1
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Davies AM, Holt AG. Modeling mitochondria, where are the numbers? Neural Regen Res 2024; 19:1435-1436. [PMID: 38051884 PMCID: PMC10883508 DOI: 10.4103/1673-5374.386402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/13/2023] [Indexed: 12/07/2023] Open
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2
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Tan DX. Mitochondrial dysfunction, a weakest link of network of aging, relation to innate intramitochondrial immunity of DNA recognition receptors. Mitochondrion 2024; 76:101886. [PMID: 38663836 DOI: 10.1016/j.mito.2024.101886] [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: 02/11/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
Aging probably is the most complexed process in biology. It is manifested by a variety of hallmarks. These hallmarks weave a network of aging; however, each hallmark is not uniformly strong for the network. It is the weakest link determining the strengthening of the network of aging, or the maximum lifespan of an organism. Therefore, only improvement of the weakest link has the chance to increase the maximum lifespan but not others. We hypothesize that mitochondrial dysfunction is the weakest link of the network of aging. It may origin from the innate intramitochondrial immunity related to the activities of pathogen DNA recognition receptors. These receptors recognize mtDNA as the PAMP or DAMP to initiate the immune or inflammatory reactions. Evidence has shown that several of these receptors including TLR9, cGAS and IFI16 can be translocated into mitochondria. The potentially intramitochondrial presented pathogen DNA recognition receptors have the capacity to attack the exposed second structures of the mtDNA during its transcriptional or especially the replicational processes, leading to the mtDNA mutation, deletion, heteroplasmy colonization, mitochondrial dysfunction, and alterations of other hallmarks, as well as aging. Pre-consumption of the intramitochondrial presented pathogen DNA recognition receptors by medical interventions including development of mitochondrial targeted small molecule which can neutralize these receptors may retard or even reverse the aging to significantly improve the maximum lifespan of the organisms.
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Affiliation(s)
- Dun-Xian Tan
- Department of Cell Systems and Anatomy, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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3
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Holt AG, Davies AM. A comparison of mtDNA deletion mutant proliferation mechanisms. J Theor Biol 2022; 551-552:111244. [PMID: 35973607 DOI: 10.1016/j.jtbi.2022.111244] [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: 04/26/2022] [Revised: 07/17/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022]
Abstract
In this paper we use simulation methods to investigate the proliferation of deletion mutations of mitochondrial DNA in neurons. We simulate three mtDNA proliferation mechanisms, namely, random drift, replicative advantage and vicious cycle. For each mechanism, we investigated the effect mutation rates have on neuron loss within a human host. We also compare heteroplasmy of each mechanism at mutation rates that yield the levels neuron loss that would be associated with dementia. Both random drift and vicious cycle predicted high levels of heteroplasmy, while replicative advantage showed a small number of dominant clones with a low background of heteroplasmy.
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4
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Holt AG, Davies AM. The Effect of Mitochondrial DNA Half-Life on Deletion Mutation Proliferation in Long Lived Cells. Acta Biotheor 2021; 69:671-695. [PMID: 34131800 DOI: 10.1007/s10441-021-09417-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/07/2021] [Indexed: 01/21/2023]
Abstract
The proliferation of mitochondrial DNA (mtDNA) with deletion mutations has been linked to aging and age related neurodegenerative conditions. In this study we model the effect of mtDNA half-life on mtDNA competition and selection. It has been proposed that mutation deletions ([Formula: see text]) have a replicative advantage over wild-type ([Formula: see text]) and that this is detrimental to the host cell, especially in post-mitotic cells. An individual cell can be viewed as forming a closed ecosystem containing a large population of independently replicating mtDNA. Within this enclosed environment a selfishly replicating [Formula: see text] would compete with the [Formula: see text] for space and resources to the detriment of the host cell. In this paper, we use a computer simulation to model cell survival in an environment where [Formula: see text] compete with [Formula: see text] such that the cell expires upon [Formula: see text] extinction. We focus on the survival time for long lived post-mitotic cells, such as neurons. We confirm previous observations that [Formula: see text] do have a replicative advantage over [Formula: see text]. As expected, cell survival times diminished with increased mutation probabilities, however, the relationship between survival time and mutation rate was non-linear, that is, a ten-fold increase in mutation probability only halved the survival time. The results of our model also showed that a modest increase in half-life had a profound affect on extending cell survival time, thereby, mitigating the replicative advantage of [Formula: see text]. Given the relevance of mitochondrial dysfunction to various neurodegenerative conditions, we propose that therapies to increase mtDNA half-life could significantly delay their onset.
