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Lisowski P, Lickfett S, Rybak-Wolf A, Menacho C, Le S, Pentimalli TM, Notopoulou S, Dykstra W, Oehler D, López-Calcerrada S, Mlody B, Otto M, Wu H, Richter Y, Roth P, Anand R, Kulka LAM, Meierhofer D, Glazar P, Legnini I, Telugu NS, Hahn T, Neuendorf N, Miller DC, Böddrich A, Polzin A, Mayatepek E, Diecke S, Olzscha H, Kirstein J, Ugalde C, Petrakis S, Cambridge S, Rajewsky N, Kühn R, Wanker EE, Priller J, Metzger JJ, Prigione A. Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure. Nat Commun 2024; 15:7027. [PMID: 39174523 PMCID: PMC11341898 DOI: 10.1038/s41467-024-51216-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
Expansion of the glutamine tract (poly-Q) in the protein huntingtin (HTT) causes the neurodegenerative disorder Huntington's disease (HD). Emerging evidence suggests that mutant HTT (mHTT) disrupts brain development. To gain mechanistic insights into the neurodevelopmental impact of human mHTT, we engineered male induced pluripotent stem cells to introduce a biallelic or monoallelic mutant 70Q expansion or to remove the poly-Q tract of HTT. The introduction of a 70Q mutation caused aberrant development of cerebral organoids with loss of neural progenitor organization. The early neurodevelopmental signature of mHTT highlighted the dysregulation of the protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2), a transcription factor involved in mitochondrial integrated stress response. CHCHD2 repression was associated with abnormal mitochondrial morpho-dynamics that was reverted upon overexpression of CHCHD2. Removing the poly-Q tract from HTT normalized CHCHD2 levels and corrected key mitochondrial defects. Hence, mHTT-mediated disruption of human neurodevelopment is paralleled by aberrant neurometabolic programming mediated by dysregulation of CHCHD2, which could then serve as an early interventional target for HD.
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Affiliation(s)
- Pawel Lisowski
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Psychiatry and Psychotherapy, Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin, Berlin, Germany
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec n/Warsaw, Poland
| | - Selene Lickfett
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Institute of Anatomy II, Heinrich-Heine-University, Düsseldorf, Germany
| | - Agnieszka Rybak-Wolf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Organoid Platform, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Carmen Menacho
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Stephanie Le
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Tancredi Massimo Pentimalli
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Sofia Notopoulou
- Institute of Applied Biosciences (INAB), Centre For Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Werner Dykstra
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht, The Netherlands
| | - Daniel Oehler
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital Düsseldorf, Cardiovascular Research Institute Düsseldorf (CARID), Düsseldorf, Germany
| | | | - Barbara Mlody
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Centogene, Rostock, Germany
| | - Maximilian Otto
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Haijia Wu
- Institute of Molecular Medicine, Medical School, Hamburg, Germany
| | | | - Philipp Roth
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ruchika Anand
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Linda A M Kulka
- Institute of Physiological Chemistry, Martin-Luther-University, Halle-Wittenberg, Germany
| | - David Meierhofer
- Quantitative RNA Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Petar Glazar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Quantitative RNA Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ivano Legnini
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Human Technopole, Milan, Italy
| | - Narasimha Swamy Telugu
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Tobias Hahn
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Nancy Neuendorf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Duncan C Miller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Annett Böddrich
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Amin Polzin
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital Düsseldorf, Cardiovascular Research Institute Düsseldorf (CARID), Düsseldorf, Germany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Sebastian Diecke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Heidi Olzscha
- Institute of Molecular Medicine, Medical School, Hamburg, Germany
- Institute of Physiological Chemistry, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Janine Kirstein
- Cell Biology, University of Bremen, Bremen, Germany
- Leibniz Institute on Aging - Fritz-Lipmann Institute, Jena, Germany
