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Padalko V, Posnik F, Adamczyk M. Mitochondrial Aconitase and Its Contribution to the Pathogenesis of Neurodegenerative Diseases. Int J Mol Sci 2024; 25:9950. [PMID: 39337438 PMCID: PMC11431987 DOI: 10.3390/ijms25189950] [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: 08/06/2024] [Revised: 08/31/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
This survey reviews modern ideas on the structure and functions of mitochondrial and cytosolic aconitase isoenzymes in eukaryotes. Cumulative experimental evidence about mitochondrial aconitases (Aco2) as one of the main targets of reactive oxygen and nitrogen species is generalized. The important role of Aco2 in maintenance of homeostasis of the intracellular iron pool and maintenance of the mitochondrial DNA is discussed. The role of Aco2 in the pathogenesis of some neurodegenerative diseases is highlighted. Inactivation or dysfunction of Aco2 as well as mutations found in the ACO2 gene appear to be significant factors in the development and promotion of various types of neurodegenerative diseases. A restoration of efficient mitochondrial functioning as a source of energy for the cell by targeting Aco2 seems to be one of the promising therapeutic directions to minimize progressive neurodegenerative disorders.
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Affiliation(s)
- Volodymyr Padalko
- Laboratory of Systems and Synthetic Biology, Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
- School of Medicine, V. N. Karazin Kharkiv National University, 61022 Kharkiv, Ukraine
| | - Filip Posnik
- Laboratory of Systems and Synthetic Biology, Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Malgorzata Adamczyk
- Laboratory of Systems and Synthetic Biology, Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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2
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Jain S, Narwal M, Omair Anwar M, Prakash N, Mohmmed A. Unravelling the anti-apoptotic role of Plasmodium falciparum Prohibitin-2 (PfPhb2) in maintaining mitochondrial homeostasis. Mitochondrion 2024:101956. [PMID: 39245193 DOI: 10.1016/j.mito.2024.101956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/16/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
The functional mitochondrion is vital for the propagation of the malaria parasite in the human host. Members of the SPFH protein family, Prohibitins (PHBs), are known to play crucial roles in maintaining mitochondrial homeostasis and cellular functions. Here, we have functionally characterized the homologue of the Plasmodium falciparumProhibitin-2 (PfPhb2) protein. A transgenic parasite line, generated using the selection-linked integration (SLI) strategy for C-terminal tagging, was utilized for cellular localization as well as for inducible knock-down of PfPhb2. We show that PfPhb2 localizes in the parasite mitochondrion during the asexual life cycle. Inducible knock-down of PfPhb2 by GlmS ribozyme caused no significant effect on the growth and multiplication of parasites. However, depletion of PfPhb2 under mitochondrial-specific stress conditions, induced by inhibiting the essential mitochondrial AAA-protease, ClpQ protease, results in enhanced inhibition of parasite growth, mitochondrial ROS production, mitochondrial membrane potential loss and led to mitochondrial fission/fragmentation, ultimately culminating in apoptosis-like cell-death. Further, PfPhb2 depletion renders the parasites more susceptible to mitochondrial targeting drug proguanil. These data suggest the functional involvement of PfPhb2 along with ClpQ protease in stabilization of various mitochondrial proteins to maintain mitochondrial homeostasis and functioning. Overall, we show that PfPhb2 has an anti-apoptotic role in maintaining mitochondrial homeostasis in the parasite.
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Affiliation(s)
- Shilpi Jain
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Monika Narwal
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Md Omair Anwar
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Neha Prakash
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Asif Mohmmed
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India.
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3
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Chowdhury A, Witte S, Aich A. Role of Mitochondrial Nucleic Acid Sensing Pathways in Health and Patho-Physiology. Front Cell Dev Biol 2022; 10:796066. [PMID: 35223833 PMCID: PMC8873532 DOI: 10.3389/fcell.2022.796066] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/14/2022] [Indexed: 12/23/2022] Open
Abstract
Mitochondria, in symbiosis with the host cell, carry out a wide variety of functions from generating energy, regulating the metabolic processes, cell death to inflammation. The most prominent function of mitochondria relies on the oxidative phosphorylation (OXPHOS) system. OXPHOS heavily influences the mitochondrial-nuclear communication through a plethora of interconnected signaling pathways. Additionally, owing to the bacterial ancestry, mitochondria also harbor a large number of Damage Associated Molecular Patterns (DAMPs). These molecules relay the information about the state of the mitochondrial health and dysfunction to the innate immune system. Consequently, depending on the intracellular or extracellular nature of detection, different inflammatory pathways are elicited. One group of DAMPs, the mitochondrial nucleic acids, hijack the antiviral DNA or RNA sensing mechanisms such as the cGAS/STING and RIG-1/MAVS pathways. A pro-inflammatory response is invoked by these signals predominantly through type I interferon (T1-IFN) cytokines. This affects a wide range of organ systems which exhibit clinical presentations of auto-immune disorders. Interestingly, tumor cells too, have devised ingenious ways to use the mitochondrial DNA mediated cGAS-STING-IRF3 response to promote neoplastic transformations and develop tumor micro-environments. Thus, mitochondrial nucleic acid-sensing pathways are fundamental in understanding the source and nature of disease initiation and development. Apart from the pathological interest, recent studies also attempt to delineate the structural considerations for the release of nucleic acids across the mitochondrial membranes. Hence, this review presents a comprehensive overview of the different aspects of mitochondrial nucleic acid-sensing. It attempts to summarize the nature of the molecular patterns involved, their release and recognition in the cytoplasm and signaling. Finally, a major emphasis is given to elaborate the resulting patho-physiologies.
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Affiliation(s)
- Arpita Chowdhury
- Department of Cellular Biochemistry, University Medical Center, Göttingen, Germany
| | - Steffen Witte
- Department of Cellular Biochemistry, University Medical Center, Göttingen, Germany
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Center, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging, from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
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4
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Human Mitochondrial RNA Processing and Modifications: Overview. Int J Mol Sci 2021; 22:ijms22157999. [PMID: 34360765 PMCID: PMC8348895 DOI: 10.3390/ijms22157999] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 01/29/2023] Open
Abstract
Mitochondria, often referred to as the powerhouses of cells, are vital organelles that are present in almost all eukaryotic organisms, including humans. They are the key energy suppliers as the site of adenosine triphosphate production, and are involved in apoptosis, calcium homeostasis, and regulation of the innate immune response. Abnormalities occurring in mitochondria, such as mitochondrial DNA (mtDNA) mutations and disturbances at any stage of mitochondrial RNA (mtRNA) processing and translation, usually lead to severe mitochondrial diseases. A fundamental line of investigation is to understand the processes that occur in these organelles and their physiological consequences. Despite substantial progress that has been made in the field of mtRNA processing and its regulation, many unknowns and controversies remain. The present review discusses the current state of knowledge of RNA processing in human mitochondria and sheds some light on the unresolved issues.
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Phadwal K, Vrahnas C, Ganley IG, MacRae VE. Mitochondrial Dysfunction: Cause or Consequence of Vascular Calcification? Front Cell Dev Biol 2021; 9:611922. [PMID: 33816463 PMCID: PMC8010668 DOI: 10.3389/fcell.2021.611922] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/04/2021] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are crucial bioenergetics powerhouses and biosynthetic hubs within cells, which can generate and sequester toxic reactive oxygen species (ROS) in response to oxidative stress. Oxidative stress-stimulated ROS production results in ATP depletion and the opening of mitochondrial permeability transition pores, leading to mitochondria dysfunction and cellular apoptosis. Mitochondrial loss of function is also a key driver in the acquisition of a senescence-associated secretory phenotype that drives senescent cells into a pro-inflammatory state. Maintaining mitochondrial homeostasis is crucial for retaining the contractile phenotype of the vascular smooth muscle cells (VSMCs), the most prominent cells of the vasculature. Loss of this contractile phenotype is associated with the loss of mitochondrial function and a metabolic shift to glycolysis. Emerging evidence suggests that mitochondrial dysfunction may play a direct role in vascular calcification and the underlying pathologies including (1) impairment of mitochondrial function by mineral dysregulation i.e., calcium and phosphate overload in patients with end-stage renal disease and (2) presence of increased ROS in patients with calcific aortic valve disease, atherosclerosis, type-II diabetes and chronic kidney disease. In this review, we discuss the cause and consequence of mitochondrial dysfunction in vascular calcification and underlying pathologies; the role of autophagy and mitophagy pathways in preventing mitochondrial dysfunction during vascular calcification and finally we discuss mitochondrial ROS, DRP1, and HIF-1 as potential novel markers and therapeutic targets for maintaining mitochondrial homeostasis in vascular calcification.
