Metabolism Leads to Impaired Cardiac Mitochondrial Function and Communication
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Molecular Mechanism of ACAD9 in Mitochondrial Respiratory Complex 1 Assembly
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.07.425795; this version posted January 9, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Molecular mechanism of ACAD9 in mitochondrial respiratory complex 1 assembly Chuanwu Xia1, Baoying Lou1, Zhuji Fu1, Al-Walid Mohsen2, Jerry Vockley2, and Jung-Ja P. Kim1 1Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA 2Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA Abstract ACAD9 belongs to the acyl-CoA dehydrogenase family, which catalyzes the α-β dehydrogenation of fatty acyl-CoA thioesters. Thus, it is involved in fatty acid β-oxidation (FAO). However, it is now known that the primary function of ACAD9 is as an essential chaperone for mitochondrial respiratory complex 1 assembly. ACAD9 interacts with ECSIT and NDUFAF1, forming the mitochondrial complex 1 assembly (MCIA) complex. Although the role of MCIA in the complex 1 assembly pathway is well studied, little is known about the molecular mechanism of the interactions among these three assembly factors. Our current studies reveal that when ECSIT interacts with ACAD9, the flavoenzyme loses the FAD cofactor and consequently loses its FAO activity, demonstrating that the two roles of ACAD9 are not compatible. ACAD9 binds to the carboxy-terminal half (C-ECSIT), and NDUFAF1 binds to the amino-terminal half of ECSIT. Although the binary complex of ACAD9 with ECSIT or with C-ECSIT is unstable and aggregates easily, the ternary complex of ACAD9-ECSIT-NDUFAF1 (i.e., the MCIA complex) is soluble and extremely stable. -
High-Throughput, Pooled Sequencing Identifies Mutations in NUBPL And
ARTICLES High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency Sarah E Calvo1–3,10, Elena J Tucker4,5,10, Alison G Compton4,10, Denise M Kirby4, Gabriel Crawford3, Noel P Burtt3, Manuel Rivas1,3, Candace Guiducci3, Damien L Bruno4, Olga A Goldberger1,2, Michelle C Redman3, Esko Wiltshire6,7, Callum J Wilson8, David Altshuler1,3,9, Stacey B Gabriel3, Mark J Daly1,3, David R Thorburn4,5 & Vamsi K Mootha1–3 Discovering the molecular basis of mitochondrial respiratory chain disease is challenging given the large number of both mitochondrial and nuclear genes that are involved. We report a strategy of focused candidate gene prediction, high-throughput sequencing and experimental validation to uncover the molecular basis of mitochondrial complex I disorders. We created seven pools of DNA from a cohort of 103 cases and 42 healthy controls and then performed deep sequencing of 103 candidate genes to identify 151 rare variants that were predicted to affect protein function. We established genetic diagnoses in 13 of 60 previously unsolved cases using confirmatory experiments, including cDNA complementation to show that mutations in NUBPL and FOXRED1 can cause complex I deficiency. Our study illustrates how large-scale sequencing, coupled with functional prediction and experimental validation, can be used to identify causal mutations in individual cases. Complex I of the mitochondrial respiratory chain is a large ~1-MDa assembly factors are probably required, as suggested by the 20 factors macromolecular machine composed of 45 protein subunits encoded necessary for assembly of the smaller complex IV9 and by cohort by both the nuclear and mitochondrial (mtDNA) genomes. -
Assembly Factors for the Membrane Arm of Human Complex I
