OXPHOS) Complex-I activity was decreased, the activities of other OXPHOS complexes including Complex-II and -IV were unaltered. Increased reactive oxygen species (ROS) levels were associated with an increase in mitochondrial biomass and apoptosis upon neem exposure. Complex-I deficiency due to the loss of Ndufa1-encoded MWFE protein inhibited neem-induced caspase activation and apoptosis, but cell death induction was enhanced. Complex II-deficiency due to the loss of succinate dehydrogenase complex subunit C (SDHC) robustly decreased caspase activation, apoptosis, and cell death. Additionally, the ablation of Complexes-I, -III, -IV, and -V together did not inhibit caspase activation. Together, we demonstrate that neem limonoids target OXPHOS system to induce cancer cell death, which does not require upregulation or activation of proapoptotic Bcl-2 family proteins.
Collapse
Affiliation(s)
- Neelu Yadav
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
| | - Sandeep Kumar
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Rahul Kumar
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Pragya Srivastava
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Leimin Sun
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA; Gastroenterology Department, Sir Run Run Shaw Hospital, Zhejiang University Medical School, Hangzhou 310016, China
| | - Peter Rapali
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Timothy Marlowe
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Andrea Schneider
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Joseph R Inigo
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Jordan O'Malley
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Ramesh Londonkar
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Raghu Gogada
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Ajay K Chaudhary
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Nagendra Yadava
- Pioneer Valley Life Sciences Institute, Springfield, MA 01107, USA
| | - Dhyan Chandra
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
| |
Collapse
|
10
|
Sen S, Domingues CC, Rouphael C, Chou C, Kim C, Yadava N. Genetic modification of human mesenchymal stem cells helps to reduce adiposity and improve glucose tolerance in an obese diabetic mouse model. Stem Cell Res Ther 2015; 6:242. [PMID: 26652025 PMCID: PMC4674936 DOI: 10.1186/s13287-015-0224-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/25/2015] [Accepted: 11/04/2015] [Indexed: 11/25/2022] Open
Abstract
Introduction Human mesenchymal stem cells (MSCs) are multipotent cells that can differentiate into fat, muscle, bone and cartilage cells. Exposure of subcutaneous abdominal adipose tissue derived AD-MSCs to high glucose (HG) leads to superoxide accumulation and up-regulation of inflammatory molecules. Our aim was to inquire how HG exposure affects MSCs differentiation and whether the mechanism is reversible. Methods We exposed human adipose tissue derived MSCs to HG (25 mM) and compared it to normal glucose (NG, 5.5 mM) exposed cells at 7, 10 and 14 days. We examined mitochondrial superoxide accumulation (Mitosox-Red), cellular oxygen consumption rate (OCR, Seahorse) and gene expression. Results HG increased reactive superoxide (ROS) accumulation noted by day 7 both in cytosol and mitochondria. The OCR between the NG and HG exposed groups however did not change until 10 days at which point OCR of HG exposed cells were reduced significantly. We noted that HG exposure upregulated mRNA expression of adipogenic (PPARG, FABP-4, CREBP alpha and beta), inflammatory (IL-6 and TNF alpha) and antioxidant (SOD2 and Catalase) genes. Next, we used AdSOD2 to upregulate SOD2 prior to HG exposure and thereby noted reduction in superoxide generation. SOD2 upregulation helped reduce mRNA over-expression of PPARG, FABP-4, IL-6 and TNFα. In a series of separate experiments, we delivered the eGFP and SOD2 upregulated MSCs (5 days post ex-vivo transduction) and saline intra-peritoneally (IP) to obese diabetic (db/db) mice. We confirmed homing-in of eGFP labeled MSCs, delivered IP, to different inflamed fat pockets, particularly omental fat. Mice receiving SOD2-MSCs showed progressive reduction in body weight and improved glucose tolerance (GTT) at 4 weeks, post MSCs transplantation compared to the GFP-MSC group (control). Conclusions High glucose evokes superoxide generation, OCR reduction and adipogenic differentiation. Mitochondrial superoxide dismutase upregulation quenches excess superoxide and reduces adipocyte inflammation. Delivery of superoxide dismutase (SOD2) using MSCs as a gene delivery vehicle reduces inflammation and improves glucose tolerance in vivo. Suppression of superoxide production and adipocyte inflammation using mitochondrial superoxide dismutase may be a novel and safe therapeutic tool to combat hyperglycemia mediated effects.
Collapse
Affiliation(s)
- Sabyasachi Sen
- Department of Medicine, Division of Endocrinology and Metabolism, The George Washington University, School of Medicine and Health Sciences, 2300 I Street, Ross Hall Suite: 450, Washington, DC, 20037, USA.
| | - Cleyton C Domingues
- Department of Medicine, Division of Endocrinology and Metabolism, The George Washington University, School of Medicine and Health Sciences, 2300 I Street, Ross Hall Suite: 450, Washington, DC, 20037, USA.
| | - Carol Rouphael
- Department of Medicine, Division of Endocrinology and Metabolism, The George Washington University, School of Medicine and Health Sciences, 2300 I Street, Ross Hall Suite: 450, Washington, DC, 20037, USA.
| | - Cyril Chou
- Pioneer Valley Life Sciences Institute, and Division of Endocrinology, Diabetes & Metabolism at Baystate Medical Center of Tufts University School of Springfield, Springfield, MA, USA.
| | - Chul Kim
- Pioneer Valley Life Sciences Institute, and Division of Endocrinology, Diabetes & Metabolism at Baystate Medical Center of Tufts University School of Springfield, Springfield, MA, USA.
| | - Nagendra Yadava
- Pioneer Valley Life Sciences Institute, and Division of Endocrinology, Diabetes & Metabolism at Baystate Medical Center of Tufts University School of Springfield, Springfield, MA, USA.
| |
Collapse
|
11
|
Levin L, Blumberg A, Barshad G, Mishmar D. Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations. Front Genet 2014; 5:448. [PMID: 25566330 PMCID: PMC4274989 DOI: 10.3389/fgene.2014.00448] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022] Open
Abstract
Most cell functions are carried out by interacting factors, thus underlying the functional importance of genetic interactions between genes, termed epistasis. Epistasis could be under strong selective pressures especially in conditions where the mutation rate of one of the interacting partners notably differs from the other. Accordingly, the order of magnitude higher mitochondrial DNA (mtDNA) mutation rate as compared to the nuclear DNA (nDNA) of all tested animals, should influence systems involving mitochondrial-nuclear (mito-nuclear) interactions. Such is the case of the energy producing oxidative phosphorylation (OXPHOS) and mitochondrial translational machineries which are comprised of factors encoded by both the mtDNA and the nDNA. Additionally, the mitochondrial RNA transcription and mtDNA replication systems are operated by nDNA-encoded proteins that bind mtDNA regulatory elements. As these systems are central to cell life there is strong selection toward mito-nuclear co-evolution to maintain their function. However, it is unclear whether (A) mito-nuclear co-evolution befalls only to retain mitochondrial functions during evolution or, also, (B) serves as an adaptive tool to adjust for the evolving energetic demands as species' complexity increases. As the first step to answer these questions we discuss evidence of both negative and adaptive (positive) selection acting on the mtDNA and nDNA-encoded genes and the effect of both types of selection on mito-nuclear interacting factors. Emphasis is given to the crucial role of recurrent ancient (nodal) mutations in such selective events. We apply this point-of-view to the three available types of mito-nuclear co-evolution: protein-protein (within the OXPHOS system), protein-RNA (mainly within the mitochondrial ribosome), and protein-DNA (at the mitochondrial replication and transcription machineries).
Collapse
Affiliation(s)
- Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| |
Collapse
|
12
|
Kim C, Patel P, Gouvin LM, Brown ML, Khalil A, Henchey EM, Heuck AP, Yadava N. Comparative Analysis of the Mitochondrial Physiology of Pancreatic β Cells. ACTA ACUST UNITED AC 2014; 3:110. [PMID: 25309834 DOI: 10.4172/2167-7662.1000110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The mitochondrial metabolism of β cells is thought to be highly specialized. Its direct comparison with other cells using isolated mitochondria is limited by the availability of islets/β cells in sufficient quantity. In this study, we have compared mitochondrial metabolism of INS1E/β cells with other cells in intact and permeabilized states. To selectively permeabilize the plasma membrane, we have evaluated the use of perfringolysin-O (PFO) in conjunction with microplate-based respirometry. PFO is a protein that binds membranes based on a threshold level of active cholesterol. Therefore, unless active cholesterol reaches a threshold level in mitochondria, they are expected to remain untouched by PFO. Cytochrome c sensitivity tests showed that in PFO-permeabilized cells, the mitochondrial integrity was completely preserved. Our data show that a time-dependent decline of the oligomycin-insensitive respiration observed in INS1E cells was due to a limitation in substrate supply to the respiratory chain. We predict that it is linked with the β cell-specific metabolism involving metabolites shuttling between the cytoplasm and mitochondria. In permeabilized β cells, the Complex l-dependent respiration was either transient or absent because of the inefficient TCA cycle. The TCA cycle insufficiency was confirmed by analysis of the CO2 evolution. This may be linked with lower levels of NAD+, which is required as a co-factor for CO2 producing reactions of the TCA cycle. β cells showed comparable OxPhos and respiratory capacities that were not affected by the inorganic phosphate (Pi) levels in the respiration medium. They showed lower ADP-stimulation of the respiration on different substrates. We believe that this study will significantly enhance our understanding of the β cell mitochondrial metabolism.