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5
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Kim E, Kim JY, Lee JY. Mathematical Modeling of p53 Pathways. Int J Mol Sci 2019; 20:ijms20205179. [PMID: 31635420 PMCID: PMC6834204 DOI: 10.3390/ijms20205179] [Citation(s) in RCA: 5] [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: 07/30/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 12/30/2022] Open
Abstract
Cells have evolved balanced systems that ensure an appropriate response to stress. The systems elicit repair responses in temporary or moderate stress but eliminate irreparable cells via apoptosis in detrimental conditions of prolonged or severe stress. The tumor suppressor p53 is a central player in these stress response systems. When activated under DNA damage stress, p53 regulates hundreds of genes that are involved in DNA repair, cell cycle, and apoptosis. Recently, increasing studies have demonstrated additional regulatory roles of p53 in metabolism and mitochondrial physiology. Due to the inherent complexity of feedback loops between p53 and its target genes, the application of mathematical modeling has emerged as a novel approach to better understand the multifaceted functions and dynamics of p53. In this review, we discuss several mathematical modeling approaches in exploring the p53 pathways.
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Affiliation(s)
- Eunjung Kim
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon 34134, Korea.
| | - Jae-Young Kim
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon 34134, Korea.
- Korea Basic Science Institute, Daejeon 34133, Korea.
| | - Joo-Yong Lee
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon 34134, Korea.
- Korea Basic Science Institute, Daejeon 34133, Korea.
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6
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Fu A, Hou Y, Yu Z, Zhao Z, Liu Z. Healthy mitochondria inhibit the metastatic melanoma in lungs. Int J Biol Sci 2019; 15:2707-2718. [PMID: 31754341 PMCID: PMC6854369 DOI: 10.7150/ijbs.38104] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/21/2019] [Indexed: 01/10/2023] Open
Abstract
Tumor mitochondria alter their functions to reprogram cell metabolism and then allow tumor cells to rapidly proliferate in the hypoxic and acidic microenvironment. However, roles of normal mitochondria played in tumor progression are still unclear. Here we investigate the normal mitochondrial effect on abnormal metabolism of tumors, and to clarify why the mitochondria have to undergo functional changes in the tumor growth. The mitochondria isolated from healthy mouse livers were intravenously injected into melanoma model mice with lung metastasis, then the tumor growth, animal survival and associated metabolic changes were studied. The results reveal that the mitochondria significantly retard tumor growth and increase survival days of animals. The anti-tumor effect of the mitochondria is related to interfering the tumor cell metabolisms, such as reducing glycolysis and producing an oxidative intracellular environment, all of which are not suitable for tumor cell proliferation. In addition, the mitochondria increases cell apoptosis, necrosis, and mitophagy. These effects are more efficient with the mitochondria isolated from young mouse livers than those from aged mice. Our study not only provides a valuable approach to invest mitochondrial function associated with tumor growth but also offer new insight into tumor therapy through interfering the tumor cell metabolism by healthy mitochondria.