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i + 12), Madrid, Spain
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Spyros Petrakis
- Institute of Applied Biosciences (INAB), Centre For Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Sidney Cambridge
- Institute of Anatomy II, Heinrich-Heine-University, Düsseldorf, Germany
- Dr. Senckenberg Anatomy, Anatomy II, Goethe-University, Frankfurt, Germany
| | - Nikolaus Rajewsky
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
- National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Ralf Kühn
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Josef Priller
- Department of Psychiatry and Psychotherapy, Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Psychiatry and Psychotherapy; School of Medicine and Health, Technical University of Munich and German Center for Mental Health (DZPG), Munich, Germany
- University of Edinburgh and UK Dementia Research Institute, Edinburgh, UK
| | - Jakob J Metzger
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - Alessandro Prigione
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
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2
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Yan J, Wang X, Fan Z, Xu Y, Zhang Y, Liu Y, Guo L, Liu D. Circ_0098823 binding with IGF2BP3 regulates DNM1L stability to promote metastasis of hepatocellular carcinoma via mitochondrial fission. Apoptosis 2024; 29:709-725. [PMID: 38459420 DOI: 10.1007/s10495-023-01903-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2023] [Indexed: 03/10/2024]
Abstract
Hepatocellular carcinoma (HCC) is highly metastatic and invasive. CircRNA participates in gene regulation of multiple tumor metastases, but little is known whether it is a bystander or an actual player in HCC metastasis. We aim to explore the molecular mechanisms of novel circRNAs in HCC metastasis. RT-qPCR was used to detect the expression of 13 circRNAs derived by the ERBB3 gene. The function of circ_0098823 and DNM1L in HCC cells were estimated by CCK-8, transwell assays, flow cytometry, electron microscope, and in vivo experiments. RNA binding protein of circ_0098823 was confirmed by RNA pull-down, mass spectrometry, and RNA immunoprecipitation. The expression of DNM1L after IGF2BP3 knockdown was detected by RT-qPCR and western blot. Circ_0098823 was significantly up-regulated both in HCC tissues and HGF induced cell lines. Circ_0098823 overexpression significantly enhanced proliferation, migration, and invasion but decreased apoptosis of HCC cells, particularly promoted mitochondrial fission. Compared with the control group, the tumors in the circ_0098823 knockdown mice were significantly smaller and lighter. Circ_0098823 silencing suppressed DNM1L expression, a key molecule for fission, which enhanced proliferation, migration and invasion, and inhibited apoptosis of HCC cell. IGF2BP3 was a binding protein of circ_0098823. The expression and mRNA stability of DNM1L were down-regulated by IGF2BP3 knockdown. IGF2BP3 knockdown significantly alleviated the excessive migration, invasion and apoptosis of HCC cells caused by circ_0098823 overexpression. This study uncovered a novel circ_0098823 with tumor-promoting effect, and the mechanism by which circ_0098823 participates in HCC progression through IGF2BP3-guided DNM1L. Our study broadens molecular understanding of HCC progression.
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Affiliation(s)
- Jiuliang Yan
- Department of Pancreatic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xiaofeng Wang
- Department of Medical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zongyu Fan
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yiqing Xu
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.85, Wujin Road, Hongkou District, Shanghai, 200080, China
| | - Yingzi Zhang
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.85, Wujin Road, Hongkou District, Shanghai, 200080, China
| | - Yi Liu
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.85, Wujin Road, Hongkou District, Shanghai, 200080, China
| | - Lei Guo
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China.
| | - Dongli Liu
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.85, Wujin Road, Hongkou District, Shanghai, 200080, China.
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Peng R, Rochon K, Stagg SM, Mears JA. The Structure of the Drp1 Lattice on Membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588123. [PMID: 38617273 PMCID: PMC11014616 DOI: 10.1101/2024.04.04.588123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanism. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. Additionally, we observed contact between Drp1 and membrane that can be assigned to variable domain sequence. We identified two states of the Drp1 lattice representing conformational changes related to membrane curvature differences. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.