Collapse
Affiliation(s)
- Chul Kim
- Pioneer Valley Life Sciences Institute, Springfield, MA, USA
| | - Pinal Patel
- Pioneer Valley Life Sciences Institute, Springfield, MA, USA
| | - Lindsey M Gouvin
- Departments of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Melissa L Brown
- Pioneer Valley Life Sciences Institute, Springfield, MA, USA
| | - Ahmed Khalil
- Department of Biology, University of Massachusetts, Amherst, MA, USA
| | | | - Alejandro P Heuck
- Departments of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Nagendra Yadava
- Pioneer Valley Life Sciences Institute, Springfield, MA, USA ; Department of Biology, University of Massachusetts, Amherst, MA, USA ; Division of Endocrinology, Diabetes & Metabolism at Baystate Medical Center of Tufts University School of Medicine, Springfield, MA, USA
| |
Collapse
|
13
|
Yadava N, Schneider SS, Jerry DJ, Kim C. Impaired mitochondrial metabolism and mammary carcinogenesis. J Mammary Gland Biol Neoplasia 2013; 18:75-87. [PMID: 23269521 PMCID: PMC3581737 DOI: 10.1007/s10911-012-9271-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 12/13/2012] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial oxidative metabolism plays a key role in meeting energetic demands of cells by oxidative phosphorylation (OxPhos). Here, we have briefly discussed (a) the dynamic relationship that exists among glycolysis, the tricarboxylic acid (TCA) cycle, and OxPhos; (b) the evidence of impaired OxPhos (i.e. mitochondrial dysfunction) in breast cancer; (c) the mechanisms by which mitochondrial dysfunction can predispose to cancer; and (d) the effects of host and environmental factors that can negatively affect mitochondrial function. We propose that impaired OxPhos could increase susceptibility to breast cancer via suppression of the p53 pathway, which plays a critical role in preventing tumorigenesis. OxPhos is sensitive to a large number of factors intrinsic to the host (e.g. inflammation) as well as environmental exposures (e.g. pesticides, herbicides and other compounds). Polymorphisms in over 143 genes can also influence the OxPhos system. Therefore, declining mitochondrial oxidative metabolism with age due to host and environmental exposures could be a common mechanism predisposing to cancer.
Collapse
Affiliation(s)
- Nagendra Yadava
- Pioneer Valley Life Sciences Institute, Springfield, MA 01107, USA.
| | | | | | | |
Collapse
|
14
|
Hoefs SJ, Rodenburg RJ, Smeitink JA, van den Heuvel LP. Molecular base of biochemical complex I deficiency. Mitochondrion 2012; 12:520-32. [DOI: 10.1016/j.mito.2012.07.106] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 07/06/2012] [Accepted: 07/10/2012] [Indexed: 12/21/2022]
|
15
|
The mitochondrial-encoded subunits of respiratory complex I (NADH:ubiquinone oxidoreductase): identifying residues important in mechanism and disease. Biochem Soc Trans 2011; 39:799-806. [PMID: 21599651 DOI: 10.1042/bst0390799] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is crucial to respiration in many aerobic organisms. The hydrophilic domain of complex I, containing nine or more redox cofactors, and comprising seven conserved core subunits, protrudes into the mitochondrial matrix or bacterial cytoplasm. The α-helical membrane-bound hydrophobic domain contains a further seven core subunits that are mitochondrial-encoded in eukaryotes and named the ND subunits (ND1-ND6 and ND4L). Complex I couples the oxidation of NADH in the hydrophilic domain to ubiquinone reduction and proton translocation in the hydrophobic domain. Although the mechanisms of NADH oxidation and intramolecular electron transfer are increasingly well understood, the mechanisms of ubiquinone reduction and proton translocation remain only poorly defined. Recently, an α-helical model of the hydrophobic domain of bacterial complex I [Efremov, Baradaran and Sazanov (2010) Nature 465, 441-447] revealed how the 63 transmembrane helices of the seven core subunits are arranged, and thus laid a foundation for the interpretation of functional data and the formulation of mechanistic proposals. In the present paper, we aim to correlate information from sequence analyses, site-directed mutagenesis studies and mutations that have been linked to human diseases, with information from the recent structural model. Thus we aim to identify and discuss residues in the ND subunits of mammalian complex I which are important in catalysis and for maintaining the enzyme's structural and functional integrity.
Collapse
|
16
|
Understanding mitochondrial complex I assembly in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:851-62. [PMID: 21924235 DOI: 10.1016/j.bbabio.2011.08.010] [Citation(s) in RCA: 298] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/17/2011] [Accepted: 08/27/2011] [Indexed: 12/12/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the largest multimeric enzyme complex of the mitochondrial respiratory chain, which is responsible for electron transport and the generation of a proton gradient across the mitochondrial inner membrane to drive ATP production. Eukaryotic complex I consists of 14 conserved subunits, which are homologous to the bacterial subunits, and more than 26 accessory subunits. In mammals, complex I consists of 45 subunits, which must be assembled correctly to form the properly functioning mature complex. Complex I dysfunction is the most common oxidative phosphorylation (OXPHOS) disorder in humans and defects in the complex I assembly process are often observed. This assembly process has been difficult to characterize because of its large size, the lack of a high resolution structure for complex I, and its dual control by nuclear and mitochondrial DNA. However, in recent years, some of the atomic structure of the complex has been resolved and new insights into complex I assembly have been generated. Furthermore, a number of proteins have been identified as assembly factors for complex I biogenesis and many patients carrying mutations in genes associated with complex I deficiency and mitochondrial diseases have been discovered. Here, we review the current knowledge of the eukaryotic complex I assembly process and new insights from the identification of novel assembly factors. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
Collapse
|
17
|
Compton S, Kim C, Griner NB, Potluri P, Scheffler IE, Sen S, Jerry DJ, Schneider S, Yadava N. Mitochondrial dysfunction impairs tumor suppressor p53 expression/function. J Biol Chem 2011; 286:20297-312. [PMID: 21502317 DOI: 10.1074/jbc.m110.163063] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, mitochondria have been suggested to act in tumor suppression. However, the underlying mechanisms by which mitochondria suppress tumorigenesis are far from being clear. In this study, we have investigated the link between mitochondrial dysfunction and the tumor suppressor protein p53 using a set of respiration-deficient (Res(-)) mammalian cell mutants with impaired assembly of the oxidative phosphorylation machinery. Our data suggest that normal mitochondrial function is required for γ-irradiation (γIR)-induced cell death, which is mainly a p53-dependent process. The Res(-) cells are protected against γIR-induced cell death due to impaired p53 expression/function. We find that the loss of complex I biogenesis in the absence of the MWFE subunit reduces the steady-state level of the p53 protein, although there is no effect on the p53 protein level in the absence of the ESSS subunit that is also essential for complex I assembly. The p53 protein level was also reduced to undetectable levels in Res(-) cells with severely impaired mitochondrial protein synthesis. This suggests that p53 protein expression is differentially regulated depending upon the type of electron transport chain/respiratory chain deficiency. Moreover, irrespective of the differences in the p53 protein expression profile, γIR-induced p53 activity is compromised in all Res(-) cells. Using two different conditional systems for complex I assembly, we also show that the effect of mitochondrial dysfunction on p53 expression/function is a reversible phenomenon. We believe that these findings will have major implications in the understanding of cancer development and therapy.