Assembly factors for the membrane arm of human complex I Byron Andrews, Joe Carroll, Shujing Ding, Ian M. Fearnley, and John E. Walker1 Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom Contributed by John E. Walker, October 14, 2013 (sent for review September 12, 2013) Mitochondrial respiratory complex I is a product of both the nuclear subunits in a fungal enzyme from Yarrowia lipolytica seem to be and mitochondrial genomes. The integration of seven subunits distributed similarly (12, 13). encoded in mitochondrial DNA into the inner membrane, their asso- The assembly of mitochondrial complex I involves building the ciation with 14 nuclear-encoded membrane subunits, the construc- 44 subunits emanating from two genomes into the two domains of tion of the extrinsic arm from 23 additional nuclear-encoded the complex. The enzyme is put together from preassembled sub- proteins, iron–sulfur clusters, and flavin mononucleotide cofactor complexes, and their subunit compositions have been characterized require the participation of assembly factors. Some are intrinsic to partially (14, 15). Extrinsic assembly factors of unknown function the complex, whereas others participate transiently. The suppres- become associated with subcomplexes that accumulate when as- sion of the expression of the NDUFA11 subunit of complex I dis- sembly and the activity of complex I are impaired by pathogenic rupted the assembly of the complex, and subcomplexes with mutations. Some assembly factor mutations also impair its activ- masses of 550 and 815 kDa accumulated. Eight of the known ex- ity (16). Other pathogenic mutations are found in all of the core trinsic assembly factors plus a hydrophobic protein, C3orf1, were subunits, and in 10 supernumerary subunits (NDUFA1, NDUFA2, associated with the subcomplexes. -
Low Abundance of the Matrix Arm of Complex I in Mitochondria Predicts Longevity in Mice
ARTICLE Received 24 Jan 2014 | Accepted 9 Apr 2014 | Published 12 May 2014 DOI: 10.1038/ncomms4837 OPEN Low abundance of the matrix arm of complex I in mitochondria predicts longevity in mice Satomi Miwa1, Howsun Jow2, Karen Baty3, Amy Johnson1, Rafal Czapiewski1, Gabriele Saretzki1, Achim Treumann3 & Thomas von Zglinicki1 Mitochondrial function is an important determinant of the ageing process; however, the mitochondrial properties that enable longevity are not well understood. Here we show that optimal assembly of mitochondrial complex I predicts longevity in mice. Using an unbiased high-coverage high-confidence approach, we demonstrate that electron transport chain proteins, especially the matrix arm subunits of complex I, are decreased in young long-living mice, which is associated with improved complex I assembly, higher complex I-linked state 3 oxygen consumption rates and decreased superoxide production, whereas the opposite is seen in old mice. Disruption of complex I assembly reduces oxidative metabolism with concomitant increase in mitochondrial superoxide production. This is rescued by knockdown of the mitochondrial chaperone, prohibitin. Disrupted complex I assembly causes premature senescence in primary cells. We propose that lower abundance of free catalytic complex I components supports complex I assembly, efficacy of substrate utilization and minimal ROS production, enabling enhanced longevity. 1 Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne NE4 5PL, UK. 2 Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle upon Tyne NE4 5PL, UK. 3 Newcastle University Protein and Proteome Analysis, Devonshire Building, Devonshire Terrace, Newcastle upon Tyne NE1 7RU, UK. Correspondence and requests for materials should be addressed to T.v.Z. -
Genome-Wide Association Study of Superovulatory Response Traits in Canadian Holsteins (Preliminary Study)
Genome-wide association study of superovulatory response traits in Canadian Holsteins (preliminary study) C. Jaton12, M. Sargolzaei13, M.K. Abo-Ismail14, F. Miglior15, C. A. Price6, A. Koeck1 and F. S. Schenkel1 1Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, Guelph, Ontario, Canada, N1G 2W1, 2Centre d’insémination artificielle du Québec (Ciaq), Saint-Hyacinthe, Québec, Canada, J2S 7B8, 3Semex Alliance, Guelph, Ontario, Canada, N1G 3Z2, 4Damanhour University, Egypt, 5Canadian Dairy Network (CDN), Guelph, Ontario, Canada, N1K 1E5, 6Université de Montréal, Faculté de médecine vétérinaire, St-Hyacinthe, Québec, Canada, J2S 2M2 INTRODUCTION Superovulation and embryo transfer are frequently used in the Canadian dairy industry to produce more offspring from elite donor cows. The technical aspect of superovulation in dairy cattle has been described by many authors around