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Lee MJ, Caruana NJ, Saner NJ, Kuang J, Stokes T, McLeod JC, Oikawa SY, Bishop DJ, Bartlett JD, Phillips SM. Resistance-only and concurrent exercise induce similar myofibrillar protein synthesis rates and associated molecular responses in moderately active men before and after training. FASEB J 2024; 38:e23392. [PMID: 38153675 DOI: 10.1096/fj.202302024r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023]
Abstract
Aerobic and resistance exercise (RE) induce distinct molecular responses. One hypothesis is that these responses are antagonistic and unfavorable for the anabolic response to RE when concurrent exercise is performed. This thesis may also depend on the participants' training status and concurrent exercise order. We measured free-living myofibrillar protein synthesis (MyoPS) rates and associated molecular responses to resistance-only and concurrent exercise (with different exercise orders), before and after training. Moderately active men completed one of three exercise interventions (matched for age, baseline strength, body composition, and aerobic capacity): resistance-only exercise (RE, n = 8), RE plus high-intensity interval exercise (RE+HIIE, n = 8), or HIIE+RE (n = 9). Participants trained 3 days/week for 10 weeks; concurrent sessions were separated by 3 h. On the first day of Weeks 1 and 10, muscle was sampled immediately before and after, and 3 h after each exercise mode and analyzed for molecular markers of MyoPS and muscle glycogen. Additional muscle, sampled pre- and post-training, was used to determine MyoPS using orally administered deuterium oxide (D2 O). In both weeks, MyoPS rates were comparable between groups. Post-exercise changes in proteins reflective of protein synthesis were also similar between groups, though MuRF1 and MAFbx mRNA exhibited some exercise order-dependent responses. In Week 10, exercise-induced changes in MyoPS and some genes (PGC-1ɑ and MuRF1) were dampened from Week 1. Concurrent exercise (in either order) did not compromise the anabolic response to resistance-only exercise, before or after training. MyoPS rates and some molecular responses to exercise are diminished after training.
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Affiliation(s)
- Matthew J Lee
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Nikeisha J Caruana
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas J Saner
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Jujiao Kuang
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Tanner Stokes
- Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan C McLeod
- Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Sara Y Oikawa
- Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - David J Bishop
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Jonathan D Bartlett
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Stuart M Phillips
- Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
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2
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Healy MD, McNally KE, Butkovič R, Chilton M, Kato K, Sacharz J, McConville C, Moody ERR, Shaw S, Planelles-Herrero VJ, Yadav SKN, Ross J, Borucu U, Palmer CS, Chen KE, Croll TI, Hall RJ, Caruana NJ, Ghai R, Nguyen THD, Heesom KJ, Saitoh S, Berger I, Schaffitzel C, Williams TA, Stroud DA, Derivery E, Collins BM, Cullen PJ. Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Cell 2023; 186:2219-2237.e29. [PMID: 37172566 PMCID: PMC10187114 DOI: 10.1016/j.cell.2023.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/23/2023] [Accepted: 04/04/2023] [Indexed: 05/15/2023]
Abstract
The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy, and in silico predictions, we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilized by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a 16th subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.
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Affiliation(s)
- Michael D Healy
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kerrie E McNally
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK; MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK.
| | - Rebeka Butkovič
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Molly Chilton
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Kohji Kato
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Joanna Sacharz
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Calum McConville
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Edmund R R Moody
- School of Biological Sciences, University of Bristol, BS8 1TD Bristol, UK
| | - Shrestha Shaw
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | | | - Sathish K N Yadav
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Jennifer Ross
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Ufuk Borucu
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Catherine S Palmer
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Kai-En Chen
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, CB2 0XY Cambridge, UK
| | - Ryan J Hall
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; Institute of Health and Sport (iHeS), Victoria University, Melbourne, VIC Australia
| | - Rajesh Ghai
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Thi H D Nguyen
- MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| | - Kate J Heesom
- Proteomics Facility, School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences and Medical School, Nagoya, Japan
| | - Imre Berger
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK; Max Planck Bristol Centre for Minimal Biology, Department of Chemistry, University of Bristol, BS8 1TS Bristol, UK
| | - Christiane Schaffitzel
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TD Bristol, UK
| | - David A Stroud
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC Australia
| | | | - Brett M Collins
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK.