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Affiliation(s)
- Kanchan Phadwal
- Functional Genetics and Development Division, The Roslin Institute and The Royal (Dick) School of Veterinary Studies (R(D)SVS), University of Edinburgh, Midlothian, United Kingdom
| | - Christina Vrahnas
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, University of Dundee, Dundee, United Kingdom
| | - Ian G. Ganley
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, University of Dundee, Dundee, United Kingdom
| | - Vicky E. MacRae
- Functional Genetics and Development Division, The Roslin Institute and The Royal (Dick) School of Veterinary Studies (R(D)SVS), University of Edinburgh, Midlothian, United Kingdom
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Ishikawa K, Nakada K. Attempts to understand the mechanisms of mitochondrial diseases: The reverse genetics of mouse models for mitochondrial disease. Biochim Biophys Acta Gen Subj 2020; 1865:129835. [PMID: 33358867 DOI: 10.1016/j.bbagen.2020.129835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/25/2020] [Accepted: 12/18/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mitochondrial disease is a general term for a disease caused by a decline in mitochondrial function. The pathology of this disease is extremely diverse and complex, and the mechanism of its pathogenesis is still unknown. Using mouse models that develop the disease via the same processes as in humans is the easiest path to understanding the underlying mechanism. However, creating a mouse model is extremely difficult due to the lack of technologies that enable editing of mitochondrial DNA (mtDNA). SCOPE OF REVIEW This paper outlines the complex pathogenesis of mitochondrial disease, and the difficulties in producing relevant mouse models. Then, the paper provides a detailed discussion on several mice created with mutations in mtDNA. The paper also introduces the pathology of mouse models with mutations including knockouts of nuclear genes that directly affect mitochondrial function. MAJOR CONCLUSIONS Several mice with mtDNA mutations and those with nuclear DNA mutations have been established. Although these models help elucidate the pathological mechanism of mitochondrial disease, they lack sufficient diversity to enable a complete understanding. Considering the variety of factors that affect the cause and mechanism of mitochondrial disease, it is necessary to account for this background diversity in mouse models as well. GENERAL SIGNIFICANCE Mouse models are indispensable for understanding the pathological mechanism of mitochondrial disease, as well as for searching new treatments. There is a need for the creation and examination of mouse models with more diverse mutations and altered nuclear backgrounds and breeding environments.
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Affiliation(s)
- Kaori Ishikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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7
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Ould Amer Y, Hebert-Chatelain E. Insight into the Interactome of Intramitochondrial PKA Using Biotinylation-Proximity Labeling. Int J Mol Sci 2020; 21:ijms21218283. [PMID: 33167377 PMCID: PMC7663848 DOI: 10.3390/ijms21218283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are fully integrated in cell signaling. Reversible phosphorylation is involved in adjusting mitochondrial physiology to the cellular needs. Protein kinase A (PKA) phosphorylates several substrates present at the external surface of mitochondria to maintain cellular homeostasis. However, few targets of PKA located inside the organelle are known. The aim of this work was to characterize the impact and the interactome of PKA located inside mitochondria. Our results show that the overexpression of intramitochondrial PKA decreases cellular respiration and increases superoxide levels. Using proximity-dependent biotinylation, followed by LC-MS/MS analysis and in silico phospho-site prediction, we identified 21 mitochondrial proteins potentially targeted by PKA. We confirmed the interaction of PKA with TIM44 using coimmunoprecipitation and observed that TIM44-S80 is a key residue for the interaction between the protein and the kinase. These findings provide insights into the interactome of intramitochondrial PKA and suggest new potential mechanisms in the regulation of mitochondrial functions.
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Affiliation(s)
- Yasmine Ould Amer
- Department of Biology, University of Moncton, Moncton, NB E1A 3E9, Canada;
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, University of Moncton, Moncton, NB E1A 3E9, Canada
| | - Etienne Hebert-Chatelain
- Department of Biology, University of Moncton, Moncton, NB E1A 3E9, Canada;
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, University of Moncton, Moncton, NB E1A 3E9, Canada
- Correspondence:
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8
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González de Cózar JM, Carretero-Junquera M, Ciesielski GL, Miettinen SM, Varjosalo M, Kaguni LS, Dufour E, Jacobs HT. A second hybrid-binding domain modulates the activity of Drosophila ribonuclease H1. J Biochem 2020; 168:515-533. [PMID: 32589740 PMCID: PMC7657459 DOI: 10.1093/jb/mvaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/15/2020] [Indexed: 11/14/2022] Open
Abstract
In eukaryotes, ribonuclease H1 (RNase H1) is involved in the processing and removal of RNA/DNA hybrids in both nuclear and mitochondrial DNA. The enzyme comprises a C-terminal catalytic domain and an N-terminal hybrid-binding domain (HBD), separated by a linker of variable length, 115 amino acids in Drosophila melanogaster (Dm). Molecular modelling predicted this extended linker to fold into a structure similar to the conserved HBD. Based on a deletion series, both the catalytic domain and the conserved HBD were required for high-affinity binding to heteroduplex substrates, while loss of the novel HBD led to an ∼90% drop in Kcat with a decreased KM, and a large increase in the stability of the RNA/DNA hybrid-enzyme complex, supporting a bipartite-binding model in which the second HBD facilitates processivity. Shotgun proteomics following in vivo cross-linking identified single-stranded DNA-binding proteins from both nuclear and mitochondrial compartments, respectively RpA-70 and mtSSB, as prominent interaction partners of Dm RNase H1. However, we were not able to document direct and stable interactions with mtSSB when the proteins were co-overexpressed in S2 cells, and functional interactions between them in vitro were minor.
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Affiliation(s)
| | | | - Grzegorz L Ciesielski
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - Sini M Miettinen
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Laurie S Kaguni
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Eric Dufour
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
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9
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Vozáriková V, Kunová N, Bauer JA, Frankovský J, Kotrasová V, Procházková K, Džugasová V, Kutejová E, Pevala V, Nosek J, Tomáška Ľ. Mitochondrial HMG-Box Containing Proteins: From Biochemical Properties to the Roles in Human Diseases. Biomolecules 2020; 10:biom10081193. [PMID: 32824374 PMCID: PMC7463775 DOI: 10.3390/biom10081193] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules are packaged into compact nucleo-protein structures called mitochondrial nucleoids (mt-nucleoids). Their compaction is mediated in part by high-mobility group (HMG)-box containing proteins (mtHMG proteins), whose additional roles include the protection of mtDNA against damage, the regulation of gene expression and the segregation of mtDNA into daughter organelles. The molecular mechanisms underlying these functions have been identified through extensive biochemical, genetic, and structural studies, particularly on yeast (Abf2) and mammalian mitochondrial transcription factor A (TFAM) mtHMG proteins. The aim of this paper is to provide a comprehensive overview of the biochemical properties of mtHMG proteins, the structural basis of their interaction with DNA, their roles in various mtDNA transactions, and the evolutionary trajectories leading to their rapid diversification. We also describe how defects in the maintenance of mtDNA in cells with dysfunctional mtHMG proteins lead to different pathologies at the cellular and organismal level.
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Affiliation(s)
- Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Ján Frankovský
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Katarína Procházková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Vladimíra Džugasová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina CH-1, 842 15 Bratislava, Slovakia;
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
- Correspondence: ; Tel.: +421-2-90149-433
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10
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Signal transducer and activator of transcription 5a (STAT5a) represses mitochondrial gene expression through direct binding to mitochondrial DNA. Biochem Biophys Res Commun 2020; 527:974-978. [PMID: 32446558 DOI: 10.1016/j.bbrc.2020.04.152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/23/2022]
Abstract
Signal transducer and activator of transcription (STAT) proteins are latent cytoplasmic transcription factors essential for cytokine signaling. Our previous study showed that interleukin-3 (IL-3) induced STAT5 translocation to mitochondria and binding to mitochondrial DNA (mtDNA) in vitro. In this report, we further demonstrated in vivo binding of endogenous STAT5a to mtDNA transcriptional control region and reduced gene expression from all three mtDNA promoters after IL-3 stimulation. To specifically define the function of mitochondrial STAT5a, we generated mitochondrial-targeting wild-type and mutant STAT5a proteins. Compared with non-targeting STAT5a, mitochondrial-targeting wild-type STAT5a significantly reduced mitochondrial gene expression in transfected HEK293 cells. The level of attenuation was amplified in cells expressing constitutively active STAT5a, but abrogated in cells expressing DNA-binding-defective STAT5a. STAT5a-mediated repression of mtDNA expression also positively correlated with STAT5a binding to the E2 subunit of pyruvate dehydrogenase complex (PDC-E2), both a gate-keeping metabolic enzyme and a component of mtDNA nucleoid in mitochondrial matrix. Metabolic shift away from mitochondrial respiration is known in many cytokine-stimulated cells and cancer cells. STAT5a-mediated repression of mitochondrial gene expression and its interaction with PDC-E2 may provide important insights into its underlying mechanisms.