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Affiliation(s)
- Ruizhi Peng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
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4
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Zhang Z, Bie X, Chen Z, Liu J, Xie Z, Li X, Xiao M, Zhang Q, Zhang Y, Yang Y, Li D. A novel variant of DNM1L expanding the clinical phenotypic spectrum: a case report and literature review. BMC Pediatr 2024; 24:104. [PMID: 38341530 PMCID: PMC10858475 DOI: 10.1186/s12887-023-04442-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/23/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Mitochondrial diseases are heterogeneous in terms of clinical manifestations and genetic characteristics. The dynamin 1-like gene (DNM1L) encodes dynamin-related protein 1 (DRP1), a member of the GTPases dynamin superfamily responsible for mitochondrial and peroxisomal fission. DNM1L variants can lead to mitochondrial fission dysfunction. CASE PRESENTATION Herein, we report a distinctive clinical phenotype associated with a novel variant of DNM1L and review the relevant literature. A 5-year-old girl presented with paroxysmal hemiplegia, astigmatism, and strabismus. Levocarnitine and coenzyme Q10 supplement showed good efficacy. Based on the patient's clinical data, trio whole-exome sequencing (trio-WES) and mtDNA sequencing were performed to identify the potential causative genes, and Sanger sequencing was used to validate the specific variation in the proband and her family members. The results showed a novel de novo heterozygous nonsense variant in exon 20 of the DNM1L gene, c.2161C>T, p.Gln721Ter, which is predicted to be a pathogenic variant according to the ACMG guidelines. The proband has a previously undescribed clinical manifestation, namely hemiparesis, which may be an additional feature of the growing phenotypic spectrum of DNM1L-related diseases. CONCLUSION Our findings elucidate a novel variant in DNM1L-related disease and reveal an expanding phenotypic spectrum associated with DNM1L variants. This report highlights the necessity of next generation sequencing for early diagnosis of patients, and that further clinical phenotypic and genotypic analysis may help to improve the understanding of DNM1L-related diseases.
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Affiliation(s)
- Zhenkun Zhang
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Xiaofan Bie
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Zhehui Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Jing Liu
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Zhenhua Xie
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Xian Li
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Mengjun Xiao
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Qiang Zhang
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Yaodong Zhang
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China.
| | - Dongxiao Li
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Children's Neurodevelopment Engineering Research Center, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
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Banerjee R, Mukherjee A, Adhikary A, Sharma S, Hussain MS, Ali ME, Nagotu S. Insights into the role of the conserved GTPase domain residues T62 and S277 in yeast Dnm1. Int J Biol Macromol 2023; 253:127381. [PMID: 37838106 DOI: 10.1016/j.ijbiomac.2023.127381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/10/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
Mitochondrial division is a highly regulated process. The master regulator of this process is the multi-domain, conserved protein called Dnm1 in yeast. In this study, we systematically analyzed two residues, T62 and S277, reported to be putatively phosphorylated in the GTPase domain of the protein. These residues lie in the G2 and G5 motifs of the GTPase domain. Both residues are important for the function of the protein, as evident from in vivo and in vitro analysis of the non-phosphorylatable and phosphomimetic variants. Dnm1T62A/D and Dnm1S277A/D showed differences with respect to the protein localization and puncta dynamics in vivo, albeit both were non-functional as assessed by mitochondrial morphology and GTPase activity. Overall, the secondary structure of the protein variants was unaltered, but local conformational changes were observed. Interestingly, both Dnm1T62A/D and Dnm1S277A/D exhibited dominant-negative behavior when expressed in cells containing endogenous Dnm1. To our knowledge, we report for the first time a single residue (S277) change that does not alter the localization of Dnm1 but makes it non-functional in a dominant-negative manner. Intriguingly, the two residues analyzed in this study are present in the same domain but exhibit variable effects when mutated to alanine or aspartic acid.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Agradeep Mukherjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ankita Adhikary
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shikha Sharma
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Nolden KA, Harwig MC, Hill RB. Human Fis1 directly interacts with Drp1 in an evolutionarily conserved manner to promote mitochondrial fission. J Biol Chem 2023; 299:105380. [PMID: 37866629 PMCID: PMC10694664 DOI: 10.1016/j.jbc.2023.105380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/30/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
Mitochondrial fission protein 1 (Fis1) and dynamin-related protein 1 (Drp1) are the only two proteins evolutionarily conserved for mitochondrial fission, and directly interact in Saccharomyces cerevisiae to facilitate membrane scission. However, it remains unclear if a direct interaction is conserved in higher eukaryotes as other Drp1 recruiters, not present in yeast, are known. Using NMR, differential scanning fluorimetry, and microscale thermophoresis, we determined that human Fis1 directly interacts with human Drp1 (KD = 12-68 μM), and appears to prevent Drp1 assembly, but not GTP hydrolysis. Similar to yeast, the Fis1-Drp1 interaction appears governed by two structural features of Fis1: its N-terminal arm and a conserved surface. Alanine scanning mutagenesis of the arm identified both loss-of-function and gain-of-function alleles with mitochondrial morphologies ranging from highly elongated (N6A) to highly fragmented (E7A), demonstrating a profound ability of Fis1 to govern morphology in human cells. An integrated analysis identified a conserved Fis1 residue, Y76, that upon substitution to alanine, but not phenylalanine, also caused highly fragmented mitochondria. The similar phenotypic effects of the E7A and Y76A substitutions, along with NMR data, support that intramolecular interactions occur between the arm and a conserved surface on Fis1 to promote Drp1-mediated fission as in S. cerevisiae. These findings indicate that some aspects of Drp1-mediated fission in humans derive from direct Fis1-Drp1 interactions that are conserved across eukaryotes.