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3
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Van Haute L, O'Connor E, Díaz-Maldonado H, Munro B, Polavarapu K, Hock DH, Arunachal G, Athanasiou-Fragkouli A, Bardhan M, Barth M, Bonneau D, Brunetti-Pierri N, Cappuccio G, Caruana NJ, Dominik N, Goel H, Helman G, Houlden H, Lenaers G, Mention K, Murphy D, Nandeesh B, Olimpio C, Powell CA, Preethish-Kumar V, Procaccio V, Rius R, Rebelo-Guiomar P, Simons C, Vengalil S, Zaki MS, Ziegler A, Thorburn DR, Stroud DA, Maroofian R, Christodoulou J, Gustafsson C, Nalini A, Lochmüller H, Minczuk M, Horvath R. TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease. Nat Commun 2023; 14:1009. [PMID: 36823193 PMCID: PMC9950373 DOI: 10.1038/s41467-023-36277-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/20/2023] [Indexed: 02/25/2023] Open
Abstract
Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT. We report for the first time that TEFM variants are associated with mitochondrial respiratory chain deficiency and a wide range of clinical presentations including mitochondrial myopathy with a treatable neuromuscular transmission defect. Mechanistically, we show muscle and primary fibroblasts from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts. Finally, tefm knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function, strengthening the genotype-phenotype correlation. Our study highlights that TEFM regulates mitochondrial transcription elongation and its defect results in variable, tissue-specific neurological and neuromuscular symptoms.
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Affiliation(s)
- Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Emily O'Connor
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Héctor Díaz-Maldonado
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Benjamin Munro
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Gautham Arunachal
- Department of Human genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Alkyoni Athanasiou-Fragkouli
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Mainak Bardhan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Magalie Barth
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Dominique Bonneau
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples Federico II, Via s. Pansini, 5, 80131, Naples, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, University of Naples Federico II, Via s. Pansini, 5, 80131, Naples, Italy
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, 3011, Australia
| | - Natalia Dominik
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Himanshu Goel
- Hunter Genetics, Waratah, University of Newcastle, Callaghan, NSW, 2298, Australia
| | - Guy Helman
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Henry Houlden
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Guy Lenaers
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Karine Mention
- Pediatric Inherited Metabolic Disorders, Hôpital Jeanne de Flandre, Lille, France
| | - David Murphy
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - Bevinahalli Nandeesh
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Catarina Olimpio
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Vincent Procaccio
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - Rocio Rius
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Cas Simons
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Alban Ziegler
- Department of Genetics, Mitovasc INSERM 1083, CNRS 6015, University Hospital of Angers, Angers, France
| | - David R Thorburn
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Reza Maroofian
- UCL London, Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, UK
| | - John Christodoulou
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Claes Gustafsson
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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4
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Tucker EJ, Baker MJ, Hock DH, Warren JT, Jaillard S, Bell KM, Sreenivasan R, Bakhshalizadeh S, Hanna CA, Caruana NJ, Wortmann SB, Rahman S, Pitceathly RDS, Donadieu J, Alimi A, Launay V, Coppo P, Christin-Maitre S, Robevska G, van den Bergen J, Kline BL, Ayers KL, Stewart PN, Stroud DA, Stojanovski D, Sinclair AH. Premature Ovarian Insufficiency in CLPB Deficiency: Transcriptomic, Proteomic and Phenotypic Insights. J Clin Endocrinol Metab 2022; 107:3328-3340. [PMID: 36074910 PMCID: PMC9693831 DOI: 10.1210/clinem/dgac528] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Premature ovarian insufficiency (POI) is a common form of female infertility that usually presents as an isolated condition but can be part of various genetic syndromes. Early diagnosis and treatment of POI can minimize comorbidity and improve health outcomes. OBJECTIVE We aimed to determine the genetic cause of syndromic POI, intellectual disability, neutropenia, and cataracts. METHODS We performed whole-exome sequencing (WES) followed by functional validation via RT-PCR, RNAseq, and quantitative proteomics, as well as clinical update of previously reported patients with variants in the caseinolytic peptidase B (CLPB) gene. RESULTS We identified causative variants in CLPB, encoding a mitochondrial disaggregase. Variants in this gene are known to cause an autosomal recessive syndrome involving 3-methylglutaconic aciduria, neurological dysfunction, cataracts, and neutropenia that is often fatal in childhood; however, there is likely a reporting bias toward severe cases. Using RNAseq and quantitative proteomics we validated causation and gained insight into genotype:phenotype correlation. Clinical follow-up of patients with CLPB deficiency who survived to adulthood identified POI and infertility as a common postpubertal ailment. CONCLUSION A novel splicing variant is associated with CLPB deficiency in an individual who survived to adulthood. POI is a common feature of postpubertal female individuals with CLPB deficiency. Patients with CLPB deficiency should be referred to pediatric gynecologists/endocrinologists for prompt POI diagnosis and hormone replacement therapy to minimize associated comorbidities.