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11
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LETM1: Essential for Mitochondrial Biology and Cation Homeostasis? Trends Biochem Sci 2019; 44:648-658. [DOI: 10.1016/j.tibs.2019.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 02/28/2019] [Accepted: 04/03/2019] [Indexed: 12/28/2022]
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12
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Durigon R, Mitchell AL, Jones AW, Manole A, Mennuni M, Hirst EM, Houlden H, Maragni G, Lattante S, Doronzio PN, Dalla Rosa I, Zollino M, Holt IJ, Spinazzola A. LETM1 couples mitochondrial DNA metabolism and nutrient preference. EMBO Mol Med 2019; 10:emmm.201708550. [PMID: 30012579 PMCID: PMC6127893 DOI: 10.15252/emmm.201708550] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The diverse clinical phenotypes of Wolf–Hirschhorn syndrome (WHS) are the result of haploinsufficiency of several genes, one of which, LETM1, encodes a protein of the mitochondrial inner membrane of uncertain function. Here, we show that LETM1 is associated with mitochondrial ribosomes, is required for mitochondrial DNA distribution and expression, and regulates the activity of an ancillary metabolic enzyme, pyruvate dehydrogenase. LETM1 deficiency in WHS alters mitochondrial morphology and DNA organization, as does substituting ketone bodies for glucose in control cells. While this change in nutrient availability leads to the death of fibroblasts with normal amounts of LETM1, WHS‐derived fibroblasts survive on ketone bodies, which can be attributed to their reduced dependence on glucose oxidation. Thus, remodeling of mitochondrial nucleoprotein complexes results from the inability of mitochondria to use specific substrates for energy production and is indicative of mitochondrial dysfunction. However, the dysfunction could be mitigated by a modified diet—for WHS, one high in lipids and low in carbohydrates.
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Affiliation(s)
- Romina Durigon
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Alice L Mitchell
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Aleck We Jones
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Andreea Manole
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Mara Mennuni
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Henry Houlden
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Serena Lattante
- Institute of Genomic Medicine, Catholic University, Rome, Italy
| | | | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Ian J Holt
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK.,Biodonostia Health Research Institute, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK .,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
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13
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Dostal V, Churchill MEA. Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:598-607. [PMID: 30807854 PMCID: PMC7806247 DOI: 10.1016/j.bbagrm.2019.01.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
In eukaryotes, cytosine methylation of nuclear DNA at CpG sequences (5mCpG) regulates epigenetic inheritance through alterations in chromatin structure. However, mitochondria lack nucleosomal chromatin, therefore the molecular mechanisms by which 5mCpG influences mitochondria must be different and are as yet unknown. Mitochondrial Transcription Factor A (TFAM) is both the primary DNA-compacting protein in the mitochondrial DNA (mtDNA) nucleoid and a transcription-initiation factor. TFAM must encounter hundreds of CpGs in mtDNA, so the occurrence of 5mCpG has the potential to impact TFAM-DNA recognition. We used biophysical approaches to determine whether 5mCpG alters any TFAM-dependent activities. 5mCpG in the heavy strand promoter (HSP1) increased the binding affinity of TFAM and induced TFAM multimerization with increased cooperativity compared to nonmethylated DNA. However, 5mCpG had no apparent effect on TFAM-dependent DNA compaction. Additionally, 5mCpG had a clear and context-dependent effect on transcription initiating from the three mitochondrial promoters. Taken together, our findings demonstrate that 5mCpG in the mitochondrial promoter region does impact TFAM-dependent activities in vitro.
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Affiliation(s)
- Vishantie Dostal
- Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mair E A Churchill
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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14
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Ultrastructure and dynamics of the actin-myosin II cytoskeleton during mitochondrial fission. Nat Cell Biol 2019; 21:603-613. [PMID: 30988424 PMCID: PMC6499663 DOI: 10.1038/s41556-019-0313-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/14/2019] [Indexed: 02/05/2023]
Abstract
Mitochondrial fission involves the preconstriction of an organelle followed by scission by dynamin-related protein Drp1. Preconstriction is facilitated by actin and non-muscle myosin II through a mechanism that remains unclear, largely due to the unknown cytoskeletal ultrastructure at mitochondrial constrictions. Here, using platinum replica electron microscopy, we show that mitochondria in cells are embedded in an interstitial cytoskeletal network that contains abundant unbranched actin filaments. Both spontaneous and induced mitochondrial constrictions typically associate with a criss-cross array of long actin filaments that comprise part of this interstitial network. Non-muscle myosin II is found adjacent to mitochondria but is not specifically enriched at the constriction sites. During ionomycin-induced mitochondrial fission, F-actin clouds colocalize with mitochondrial constriction sites, whereas dynamic myosin II clouds are present in the vicinity of constrictions. We propose that myosin II promotes mitochondrial constriction by inducing stochastic deformations of the interstitial actin network, which applies pressure on the mitochondrial surface and thus initiates curvature-sensing mechanisms that complete mitochondrial constriction.
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15
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Hernando-Rodríguez B, Artal-Sanz M. Mitochondrial Quality Control Mechanisms and the PHB (Prohibitin) Complex. Cells 2018; 7:cells7120238. [PMID: 30501123 PMCID: PMC6315423 DOI: 10.3390/cells7120238] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial functions are essential for life, critical for development, maintenance of stem cells, adaptation to physiological changes, responses to stress, and aging. The complexity of mitochondrial biogenesis requires coordinated nuclear and mitochondrial gene expression, owing to the need of stoichiometrically assemble the oxidative phosphorylation (OXPHOS) system for ATP production. It requires, in addition, the import of a large number of proteins from the cytosol to keep optimal mitochondrial function and metabolism. Moreover, mitochondria require lipid supply for membrane biogenesis, while it is itself essential for the synthesis of membrane lipids. To achieve mitochondrial homeostasis, multiple mechanisms of quality control have evolved to ensure that mitochondrial function meets cell, tissue, and organismal demands. Herein, we give an overview of mitochondrial mechanisms that are activated in response to stress, including mitochondrial dynamics, mitophagy and the mitochondrial unfolded protein response (UPRmt). We then discuss the role of these stress responses in aging, with particular focus on Caenorhabditis elegans. Finally, we review observations that point to the mitochondrial prohibitin (PHB) complex as a key player in mitochondrial homeostasis, being essential for mitochondrial biogenesis and degradation, and responding to mitochondrial stress. Understanding how mitochondria responds to stress and how such responses are regulated is pivotal to combat aging and disease.
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Affiliation(s)
- Blanca Hernando-Rodríguez
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, 41013 Seville, Spain.
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain.
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, 41013 Seville, Spain.
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain.
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16
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Human mitochondrial degradosome prevents harmful mitochondrial R loops and mitochondrial genome instability. Proc Natl Acad Sci U S A 2018; 115:11024-11029. [PMID: 30301808 DOI: 10.1073/pnas.1807258115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
R loops are nucleic acid structures comprising an DNA-RNA hybrid and a displaced single-stranded DNA. These structures may occur transiently during transcription, playing essential biological functions. However, persistent R loops may become pathological as they are important drivers of genome instability and have been associated with human diseases. The mitochondrial degradosome is a functionally conserved complex from bacteria to human mitochondria. It is composed of the ATP-dependent RNA and DNA helicase SUV3 and the PNPase ribonuclease, playing a central role in mitochondrial RNA surveillance and degradation. Here we describe a new role for the mitochondrial degradosome in preventing the accumulation of pathological R loops in the mitochondrial DNA, in addition to preventing dsRNA accumulation. Our data indicate that, similar to the molecular mechanisms acting in the nucleus, RNA surveillance mechanisms in the mitochondria are crucial to maintain its genome integrity by counteracting pathological R-loop accumulation.