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Affiliation(s)
- Kelsey A Nolden
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Megan C Harwig
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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7
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Na SB, Seo BJ, Hong TK, Oh SY, Hong YJ, Song JH, Uhm SJ, Hong K, Do JT. Altered Mitochondrial Function and Accelerated Aging Phenotype in Neural Stem Cells Derived from Dnm1l Knockout Embryonic Stem Cells. Int J Mol Sci 2023; 24:14291. [PMID: 37762596 PMCID: PMC10532274 DOI: 10.3390/ijms241814291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Mitochondria are crucial for cellular energy metabolism and are involved in signaling, aging, and cell death. They undergo dynamic changes through fusion and fission to adapt to different cellular states. In this study, we investigated the effect of knocking out the dynamin 1-like protein (Dnm1l) gene, a key regulator of mitochondrial fission, in neural stem cells (NSCs) differentiated from Dnm1l knockout embryonic stem cells (Dnm1l-/- ESCs). Dnm1l-/- ESC-derived NSCs (Dnm1l-/- NSCs) exhibited similar morphology and NSC marker expression (Sox2, Nestin, and Pax6) to brain-derived NSCs, but lower Nestin and Pax6 expression than both wild-type ESC-derived NSCs (WT-NSCs) and brain-derived NSCs. In addition, compared with WT-NSCs, Dnm1l-/- NSCs exhibited distinct mitochondrial morphology and function, contained more elongated mitochondria, showed reduced mitochondrial respiratory capacity, and showed a metabolic shift toward glycolysis for ATP production. Notably, Dnm1l-/- NSCs exhibited impaired self-renewal ability and accelerated cellular aging during prolonged culture, resulting in decreased proliferation and cell death. Furthermore, Dnm1l-/- NSCs showed elevated levels of inflammation and cell stress markers, suggesting a connection between Dnm1l deficiency and premature aging in NSCs. Therefore, the compromised self-renewal ability and accelerated cellular aging of Dnm1l-/- NSCs may be attributed to mitochondrial fission defects.
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Affiliation(s)
- Seung-Bin Na
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.-B.N.); (B.-J.S.); (T.-K.H.); (S.-Y.O.); (Y.-J.H.); (J.-H.S.); (K.H.)
| | - Bong-Jong Seo
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.-B.N.); (B.-J.S.); (T.-K.H.); (S.-Y.O.); (Y.-J.H.); (J.-H.S.); (K.H.)
| | - Tae-Kyung Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.-B.N.); (B.-J.S.); (T.-K.H.); (S.-Y.O.); (Y.-J.H.); (J.-H.S.); (K.H.)
| | - Seung-Yeon Oh
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.-B.N.); (B.-J.S.); (T.-K.H.); (S.-Y.O.); (Y.-J.H.); (J.-H.S.); (K.H.)
| | - Yean-Ju Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.-B.N.); (B.-J.S.); (T.-K.H.); (S.-Y.O.); (Y.-J.H.); (J.-H.S.); (K.H.)
| | - Jae-Hoon Song
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.-B.N.); (B.-J.S.); (T.-K.H.); (S.-Y.O.); (Y.-J.H.); (J.-H.S.); (K.H.)
| | - Sang-Jun Uhm
- Department of Animal Science, Sangji University, Wonju 26339, Republic of Korea;
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.-B.N.); (B.-J.S.); (T.-K.H.); (S.-Y.O.); (Y.-J.H.); (J.-H.S.); (K.H.)
| | - Jeong-Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.-B.N.); (B.-J.S.); (T.-K.H.); (S.-Y.O.); (Y.-J.H.); (J.-H.S.); (K.H.)