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Affiliation(s)
- Elena J Tucker
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Megan J Baker
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Julia T Warren
- Division of Hematology-Oncology, Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sylvie Jaillard
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033 Rennes, France
| | - Katrina M Bell
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Rajini Sreenivasan
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shabnam Bakhshalizadeh
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Chloe A Hanna
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Gynaecology, The Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, 3011, Australia
| | - Saskia B Wortmann
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg 5020, Austria
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboudumc, Nijmegen 6524, The Netherlands
| | - Shamima Rahman
- Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, and Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Jean Donadieu
- Sorbonne Université, Service d’Hémato-oncologie Pédiatrique, Assistance Publique-Hopitaux de Paris (AP-HP), Hôpital Trousseau, Paris 75006, France
- Registre Français des Neutropénies Congénitales, Hôpital Trousseau, Paris 75006, France
- Centre de Référence des Neutropénies Chroniques, AP-HP, Hôpital Trousseau, Paris 75006, France
| | - Aurelia Alimi
- Sorbonne Université, Service d’Hémato-oncologie Pédiatrique, Assistance Publique-Hopitaux de Paris (AP-HP), Hôpital Trousseau, Paris 75006, France
- Registre Français des Neutropénies Congénitales, Hôpital Trousseau, Paris 75006, France
- Centre de Référence des Neutropénies Chroniques, AP-HP, Hôpital Trousseau, Paris 75006, France
| | - Vincent Launay
- Hematologie, Centre Hospitalier de St Brieuc, Paris 22027, France
| | - Paul Coppo
- Sorbonne Université, Service d’hématologie Hôpital Saint-Antoine, AP-HP, Paris75006, France
| | - Sophie Christin-Maitre
- Sorbonne Université, Service d’Endocrinologie, diabétologie et médecine de la reproduction Hôpital Saint-Antoine, AP-HP, Paris75006, France
| | - Gorjana Robevska
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Jocelyn van den Bergen
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Brianna L Kline
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Katie L Ayers
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Phoebe N Stewart
- Department of Paediatrics, The Royal Hobart Hospital, Tasmania 7000, Australia
| | - David A Stroud
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew H Sinclair
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
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5
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Robinson DRL, Hock DH, Muellner-Wong L, Kugapreethan R, Reljic B, Surgenor EE, Rodrigues CHM, Caruana NJ, Stroud DA. Applying Sodium Carbonate Extraction Mass Spectrometry to Investigate Defects in the Mitochondrial Respiratory Chain. Front Cell Dev Biol 2022; 10:786268. [PMID: 35300415 PMCID: PMC8921082 DOI: 10.3389/fcell.2022.786268] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/03/2022] [Indexed: 12/03/2022] Open
Abstract
Mitochondria are complex organelles containing 13 proteins encoded by mitochondrial DNA and over 1,000 proteins encoded on nuclear DNA. Many mitochondrial proteins are associated with the inner or outer mitochondrial membranes, either peripherally or as integral membrane proteins, while others reside in either of the two soluble mitochondrial compartments, the mitochondrial matrix and the intermembrane space. The biogenesis of the five complexes of the oxidative phosphorylation system are exemplars of this complexity. These large multi-subunit complexes are comprised of more than 80 proteins with both membrane integral and peripheral associations and require soluble, membrane integral and peripherally associated assembly factor proteins for their biogenesis. Mutations causing human mitochondrial disease can lead to defective complex assembly due to the loss or altered function of the affected protein and subsequent destabilization of its interactors. Here we couple sodium carbonate extraction with quantitative mass spectrometry (SCE-MS) to track changes in the membrane association of the mitochondrial proteome across multiple human knockout cell lines. In addition to identifying the membrane association status of over 840 human mitochondrial proteins, we show how SCE-MS can be used to understand the impacts of defective complex assembly on protein solubility, giving insights into how specific subunits and sub-complexes become destabilized.