Collapse
Affiliation(s)
- Shannon Compton
- Pioneer Valley Life Sciences Institute, Springfield, Massachusetts 01107, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Gershoni M, Fuchs A, Shani N, Fridman Y, Corral-Debrinski M, Aharoni A, Frishman D, Mishmar D. Coevolution predicts direct interactions between mtDNA-encoded and nDNA-encoded subunits of oxidative phosphorylation complex i. J Mol Biol 2010; 404:158-71. [PMID: 20868692 DOI: 10.1016/j.jmb.2010.09.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 09/05/2010] [Accepted: 09/13/2010] [Indexed: 10/19/2022]
Abstract
Despite years of research, the structure of the largest mammalian oxidative phosphorylation (OXPHOS) complex, NADH-ubiquinone oxidoreductase (complex I), and the interactions among its 45 subunits are not fully understood. Since complex I harbors subunits encoded by mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) genomes, with the former evolving ∼10 times faster than the latter, tight cytonuclear coevolution is expected and observed. Recently, we identified three nDNA-encoded complex I subunits that underwent accelerated amino acid replacement, suggesting their adjustment to the elevated mtDNA rate of change. Hence, they constitute excellent candidates for binding mtDNA-encoded subunits. Here, we further disentangle the network of physical cytonuclear interactions within complex I by analyzing subunits coevolution. Firstly, relying on the bioinformatic analysis of 10 protein complexes possessing solved structures, we show that signals of coevolution identified physically interacting subunits with nearly 90% accuracy, thus lending support to our approach. When applying this approach to cytonuclear interaction within complex I, we predict that the 'rate-accelerated' nDNA-encoded subunits of complex I, NDUFC2 and NDUFA1, likely interact with the mtDNA-encoded subunits ND5/ND4 and ND5/ND4/ND1, respectively. Furthermore, we predicted interactions among mtDNA-encoded complex I subunits. Using the yeast two-hybrid system, we experimentally confirmed the predicted interactions of human NDUFC2 with ND4, the interactions of human NDUFA1 with ND1 and ND4, and the lack of interaction of NDUFC2 with ND3 and NDUFA1, thus providing a proof of concept for our approach. Our study shows, for the first time, evidence for direct interactions between nDNA-encoded and mtDNA-encoded subunits of human OXPHOS complex I and paves the path towards deciphering subunit interactions within complexes lacking three-dimensional structures. Our subunit-interactions-predicting method, ComplexCorr, is available at http://webclu.bio.wzw.tum.de/complexcorr.
Collapse
Affiliation(s)
- Moran Gershoni
- Department of Life Sciences and the Nation Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Morán M, Rivera H, Sánchez-Aragó M, Blázquez A, Merinero B, Ugalde C, Arenas J, Cuezva JM, Martín MA. Mitochondrial bioenergetics and dynamics interplay in complex I-deficient fibroblasts. Biochim Biophys Acta Mol Basis Dis 2010; 1802:443-53. [PMID: 20153825 DOI: 10.1016/j.bbadis.2010.02.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 02/03/2010] [Accepted: 02/08/2010] [Indexed: 11/17/2022]
Abstract
BACKGROUND Complex I (CI) deficiency is the most frequent cause of OXPHOS disorders. Recent studies have shown increases in reactive oxygen species (ROS) production and mitochondrial network disturbances in patients' fibroblasts harbouring mutations in CI subunits. OBJECTIVES The present work evaluates the impact of mutations in the NDUFA1 and NDUFV1 genes of CI on mitochondrial bioenergetics and dynamics, in fibroblasts from patients suffering isolated CI deficiency. RESULTS Decreased oxygen consumption rate and slow growth rate were found in patients with severe CI deficiency. Mitochondrial diameter was slightly increased in patients' cells cultured in galactose or treated with 2'-deoxyglucose without evidence of mitochondrial fragmentation. Expression levels of the main proteins involved in mitochondrial dynamics, OPA1, MFN2, and DRP1, were slightly augmented in all patients' cells lines. The study of mitochondrial dynamics showed delayed recovery of the mitochondrial network after treatment with the uncoupler carbonyl cyanide m-chlorophenyl hydrazone (cccp) in patients with severe CI deficiency. Intracellular ROS levels were not increased neither in glucose nor galactose medium in patients' fibroblasts. CONCLUSION Our main finding was that severe CI deficiency in patients harbouring mutations in the NDUFA1 and NDUFV1 genes is linked to a delayed mitochondrial network recovery after cccp treatment. However, the CI deficiency is neither associated with massive mitochondrial fragmentation nor with increased ROS levels. The different genetic backgrounds of patients with OXPHOS disorders would explain, at least partially, differences in the pathophysiological manifestations of CI deficiency.
Collapse
Affiliation(s)
- M Morán
- Centro de Investigación, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Sharma LK, Lu J, Bai Y. Mitochondrial respiratory complex I: structure, function and implication in human diseases. Curr Med Chem 2009; 16:1266-77. [PMID: 19355884 DOI: 10.2174/092986709787846578] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondria are ubiquitous organelles in eukaryotic cells whose primary function is to generate energy supplies in the form of ATP through oxidative phosphorylation. As the entry point for most electrons into the respiratory chain, NADH:ubiquinone oxidoreductase, or complex I, is the largest and least understood component of the mitochondrial oxidative phosphorylation system. Substantial progress has been made in recent years in understanding its subunit composition, its assembly, the interaction among complex I and other respiratory components, and its role in oxidative stress and apoptosis. This review provides an updated overview of the structure of complex I, as well as its cellular functions, and discusses the implication of complex I dysfunction in various human diseases.
Collapse
Affiliation(s)
- Lokendra K Sharma
- Department of Cellular and Structural Biology, University of Texas Health Sciences Center at San Antonio, San Antonio, TX 78229, USA
| | | | | |
Collapse
|
21
|
A neonatal polyvisceral failure linked to a de novo homoplasmic mutation in the mitochondrially encoded cytochrome b gene. Mitochondrion 2009; 9:346-52. [PMID: 19563916 DOI: 10.1016/j.mito.2009.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 04/25/2009] [Accepted: 06/19/2009] [Indexed: 11/22/2022]
Abstract
Mutations within the mitochondrially encoded cytochrome b (MTCYB) gene are heteroplasmic and lead to severe exercise intolerance. We describe an unusual clinical presentation secondary to a novel homoplasmic mutation within MTCYB. The m.15635T>C transition (S297P) was carried by a newborn who presented with a polyvisceral failure. This mutation was responsible for a complex III deficiency. It was homoplasmic in all tissues tested and was undetectable in patient's mother. Functional analyses, including studies on patient's cybrid cell lines, demonstrate the pathogenicity of this variant. Our data show that mutations within MTCYB can be responsible for severe phenotype at birth.
Collapse
|
22
|
Chinta SJ, Rane A, Yadava N, Andersen JK, Nicholls DG, Polster BM. Reactive oxygen species regulation by AIF- and complex I-depleted brain mitochondria. Free Radic Biol Med 2009; 46:939-47. [PMID: 19280713 PMCID: PMC2775507 DOI: 10.1016/j.freeradbiomed.2009.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Apoptosis-inducing factor (AIF)-deficient harlequin (Hq) mice undergo neurodegeneration associated with a 40-50% reduction in complex I level and activity. We tested the hypothesis that AIF and complex I regulate reactive oxygen species (ROS) production by brain mitochondria. Isolated Hq brain mitochondria oxidizing complex I substrates displayed no difference compared to wild type (WT) in basal ROS production, H2O2 removal, or ROS production stimulated by complex I inhibitors rotenone or 1-methyl-4-phenylpyridinium. In contrast, ROS production caused by reverse electron transfer to complex I was attenuated by approximately 50% in Hq mitochondria oxidizing the complex II substrate succinate. Basal and rotenone-stimulated rates of H2O2 release from in situ mitochondria did not differ between Hq and WT synaptosomes metabolizing glucose, nor did the level of in vivo oxidative protein carbonyl modifications detected in synaptosomes, brain mitochondria, or homogenates. Our results suggest that AIF does not directly modulate ROS release from brain mitochondria. In addition, they demonstrate that in contrast to ROS produced by mitochondria oxidizing succinate, ROS release from in situ synaptosomal mitochondria or from isolated brain mitochondria oxidizing complex I substrates is not proportional to the amount of complex I. These findings raise the important possibility that complex I contributes less to physiological ROS production by brain mitochondria than previously suggested.