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Affiliation(s)
- Ailing Fu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yixue Hou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhenyao Yu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zizhen Zhao
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zesheng Liu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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7
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Lakshmanan LN, Yee Z, Ng LF, Gunawan R, Halliwell B, Gruber J. Clonal expansion of mitochondrial DNA deletions is a private mechanism of aging in long-lived animals. Aging Cell 2018; 17:e12814. [PMID: 30043489 PMCID: PMC6156498 DOI: 10.1111/acel.12814] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 02/06/2023] Open
Abstract
Disruption of mitochondrial metabolism and loss of mitochondrial DNA (mtDNA) integrity are widely considered as evolutionarily conserved (public) mechanisms of aging (López-Otín et al., Cell, 153, 2013 and 1194). Human aging is associated with loss in skeletal muscle mass and function (Sarcopenia), contributing significantly to morbidity and mortality. Muscle aging is associated with loss of mtDNA integrity. In humans, clonally expanded mtDNA deletions colocalize with sites of fiber breakage and atrophy in skeletal muscle. mtDNA deletions may therefore play an important, possibly causal role in sarcopenia. The nematode Caenorhabditis elegans also exhibits age-dependent decline in mitochondrial function and a form of sarcopenia. However, it is unclear if mtDNA deletions play a role in C. elegans aging. Here, we report identification of 266 novel mtDNA deletions in aging nematodes. Analysis of the mtDNA mutation spectrum and quantification of mutation burden indicates that (a) mtDNA deletions in nematode are extremely rare, (b) there is no significant age-dependent increase in mtDNA deletions, and (c) there is little evidence for clonal expansion driving mtDNA deletion dynamics. Thus, mtDNA deletions are unlikely to drive the age-dependent functional decline commonly observed in C. elegans. Computational modeling of mtDNA dynamics in C. elegans indicates that the lifespan of short-lived animals such as C. elegans is likely too short to allow for significant clonal expansion of mtDNA deletions. Together, these findings suggest that clonal expansion of mtDNA deletions is likely a private mechanism of aging predominantly relevant in long-lived animals such as humans and rhesus monkey and possibly in rodents.
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Affiliation(s)
- Lakshmi Narayanan Lakshmanan
- Institute for Chemical and BioengineeringETH ZurichZurichSwitzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment GenopodeLausanneSwitzerland
| | - Zhuangli Yee
- Department of BiochemistryYong Loo Lin School of Medicine, National University of SingaporeSingapore
| | - Li Fang Ng
- Ageing Research Laboratory, Science DivisionYale‐NUS CollegeSingaporeSingapore
| | - Rudiyanto Gunawan
- Institute for Chemical and BioengineeringETH ZurichZurichSwitzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment GenopodeLausanneSwitzerland
| | - Barry Halliwell
- Department of BiochemistryYong Loo Lin School of Medicine, National University of SingaporeSingapore
| | - Jan Gruber
- Department of BiochemistryYong Loo Lin School of Medicine, National University of SingaporeSingapore
- Ageing Research Laboratory, Science DivisionYale‐NUS CollegeSingaporeSingapore
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8
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Coccarelli A, Hasan HM, Carson J, Parthimos D, Nithiarasu P. Influence of ageing on human body blood flow and heat transfer: A detailed computational modelling study. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2018; 34:e3120. [PMID: 29932495 PMCID: PMC6220937 DOI: 10.1002/cnm.3120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 05/17/2023]
Abstract
Ageing plays a fundamental role in arterial blood transport and heat transfer within a human body. The aim of this work is to provide a comprehensive methodology, based on biomechanical considerations, for modelling arterial flow and energy exchange mechanisms in the body accounting for age-induced changes. The study outlines a framework for age-related modifications within several interlinked subsystems, which include arterial stiffening, heart contractility variations, tissue volume and property changes, and thermoregulatory system deterioration. Some of the proposed age-dependent governing equations are directly extrapolated from experimental data sets. The computational framework is demonstrated through numerical experiments, which show the impact of such age-related changes on arterial blood pressure, local temperature distribution, and global body thermal response. The proposed numerical experiments show that the age-related changes in arterial convection do not significantly affect the tissue temperature distribution. Results also highlight age-related effects on the sweating mechanism, which lead to a significant reduction in heat dissipation and a subsequent rise in skin and core temperatures.