the world, but the genetic and genomic aspect of this technique has still to be discovered. Superovulatory response is moderately heritable in Holstein dairy cattle (Jaton et al., 2015), so that it could be possible to genetically select donors that would produce more embryos. Moreover, finding genes that impact the superovulatory response may also help with to select of a donors that would respond well to superovulation. To our knowledge, very few studies have performed a genome-wide association study (GWAS) in dairy cattle for traits related to superovulatory response. One study performed a GWAS for fertility traits such as fertilization and blastocyst rate of Holstein cows and found significant SNPs associated with those traits (Huang et al., 2010). Another study done on Japanese black cattle identified a genetic variant in the Glutamate Receptor AMPA 1 (GRIA1) gene that has an impact on the ovulation rate (Sugimoto et al., 2010). -
NDUFA8 (E-3): Sc-398098
SANTA CRUZ BIOTECHNOLOGY, INC. NDUFA8 (E-3): sc-398098 BACKGROUND APPLICATIONS NDUFA8 (NDUFA8 NADH dehydrogenase (ubiquinone) 1 a subcomplex, 8), NDUFA8 (E-3) is recommended for detection of NDUFA8 of mouse, rat and also known as complex I-PGIV (CI-PGIV) or PGIV, is a 172 amino acid mitochon- human origin by Western Blotting (starting dilution 1:100, dilution range drial protein belonging to the complex I NDUFA8 subunit family. Existing as a 1:100-1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein subunit of the multi-protein membrane respiratory chain NADH dehydrogenase (1 ml of cell lysate)], immunofluorescence (starting dilution 1:50, dilution complex (complex I), NDUFA8 functions as an accessory protein that facilitates range 1:50-1:500) and solid phase ELISA (starting dilution 1:30, dilution the transfer of electrons from NADH to the respiratory chain. NDUFA8 is most range 1:30-1:3000). highly expressed in heart and skeletal muscle and contains two CHCH domains. Suitable for use as control antibody for NDUFA8 siRNA (h): sc-92963, The gene encoding NDUFA8 maps to human chromosome 9, which houses over NDUFA8 siRNA (m): sc-149875, NDUFA8 shRNA Plasmid (h): sc-92963-SH, 900 genes and comprises nearly 4% of the human genome. Hereditary hemor- NDUFA8 shRNA Plasmid (m): sc-149875-SH, NDUFA8 shRNA (h) Lentiviral rhagic telangiectasia, which is characterized by harmful vascular defects, and Particles: sc-92963-V and NDUFA8 shRNA (m) Lentiviral Particles: Familial dysautonomia, are both associated with chromosome 9. sc-149875-V. REFERENCES Molecular Weight of NDUFA8: 20 kDa. -
The LYR Protein Subunit NB4M/NDUFA6 of Mitochondrial Complex I Anchors an Acyl Carrier Protein and Is Essential for Catalytic Activity
The LYR protein subunit NB4M/NDUFA6 of mitochondrial complex I anchors an acyl carrier protein and is essential for catalytic activity Heike Angerera, Michael Radermacherb, Michalina Mankowska a, Mirco Stegerc, Klaus Zwickerd, Heinrich Heidec, Ilka Wittigc,e, Ulrich Brandte,f, and Volker Zickermanna,e,1 aInstitute of Biochemistry II, Structural Bioenergetics Group, Medical School, Goethe University Frankfurt, 60438 Frankfurt, Germany; bDepartment of Molecular Physiology and Biophysics, College of Medicine, University of Vermont, Burlington, VT 05405; cFunctional Proteomics, SFB 815 Core Unit, and dInstitute of Biochemistry I, Medical School, Goethe University Frankfurt, 60590 Frankfurt, Germany; eCluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Germany; and fNijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands Edited by Wolfgang Baumeister, Max Planck Institute of Biochemistry, Martinsried, Germany, and approved February 25, 2014 (received for review December 4, 2013) Mitochondrial complex I is the largest and most complicated enzyme is identical to LYR motif containing protein 6 (LYRM6). Sever- of the oxidative phosphorylation system. It comprises a number al other LYRM proteins were shown to be associated with of so-called accessory subunits of largely unknown structure and the maintenance of mitochondrial homeostasis. LYRM4 (alterna- function. Here we studied subunit NB4M [NDUFA6, LYR motif tive designation ISD11, iron-sulfur protein biogenesis -