Collapse
|
23
|
Potluri P, Davila A, Ruiz-Pesini E, Mishmar D, O'Hearn S, Hancock S, Simon M, Scheffler IE, Wallace DC, Procaccio V. A novel NDUFA1 mutation leads to a progressive mitochondrial complex I-specific neurodegenerative disease. Mol Genet Metab 2009; 96:189-95. [PMID: 19185523 PMCID: PMC2693342 DOI: 10.1016/j.ymgme.2008.12.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 12/09/2008] [Accepted: 12/09/2008] [Indexed: 10/21/2022]
Abstract
Mitochondrial diseases have been shown to result from mutations in mitochondrial genes located in either the nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). Mitochondrial OXPHOS complex I has 45 subunits encoded by 38 nuclear and 7 mitochondrial genes. Two male patients in a putative X-linked pedigree exhibiting a progressive neurodegenerative disorder and a severe muscle complex I enzyme defect were analyzed for mutations in the 38 nDNA and seven mtDNA encoded complex I subunits. The nDNA X-linked NDUFA1 gene (MWFE polypeptide) was discovered to harbor a novel missense mutation which changed a highly conserved glycine at position 32 to an arginine, shown to segregate with the disease. When this mutation was introduced into a NDUFA1 null hamster cell line, a substantial decrease in the complex I assembly and activity was observed. When the mtDNA of the patient was analyzed, potentially relevant missense mutations were observed in the complex I genes. Transmitochondrial cybrids containing the patient's mtDNA resulted in a mild complex I deficiency. Interestingly enough, the nDNA encoded MWFE polypeptide has been shown to interact with various mtDNA encoded complex I subunits. Therefore, we hypothesize that the novel G32R mutation in NDUFA1 is causing complex I deficiency either by itself or in synergy with additional mtDNA variants.
Collapse
Affiliation(s)
- Prasanth Potluri
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG), University of California, 2034 Hewitt Hall, Irvine, CA 92697-3940, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Comparative genomics of the oxidative phosphorylation system in fungi. Fungal Genet Biol 2008; 45:1248-56. [DOI: 10.1016/j.fgb.2008.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 04/29/2008] [Accepted: 06/18/2008] [Indexed: 11/22/2022]
|
25
|
Lazarou M, Thorburn DR, Ryan MT, McKenzie M. Assembly of mitochondrial complex I and defects in disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1793:78-88. [PMID: 18501715 DOI: 10.1016/j.bbamcr.2008.04.015] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 04/15/2008] [Accepted: 04/25/2008] [Indexed: 12/19/2022]
Abstract
Isolated complex I deficiency is the most common cause of respiratory chain dysfunction. Defects in human complex I result in energy generation disorders and they are also implicated in neurodegenerative disease and altered apoptotic signaling. Complex I dysfunction often occurs as a result of its impaired assembly. The assembly process of complex I is poorly understood, complicated by the fact that in mammals, it is composed of 45 different subunits and is regulated by both nuclear and mitochondrial genomes. However, in recent years we have gained new insights into complex I biogenesis and a number of assembly factors involved in this process have also been identified. In most cases, these factors have been discovered through their gene mutations that lead to specific complex I defects and result in mitochondrial disease. Here we review how complex I is assembled and the factors required to mediate this process.
Collapse
Affiliation(s)
- Michael Lazarou
- Department of Biochemistry, La Trobe University, 3086 Melbourne, Australia
| | | | | | | |
Collapse
|
26
|
Piskacek M, Zotova L, Zsurka G, Schweyen RJ. Conditional knockdown of hMRS2 results in loss of mitochondrial Mg(2+) uptake and cell death. J Cell Mol Med 2008; 13:693-700. [PMID: 18384665 PMCID: PMC3822876 DOI: 10.1111/j.1582-4934.2008.00328.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The human gene MRS2L encodes a mitochondrial protein distantly related to CorA Mg2+ transport proteins. Constitutive shRNA-mediated knockdown of hMRS2 in human HEK-293 cell line was found here to cause death. To further study its role in Mg2+ transport, we have established stable cell lines with conditionally expressing shRNAs directed against hMRS2L. The cells expressing shRNA for several generations exhibited lower steady-state levels of free mitochondrial Mg2+ ([Mg2+]m) and reduced capacity of mitochondrial Mg2+ uptake than control cells. Long-term expression of shRNAs resulted in loss of mitochondrial respiratory complex I, decreased mitochondrial membrane potential and cell death. We conclude that hMrs2 is the major transport protein for Mg + uptake into mitochondria and that expression of hMrs2 is essential for the maintenance of respiratory complex I and cell viability.
Collapse
|
27
|
Vogel RO, Smeitink JAM, Nijtmans LGJ. Human mitochondrial complex I assembly: A dynamic and versatile process. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1215-27. [PMID: 17854760 DOI: 10.1016/j.bbabio.2007.07.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 07/24/2007] [Accepted: 07/26/2007] [Indexed: 12/12/2022]
Abstract
One can but admire the intricate way in which biomolecular structures are formed and cooperate to allow proper cellular function. A prominent example of such intricacy is the assembly of the five inner membrane embedded enzymatic complexes of the mitochondrial oxidative phosphorylation (OXPHOS) system, which involves the stepwise combination of >80 subunits and prosthetic groups encoded by both the mitochondrial and nuclear genomes. This review will focus on the assembly of the most complicated OXPHOS structure: complex I (NADH:ubiquinone oxidoreductase, EC 1.6.5.3). Recent studies into complex I assembly in human cells have resulted in several models elucidating a thus far enigmatic process. In this review, special attention will be given to the overlap between the various assembly models proposed in different organisms. Complex I being a complicated structure, its assembly must be prone to some form of coordination. This is where chaperone proteins come into play, some of which may relate complex I assembly to processes such as apoptosis and even immunity.
Collapse
Affiliation(s)
- Rutger O Vogel
- Nijmegen Centre for Mitochondrial Disorders, Department of Pediatrics, Radboud University Nijmegen Medical Centre, Geert Grooteplein 10, 6500 HB Nijmegen, The Netherlands
| | | | | |
Collapse
|
28
|
Yadava N, Potluri P, Scheffler IE. Investigations of the potential effects of phosphorylation of the MWFE and ESSS subunits on complex I activity and assembly. Int J Biochem Cell Biol 2007; 40:447-60. [PMID: 17931954 DOI: 10.1016/j.biocel.2007.08.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 08/16/2007] [Accepted: 08/21/2007] [Indexed: 11/18/2022]
Abstract
There have been several reports on the phosphorylation of various subunits of NADH-ubiquinone oxidoreductase (complex I) in mammalian mitochondria. The effects of phosphorylation on assembly or activity of these subunits have not been investigated directly. The cAMP-dependent phosphorylation of the MWFE and ESSS subunits in isolated bovine heart mitochondria has been recently reported. We have investigated the significance of potential phosphorylation of these two subunits in complex I assembly and function by mutational analysis of the phosphorylation sites. Chinese hamster mutant cell lines missing either the MWFE or the ESSS subunits were transfected and complemented with the corresponding wild type and mutant cDNAs made by site-directed mutagenesis. In MWFE the serine 55 was substituted by alanine, glutamate, glutamine, and aspartate (S55A, S55E, S55Q, and S55D, respectively). The glutamate substitutions might be expected to mimic the phosphorylated state of the protein. With the exception of the MWFE(S55A) mutant protein the assembly of complex I was completely blocked, and no activity could be detected. Various substitutions in the ESSS protein (S2A, S2E, S8A, S8E, T21A, T21E, S30A, S30E) appeared to cause lower levels of mature protein and a significantly reduced complex I activity measured polarographically. The ESSS (S2/8A) double mutant protein caused a complete failure to assemble. These mutational analyses suggest that if phosphorylation occurs in vivo, the effects on complex I activity are significant.
Collapse
Affiliation(s)
- N Yadava
- Buck Institute for Age Research, Novato, CA 94945, United States
| | | | | |
Collapse
|
29
|
McKenzie M, Lazarou M, Thorburn DR, Ryan MT. Analysis of mitochondrial subunit assembly into respiratory chain complexes using Blue Native polyacrylamide gel electrophoresis. Anal Biochem 2007; 364:128-37. [PMID: 17391635 DOI: 10.1016/j.ab.2007.02.022] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Revised: 02/16/2007] [Accepted: 02/16/2007] [Indexed: 12/01/2022]
Abstract
The mitochondrial respiratory chain consists of multi-subunit protein complexes embedded in the inner membrane. Although the majority of subunits are encoded by nuclear genes and are imported into mitochondria, 13 subunits in humans are encoded by mitochondrial DNA. The coordinated assembly of subunits encoded from two genomes is a poorly understood process, with assembly pathway defects being a major determinant in mitochondrial disease. In this study, we monitored the assembly of human respiratory complexes using radiolabeled, mitochondrially encoded subunits in conjunction with Blue Native polyacrylamide gel electrophoresis. The efficiency of assembly was found to differ markedly between complexes, and intermediate complexes containing newly synthesized mitochondrial DNA-encoded subunits could be observed for complexes I, III, and IV. In particular, we detected human cytochrome b as a monomer and as a component of a novel approximately 120 kDa intermediate complex at early chase times before being totally assembled into mature complex III. Furthermore, we show that this approach is highly suited for the rapid detection of respiratory complex assembly defects in fibroblasts from patients with mitochondrial disease and, thus, has potential diagnostic applications.