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8
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Bauer BL, Rochon K, Liu JC, Ramachandran R, Mears JA. Disease-associated mutations in Drp1 have fundamentally different effects on the mitochondrial fission machinery. Hum Mol Genet 2023; 32:1975-1987. [PMID: 36795043 PMCID: PMC10244223 DOI: 10.1093/hmg/ddad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Patient mutations have been identified throughout dynamin-related protein 1 (Drp1), the key protein mediator of mitochondrial fission. These changes generally impact young children and often result in severe neurological defects and, in some instances, death. Until now, the underlying functional defect leading to patient phenotypes has been largely speculative. We therefore analyzed six disease-associated mutations throughout the GTPase and middle domains (MD) of Drp1. The MD plays a role in Drp1 oligomerization, and three mutations in this region were predictably impaired in self-assembly. However, another mutant in this region (F370C) retained oligomerization capability on pre-curved membranes despite being assembly-limited in solution. Instead, this mutation impaired membrane remodeling of liposomes, which highlights the importance of Drp1 in generating local membrane curvature before fission. Two GTPase domain mutations were also observed in different patients. The G32A mutation was impaired in GTP hydrolysis both in solution and in the presence of lipid but remains capable of self-assembly on these lipid templates. The G223V mutation also exhibited decreased GTPase activity and was able to assemble on pre-curved lipid templates; however, this change impaired membrane remodeling of unilamellar liposomes similar to F370C. This demonstrates that the Drp1 GTPase domain also contributes to self-assembly interactions that drive membrane curvature. Overall, the functional defects caused by mutations in Drp1 are highly variable even for mutations that reside within the same functional domain. This study provides a framework for characterizing additional Drp1 mutations to provide a comprehensive understanding of functional sites within this essential protein.
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Affiliation(s)
- Brianna L Bauer
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jasmine C Liu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44016, USA
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9
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Nolden KA, Harwig MC, Hill RB. Human Fis1 directly interacts with Drp1 in an evolutionarily conserved manner to promote mitochondrial fission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539292. [PMID: 37205551 PMCID: PMC10187221 DOI: 10.1101/2023.05.03.539292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mitochondrial Fission Protein 1 (Fis1) and Dynamin Related Protein 1 (Drp1) are the only two proteins evolutionarily conserved for mitochondrial fission, and directly interact in S. cerevisiae to facilitate membrane scission. However, it remains unclear if a direct interaction is conserved in higher eukaryotes as other Drp1 recruiters, not present in yeast, are known. Using NMR, differential scanning fluorimetry, and microscale thermophoresis, we determined that human Fis1 directly interacts with human Drp1 ( K D = 12-68 µM), and appears to prevent Drp1 assembly, but not GTP hydrolysis. Similar to yeast, the Fis1-Drp1 interaction appears governed by two structural features of Fis1: its N-terminal arm and a conserved surface. Alanine scanning mutagenesis of the arm identified both loss- and gain-of-function alleles with mitochondrial morphologies ranging from highly elongated (N6A) to highly fragmented (E7A) demonstrating a profound ability of Fis1 to govern morphology in human cells. An integrated analysis identified a conserved Fis1 residue, Y76, that upon substitution to alanine, but not phenylalanine, also caused highly fragmented mitochondria. The similar phenotypic effects of the E7A and Y76A substitutions, along with NMR data, support that intramolecular interactions occur between the arm and a conserved surface on Fis1 to promote Drp1-mediated fission as in S. cerevisiae . These findings indicate that some aspects of Drp1-mediated fission in humans derive from direct Fis1-Drp1 interactions that are conserved across eukaryotes.