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Affiliation(s)
- Alberto Coccarelli
- Biomedical Engineering Group, Zienkiewicz Centre for Computational Engineering, College of EngineeringSwansea UniversityUK
| | - Hayder M. Hasan
- Biomedical Engineering Group, Zienkiewicz Centre for Computational Engineering, College of EngineeringSwansea UniversityUK
| | - Jason Carson
- Biomedical Engineering Group, Zienkiewicz Centre for Computational Engineering, College of EngineeringSwansea UniversityUK
| | | | - Perumal Nithiarasu
- Biomedical Engineering Group, Zienkiewicz Centre for Computational Engineering, College of EngineeringSwansea UniversityUK
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9
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Resolving the Enigma of the Clonal Expansion of mtDNA Deletions. Genes (Basel) 2018; 9:genes9030126. [PMID: 29495484 PMCID: PMC5867847 DOI: 10.3390/genes9030126] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/31/2022] Open
Abstract
Mitochondria are cell organelles that are special since they contain their own genetic material in the form of mitochondrial DNA (mtDNA). Damage and mutations of mtDNA are not only involved in several inherited human diseases but are also widely thought to play an important role during aging. In both cases, point mutations or large deletions accumulate inside cells, leading to functional impairment once a certain threshold has been surpassed. In most cases, it is a single type of mutant that clonally expands and out-competes the wild type mtDNA, with different mutant molecules being amplified in different cells. The challenge is to explain where the selection advantage for the accumulation comes from, why such a large range of different deletions seem to possess this advantage, and how this process can scale to species with different lifespans such as those of rats and man. From this perspective, we provide an overview of current ideas, present an update of our own proposal, and discuss the wider relevance of the phenomenon for aging.
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10
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Mc Auley MT, Guimera AM, Hodgson D, Mcdonald N, Mooney KM, Morgan AE, Proctor CJ. Modelling the molecular mechanisms of aging. Biosci Rep 2017; 37:BSR20160177. [PMID: 28096317 PMCID: PMC5322748 DOI: 10.1042/bsr20160177] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/15/2016] [Accepted: 01/16/2017] [Indexed: 01/09/2023] Open
Abstract
The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field.
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Affiliation(s)
- Mark T Mc Auley
- Faculty of Science and Engineering, University of Chester, Chester, U.K
| | - Alvaro Martinez Guimera
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, U.K
| | - David Hodgson
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - Neil Mcdonald
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, U.K
| | | | - Amy E Morgan
- Faculty of Science and Engineering, University of Chester, Chester, U.K
| | - Carole J Proctor
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K.
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
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11
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Volmering E, Niehusmann P, Peeva V, Grote A, Zsurka G, Altmüller J, Nürnberg P, Becker AJ, Schoch S, Elger CE, Kunz WS. Neuropathological signs of inflammation correlate with mitochondrial DNA deletions in mesial temporal lobe epilepsy. Acta Neuropathol 2016; 132:277-288. [PMID: 26993140 DOI: 10.1007/s00401-016-1561-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/26/2016] [Accepted: 03/11/2016] [Indexed: 11/27/2022]
Abstract
Accumulation of mitochondrial DNA (mtDNA) deletions has been proposed to be responsible for the presence of respiratory-deficient neurons in several CNS diseases. Deletions are thought to originate from double-strand breaks due to attack of reactive oxygen species (ROS) of putative inflammatory origin. In epileptogenesis, emerging evidence points to chronic inflammation as an important feature. Here we aimed to analyze the potential association of inflammation and mtDNA deletions in the hippocampal tissue of patients with mesial temporal lobe epilepsy (mTLE) and hippocampal sclerosis (HS). Hippocampal and parahippocampal tissue samples from 74 patients with drug-refractory mTLE served for mtDNA analysis by multiplex PCR as well as long-range PCR, single-molecule PCR and ultra-deep sequencing of mtDNA in selected samples. Patients were sub-classified according to neuropathological findings. Semi-quantitative assessment of neuronal cell loss was performed in the hippocampal regions CA1-CA4. Inflammatory infiltrates were quantified by cell counts in the CA1, CA3 and CA4 regions from well preserved hippocampal samples (n = 33). Samples with HS showed a significantly increased frequency of a 7436-bp mtDNA deletion (p < 0.0001) and a higher proportion of somatic G>T transversions compared to mTLE patients with different histopathology. Interestingly, the number of T-lymphocytes in the hippocampal CA1, CA3 and CA4 regions was, similar to the 7436-bp mtDNA deletion, significantly increased in samples with HS compared to other subgroups. Our findings show a coincidence of HS, increased somatic G>T transversions, the presence of a specific mtDNA deletion, and increased inflammatory infiltrates. These results support the hypothesis that chronic inflammation leads to mitochondrial dysfunction by ROS-mediated mtDNA mutagenesis which promotes epileptogenesis and neuronal cell loss in patients with mTLE and HS.