Collapse
Affiliation(s)
- Matthew McKenzie
- Department of Biochemistry, La Trobe University, Melbourne, VIC 3086, Australia.
| | | | | | | |
Collapse
|
30
|
Fernandez-Moreira D, Ugalde C, Smeets R, Rodenburg RJT, Lopez-Laso E, Ruiz-Falco ML, Briones P, Martin MA, Smeitink JAM, Arenas J. X-linked NDUFA1 gene mutations associated with mitochondrial encephalomyopathy. Ann Neurol 2007; 61:73-83. [PMID: 17262856 DOI: 10.1002/ana.21036] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Mitochondrial complex I deficiency is the commonest diagnosed respiratory chain defect, being genetically heterogeneous. The male preponderance of previous patient cohorts suggested an X-linked underlying genetic defect. We investigated mutations in the X-chromosomal complex I structural genes, NDUFA1 and NDUFB11, as a novel cause of mitochondrial encephalomyopathy. METHODS We sequenced 12 nuclear genes and the mitochondrial DNA-encoded complex I genes in 26 patients with respiratory chain complex I defect. Novel mutations were confirmed by polymerase chain reaction restriction length polymorphism. Assembly/stability studies in fibroblasts were performed using two-dimensional blue native gel electrophoresis. RESULTS Two novel p.Gly8Arg and p.Arg37Ser hemizygous mutations in NDUFA1 were identified in two unrelated male patients presenting with Leigh's syndrome and with myoclonic epilepsy and developmental delay, respectively. Two-dimensional blue native gel electrophoresis showed decreased levels of intact complex I with no accumulation of lower molecular weight subcomplexes, indicating that assembly, stability, or both are compromised. INTERPRETATION Mutations in the X-linked NDUFA1 gene result in complex I defect and encephalomyopathy. Assembly/stability analysis might give an explanation for the different clinical phenotypes and become useful for future diagnostic purposes.
Collapse
|
31
|
Petruzzella V, Tessa A, Torraco A, Fattori F, Dotti MT, Bruno C, Cardaioli E, Papa S, Federico A, Santorelli FM. The NDUFB11 gene is not a modifier in Leber hereditary optic neuropathy. Biochem Biophys Res Commun 2007; 355:181-7. [PMID: 17292333 DOI: 10.1016/j.bbrc.2007.01.140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Accepted: 01/24/2007] [Indexed: 11/24/2022]
Abstract
Over 95% of Leber hereditary optic neuropathy (LHON) cases are due to mutations in mitochondrial DNA-encoded subunits of NADH:ubiquinone oxidoreductase (E.C.1.6.5.3., complex I). A recessive X-linked susceptibility gene that acts synergistically with the primary mtDNA mutation to produce visual loss is suggested by the high male-to-female ratio among LHON patients. The ESSS protein is a recently isolated subunit of bovine heart mitochondrial complex I. We revisited the genomic sequence of NDUFB11, the human homolog mapping to chromosome Xp11.23, and identified two mRNA isoforms showing different expression profiles in human tissues. Cultured skin fibroblasts from four LHON patients showed a pattern of expression similar to normal controls. Moreover, NDUFB11 did not seem to influence risk and age at onset of visual loss in a total of 65 individuals from 35 Italian LHON families. Also, the gene was not affected in 11 children with a severe encephalopathy associated with decreased complex I activity in skeletal muscle.
Collapse
Affiliation(s)
- Vittoria Petruzzella
- Department of Medical Biochemistry, Medical Biology and Medical Physics, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Janssen RJRJ, Nijtmans LG, van den Heuvel LP, Smeitink JAM. Mitochondrial complex I: structure, function and pathology. J Inherit Metab Dis 2006; 29:499-515. [PMID: 16838076 DOI: 10.1007/s10545-006-0362-4] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 05/31/2006] [Accepted: 06/01/2006] [Indexed: 10/24/2022]
Abstract
Oxidative phosphorylation (OXPHOS) has a prominent role in energy metabolism of the cell. Being under bigenomic control, correct biogenesis and functioning of the OXPHOS system is dependent on the finely tuned interaction between the nuclear and the mitochondrial genome. This suggests that disturbances of the system can be caused by numerous genetic defects and can result in a variety of metabolic and biochemical alterations. Consequently, OXPHOS deficiencies manifest as a broad clinical spectrum. Complex I, the biggest and most complicated enzyme complex of the OXPHOS system, has been subjected to thorough investigation in recent years. Significant progress has been made in the field of structure, composition, assembly, and pathology. Important gains in the understanding of the Goliath of the OXPHOS system are: exposing the electron transfer mechanism and solving the crystal structure of the peripheral arm, characterization of almost all subunits and some of their functions, and creating models to elucidate the assembly process with concomitant identification of assembly chaperones. Unravelling the intricate mechanisms underlying the functioning of this membrane-bound enzyme complex in health and disease will pave the way for developing adequate diagnostic procedures and advanced therapeutic treatment strategies.
Collapse
Affiliation(s)
- Rolf J R J Janssen
- Nijmegen Centre for Mitochondrial Disorders, Laboratory of Paediatrics and Neurology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | | | | |
Collapse
|
33
|
Mishmar D, Ruiz-Pesini E, Mondragon-Palomino M, Procaccio V, Gaut B, Wallace DC. Adaptive selection of mitochondrial complex I subunits during primate radiation. Gene 2006; 378:11-8. [PMID: 16828987 DOI: 10.1016/j.gene.2006.03.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2006] [Revised: 03/17/2006] [Accepted: 03/24/2006] [Indexed: 12/23/2022]
Abstract
Mammalian oxidative phosphorylation (OXPHOS) complexes I, III, IV and V are assembled from both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) encoded subunits, with complex I encompassing 39 nDNA and seven mtDNA subunits. Yet the sequence variation of the mtDNA genes is more than ten fold greater than that of the nDNA encoded genes of the OXPHOS complexes and the mtDNA proteins have been found to be influenced by positive (adaptive) selection. To maintain a functional complex I, nDNA and mtDNA subunits must interact, implying that certain nDNA complex I genes may also have been influenced by positive selection. To determine if positive selection has influenced nDNA complex I genes, we analyzed the DNA sequences of all of the nDNA and mtDNA encoded complex I subunits from orangutan, gorilla, chimpanzee, human and all available vertebrate sequences. This revealed that three nDNA complex I genes (NDUFC2, NDUFA1, and NDUFA4) had significantly increased amino acid substitution rates by both PAML and Z-test, suggesting that they have been subjected to adaptive selection during primate radiation. Since all three of these subunits reside in the membrane domain of complex I along with the mtDNA subunits, we compared amino acid changes in these three nDNA genes with those of the mtDNA genes across species. Changes in the nDNA NDUFC2 cysteine 39 were found to correlate with those in the mtDNA ND5 cysteine 330. Therefore, adaptive selection has influenced some nDNA complex I genes and nDNA and mtDNA complex I genes may have co-evolved.
Collapse
Affiliation(s)
- Dan Mishmar
- The Center for Molecular and Mitochondrial Medicine and Genetics, Hewitt Hall, room 2014, University of California, Irvine, Irvine, CA 92697-3940, USA
| | | | | | | | | | | |
Collapse
|
34
|
Krause F. Detection and analysis of protein–protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes. Electrophoresis 2006; 27:2759-81. [PMID: 16817166 DOI: 10.1002/elps.200600049] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
It is an essential and challenging task to unravel protein-protein interactions in their actual in vivo context. Native gel systems provide a separation platform allowing the analysis of protein complexes on a rather proteome-wide scale in a single experiment. This review focus on blue-native (BN)-PAGE as the most versatile and successful gel-based approach to separate soluble and membrane protein complexes of intricate protein mixtures derived from all biological sources. BN-PAGE is a charge-shift method with a running pH of 7.5 relying on the gentle binding of anionic CBB dye to all membrane and many soluble protein complexes, leading to separation of protein species essentially according to their size and superior resolution than other fractionation techniques can offer. The closely related colorless-native (CN)-PAGE, whose applicability is restricted to protein species with intrinsic negative net charge, proved to provide an especially mild separation capable of preserving weak protein-protein interactions better than BN-PAGE. The essential conditions determining the success of detecting protein-protein interactions are the sample preparations, e.g. the efficiency/mildness of the detergent solubilization of membrane protein complexes. A broad overview about the achievements of BN- and CN-PAGE studies to elucidate protein-protein interactions in organelles and prokaryotes is presented, e.g. the mitochondrial protein import machinery and oxidative phosphorylation supercomplexes. In many cases, solubilization with digitonin was demonstrated to facilitate an efficient and particularly gentle extraction of membrane protein complexes prone to dissociation by treatment with other detergents. In general, analyses of protein interactomes should be carried out by both BN- and CN-PAGE.