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17
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Huangyang P, Simon MC. Hidden features: exploring the non-canonical functions of metabolic enzymes. Dis Model Mech 2018; 11:11/8/dmm033365. [PMID: 29991493 PMCID: PMC6124551 DOI: 10.1242/dmm.033365] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The study of cellular metabolism has been rigorously revisited over the past decade, especially in the field of cancer research, revealing new insights that expand our understanding of malignancy. Among these insights is the discovery that various metabolic enzymes have surprising activities outside of their established metabolic roles, including in the regulation of gene expression, DNA damage repair, cell cycle progression and apoptosis. Many of these newly identified functions are activated in response to growth factor signaling, nutrient and oxygen availability, and external stress. As such, multifaceted enzymes directly link metabolism to gene transcription and diverse physiological and pathological processes to maintain cell homeostasis. In this Review, we summarize the current understanding of non-canonical functions of multifaceted metabolic enzymes in disease settings, especially cancer, and discuss specific circumstances in which they are employed. We also highlight the important role of subcellular localization in activating these novel functions. Understanding their non-canonical properties should enhance the development of new therapeutic strategies for cancer treatment. Summary: This Review summarizes recent findings about multifaceted metabolic enzymes with non-canonical activities outside their core biochemical functions, and how they may provide new therapeutic strategies for cancers.
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Affiliation(s)
- Peiwei Huangyang
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Departments of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA .,Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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18
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COMP-prohibitin 2 interaction maintains mitochondrial homeostasis and controls smooth muscle cell identity. Cell Death Dis 2018; 9:676. [PMID: 29867124 PMCID: PMC5986769 DOI: 10.1038/s41419-018-0703-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/06/2018] [Accepted: 05/14/2018] [Indexed: 12/22/2022]
Abstract
Vascular smooth muscle cells (VSMCs) are highly phenotypically plastic, and loss of the contractile phenotype in VSMCs has been recognized at the early onset of the pathology of a variety of vascular diseases. However, the endogenous regulatory mechanism to maintain contractile phenotype in VSMCs remains elusive. Moreover, little has been known about the role of the mitochondrial bioenergetics in terms of VSMC homeostasis. Herein, we asked if glycoprotein COMP (Cartilage oligomeric matrix protein) is involved in mitochondrial bioenergetics and therefore regulates VSMCs homeostasis. By using fluorescence assay, subcellular western blot and liquid chromatography tandem mass spectrometry analysis, we found that extracellular matrix protein COMP unexpectedly localized within mitochondria. Further mitochondrial transplantation revealed that both mitochondrial and non-mitochondrial COMP maintained VSMC identity. Moreover, microarray analysis revealed that COMP deficiency impaired mitochondrial oxidative phosphorylation in VSMCs. Further study confirmed that COMP deficiency caused mitochondrial oxidative phosphorylation dysfunction accompanied by morphological abnormality. Moreover, the interactome of mitochondrial COMP revealed that COMP interacted with prohibitin 2, and COMP-prohibitin 2 interaction maintained mitochondrial homeostasis. Additionally, disruption of COMP-prohibitin 2 interaction caused VSMC dedifferentiation in vitro and enhanced the neointima formation post rat carotid artery injury in vivo. In conclusion, COMP-prohibitin 2 interaction in mitochondria plays an important role in maintaining the contractile phenotype of VSMCs by regulating mitochondrial oxidative phosphorylation. Maintaining the homeostasis of mitochondrial respiration through COMP-prohibitin 2 interaction may shed light on prevention of vascular disease.
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19
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Yuan G, Chen X, Liu Z, Wei W, Shu Q, Abou-Hamdan H, Jiang L, Li X, Chen R, Désaubry L, Zhou F, Xie D. Flavagline analog FL3 induces cell cycle arrest in urothelial carcinoma cell of the bladder by inhibiting the Akt/PHB interaction to activate the GADD45α pathway. J Exp Clin Cancer Res 2018; 37:21. [PMID: 29415747 PMCID: PMC5804081 DOI: 10.1186/s13046-018-0695-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/31/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Prohibitin 1 (PHB) is a potential target for the treatment of urothelial carcinoma of the bladder (UCB). FL3 is a newly synthesized agent that inhibits cancer cell proliferation by targeting the PHB protein; however, the effect of FL3 in UCB cells remains unexplored. METHODS FL3 was identified to be a potent inhibitor of UCB cell viability using CCK-8 (cell counting kit-8) assay. Then a series of in vitro and in vivo experiments were conducted to further demonstrate the inhibitory effect of FL3 on UCB cell proliferation and to determine the underlying mechanisms. RESULTS FL3 inhibited UCB cell proliferation and growth both in vitro and in vivo. By targeting the PHB protein, FL3 inhibited the interaction of Akt and PHB as well as Akt-mediated PHB phosphorylation, which consequently decreases the localization of PHB in the mitochondria. In addition, FL3 treatment resulted in cell cycle arrest in the G2/M phase, and this inhibitory effect of FL3 could be mimicked by knockdown of PHB. Through the microarray analysis of mRNA expression after FL3 treatment and knockdown of PHB, we found that the mRNA expression of the growth arrest and DNA damage-inducible alpha (GADD45α) gene were significantly upregulated. When knocked down the expression of GADD45α, the inhibitory effect of FL3 on cell cycle was rescued, suggesting that FL3-induced cell cycle inhibition is GADD45α dependent. CONCLUSION Our data provide that FL3 inhibits the interaction of Akt and PHB, which in turn activates the GADD45α-dependent cell cycle inhibition in the G2/M phase.
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Affiliation(s)
- Gangjun Yuan
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xin Chen
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhuowei Liu
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wensu Wei
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qinghai Shu
- School of Material Science and Engineering, Beijing Institute of Technology, Beijing, China
| | - Hussein Abou-Hamdan
- Therapeutic Innovation Laboratory, UMR7200, CNRS/University of Strasbourg, Strasbourg, France
| | - Lijuan Jiang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xiangdong Li
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Rixin Chen
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Laurent Désaubry
- Therapeutic Innovation Laboratory, UMR7200, CNRS/University of Strasbourg, Strasbourg, France.
- Sino-French Joint Lab of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.
| | - Fangjian Zhou
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Dan Xie
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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20
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Nagalakshmi B., Sagarkar S, Sakharkar AJ. Epigenetic Mechanisms of Traumatic Brain Injuries. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:263-298. [DOI: 10.1016/bs.pmbts.2017.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Morin JA, Cerrón F, Jarillo J, Beltran-Heredia E, Ciesielski GL, Arias-Gonzalez JR, Kaguni LS, Cao FJ, Ibarra B. DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein. Nucleic Acids Res 2017; 45:7237-7248. [PMID: 28486639 PMCID: PMC5499585 DOI: 10.1093/nar/gkx395] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/27/2017] [Indexed: 12/02/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions. To study this possibility, we used optical tweezers to determine and compare the structure and energetics of long, individual HmtSSB–DNA complexes assembled on preformed ssDNA and on ssDNA generated gradually during ‘in situ’ DNA synthesis. We show that HmtSSB binds to preformed ssDNA in two major modes, depending on salt and protein concentration. However, when protein binding was coupled to strand-displacement DNA synthesis, only one of the two binding modes was observed under all experimental conditions. Our results reveal a key role for the gradual generation of ssDNA in modulating the binding mode of a multimeric SSB protein and consequently, in generating the appropriate nucleoprotein structure for DNA synthetic reactions required for genome maintenance.
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Affiliation(s)
- José A Morin
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain
| | - Fernando Cerrón
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain
| | - Javier Jarillo
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Elena Beltran-Heredia
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Grzegorz L Ciesielski
- Institute of Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland.,Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) and CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología', 28049 Madrid, Spain
| | - Laurie S Kaguni
- Institute of Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland.,Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - Francisco J Cao
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) and CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología', 28049 Madrid, Spain
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22
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Pawar T, Bjørås M, Klungland A, Eide L. Metabolism and DNA repair shape a specific modification pattern in mitochondrial DNA. Mitochondrion 2017; 40:16-28. [PMID: 28893634 DOI: 10.1016/j.mito.2017.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 11/28/2022]
Abstract
The mitochondrial DNA (mtDNA) resides in the vicinity of energy-rich reactions. Thus, chemical modifications of mtDNA might mirror mitochondrial processes and could serve as biomarkers of metabolic processes in the mitochondria. This hypothesis was tested by assessing modifications at 17 different sites in the mtDNA as a function of cell type, oxidative stress and mitochondrial activity. Two mouse mutants with a metabolic phenotype were compared to wild-type (WT) mice: the ogg1-/- mouse that lacks the 8-oxoguanine DNA glycosylase (OGG1), and the alkbh7-/- mouse missing the ALKBH7 protein that has been implicated in fatty acid oxidation. It was found that cell type, oxidative stress and mitochondrial complex activity shaped distinct modification patterns in mtDNA, and that OGG1 and ALKBH7 independently modulated these modification patterns. The modifications included ribonucleotides, which also accumulated in mtDNA with age. Interestingly, this age-dependent accumulation most likely involves DNA repair, as mtDNA from ogg1-/- mice did not accumulate modifications with age. On the other hand, alkbh7-/- mtDNA accumulated more modifications with age than WT mtDNA. Our results show that mtDNA is dynamically modified with metabolic activity and imply a novel synergy between metabolism and mtDNA repair proteins.