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Affiliation(s)
- David R L Robinson
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Linden Muellner-Wong
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.,The Royal Children's Hospital, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Roopasingam Kugapreethan
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Boris Reljic
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Elliot E Surgenor
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Carlos H M Rodrigues
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.,Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.,Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.,The Royal Children's Hospital, Murdoch Children's Research Institute, Parkville, VIC, Australia
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Van Bergen NJ, Hock DH, Spencer L, Massey S, Stait T, Stark Z, Lunke S, Roesley A, Peters H, Lee JY, Le Fevre A, Heath O, Mignone C, Yang JYM, Ryan MM, D’Arcy C, Nash M, Smith S, Caruana NJ, Thorburn DR, Stroud DA, White SM, Christodoulou J, Brown NJ. Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function. Int J Mol Sci 2022; 23:ijms23020986. [PMID: 35055180 PMCID: PMC8777681 DOI: 10.3390/ijms23020986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/04/2022] Open
Abstract
Pyridine Nucleotide-Disulfide Oxidoreductase Domain 2 (PYROXD2; previously called YueF) is a mitochondrial inner membrane/matrix-residing protein and is reported to regulate mitochondrial function. The clinical importance of PYROXD2 has been unclear, and little is known of the protein’s precise biological function. In the present paper, we report biallelic variants in PYROXD2 identified by genome sequencing in a patient with suspected mitochondrial disease. The child presented with acute neurological deterioration, unresponsive episodes, and extreme metabolic acidosis, and received rapid genomic testing. He died shortly after. Magnetic resonance imaging (MRI) brain imaging showed changes resembling Leigh syndrome, one of the more common childhood mitochondrial neurological diseases. Functional studies in patient fibroblasts showed a heightened sensitivity to mitochondrial metabolic stress and increased mitochondrial superoxide levels. Quantitative proteomic analysis demonstrated decreased levels of subunits of the mitochondrial respiratory chain complex I, and both the small and large subunits of the mitochondrial ribosome, suggesting a mitoribosomal defect. Our findings support the critical role of PYROXD2 in human cells, and suggest that the biallelic PYROXD2 variants are associated with mitochondrial dysfunction, and can plausibly explain the child’s clinical presentation.
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Affiliation(s)
- Nicole J. Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
| | - Daniella H. Hock
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
| | - Lucy Spencer
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Tegan Stait
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Australian Genomics Health Alliance, Parkville, VIC 3052, Australia
| | - Sebastian Lunke
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ain Roesley
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - Heidi Peters
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Joy Yaplito Lee
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Anna Le Fevre
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - Oliver Heath
- Department of Metabolic Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (H.P.); (O.H.)
| | - Cristina Mignone
- Medical Imaging Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Joseph Yuan-Mou Yang
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Department of Neurosurgery, Neuroscience Advanced Clinical Imaging Service (NACIS), The Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Developmental Imaging, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
- Neuroscience Research, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Monique M. Ryan
- Neurology Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Colleen D’Arcy
- Anatomical Pathology Department, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Margot Nash
- General Medicine, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Sile Smith
- Paediatric Intensive Care Unit, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Nikeisha J. Caruana
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC 3011, Australia
| | - David R. Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - David A. Stroud
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (D.H.H.); (N.J.C.)
| | - Susan M. White
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia; (L.S.); (S.M.); (T.S.); (D.R.T.); (D.A.S.)