Collapse
Affiliation(s)
- Frank Krause
- Department of Chemistry, Physical Biochemistry, Darmstadt University of Technology, Germany.
| |
Collapse
|
35
|
Noack H, Bednarek T, Heidler J, Ladig R, Holtz J, Szibor M. TFAM-dependent and independent dynamics of mtDNA levels in C2C12 myoblasts caused by redox stress. Biochim Biophys Acta Gen Subj 2006; 1760:141-50. [PMID: 16439064 DOI: 10.1016/j.bbagen.2005.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 11/11/2005] [Accepted: 12/07/2005] [Indexed: 11/29/2022]
Abstract
TFAM is an essential protein factor for the initiation of transcription of the mtDNA. It also functions as a packaging factor, which stabilizes the mtDNA pool. To investigate the regulatory role of TFAM for regeneration and proliferation of the mtDNA pool, we exposed the muscle cell line C2C12 to a severe redox stress (H2O2) or to a moderate redox stress (GSH depletion), determined the dynamics of the mtDNA levels and correlated this with the TFAM protein levels. H2O2 caused a concentration-dependent loss of mtDNA molecules. The mtDNA levels recovered slowly within 3 days after H2O2 stress. The TFAM protein was less degraded than the mtDNA indicating an accumulation of TFAM protein per mtDNA after H2O2 stress. Overexpression of TFAM did not protect against the mtDNA loss after H2O2 stress but shortened the recovery time. GSH depletion led to a proliferation of the mtDNA pool. Although the mtDNA levels increased the TFAM protein levels were unaffected by the GSH depletion. We conclude that the accumulation of the TFAM protein after H2O2 stress contributes to the regeneration of the mtDNA pool but that other mechanisms, independent from the TFAM protein amount have to be postulated to explain the proliferation of the mtDNA pool after GSH depletion.
Collapse
Affiliation(s)
- Heiko Noack
- Institute of Pathophysiology, Martin-Luther-University Halle-Wittenberg, ZAMED, Heinrich-Damerow-Str. 1, 06097 Halle, Germany.
| | | | | | | | | | | |
Collapse
|
36
|
Friedrich T, Stolpe S, Schneider D, Barquera B, Hellwig P. Ion translocation by the Escherichia coli NADH:ubiquinone oxidoreductase (complex I). Biochem Soc Trans 2005; 33:836-9. [PMID: 16042610 DOI: 10.1042/bst0330836] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The energy-converting NADH:ubiquinone oxidoreductase, also known as respiratory complex I, couples the transfer of electrons from NADH to ubiquinone with the translocation of ions across the membrane. It was assumed that the complex exclusively works as a proton pump. Recently, it has been proposed that complex I from Klebsiella pneumoniae and Escherichia coli work as Na+ pumps. We have used an E. coli complex I preparation to determine the type of ion(s) translocated by means of enzyme activity, generation of a membrane potential and redox-induced Fourier-transform infrared spectroscopy. We did not find any indications for Na+ translocation by the E. coli complex I.
Collapse
Affiliation(s)
- T Friedrich
- Institut für Org. Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, D-79104 Freiburg, Germany.
| | | | | | | | | |
Collapse
|
37
|
Mamelak AJ, Kowalski J, Murphy K, Yadava N, Zahurak M, Kouba DJ, Howell BG, Tzu J, Cummins DL, Liégeois NJ, Berg K, Sauder DN. Downregulation of NDUFA1 and other oxidative phosphorylation-related genes is a consistent feature of basal cell carcinoma. Exp Dermatol 2005; 14:336-48. [PMID: 15854127 DOI: 10.1111/j.0906-6705.2005.00278.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Basal cell carcinoma (BCC) is the most common cutaneous malignancy that, like other tumours, possesses a heterogeneous genetic composition. In order to select genes with consistent changes in expression among these tumours, we analysed BCC microarray expression data by using a novel approach, termed correlative analysis of microarrays (CAM). CAM is a nested, non-parametric method designed to qualitatively select candidates based on their individual, similar effects upon an array-wide closeness measure. We applied the CAM method to expression data generated by two-channel cDNA microarray experiments, where 21 BCC and patient-matched normal skin specimens were examined. Fifteen candidate genes were selected, with six overexpressed and nine underexpressed in BCC vs. normal skin. Five of the nine consistently downregulated genes in the tumour samples are involved in mitochondrial function and the oxidative phosphorylation (OXPHOS) pathway. One of these genes was the 7.5-kDa subunit, NADH dehydrogenase (ubiquinone) alpha subcomplex-1 (NDUFA1), an accessory component of OXPHOS complex-I that is essential for respiratory activity. These findings support the hypothesis that irregularities in mitochondrial function are involved in neoplasia. Suppression of NDUFA1 expression could represent a key pathogenic mechanism in the development of BCC.
Collapse
Affiliation(s)
- Adam J Mamelak
- Department of Dermatology, Johns Hopkins University, Baltimore, MD 21287-0900, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Pineau B, Mathieu C, Gérard-Hirne C, De Paepe R, Chétrit P. Targeting the NAD7 subunit to mitochondria restores a functional complex I and a wild type phenotype in the Nicotiana sylvestris CMS II mutant lacking nad7. J Biol Chem 2005; 280:25994-6001. [PMID: 15849190 DOI: 10.1074/jbc.m500508200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial DNA of the Nicotiana sylvestris CMSII mutant carries a 72-kb deletion comprising the single copy nad7 gene that encodes the NAD7 subunit of the respiratory complex I (NADH-ubiquinone oxidoreductase). CMSII plants lack rotenone-sensitive complex I activity and are impaired in physiological and phenotypical traits. To check whether these changes directly result from the deletion of nad7, we constructed CMS transgenic plants (termed as CMSnad7) carrying an edited nad7 cDNA fused to the CAMV 35S promoter and to a mitochondrial targeting sequence. The nad7 sequence was transcribed and translated and the NAD7 protein directed to mitochondria in CMSnad7 transgenic plants, which recovered both wild type morphology and growth features. Blue-native/SDS gel electrophoresis and enzymatic assays showed that, whereas fully assembled complex I was absent from CMSII mitochondria, a functional complex was present in CMSnad7 mitochondria. Furthermore, a supercomplex involving complex I and complex III was present in CMSnad7 as in the wild type. Taken together, these data demonstrate that lack of complex I in CMSII was indeed the direct consequence of the absence of nad7. Hence, NAD7 is a key element for complex assembly in plants. These results also show that allotopic expression from the nucleus can fully complement the lack of a mitochondrial-encoded complex I gene.
Collapse
Affiliation(s)
- Bernard Pineau
- Institut de Biotechnologie des Plantes, Laboratoire Mitochondries et Métabolisme Centre National de la Recherche Scientifique-Université Paris-Sud, Unite Mixte de Recherche 8618, 91405 Orsay, France
| | | | | | | | | |
Collapse
|
39
|
Duarte M, Schulte U, Ushakova AV, Videira A. Neurospora strains harboring mitochondrial disease-associated mutations in iron-sulfur subunits of complex I. Genetics 2005; 171:91-9. [PMID: 15956670 PMCID: PMC1456533 DOI: 10.1534/genetics.105.041517] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We subjected the genes encoding the 19.3-, 21.3c-, and 51-kDa iron-sulfur subunits of respiratory chain complex I from Neurospora crassa to site-directed mutagenesis to mimic mutations in human complex I subunits associated with mitochondrial diseases. The V135M substitution was introduced into the 19.3-kDa cDNA, the P88L and R111H substitutions were separately introduced into the 21.3c-kDa cDNA, and the A353V and T435M alterations were separately introduced into the 51-kDa cDNA. The altered cDNAs were expressed in the corresponding null-mutants under the control of a heterologous promoter. With the exception of the A353V polypeptide, all mutated subunits were able to promote assembly of a functional complex I, rescuing the phenotypes of the respective null-mutants. Complex I from these strains displays spectroscopic and enzymatic properties similar to those observed in the wild-type strain. A decrease in total complex I amounts may be the major impact of the mutations, although expression levels of mutant genes from the heterologous promoter were sometimes lower and may also account for complex I levels. We discuss these findings in relation to the involvement of complex I deficiencies in mitochondrial disease.