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Affiliation(s)
- Tina Pawar
- Department of Medical Biochemistry, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway; Department of clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway.
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23
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Gao Z, Luo G, Ni B. Progress in mass spectrometry-based proteomic research of tumor hypoxia (Review). Oncol Rep 2017; 38:676-684. [PMID: 28656308 DOI: 10.3892/or.2017.5748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 05/31/2017] [Indexed: 11/06/2022] Open
Abstract
A hypoxic microenvironment effects various signaling pathways in the human body, including those that are critical for normal physiology and those that support tumorigenesis or cancer progression. A hypoxic tumor microenvironment, in particular, modulates cell migration, invasion and resistance to radiotherapy and chemotherapy. Development of the mass spectrometry (MS) technique has allowed for expansion of proteomic study to a wide variety of fields, with the study of tumor hypoxia being among the latest to enjoy its benefits. In such studies, changes in the proteome of tumor tissue or cells induced by the hypoxic conditions are analyzed. A multitude of hypoxic regulatory proteins have already been identified, increasing our understanding of the mechanisms underlying tumor occurrence and development and representing candidate reference markers for tumor diagnosis and therapy. The present review provides the first summary of the collective studies on tumor microenvironment hypoxia that have been completed using MS-based proteomic techniques, providing a systematic discussion of the benefits and current challenges of the various applications.
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Affiliation(s)
- Zhiqi Gao
- Department of Pathophysiology and High Altitude Pathology/Key Laboratory of High Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Gang Luo
- Department of Pathophysiology and High Altitude Pathology/Key Laboratory of High Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Bing Ni
- Department of Pathophysiology and High Altitude Pathology/Key Laboratory of High Altitude Environment Medicine (Third Military Medical University), Ministry of Education/Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P.R. China
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24
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Mitochondrial Nucleoid: Shield and Switch of the Mitochondrial Genome. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:8060949. [PMID: 28680532 PMCID: PMC5478868 DOI: 10.1155/2017/8060949] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/06/2017] [Accepted: 04/03/2017] [Indexed: 11/18/2022]
Abstract
Mitochondria preserve very complex and distinctively unique machinery to maintain and express the content of mitochondrial DNA (mtDNA). Similar to chromosomes, mtDNA is packaged into discrete mtDNA-protein complexes referred to as a nucleoid. In addition to its role as a mtDNA shield, over 50 nucleoid-associated proteins play roles in mtDNA maintenance and gene expression through either temporary or permanent association with mtDNA or other nucleoid-associated proteins. The number of mtDNA(s) contained within a single nucleoid is a fundamental question but remains a somewhat controversial issue. Disturbance in nucleoid components and mutations in mtDNA were identified as significant in various diseases, including carcinogenesis. Significant interest in the nucleoid structure and its regulation has been stimulated in relation to mitochondrial diseases, which encompass diseases in multicellular organisms and are associated with accumulation of numerous mutations in mtDNA. In this review, mitochondrial nucleoid structure, nucleoid-associated proteins, and their regulatory roles in mitochondrial metabolism are briefly addressed to provide an overview of the emerging research field involving mitochondrial biology.
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25
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Abstract
Mitochondrial DNA (mtDNA) in cells is organized in nucleoids containing DNA and various proteins. This review discusses questions of organization and structural dynamics of nucleoids as well as their protein components. The structures of mt-nucleoid from different organisms are compared. The currently accepted model of nucleoid organization is described and questions needing answers for better understanding of the fine mechanisms of the mitochondrial genetic apparatus functioning are discussed.
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Affiliation(s)
- A A Kolesnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
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26
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Single-molecule studies of high-mobility group B architectural DNA bending proteins. Biophys Rev 2016; 9:17-40. [PMID: 28303166 PMCID: PMC5331113 DOI: 10.1007/s12551-016-0236-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/23/2022] Open
Abstract
Protein–DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function. These roles vary from the maintenance of chromatin structure and facilitation of ribosomal RNA transcription (yeast high-mobility group 1 protein) to regulatory and packaging roles (human mitochondrial transcription factor A). We describe how these HMGB proteins bind, bend, bridge, loop and compact DNA to perform these functions. We also describe how single molecule experiments observe multiple rates for dissociation of HMGB proteins from DNA, while only one rate is observed in bulk experiments. The measured single-molecule kinetics reveals a local, microscopic mechanism by which HMGB proteins alter DNA flexibility, along with a second, much slower macroscopic rate that describes the complete dissociation of the protein from DNA.
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27
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Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are fingerprints of epigenetic modifications. These bases have been found in the mitochondrial DNA (mtDNA) and together with the discovery of mitochondrial localization of DNA methyltransferases, this implies that mtDNA is under epigenetic regulation. However, the indirect methods hitherto used to assess mitochondrial 5mC and 5hmC require attention as they readily generate artificial signals that may lead to erroneous conclusions. Here, we demonstrate how three independent, frequently used methods to identify epigenetic modification of DNA readily generate false mtDNA epigenetic signals. The three methods were selective 5mC/5hmC-mediated inhibition of restriction enzymes, bisulfite conversion and 5hmC glucosylation-dependent immunocapture. Adequate controls for all methods are suggested.
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Affiliation(s)
- Tina Pawar
- a Department of Medical Biochemistry , Institute of Clinical Medicine, University of Oslo , Oslo , Norway
| | - Lars Eide
- a Department of Medical Biochemistry , Institute of Clinical Medicine, University of Oslo , Oslo , Norway
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28
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Darbandi S, Darbandi M, Khorshid HRK, Sadeghi MR, Al-Hasani S, Agarwal A, Shirazi A, Heidari M, Akhondi MM. Experimental strategies towards increasing intracellular mitochondrial activity in oocytes: A systematic review. Mitochondrion 2016; 30:8-17. [PMID: 27234976 DOI: 10.1016/j.mito.2016.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 04/04/2016] [Accepted: 05/20/2016] [Indexed: 12/19/2022]
Abstract
PURPOSE The mitochondrial complement is critical in sustaining the earliest stages of life. To improve the Assisted Reproductive Technology (ART), current methods of interest were evaluated for increasing the activity and copy number of mitochondria in the oocyte cell. METHODS This covered the researches from 1966 to September 2015. RESULTS The results provided ten methods that can be studied individually or simultaneously. CONCLUSION Though the use of these techniques generated great concern about heteroplasmy observation in humans, it seems that with study on these suggested methods there is real hope for effective treatments of old oocyte or oocytes containing mitochondrial problems in the near future.
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Affiliation(s)
- Sara Darbandi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
| | - Mahsa Darbandi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
| | | | - Mohammad Reza Sadeghi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
| | - Safaa Al-Hasani
- Reproductive Medicine Unit, University of Schleswig-Holstein, Luebeck, Germany.