Human CLPB) Is a Potent Mitochondrial Protein Disaggregase That Is Inactivated By
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.17.911016; this version posted January 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Skd3 (human CLPB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations Ryan R. Cupo1,2 and James Shorter1,2* 1Department of Biochemistry and Biophysics, 2Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, U.S.A. *Correspondence: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.17.911016; this version posted January 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Cells have evolved specialized protein disaggregases to reverse toxic protein aggregation and restore protein functionality. In nonmetazoan eukaryotes, the AAA+ disaggregase Hsp78 resolubilizes and reactivates proteins in mitochondria. Curiously, metazoa lack Hsp78. Hence, whether metazoan mitochondria reactivate aggregated proteins is unknown. Here, we establish that a mitochondrial AAA+ protein, Skd3 (human CLPB), couples ATP hydrolysis to protein disaggregation and reactivation. The Skd3 ankyrin-repeat domain combines with conserved AAA+ elements to enable stand-alone disaggregase activity. A mitochondrial inner-membrane protease, PARL, removes an autoinhibitory peptide from Skd3 to greatly enhance disaggregase activity. Indeed, PARL-activated Skd3 dissolves α-synuclein fibrils connected to Parkinson’s disease. Human cells lacking Skd3 exhibit reduced solubility of various mitochondrial proteins, including anti-apoptotic Hax1. -
Skd3 (Human CLPB) Is a Potent Mitochondrial Protein Disaggregase That Is Inactivated By
bioRxiv preprint first posted online Jan. 18, 2020; doi: http://dx.doi.org/10.1101/2020.01.17.911016. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Skd3 (human CLPB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations Ryan R. Cupo1,2 and James Shorter1,2* 1Department of Biochemistry and Biophysics, 2Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, U.S.A. *Correspondence: [email protected] 1 bioRxiv preprint first posted online Jan. 18, 2020; doi: http://dx.doi.org/10.1101/2020.01.17.911016. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. ABSTRACT Cells have evolved specialized protein disaggregases to reverse toxic protein aggregation and restore protein functionality. In nonmetazoan eukaryotes, the AAA+ disaggregase Hsp78 resolubilizes and reactivates proteins in mitochondria. Curiously, metazoa lack Hsp78. Hence, whether metazoan mitochondria reactivate aggregated proteins is unknown. Here, we establish that a mitochondrial AAA+ protein, Skd3 (human CLPB), couples ATP hydrolysis to protein disaggregation and reactivation. The Skd3 ankyrin-repeat domain combines with conserved AAA+ elements to enable stand-alone disaggregase activity. A mitochondrial inner-membrane protease, PARL, removes an autoinhibitory peptide from Skd3 to greatly enhance disaggregase activity. Indeed, PARL-activated Skd3 dissolves α-synuclein fibrils connected to Parkinson’s disease. -
THE FUNCTIONAL SIGNIFICANCE of MITOCHONDRIAL SUPERCOMPLEXES in C. ELEGANS by WICHIT SUTHAMMARAK Submitted in Partial Fulfillment
THE FUNCTIONAL SIGNIFICANCE OF MITOCHONDRIAL SUPERCOMPLEXES in C. ELEGANS by WICHIT SUTHAMMARAK Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Advisor: Drs. Margaret M. Sedensky & Philip G. Morgan Department of Genetics CASE WESTERN RESERVE UNIVERSITY January, 2011 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of _____________________________________________________ candidate for the ______________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Dedicated to my family, my teachers and all of my beloved ones for their love and support ii ACKNOWLEDGEMENTS My advanced academic journey began 5 years ago on the opposite side of the world. I traveled to the United States from Thailand in search of a better understanding of science so that one day I can return to my homeland and apply the knowledge and experience I have gained to improve the lives of those affected by sickness and disease yet unanswered by science. Ultimately, I hoped to make the academic transition into the scholarly community by proving myself through scientific research and understanding so that I can make a meaningful contribution to both the scientific and medical communities. The following dissertation would not have been possible without the help, support, and guidance of a lot of people both near and far. I wish to thank all who have aided me in one way or another on this long yet rewarding journey. My sincerest thanks and appreciation goes to my advisors Philip Morgan and Margaret Sedensky. -