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Discipline of Child and Adolescent Health, University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
| | - Natasha J. Brown
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia; (Z.S.); (S.L.); (J.Y.L.); (J.Y.-M.Y.); (S.M.W.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (A.R.); (A.L.F.)
- Correspondence: (N.J.V.B.); (J.C.); (N.J.B.)
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7
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Lin W, Saner NJ, Weng X, Caruana NJ, Botella J, Kuang J, Lee MJC, Jamnick NA, Pitchford NW, Garnham A, Bartlett JD, Chen H, Bishop DJ. The Effect of Sleep Restriction, With or Without Exercise, on Skeletal Muscle Transcriptomic Profiles in Healthy Young Males. Front Endocrinol (Lausanne) 2022; 13:863224. [PMID: 35937838 PMCID: PMC9355502 DOI: 10.3389/fendo.2022.863224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Inadequate sleep is associated with many detrimental health effects, including increased risk of developing insulin resistance and type 2 diabetes. These effects have been associated with changes to the skeletal muscle transcriptome, although this has not been characterised in response to a period of sleep restriction. Exercise induces a beneficial transcriptional response within skeletal muscle that may counteract some of the negative effects associated with sleep restriction. We hypothesised that sleep restriction would down-regulate transcriptional pathways associated with glucose metabolism, but that performing exercise would mitigate these effects. METHODS 20 healthy young males were allocated to one of three experimental groups: a Normal Sleep (NS) group (8 h time in bed per night (TIB), for five nights (11 pm - 7 am)), a Sleep Restriction (SR) group (4 h TIB, for five nights (3 am - 7 am)), and a Sleep Restriction and Exercise group (SR+EX) (4 h TIB, for five nights (3 am - 7 am) and three high-intensity interval exercise (HIIE) sessions (performed at 10 am)). RNA sequencing was performed on muscle samples collected pre- and post-intervention. Our data was then compared to skeletal muscle transcriptomic data previously reported following sleep deprivation (24 h without sleep). RESULTS Gene set enrichment analysis (GSEA) indicated there was an increased enrichment of inflammatory and immune response related pathways in the SR group post-intervention. However, in the SR+EX group the direction of enrichment in these same pathways occurred in the opposite directions. Despite this, there were no significant changes at the individual gene level from pre- to post-intervention. A set of genes previously shown to be decreased with sleep deprivation was also decreased in the SR group, but increased in the SR+EX group. CONCLUSION The alterations to inflammatory and immune related pathways in skeletal muscle, following five nights of sleep restriction, provide insight regarding the transcriptional changes that underpin the detrimental effects associated with sleep loss. Performing three sessions of HIIE during sleep restriction attenuated some of these transcriptional changes. Overall, the transcriptional alterations observed with a moderate period of sleep restriction were less evident than previously reported changes following a period of sleep deprivation.
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Affiliation(s)
- Wentao Lin
- College of Exercise and Health, Guangzhou Sport University, Guangzhou, China
| | - Nicholas J. Saner
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- Human Integrative Physiology, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Xiquan Weng
- College of Exercise and Health, Guangzhou Sport University, Guangzhou, China
| | - Nikeisha J. Caruana
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Javier Botella
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Jujiao Kuang
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
| | - Matthew J-C. Lee
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
| | - Nicholas A. Jamnick
- Metabolic Research Unit, Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Nathan W. Pitchford
- School of Health Sciences, University of Tasmania, Launceston, TAS, Australia
| | - Andrew Garnham
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
| | | | - Hao Chen
- College of Exercise and Health, Guangzhou Sport University, Guangzhou, China
- *Correspondence: Hao Chen, ; David J. Bishop,
| | - David J. Bishop
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- *Correspondence: Hao Chen, ; David J. Bishop,
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Granata C, Caruana NJ, Botella J, Jamnick NA, Huynh K, Kuang J, Janssen HA, Reljic B, Mellett NA, Laskowski A, Stait TL, Frazier AE, Coughlan MT, Meikle PJ, Thorburn DR, Stroud DA, Bishop DJ. High-intensity training induces non-stoichiometric changes in the mitochondrial proteome of human skeletal muscle without reorganisation of respiratory chain content. Nat Commun 2021; 12:7056. [PMID: 34862379 PMCID: PMC8642543 DOI: 10.1038/s41467-021-27153-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/26/2021] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial defects are implicated in multiple diseases and aging. Exercise training is an accessible, inexpensive therapeutic intervention that can improve mitochondrial bioenergetics and quality of life. By combining multiple omics techniques with biochemical and in silico normalisation, we removed the bias arising from the training-induced increase in mitochondrial content to unearth an intricate and previously undemonstrated network of differentially prioritised mitochondrial adaptations. We show that changes in hundreds of transcripts, proteins, and lipids are not stoichiometrically linked to the overall increase in mitochondrial content. Our findings suggest enhancing electron flow to oxidative phosphorylation (OXPHOS) is more important to improve ATP generation than increasing the abundance of the OXPHOS machinery, and do not support the hypothesis that training-induced supercomplex formation enhances mitochondrial bioenergetics. Our study provides an analytical approach allowing unbiased and in-depth investigations of training-induced mitochondrial adaptations, challenging our current understanding, and calling for careful reinterpretation of previous findings.