| | - Ashok Agarwal
- Center for Reproductive Medicine, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Abolfazl Shirazi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
| | - Mahnaz Heidari
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran. M.@avicenna.ar.ir
| | - Mohammad Mehdi Akhondi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
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Wideman JG, Muñoz-Gómez SA. The evolution of ERMIONE in mitochondrial biogenesis and lipid homeostasis: An evolutionary view from comparative cell biology. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:900-912. [PMID: 26825688 DOI: 10.1016/j.bbalip.2016.01.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 12/17/2022]
Abstract
The ER-mitochondria organizing network (ERMIONE) in Saccharomyces cerevisiae is involved in maintaining mitochondrial morphology and lipid homeostasis. ERMES and MICOS are two scaffolding complexes of ERMIONE that contribute to these processes. ERMES is ancient but has been lost in several lineages including animals, plants, and SAR (stramenopiles, alveolates and rhizaria). On the other hand, MICOS is ancient and has remained present in all organisms bearing mitochondrial cristae. The ERMIONE precursor evolved in the α-proteobacterial ancestor of mitochondria which had the central subunit of MICOS, Mic60. The subsequent evolution of ERMIONE and its interactors in eukaryotes reflects the integrative co-evolution of mitochondria and their hosts and the adaptive paths that some lineages have followed in their specialization to certain environments. By approaching the ERMIONE from a perspective of comparative evolutionary cell biology, we hope to shed light on not only its evolutionary history, but also how ERMIONE components may function in organisms other than S. cerevisiae. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
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Affiliation(s)
| | - Sergio A Muñoz-Gómez
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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30
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Jokinen R, Marttinen P, Stewart JB, Neil Dear T, Battersby BJ. Tissue-specific modulation of mitochondrial DNA segregation by a defect in mitochondrial division. Hum Mol Genet 2015; 25:706-14. [PMID: 26681804 DOI: 10.1093/hmg/ddv508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/08/2015] [Indexed: 01/19/2023] Open
Abstract
Mitochondria are dynamic organelles that divide and fuse by remodeling an outer and inner membrane in response to developmental, physiological and stress stimuli. These events are coordinated by conserved dynamin-related GTPases. The dynamics of mitochondrial morphology require coordination with mitochondrial DNA (mtDNA) to ensure faithful genome transmission, however, this process remains poorly understood. Mitochondrial division is linked to the segregation of mtDNA but how it affects cases of mtDNA heteroplasmy, where two or more mtDNA variants/mutations co-exist in a cell, is unknown. Segregation of heteroplasmic human pathogenic mtDNA mutations is a critical factor in the onset and severity of human mitochondrial diseases. Here, we investigated the coupling of mitochondrial morphology to the transmission and segregation of mtDNA in mammals by taking advantage of two genetically modified mouse models: one with a dominant-negative mutation in the dynamin-related protein 1 (Drp1 or Dnm1l) that impairs mitochondrial fission and the other, heteroplasmic mice segregating two neutral mtDNA haplotypes (BALB and NZB). We show a tissue-specific response to mtDNA segregation from a defect in mitochondrial fission. Only mtDNA segregation in the hematopoietic compartment is modulated from impaired Dnm1l function. In contrast, no effect was observed in other tissues arising from the three germ layers during development and in mtDNA transmission through the female germline. Our data suggest a robust organization of a heteroplasmic mtDNA segregating unit across mammalian cell types that can overcome impaired mitochondrial division to ensure faithful transmission of the mitochondrial genome.
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Affiliation(s)
- Riikka Jokinen
- Research Programs Unit - Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Paula Marttinen
- Research Programs Unit - Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany and
| | - T Neil Dear
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Brendan J Battersby
- Research Programs Unit - Molecular Neurology, University of Helsinki, Helsinki, Finland,
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31
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Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation. Nat Commun 2015; 5:3077. [PMID: 24435062 PMCID: PMC3936014 DOI: 10.1038/ncomms4077] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/06/2013] [Indexed: 12/19/2022] Open
Abstract
TFAM (transcription factor A, mitochondrial) is a DNA-binding protein that activates transcription at the two major promoters of mitochondrial DNA (mtDNA)--the light strand promoter (LSP) and the heavy strand promoter 1 (HSP1). Equally important, it coats and packages the mitochondrial genome. TFAM has been shown to impose a U-turn on LSP DNA; however, whether this distortion is relevant at other sites is unknown. Here we present crystal structures of TFAM bound to HSP1 and to nonspecific DNA. In both, TFAM similarly distorts the DNA into a U-turn. Yet, TFAM binds to HSP1 in the opposite orientation from LSP explaining why transcription from LSP requires DNA bending, whereas transcription at HSP1 does not. Moreover, the crystal structures reveal dimerization of DNA-bound TFAM. This dimerization is dispensable for DNA bending and transcriptional activation but is important in DNA compaction. We propose that TFAM dimerization enhances mitochondrial DNA compaction by promoting looping of the DNA.
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32
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Akhmedov AT, Marín-García J. Mitochondrial DNA maintenance: an appraisal. Mol Cell Biochem 2015; 409:283-305. [DOI: 10.1007/s11010-015-2532-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/06/2015] [Indexed: 12/13/2022]
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33
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Primer removal during mammalian mitochondrial DNA replication. DNA Repair (Amst) 2015; 34:28-38. [PMID: 26303841 DOI: 10.1016/j.dnarep.2015.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 12/17/2022]
Abstract
The small circular mitochondrial genome in mammalian cells is replicated by a dedicated replisome, defects in which can cause mitochondrial disease in humans. A fundamental step in mitochondrial DNA (mtDNA) replication and maintenance is the removal of the RNA primers needed for replication initiation. The nucleases RNase H1, FEN1, DNA2, and MGME1 have been implicated in this process. Here we review the role of these nucleases in the light of primer removal pathways in mitochondria, highlight associations with disease, as well as consider the implications for mtDNA replication initiation.
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34
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Piechota J, Bereza M, Sokołowska A, Suszyński K, Lech K, Jańska H. Unraveling the functions of type II-prohibitins in Arabidopsis mitochondria. PLANT MOLECULAR BIOLOGY 2015; 88:249-267. [PMID: 25896400 DOI: 10.1007/s11103-015-0320-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
In yeast and mammals, prohibitins (PHBs) are considered as structural proteins that form a scaffold-like structure for interacting with a set of proteins involved in various processes occurring in the mitochondria. The role of PHB in plant mitochondria is poorly understood. In the study, the model organism Arabidopsis thaliana was used to identify the possible roles of type-II PHBs (homologs of yeast Phb2p) in plant mitochondria. The obtained results suggest that the plant PHB complex participates in the assembly of multisubunit complexes; namely, respiratory complex I and enzymatic complexes carrying lipoic acid as a cofactor (pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and glycine decarboxylase). PHBs physically interact with subunits of these complexes. Knockout of two Arabidopsis type-II prohibitins (AtPHB2 and AtPHB6) results in a decreased abundance of these complexes along with a reduction in mitochondrial acyl carrier proteins. Also, the absence of AtPHB2 and AtPHB6 influences the expression of the mitochondrial genome and leads to the activation of alternative respiratory pathways, namely alternative oxidase and external NADH-dependent alternative dehydrogenases.
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Affiliation(s)
- Janusz Piechota
- Department of Biotechnology, University of Wroclaw, F. Juliot-Curie 14a, 50-383, Wroclaw, Poland,
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35
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Bavelloni A, Piazzi M, Raffini M, Faenza I, Blalock WL. Prohibitin 2: At a communications crossroads. IUBMB Life 2015; 67:239-54. [PMID: 25904163 DOI: 10.1002/iub.1366] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/06/2015] [Indexed: 01/02/2023]
Abstract
Prohibitins (PHBs) are a highly conserved class of proteins first discovered as inhibitors of cellular proliferation. Since then PHBs have been found to have a significant role in transcription, nuclear signaling, mitochondrial structural integrity, cell division, and cellular membrane metabolism, placing these proteins among the key regulators of pathologies such as cancer, neuromuscular degeneration, and other metabolic diseases. The human genome encodes two PHB proteins, prohibitin 1 (PHB1) and prohibitin 2 (PHB2), which function not only as a heterodimeric complex, but also independently. While many previous reviews have focused on the better characterized prohibitin, PHB1, this review focuses on PHB2 and new data concerning its cellular functions both in complex with PHB1 and independent of PHB1.