Collapse
Affiliation(s)
- Margarida Duarte
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | | | | | | |
Collapse
|
40
|
Scheffler IE, Yadava N, Potluri P. Molecular genetics of complex I-deficient Chinese hamster cell lines. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1659:160-71. [PMID: 15576048 DOI: 10.1016/j.bbabio.2004.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Revised: 07/28/2004] [Accepted: 08/09/2004] [Indexed: 11/22/2022]
Abstract
The work from our laboratory on complex I-deficient Chinese hamster cell mutants is reviewed. Several complementation groups with a complete defect have been identified. Three of these are due to X-linked mutations, and the mutated genes for two have been identified. We describe null mutants in the genes for the subunits MWFE (gene: NDUFA1) and ESSS. They represent small integral membrane proteins localized in the Ialpha (Igamma) and Ibeta subcomplexes, respectively [J. Hirst, J. Carroll, I.M. Fearnley, R.J. Shannon, J.E. Walker. The nuclear encoded subunits of complex I from bovine heart mitochondria. Biochim. Biophys. Acta 1604 (7-10-2003) 135-150.]. Both are absolutely essential for assembly and activity of complex I. Epitope-tagged versions of these proteins can be expressed from a poly-cistronic vector to complement the mutants, or to be co-expressed with the endogenous proteins in other hamster cell lines (mutant or wild type), or human cells. Structure-function analyses can be performed with proteins altered by site-directed mutagenesis. A cell line has been constructed in which the MWFE subunit is conditionally expressed, opening a window on the kinetics of assembly of complex I. Its targeting, import into mitochondria, and orientation in the inner membrane have also been investigated. The two proteins have recently been shown to be the targets for a cAMP-dependent kinase [R. Chen, I.M. Fearnley, S.Y. Peak_Chew, J.E. Walker. The phosphorylation of subunits of complex I from bovine heart mitochondria. J. Biol. Chem. xx (2004) xx-xx.]. The epitope-tagged proteins can be cross-linked with other complex I subunits.
Collapse
Affiliation(s)
- Immo E Scheffler
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA.
| | | | | |
Collapse
|
41
|
Potluri P, Yadava N, Scheffler IE. The role of the ESSS protein in the assembly of a functional and stable mammalian mitochondrial complex I (NADH-ubiquinone oxidoreductase). ACTA ACUST UNITED AC 2004; 271:3265-73. [PMID: 15265046 DOI: 10.1111/j.1432-1033.2004.04260.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ESSS protein is a recently identified subunit of mammalian mitochondrial complex I. It is a relatively small integral membrane protein (122 amino acids) found in the beta-subcomplex. Genomic sequence database searches reveal its localization to the X-chromosome in humans and mouse. The ESSS cDNA from Chinese hamster cells was cloned and shown to complement one complementation group of our previously described mutants with a proposed X-linkage. Sequence analyses of the ESSS cDNA in these mutants revealed chain termination mutations. In two of these mutants the protein is truncated at the C-terminus of the targeting sequence; the mutants are null mutants for the ESSS subunit. There is no detectable complex I assembly and activity in the absence of the ESSS subunit as revealed by blue native polyacrylamide gel electrophoresis (BN/PAGE) analysis and polarography. Complex I activity can be restored with ESSS subunits tagged with either hemagglutinin (HA) or hexahistidine (His6) epitopes at the C-terminus. Although, the accumulation of ESSS-HA is not dependent upon the presence of mtDNA-encoded subunits (ND1-6,4 L), it is incorporated into complex I only in presence of compatible complex I subunits from the same species.
Collapse
Affiliation(s)
- Prasanth Potluri
- Division of Biology, Molecular Biology Section, University of California, San Diego, California 92093-0322, USA
| | | | | |
Collapse
|
42
|
Shaffer AL, Shapiro-Shelef M, Iwakoshi NN, Lee AH, Qian SB, Zhao H, Yu X, Yang L, Tan BK, Rosenwald A, Hurt EM, Petroulakis E, Sonenberg N, Yewdell JW, Calame K, Glimcher LH, Staudt LM. XBP1, downstream of Blimp-1, expands the secretory apparatus and other organelles, and increases protein synthesis in plasma cell differentiation. Immunity 2004; 21:81-93. [PMID: 15345222 DOI: 10.1016/j.immuni.2004.06.010] [Citation(s) in RCA: 750] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Revised: 04/23/2004] [Accepted: 05/19/2004] [Indexed: 11/27/2022]
Abstract
The differentiation of B cells into immunoglobulin-secreting plasma cells is controlled by two transcription factors, Blimp-1 and XBP1. By gene expression profiling, we defined a set of genes whose induction during mouse plasmacytic differentiation is dependent on Blimp-1 and/or XBP1. Blimp-1-deficient B cells failed to upregulate most plasma cell-specific genes, including xbp1. Differentiating xbp1-deficient B cells induced Blimp-1 normally but failed to upregulate genes encoding many secretory pathway components. Conversely, ectopic expression of XBP1 induced a wide spectrum of secretory pathway genes and physically expanded the endoplasmic reticulum. In addition, XBP1 increased cell size, lysosome content, mitochondrial mass and function, ribosome numbers, and total protein synthesis. Thus, XBP1 coordinates diverse changes in cellular structure and function resulting in the characteristic phenotype of professional secretory cells.
Collapse
Affiliation(s)
- A L Shaffer
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
PURPOSE OF REVIEW Disturbances in the mitochondrial oxidative phosphorylation pathway most often lead to devastating disorders with a fatal outcome. Of these, complex I deficiency is the most frequently encountered. Recent characterization of the mitochondrial and nuclear DNA-encoded complex I subunits has allowed mutational analysis and reliable prenatal diagnosis. Nevertheless, complex-I-deficient patients without a mutation in any of the known subunits remain. It is assumed that these patients harbour defects in proteins involved in the assembly of this largest member of the oxidative phosphorylation complexes. This review describes current understanding of complex I assembly, new developments and future perspectives. RECENT FINDINGS The first model of human complex I assembly has been proposed recently. New insights into supercomplex assembly and stability may help to explain combined deficiencies. Recent functional characterization of some of the 32 accessory subunits of the complex may link these subunits to complex I biogenesis and activity regulation. SUMMARY Research on complex I assembly is increasing rapidly. However, comparison between theoretical and experimental models of complex I assembly is still problematic. The growing understanding of complex I assembly at the subunit and supercomplex level will clarify the picture in the future. The elucidation of complex I assembly, by combining patient data with new experimental methods, will facilitate the diagnosis of (and possibly therapy for) many uncharacterized mitochondrial disorders.
Collapse
Affiliation(s)
- Rutger Vogel
- Nijmegen Centre for Mitochondrial Disorders at the Department of Paediatrics, University Medical Centre Nijmegen, Nijmegen, The Netherlands
| | | | | | | | | |
Collapse
|
44
|
Chen R, Fearnley IM, Peak-Chew SY, Walker JE. The phosphorylation of subunits of complex I from bovine heart mitochondria. J Biol Chem 2004; 279:26036-45. [PMID: 15056672 DOI: 10.1074/jbc.m402710200] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In bovine heart mitochondria and in submitochondrial particles, membrane-associated proteins with apparent molecular masses of 18 and 10 kDa become strongly radiolabeled by [(32)P]ATP in a cAMP-dependent manner. The 18-kDa phosphorylated protein is subunit ESSS from complex I and not as previously reported the 18 k subunit (with the N-terminal sequence AQDQ). The phosphorylated residue in subunit ESSS is serine 20. In the 10 kDa band, the complex I subunit MWFE was phosphorylated on serine 55. In the presence of protein kinase A and cAMP, the same subunits of purified complex I were phosphorylated by [(32)P]ATP at the same sites. Subunits ESSS and MWFE both contribute to the membrane arm of complex I. Each has a single hydrophobic region probably folded into a membrane spanning alpha-helix. It is likely that the phosphorylation site of subunit ESSS lies in the mitochondrial matrix and that the site in subunit MWFE is in the intermembrane space. Subunit ESSS has no known role, but subunit MWFE is required for assembly into complex I of seven hydrophobic subunits encoded in the mitochondrial genome. The possible effects of phosphorylation of these subunits on the activity and/or the assembly of complex I remain to be explored.