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Affiliation(s)
- Cesare Granata
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia.
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University, 40225, Düsseldorf, Germany.
| | - Nikeisha J Caruana
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Javier Botella
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
| | - Nicholas A Jamnick
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
- Metabolic Research Unit, School of Medicine and Institute for Mental and Physical Health and Clinical Translation (iMPACT), Deakin University, Geelong, VIC, Australia
| | - Kevin Huynh
- Baker Heart & Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Jujiao Kuang
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
| | - Hans A Janssen
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia
| | - Boris Reljic
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | | | - Adrienne Laskowski
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Tegan L Stait
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Melinda T Coughlan
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Baker Heart & Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Peter J Meikle
- Baker Heart & Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, 3052, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - David A Stroud
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
| | - David J Bishop
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, VIC, 3011, Australia.
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9
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Caruana NJ, Strugnell JM, Finn J, Faou P, Plummer KM, Cooke IR. Quantitative Proteomic Analysis of the Slime and Ventral Mantle Glands of the Striped Pyjama Squid ( Sepioloidea lineolata). J Proteome Res 2020; 19:1491-1501. [PMID: 32091901 DOI: 10.1021/acs.jproteome.9b00738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cephalopods are known to produce an extensive range of secretions including ink, mucus, and venom. Sepiadariidae, a family of small, benthic bobtail squids, are notable for the high volume of viscous slime they emit when stressed. One species, Sepioloidea lineolata (striped pyjama squid), is covered with glands along the perimeter of the ventral mantle, and these structures are hypothesized to be the source of its slime. Using label-free quantitative proteomics, we analyzed five tissue types (dorsal and ventral mantle muscle, dorsal and ventral epithelium, and ventral mantle glands) and the slime from four individuals. In doing so, we were able to determine the relationship between the slime and the tissues as well as highlight proteins that were specifically identified within the slime and ventral mantle glands. A total of 28 proteins were identified to be highly enriched in slime, and these were composed of peptidases and protease inhibitors. Seven of these proteins contained predicted signal peptides, indicating classical secretion, with four proteins having no identifiable domains or similarity to any known proteins. The ventral mantle glands also appear to be the tissue with the closest overall proteomic composition to the slime; therefore, it is likely that the slime originates, at least in part, from these glands.