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Affiliation(s)
- Alberto Bavelloni
- Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopedic Institute, Bologna, Italy.,Laboratory RAMSES, Rizzoli Orthopedic Institute, Bologna, Italy
| | - Manuela Piazzi
- Department of Biomedical Sciences, University of Bologna, Bologna, Italy
| | - Mirco Raffini
- Laboratory RAMSES, Rizzoli Orthopedic Institute, Bologna, Italy
| | - Irene Faenza
- Department of Biomedical Sciences, University of Bologna, Bologna, Italy
| | - William L Blalock
- Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopedic Institute, Bologna, Italy.,National Research Council of Italy, Institute of Molecular Genetics, Bologna, Italy
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36
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Strand JM, Skinnes R, Scheffler K, Rootvelt T, Woldseth B, Bjørås M, Eide L. Genome instability in Maple Syrup Urine Disease correlates with impaired mitochondrial biogenesis. Metabolism 2014; 63:1063-70. [PMID: 24928662 DOI: 10.1016/j.metabol.2014.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/09/2014] [Accepted: 05/04/2014] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The mitochondrial branched-chain ketoacid dehydrogenase (BCKD) catalyzes the degradation of branched-chain amino acids (BCAA), which have been shown to induce oxidative stress. Maple Syrup Urine Disease (MSUD) is caused by impaired activity of BCKD, suggesting that oxidative stress and resulting DNA damage could contribute to pathology. We evaluated the potential effect of BCKD deficiency on genome integrity and mitochondrial function as a downstream target. METHODS Primary fibroblasts from MSUD patients and controls were either cultivated under normal conditions or exposed to metabolic or oxidative stress. DNA was analyzed for damage and mitochondrial function was evaluated by gene expression analyses, functional assays and immunofluorescent methods. RESULTS Patient fibroblasts accumulated damage in mitochondrial DNA (mtDNA) and nuclear DNA, with a corresponding reduction in mitochondrial transcription, mtDNA copy number and pyruvate dehydrogenase. We found no evidence of increased level of reactive oxygen species (ROS) in patient fibroblasts under normal conditions, suggesting that the genotoxic effect is ascribed to accumulating metabolites. CONCLUSIONS Impaired BCKD activity as in MSUD, results in accumulation of DNA damage and corresponding mitochondrial dysfunction.
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Affiliation(s)
- Janne M Strand
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway; Department of Microbiology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Ragnhild Skinnes
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Katja Scheffler
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway; Department of Microbiology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Terje Rootvelt
- Women and Children's Division, Oslo University Hospital, Oslo, Norway
| | - Berit Woldseth
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Magnar Bjørås
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway; Department of Microbiology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.
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37
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Hensen F, Cansiz S, Gerhold JM, Spelbrink JN. To be or not to be a nucleoid protein: A comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins. Biochimie 2014; 100:219-26. [DOI: 10.1016/j.biochi.2013.09.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/17/2013] [Indexed: 01/09/2023]
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38
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Muftuoglu M, Mori MP, de Souza-Pinto NC. Formation and repair of oxidative damage in the mitochondrial DNA. Mitochondrion 2014; 17:164-81. [PMID: 24704805 DOI: 10.1016/j.mito.2014.03.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 03/18/2014] [Accepted: 03/18/2014] [Indexed: 12/13/2022]
Abstract
The mitochondrial DNA (mtDNA) encodes for only 13 polypeptides, components of 4 of the 5 oxidative phosphorylation complexes. But despite this apparently small numeric contribution, all 13 subunits are essential for the proper functioning of the oxidative phosphorylation circuit. Thus, accumulation of lesions, mutations and deletions/insertions in the mtDNA could have severe functional consequences, including mitochondrial diseases, aging and age-related diseases. The DNA is a chemically unstable molecule, which can be easily oxidized, alkylated, deaminated and suffer other types of chemical modifications, throughout evolution the organisms that survived were those who developed efficient DNA repair processes. In the last two decades, it has become clear that mitochondria have DNA repair pathways, which operate, at least for some types of lesions, as efficiently as the nuclear DNA repair pathways. The mtDNA is localized in a particularly oxidizing environment, making it prone to accumulate oxidatively generated DNA modifications (ODMs). In this article, we: i) review the major types of ODMs formed in mtDNA and the known repair pathways that remove them; ii) discuss the possible involvement of other repair pathways, just recently characterized in mitochondria, in the repair of these modifications; and iii) address the role of DNA repair in mitochondrial function and a possible cross-talk with other pathways that may potentially participate in mitochondrial genomic stability, such as mitochondrial dynamics and nuclear-mitochondrial signaling. Oxidative stress and ODMs have been increasingly implicated in disease and aging, and thus we discuss how variations in DNA repair efficiency may contribute to the etiology of such conditions or even modulate their clinical outcomes.
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Affiliation(s)
- Meltem Muftuoglu
- Department of Molecular Biology and Genetics, Acibadem University, Atasehir, 34752 Istanbul, Turkey
| | - Mateus P Mori
- Depto. de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000 Brazil
| | - Nadja C de Souza-Pinto
- Depto. de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000 Brazil.
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39
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Bogenhagen DF, Martin DW, Koller A. Initial steps in RNA processing and ribosome assembly occur at mitochondrial DNA nucleoids. Cell Metab 2014; 19:618-29. [PMID: 24703694 DOI: 10.1016/j.cmet.2014.03.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/17/2013] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
Abstract
Mammalian mitochondrial DNA (mtDNA) resides in compact nucleoids, where it is replicated and transcribed into long primary transcripts processed to generate rRNAs, tRNAs, and mRNAs encoding 13 proteins. This situation differs from bacteria and eukaryotic nucleoli, which have dedicated rRNA transcription units. The assembly of rRNAs into mitoribosomes has received little study. We show that mitochondrial RNA processing enzymes involved in tRNA excision, ribonuclease P (RNase P) and ELAC2, as well as a subset of nascent mitochondrial ribosomal proteins (MRPs) associate with nucleoids to initiate RNA processing and ribosome assembly. SILAC pulse-chase labeling experiments show that nascent MRPs recruited to the nucleoid fraction were highly labeled after the pulse in a transcription-dependent manner and decreased in labeling intensity during the chase. These results provide insight into the landscape of binding events required for mitochondrial ribosome assembly and firmly establish the mtDNA nucleoid as a control center for mitochondrial biogenesis.
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Affiliation(s)
- Daniel F Bogenhagen
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA.
| | - Dwight W Martin
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794-8160, USA; Proteomics Center, Stony Brook University, Stony Brook, NY 11794-8691, USA
| | - Antonius Koller
- Proteomics Center, Stony Brook University, Stony Brook, NY 11794-8691, USA
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40
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Friedman JR, Nunnari J. Mitochondrial form and function. Nature 2014; 505:335-43. [PMID: 24429632 DOI: 10.1038/nature12985] [Citation(s) in RCA: 1173] [Impact Index Per Article: 117.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/22/2013] [Indexed: 02/08/2023]
Abstract
Mitochondria are one of the major ancient endomembrane systems in eukaryotic cells. Owing to their ability to produce ATP through respiration, they became a driving force in evolution. As an essential step in the process of eukaryotic evolution, the size of the mitochondrial chromosome was drastically reduced, and the behaviour of mitochondria within eukaryotic cells radically changed. Recent advances have revealed how the organelle's behaviour has evolved to allow the accurate transmission of its genome and to become responsive to the needs of the cell and its own dysfunction.
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Affiliation(s)
- Jonathan R Friedman
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, California 95616, USA
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, California 95616, USA
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41
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Mitochondrial DNA mutations and breast tumorigenesis. Biochim Biophys Acta Rev Cancer 2013; 1836:336-44. [PMID: 24140413 DOI: 10.1016/j.bbcan.2013.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 10/02/2013] [Accepted: 10/05/2013] [Indexed: 12/15/2022]
Abstract
Breast cancer is a heterogeneous disease and genetic factors play an important role in its genesis. Although mutations in tumor suppressors and oncogenes encoded by the nuclear genome are known to play a critical role in breast tumorigenesis, the contribution of the mitochondrial genome to this process is unclear. Like the nuclear genome, the mitochondrial genome also encodes proteins critical for mitochondrion functions such as oxidative phosphorylation (OXPHOS), which is known to be defective in cancer including breast cancer. Mitochondrial DNA (mtDNA) is more susceptible to mutations due to limited repair mechanisms compared to nuclear DNA (nDNA). Thus changes in mitochondrial genes could also contribute to the development of breast cancer. In this review we discuss mtDNA mutations that affect OXPHOS. Continuous acquisition of mtDNA mutations and selection of advantageous mutations ultimately leads to generation of cells that propagate uncontrollably to form tumors. Since irreversible damage to OXPHOS leads to a shift in energy metabolism towards enhanced aerobic glycolysis in most cancers, mutations in mtDNA represent an early event during breast tumorigenesis, and thus may serve as potential biomarkers for early detection and prognosis of breast cancer. Because mtDNA mutations lead to defective OXPHOS, development of agents that target OXPHOS will provide specificity for preventative and therapeutic agents against breast cancer with minimal toxicity.