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10
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Robertson GL, Riffle S, Patel M, Bodnya C, Marshall A, Beasley HK, Garza-Lopez E, Shao J, Vue Z, Hinton A, Stoll MS, de Wet S, Theart RP, Chakrabarty RP, Loos B, Chandel NS, Mears JA, Gama V. DRP1 mutations associated with EMPF1 encephalopathy alter mitochondrial membrane potential and metabolic programs. J Cell Sci 2023; 136:jcs260370. [PMID: 36763487 PMCID: PMC10657212 DOI: 10.1242/jcs.260370] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/22/2022] [Indexed: 02/11/2023] Open
Abstract
Mitochondria and peroxisomes are dynamic signaling organelles that constantly undergo fission, driven by the large GTPase dynamin-related protein 1 (DRP1; encoded by DNM1L). Patients with de novo heterozygous missense mutations in DNM1L present with encephalopathy due to defective mitochondrial and peroxisomal fission (EMPF1) - a devastating neurodevelopmental disease with no effective treatment. To interrogate the mechanisms by which DRP1 mutations cause cellular dysfunction, we used human-derived fibroblasts from patients who present with EMPF1. In addition to elongated mitochondrial morphology and lack of fission, patient cells display lower coupling efficiency, increased proton leak and upregulation of glycolysis. Mitochondrial hyperfusion also results in aberrant cristae structure and hyperpolarized mitochondrial membrane potential. Peroxisomes show a severely elongated morphology in patient cells, which is associated with reduced respiration when cells are reliant on fatty acid oxidation. Metabolomic analyses revealed impaired methionine cycle and synthesis of pyrimidine nucleotides. Our study provides insight into the role of mitochondrial dynamics in cristae maintenance and the metabolic capacity of the cell, as well as the disease mechanism underlying EMPF1.
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Affiliation(s)
| | - Stellan Riffle
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Mira Patel
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Caroline Bodnya
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Andrea Marshall
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Heather K. Beasley
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Edgar Garza-Lopez
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Jianqiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA 52246, USA
| | - Zer Vue
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Antentor Hinton
- Vanderbilt University, Molecular Physiology and Biophysics, Nashville, TN 37232, USA
| | - Maria S. Stoll
- Case Western Reserve University, Department of Pharmacology and Center for Mitochondrial Diseases, Cleveland, OH 44106, USA
| | - Sholto de Wet
- Stellenbosch University, Department of Physiological Sciences, Matieland, 7602, Stellenbosch, South Africa
| | - Rensu P. Theart
- Stellenbosch University, Department of Electrical and Electronic Engineering, Matieland, 7602, Stellenbosch, South Africa
| | - Ram Prosad Chakrabarty
- Northwestern University, Feinberg School of Medicine Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
| | - Ben Loos
- Stellenbosch University, Department of Electrical and Electronic Engineering, Matieland, 7602, Stellenbosch, South Africa
| | - Navdeep S. Chandel
- Northwestern University, Feinberg School of Medicine Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
- Northwestern University, Feinberg School of Medicine Department of Biochemistry and Molecular Genetics, Chicago, IL 60611, USA
| | - Jason A. Mears
- Case Western Reserve University, Department of Pharmacology and Center for Mitochondrial Diseases, Cleveland, OH 44106, USA
| | - Vivian Gama
- Vanderbilt University, Cell and Developmental Biology, Nashville, TN 37232, USA
- Vanderbilt University, Vanderbilt Center for Stem Cell Biology, Nashville, TN 37232, USA
- Vanderbilt University, Vanderbilt Brain Institute, Nashville, TN 37232, USA
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11
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Collier JJ, Oláhová M, McWilliams TG, Taylor RW. Mitochondrial signalling and homeostasis: from cell biology to neurological disease. Trends Neurosci 2023; 46:137-152. [PMID: 36635110 DOI: 10.1016/j.tins.2022.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023]
Abstract
Efforts to understand how mitochondrial dysfunction contributes to neurodegeneration have primarily focussed on the role of mitochondria in neuronal energy metabolism. However, progress in understanding the etiological nature of emerging mitochondrial functions has yielded new ideas about the mitochondrial basis of neurological disease. Studies aimed at deciphering how mitochondria signal through interorganellar contacts, vesicular trafficking, and metabolic transmission have revealed that mitochondrial regulation of immunometabolism, cell death, organelle dynamics, and neuroimmune interplay are critical determinants of neural health. Moreover, the homeostatic mechanisms that exist to protect mitochondrial health through turnover via nanoscale proteostasis and lysosomal degradation have become integrated within mitochondrial signalling pathways to support metabolic plasticity and stress responses in the nervous system. This review highlights how these distinct mitochondrial pathways converge to influence neurological health and contribute to disease pathology.
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Affiliation(s)
- Jack J Collier
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Thomas G McWilliams
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders of Adults and Children, Newcastle University, Newcastle upon Tyne, UK.
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