Collapse
Affiliation(s)
- Ruming Chen
- Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK
| | | | | | | |
Collapse
|
45
|
Yadava N, Houchens T, Potluri P, Scheffler IE. Development and Characterization of a Conditional Mitochondrial Complex I Assembly System. J Biol Chem 2004; 279:12406-13. [PMID: 14722084 DOI: 10.1074/jbc.m313588200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We developed a conditional complex I assembly system in a Chinese hamster fibroblast mutant line, CCL16-B2, that does not express the NDUFA1 gene (encoding the MWFE protein). In this mutant, a hemagglutinin (HA) epitope-tagged MWFE protein was expressed from a doxycycline-inducible promoter. The expression of the protein was absolutely dependent on the presence of doxycycline, and the gene could be turned off completely by removal of doxycycline. These experiments demonstrated a key role of MWFE in the pathway of complex I assembly. Upon induction the MWFE.HA protein reached steady-state levels within 24 h, but the appearance of fully active complex I was delayed by another approximately 24 h. The MWFE appeared in a precomplex that probably includes one or more subunits encoded by mtDNA. The fate of MWFE and the stability of complex I were themselves very tightly linked to the activity of mitochondrial protein synthesis and to the assembly of subunits encoded by mtDNA (ND1-6 and ND4L). This novel conditional system can shed light not only on the mechanism of complex I assembly but emphasizes the role of subunits previously thought of as "accessory." It promises to have broader applications in the study of cellular energy metabolism and production of reactive oxygen species and related processes.
Collapse
Affiliation(s)
- Nagendra Yadava
- Section of Molecular Biology, Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093-0322, USA
| | | | | | | |
Collapse
|
46
|
Scacco S, Petruzzella V, Budde S, Vergari R, Tamborra R, Panelli D, van den Heuvel LP, Smeitink JA, Papa S. Pathological mutations of the human NDUFS4 gene of the 18-kDa (AQDQ) subunit of complex I affect the expression of the protein and the assembly and function of the complex. J Biol Chem 2003; 278:44161-7. [PMID: 12944388 DOI: 10.1074/jbc.m307615200] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Presented is a study of the impact on the structure and function of human complex I of three different homozygous mutations in the NDUFS4 gene coding for the 18-kDa subunit of respiratory complex I, inherited by autosomal recessive mode in three children affected by a fatal neurological Leigh-like syndrome. The mutations consisted, respectively, of a AAGTC duplication at position 466-470 of the coding sequence, a single base deletion at position 289/290, and a G44A nonsense mutation in the first exon of the gene. All three mutations were found to be associated with a defect of the assembly of a functional complex in the inner mitochondrial membrane. In all the mutations, in addition to destruction of the carboxyl-terminal segment of the 18-kDa subunit, the amino-terminal segment of the protein was also missing. In the mutation that was expected to produce a truncated subunit, the disappearance of the protein was associated with an almost complete disappearance of the NDUFS4 transcript. These observations show the essential role of the NDUFS4 gene in the structure and function of complex I and give insight into the pathogenic mechanism of NDUFS4 gene mutations in a severe defect of complex I.
Collapse
Affiliation(s)
- Salvatore Scacco
- Department of Medical Biochemistry and Medical Biology, University of Bari, 70124 Bari, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Hirst J, Carroll J, Fearnley IM, Shannon RJ, Walker JE. The nuclear encoded subunits of complex I from bovine heart mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1604:135-50. [PMID: 12837546 DOI: 10.1016/s0005-2728(03)00059-8] [Citation(s) in RCA: 292] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria is a complicated, multi-subunit, membrane-bound assembly. Recently, the subunit compositions of complex I and three of its subcomplexes have been reevaluated comprehensively. The subunits were fractionated by three independent methods, each based on a different property of the subunits. Forty-six different subunits, with a combined molecular mass of 980 kDa, were identified. The three subcomplexes, I alpha, I beta and I lambda, correlate with parts of the membrane extrinsic and membrane-bound domains of the complex. Therefore, the partitioning of subunits amongst these subcomplexes has provided information about their arrangement within the L-shaped structure. The sequences of 45 subunits of complex I have been determined. Seven of them are encoded by mitochondrial DNA, and 38 are products of the nuclear genome, imported into the mitochondrion from the cytoplasm. Post-translational modifications of many of the nuclear encoded subunits of complex I have been identified. The seven mitochondrially encoded subunits, and seven of the nuclear encoded subunits, are homologues of the 14 subunits found in prokaryotic complexes I. They are considered to be sufficient for energy transduction by complex I, and they are known as the core subunits. The core subunits bind a flavin mononucleotide (FMN) at the active site for NADH oxidation, up to eight iron-sulfur clusters, and one or more ubiquinone molecules. The locations of some of the cofactors can be inferred from the sequences of the core subunits. The remaining 31 subunits of bovine complex I are the supernumerary subunits, which may be important either for the stability of the complex, or for its assembly. Sequence relationships suggest that some of them carry out reactions unrelated to the NADH:ubiquinone oxidoreductase activity of the complex.
Collapse
Affiliation(s)
- Judy Hirst
- Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, UK.
| | | | | | | | | |
Collapse
|
48
|
Heazlewood JL, Howell KA, Millar AH. Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1604:159-69. [PMID: 12837548 DOI: 10.1016/s0005-2728(03)00045-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The NADH:ubiquinone oxidoreductase of the mitochondrial respiratory chain is a large multisubunit complex in eukaryotes containing 30-40 different subunits. Analysis of this complex using blue-native gel electrophoresis coupled to tandem mass spectrometry (MS) has identified a series of 30 different proteins from the model dicot plant, Arabidopsis, and 24 different proteins from the model monocot plant, rice. These proteins have been linked back to genes from plant genome sequencing and comparison of this dataset made with predicted orthologs of complex I components in these plants. This analysis reveals that plants contain the series of 14 highly conserved complex I subunits found in other eukaryotic and related prokaryotic enzymes and a small set of 9 proteins widely found in eukaryotic complexes. A significant number of the proteins present in bovine complex I but absent from fungal complex I are also absent from plant complex I and are not encoded in plant genomes. A series of plant-specific nuclear-encoded complex I associated subunits were identified, including a series of ferripyochelin-binding protein-like subunits and a range of small proteins of unknown function. This represents a post-genomic and large-scale analysis of complex I composition in higher plants.
Collapse
Affiliation(s)
- Joshua L Heazlewood
- Plant Molecular Biology Group, Biochemistry and Molecular Biology, School of Biomedical and Chemical Sciences, Faculty of Life and Physical Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley 6009, Western Australia, Australia
| | | | | |
Collapse
|
49
|
Marques I, Duarte M, Videira A. The 9.8 kDa subunit of complex I, related to bacterial Na(+)-translocating NADH dehydrogenases, is required for enzyme assembly and function in Neurospora crassa. J Mol Biol 2003; 329:283-90. [PMID: 12758076 DOI: 10.1016/s0022-2836(03)00443-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nuclear gene encoding a 9.8 kDa subunit of complex I, the homologue of mammalian MWFE protein, was identified in the genome of Neurospora crassa. The gene was cloned and inactivated in vivo by the generation of repeat-induced point mutations. Fungal mutant strains lacking the 9.8 kDa polypeptide were subsequently isolated. Analyses of mitochondrial proteins from mutant nuo9.8 indicate that the membrane and peripheral arms of complex I fail to assemble. Respiration of mutant mitochondria on matrix NADH is rotenone-insensitive, confirming that the 9.8 kDa protein is required for the assembly and activity of complex I. We found a similarity between the MWFE homologues and the C-terminal part of the nqrA subunit of bacterial Na(+)-translocating NADH:quinone oxidoreductases (Na(+)-NQR), suggesting a link between proton-pumping and sodium-pumping NADH dehydrogenases.
Collapse
Affiliation(s)
- Isabel Marques
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | | | | |
Collapse
|
50
|
Qi X, Lewin AS, Hauswirth WW, Guy J. Suppression of complex I gene expression induces optic neuropathy. Ann Neurol 2003; 53:198-205. [PMID: 12557286 DOI: 10.1002/ana.10426] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Optic nerve degeneration is a feature common to diseases with mutations in genes that encode complex I of the respiratory chain. Vulnerability of this central nervous system tract is a mystery, because of the paucity of animal models used to investigate effects of the mutated DNA in tissues rather than isolated in cultured cells. Using a ribozyme designed to degrade the mRNA encoding a critical nuclear-encoded subunit gene of complex I (NDUFA1), we tested whether oxidative phosphorylation deficiency can recapitulate the optic neuropathy of mitochondrial disease. Injection of adenoassociated virus expressing this ribozyme led to axonal destruction and demyelination, the hallmarks of Leber hereditary optic neuropathy.
Collapse
Affiliation(s)
- Xiaoping Qi
- Department of Ophthalmology, University of Florida, College of Medicine, Gainesville 32610, USA
| | | | | | | |
Collapse
|