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42
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Lee KW, Okot-Kotber C, LaComb JF, Bogenhagen DF. Mitochondrial ribosomal RNA (rRNA) methyltransferase family members are positioned to modify nascent rRNA in foci near the mitochondrial DNA nucleoid. J Biol Chem 2013; 288:31386-99. [PMID: 24036117 DOI: 10.1074/jbc.m113.515692] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have identified RNMTL1, MRM1, and MRM2 (FtsJ2) as members of the RNA methyltransferase family that may be responsible for the three known 2'-O-ribose modifications of the 16 S rRNA core of the large mitochondrial ribosome subunit. These proteins are confined to foci located in the vicinity of mtDNA nucleoids. They show distinct patterns of association with mtDNA nucleoids and/or mitochondrial ribosomes in cell fractionation studies. We focused on the role of the least studied protein in this set, RNMTL1, to show that this protein interacts with the large ribosomal subunit as well as with a series of non-ribosomal proteins that may be involved in coupling of the rate of rRNA transcription and ribosome assembly in mitochondria. siRNA-directed silencing of RNMTL1 resulted in a significant inhibition of translation on mitochondrial ribosomes. Our results are consistent with a role for RNMTL1 in methylation of G(1370) of human 16 S rRNA.
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Affiliation(s)
- Ken-Wing Lee
- From the Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
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43
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Warda M, Kim HK, Kim N, Ko KS, Rhee BD, Han J. A matter of life, death and diseases: mitochondria from a proteomic perspective. Expert Rev Proteomics 2013; 10:97-111. [PMID: 23414362 DOI: 10.1586/epr.12.69] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mitochondria are highly ordered, integrated organelles that energize cellular activities and contribute to programmed death by initiating disciplined apoptotic cascades. This review seeks to clarify our understanding of mitochondrial structural-functional integrity beyond the resolved nuclear genome by unraveling the dynamic mitochondrial proteome and elucidating proteome/genome interplay. The roles of mechanochemical coupling between mitoskeleton and cytoskeleton and crosstalk with other organelles in orchestrating cellular outcomes are explained. The authors also review the modulation of mitochondrial-related oxidative stress on apoptosis and cancer development and the context is applied to interpret pathogenetic events in neurodegenerative disorders and cardiovascular diseases. The accumulated proteomics evidence is used to describe the integral role that mitochondria play and how they influence other intracellular organelles. Possible mitochondrial-targeted therapeutic interventions are also discussed.
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Affiliation(s)
- Mohamad Warda
- Biochemistry, Molecular Biology and Chemistry of Nutrition Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
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44
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Kolesnikov AA, Gerasimov ES. Diversity of mitochondrial genome organization. BIOCHEMISTRY (MOSCOW) 2013; 77:1424-35. [PMID: 23379519 DOI: 10.1134/s0006297912130020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we discuss types of mitochondrial genome structural organization (architecture), which includes the following characteristic features: size and the shape of DNA molecule, number of encoded genes, presence of cryptogenes, and editing of primary transcripts.
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Affiliation(s)
- A A Kolesnikov
- Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia.
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45
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Zhang SB, Maguire D, Zhang M, Zhang A, Zhang L, Swarts S, Okunieff P. Maternal Bias in Mouse Radiosensitivity: The Role of the Mitochondrial PTP. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 789:251-256. [DOI: 10.1007/978-1-4614-7411-1_34] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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46
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Cheng J, Gao F, Chen X, Wu J, Xing C, Lv Z, Xu W, Xie Q, Wu L, Ye S, Xie H, Zheng S, Zhou L. Prohibitin-2 promotes hepatocellular carcinoma malignancy progression in hypoxia based on a label-free quantitative proteomics strategy. Mol Carcinog 2013; 53:820-32. [PMID: 23661548 DOI: 10.1002/mc.22040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 11/20/2012] [Accepted: 12/12/2012] [Indexed: 02/05/2023]
Abstract
The rapid growth of hepatocellular carcinoma (HCC) leading to tumor hypoxia is a common pathological phenomenon. Meanwhile, tumor hypoxia can promote a change in the biological properties of tumor cells. It may enhance the survival of tumor cells under stress conditions, resulting in resistance to apoptosis and angiogenesis. The moleculars that could modulate the malignant phenotypes of HCC cells remain largely unknown. Based on label-free quantitative proteomic data, we found a significant upregulation of prohibitin-2 (PHB2) in HCC tissues. Treatment of hepatoma cells with small interfering RNAs against PHB2 suppressed cell growth and colony formation, led to G1 phase arrest and sensitized HCC cells to apoptosis. Moreover, inhibition of PHB2 expression dramatically repressed the ability of HCC cells to adapt to hypoxic microenvironments and resist chemotherapy-induced apoptosis. Thus, PHB2 in HCC supports the development and progression of hepatocellular malignancy to hypoxia, and implicates the potential antagonist function of PHB2 in transarterial chemoembolization treatment.
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Affiliation(s)
- Jun Cheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P.R., China; Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang University, Hangzhou, P.R., China
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47
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Kolesar JE, Wang CY, Taguchi YV, Chou SH, Kaufman BA. Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome. Nucleic Acids Res 2012; 41:e58. [PMID: 23275548 PMCID: PMC3575812 DOI: 10.1093/nar/gks1324] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The mitochondrial genome exists in numerous structural conformations, complicating the study of mitochondrial DNA (mtDNA) metabolism. Here, we describe the development of 2D intact mtDNA agarose gel electrophoresis (2D-IMAGE) for the separation and detection of approximately two-dozen distinct topoisomers. Although the major topoisomers were well conserved across many cell and tissue types, unique differences in certain cells and tissues were also observed. RNase treatment revealed that partially hybridized RNAs associated primarily with covalently closed circular DNA, consistent with this structure being the template for transcription. Circular structures composed of RNA:DNA hybrids contained only heavy-strand DNA sequences, implicating them as lagging-strand replication intermediates. During recovery from replicative arrest, 2D-IMAGE showed changes in both template selection and replication products. These studies suggest that discrete topoisomers are associated with specific mtDNA-directed processes. Because of the increased resolution, 2D-IMAGE has the potential to identify novel mtDNA intermediates involved in replication or transcription, or pathology including oxidative linearization, deletions or depletion.
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Affiliation(s)
- Jill E Kolesar
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street VET220E, Philadelphia, PA 19104, USA
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Bernt M, Braband A, Schierwater B, Stadler PF. Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol 2012; 69:328-38. [PMID: 23142697 DOI: 10.1016/j.ympev.2012.10.020] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 10/20/2012] [Accepted: 10/22/2012] [Indexed: 11/30/2022]
Abstract
Many years of extensive studies of metazoan mitochondrial genomes have established differences in gene arrangements and genetic codes as valuable phylogenetic markers. Understanding the underlying mechanisms of replication, transcription and the role of the control regions which cause e.g. different gene orders is important to assess the phylogenetic signal of such events. This review summarises and discusses, for the Metazoa, the general aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of gene rearrangements. As whole genome sequencing projects accumulate, more and more observations about mitochondrial gene transfer to the nucleus are reported. Thus occurrence and phylogenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review.
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Affiliation(s)
- Matthias Bernt
- Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.
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Dual functions of α-ketoglutarate dehydrogenase E2 in the Krebs cycle and mitochondrial DNA inheritance in Trypanosoma brucei. EUKARYOTIC CELL 2012; 12:78-90. [PMID: 23125353 DOI: 10.1128/ec.00269-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The dihydrolipoyl succinyltransferase (E2) of the multisubunit α-ketoglutarate dehydrogenase complex (α-KD) is an essential Krebs cycle enzyme commonly found in the matrices of mitochondria. African trypanosomes developmentally regulate mitochondrial carbohydrate metabolism and lack a functional Krebs cycle in the bloodstream of mammals. We found that despite the absence of a functional α-KD, bloodstream form (BF) trypanosomes express α-KDE2, which localized to the mitochondrial matrix and inner membrane. Furthermore, α-KDE2 fractionated with the mitochondrial genome, the kinetoplast DNA (kDNA), in a complex with the flagellum. A role for α-KDE2 in kDNA maintenance was revealed in α-KDE2 RNA interference (RNAi) knockdowns. Following RNAi induction, bloodstream trypanosomes showed pronounced growth reduction and often failed to equally distribute kDNA to daughter cells, resulting in accumulation of cells devoid of kDNA (dyskinetoplastic) or containing two kinetoplasts. Dyskinetoplastic trypanosomes lacked mitochondrial membrane potential and contained mitochondria of substantially reduced volume. These results indicate that α-KDE2 is bifunctional, both as a metabolic enzyme and as a mitochondrial inheritance factor necessary for the distribution of kDNA networks to daughter cells at cytokinesis.
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Campbell CT, Kolesar JE, Kaufman BA. Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:921-9. [DOI: 10.1016/j.bbagrm.2012.03.002] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/08/2012] [Accepted: 03/15/2012] [Indexed: 10/28/2022]
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