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Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland 4811, Australia
| | - Julian Finn
- Sciences, Museums Victoria, Carlton, Victoria 3053, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ira R Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland 4811, Australia
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Caruana NJ, Strugnell JM, Faou P, Finn J, Cooke IR. Comparative Proteomic Analysis of Slime from the Striped Pyjama Squid, Sepioloidea lineolata, and the Southern Bottletail Squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae). J Proteome Res 2019; 18:890-899. [PMID: 30628786 DOI: 10.1021/acs.jproteome.8b00569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sepioloidea lineolata, the striped pyjama squid (family Sepiadariidae), is a small species of benthic bobtail squid distributed along the Southern Indo-Pacific coast of Australia. Like other sepiadariid squids, it is known to secrete large volumes of viscous slime when stressed. In order to identify key proteins involved in the function of sepiadariid slimes, we compared the slime proteome of Sepioloidea lineolata with that of a closely related species, Sepiadarium austrinum. Of the 550 protein groups identified in Sepioloidea lineolata slime, 321 had orthologs in Sepiadarium austrinum, and the abundance of these (iBAQ) was highly correlated between species. Both slimes were dominated by a small number of abundant proteins, and several of these were short secreted proteins with no homologues outside the class Cephalopoda. No mucins were identified within either species' slime, suggesting that it is structurally distinct from mucin polymer-based gels found in many vertebrate and echinoderm secretions. The extent of N-glycosylation in the slime of Sepioloidea lineolata was also studied via glycan cleavage with Peptide: N-glycosidase F (PNGase-F). Although very few (four) proteins showed strong evidence of N-glycosylation, we found that treatment with PNGase-F led to a slight increase in peptide identification rates compared with controls.
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Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution , La Trobe University , Melbourne , VIC 3086 , Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution , La Trobe University , Melbourne , VIC 3086 , Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture , James Cook University , Townsville , QLD 4811 , Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , VIC 3086 , Australia
| | - Julian Finn
- Sciences , Museums Victoria , Carlton , VIC 3053 , Australia
| | - Ira R Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , VIC 3086 , Australia.,Department of Molecular and Cell Biology , James Cook University , Townsville , QLD 4811 , Australia
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11
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Caruana NJ, Cooke IR, Faou P, Finn J, Hall NE, Norman M, Pineda SS, Strugnell JM. A combined proteomic and transcriptomic analysis of slime secreted by the southern bottletail squid, Sepiadarium austrinum (Cephalopoda). J Proteomics 2016; 148:170-82. [PMID: 27476034 DOI: 10.1016/j.jprot.2016.07.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/20/2016] [Accepted: 07/24/2016] [Indexed: 10/21/2022]
Abstract
UNLABELLED Sepiadarium austrinum, the southern bottletail squid, is a small squid that inhabits soft sediments along Australia's south-east coast. When provoked, it rapidly secretes large volumes of slime, presumably as a form of chemical defense. We analyzed the proteomic composition of this slime using tandem mass spectrometry and transcriptomics and found that it was remarkably complex with 1735 identified protein groups (FDR:0.01). To investigate the chemical defense hypothesis we performed an Artemia toxicity assay and used sequence analysis to search for toxin-like molecules. Although the slime did not appear to be toxic to Artemia we found 13 proteins in slime with the hallmarks of toxins, namely cysteine richness, short length, a signal peptide and/or homology to known toxins. These included three short (80-130AA) cysteine rich secreted proteins with no homology to proteins on the NCBI or UniProt databases. Other protein families found included, CAP, phospholipase-B, ShKT-like peptides, peptidase S10, Kunitz BPTI and DNase II. Quantitative analysis using intensity based absolute quantification (iBAQ via MaxQuant) revealed 20 highly abundant proteins, accounting for 67% of iBAQ signal, and three of these were toxin-like. No mucin homologues were found suggesting that the structure of the slime gel may be formed by an unknown mechanism. BIOLOGICAL SIGNIFICANCE This study is the first known instance of a slime secretion from a cephalopod to be analyzed by proteomics methods and is the first investigation of a member of the family Sepiadariidae using proteomic methods. 1735 proteins were identified with 13 of these fitting criteria established for the identification of putative toxins. The slime is dominated by 20 highly abundant proteins with secreted, cysteine rich proteins. The study highlights the importance of 'omics approaches in understanding novel organisms.
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Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, Vic 3086, Australia.
| | - Ira R Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, Qld 4811, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Vic 3086, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Vic 3086, Australia
| | - Julian Finn
- Sciences, Museum Victoria, Carlton, Vic 3053, Australia
| | - Nathan E Hall
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Vic 3053, Australia
| | - Mark Norman
- Sciences, Museum Victoria, Carlton, Vic 3053, Australia
| | - Sandy S Pineda
- Institute for Molecular Bioscience, The University of Queensland, QLD 4072, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, Vic 3086, Australia
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