Mitochondrial Medicine in the Omics Era
Mitochondrial Medicine in the Omics Era Joyeeta Rahman1 and Shamima Rahman1,2* 1 Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health and 2 Metabolic Unit, Great Ormond Street Hospital NHS Foundation Trust, London, UK *Correspondence to: Professor Shamima Rahman Mitochondrial Research Group Genetics and Genomic Medicine UCL Great Ormond Street Institute of Child Health London WC1N 1EH, UK. Telephone: +44 (0)2079052608 [email protected] Keywords: Mitochondrial disease, OXPHOS, signalling, omics, genomics, transcriptomics, proteomics, metabolomics, mitochondrial stress response, treatment 1 Abstract Mitochondria are dynamic bioenergetic organelles whose maintenance requires ~1500 proteins from two genomes. Mutations in either the mitochondrial or nuclear genome can disrupt a plethora of cellular metabolic and homeostatic functions. Mitochondrial diseases represent one the most common and severe groups of inherited genetic disorders, characterised by clinical, biochemical, and genetic heterogeneity, diagnostic odysseys, and lack of curative therapies. This review aims to discuss recent advances in mitochondrial biology and medicine arising from widespread utilisation of high-throughput omics technologies, and also includes a broad discussion of emerging therapies for mitochondrial disease. New insights into both bioenergetic and biosynthetic mitochondrial functionalities have expedited the genetic diagnosis of primary mitochondrial disorders, and identified novel mitochondrial pathomechanisms and new targets -
The Dawn of the Crispr-Free Genome Editing Era
Mitsui & Co. Global Strategic Studies Institute Monthly Report, November 2020 THE DAWN OF THE CRISPR-FREE GENOME EDITING ERA —THE DEVELOPMENT OF GENOME EDITING TECHNOLOGY— Yutaka Abe Technology Foresight Center and Industry Innovation Dept., Technology & Innovation Studies Div. Mitsui & Co. Global Strategic Studies Institute OVERVIEW The genome editing technology CRISPR-Cas9, which drew attention in the 2020 Nobel Prize in Chemistry, has been applied in various fields and has a concrete record in improving productivity and others. As such, future social implementation is expected to progress steadily. CRISPR-Cas9 has some drawbacks that need to be resolved, such as the possibility of altering the genetic information in unintended locations and the adverse effects to the organism caused by the activated immune functions due to DNA cleavage. While there are moves to improve CRISPR-Cas9 currently, research and development are underway into so- called CRISPR-free technologies, such as RNA editing technology and mitochondrial DNA editing technology that edit the genome without cutting DNA. Applications of CRISPR-free technology include RNA therapeutics and the treatment and cure of mitochondrial diseases, and these technological trends warrant attention. On October 7, 2020, the Royal Swedish Academy of Sciences announced that it would award the Nobel Prize in Chemistry to two scientists involved in the development of genome editing technology. This is a rapid award of the prize, having been just eight years since the paper1 was published in June 2012, and shows how innovative the genome editing technology CRISPR-Cas92 is. Since the effectiveness of CRISPR-Cas9 was shown in cultured cells in 2013, it has been used not only in the medical and healthcare fields but also in the areas of agriculture, livestock, and fisheries, and concrete results3 have been produced.