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Affiliation(s)
- Elisa Volmering
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Pitt Niehusmann
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
- Department of Neuro-/Pathology, Oslo University Hospital, Oslo, Norway
| | - Viktoriya Peeva
- Division of Neurochemistry, Department of Epileptology, University Bonn Medical Center, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Alexander Grote
- Department of Neurosurgery, University of Bonn Medical Center, Bonn, Germany
| | - Gábor Zsurka
- Division of Neurochemistry, Department of Epileptology, University Bonn Medical Center, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Albert J Becker
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
- Translational Epilepsy Research Section, University of Bonn Medical Center, Bonn, Germany
| | - Susanne Schoch
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
- Translational Epilepsy Research Section, University of Bonn Medical Center, Bonn, Germany
| | - Christian E Elger
- Division of Neurochemistry, Department of Epileptology, University Bonn Medical Center, Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Wolfram S Kunz
- Division of Neurochemistry, Department of Epileptology, University Bonn Medical Center, Sigmund-Freud-Str. 25, 53105, Bonn, Germany.
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12
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Analysis of Replicating Mitochondrial DNA by In Organello Labeling and Two-Dimensional Agarose Gel Electrophoresis. Methods Mol Biol 2016; 1351:95-113. [PMID: 26530677 DOI: 10.1007/978-1-4939-3040-1_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Our understanding of the mechanisms of DNA replication in a broad range of organisms and viruses has benefited from the application of two-dimensional agarose gel electrophoresis (2D-AGE). The method resolves DNA molecules on the basis of size and shape and is technically straightforward. 2D-AGE sparked controversy in the field of mitochondria when it revealed replicating molecules with lengthy tracts of RNA, a phenomenon never before reported in nature. More recently, radioisotope labeling of the DNA in the mitochondria has been coupled with 2D-AGE. In its first application, this procedure helped to delineate the "bootlace mechanism of mitochondrial DNA replication," in which processed mitochondrial transcripts are hybridized to the lagging strand template at the replication fork as the leading DNA strand is synthesized. This chapter provides details of the method, how it has been applied to date and concludes with some potential future applications of the technique.
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13
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Loshchenova PS, Sinitsyna OI, Fedoseeva LA, Stefanova NA, Kolosova NG. Influence of antioxidant SkQ1 on accumulation of mitochondrial DNA deletions in the hippocampus of senescence-accelerated OXYS rats. BIOCHEMISTRY (MOSCOW) 2015; 80:596-603. [DOI: 10.1134/s0006297915050120] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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Holt IJ, Speijer D, Kirkwood TBL. The road to rack and ruin: selecting deleterious mitochondrial DNA variants. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130451. [PMID: 24864317 DOI: 10.1098/rstb.2013.0451] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondria constitute the major energy-producing compartment of the eukaryotic cell. These organelles contain many molecules of DNA that contribute only a handful of proteins required for energy production. Mutations in the DNA of mitochondria were identified as a cause of human disease a quarter of a century ago, and they have subsequently been implicated in ageing. The process whereby deleterious variants come to dominate a cell, tissue or human is the subject of debate. It is likely to involve multiple, often competing, factors, as selection pressures on mitochondrial DNA can be both indirect and intermittent, and are subjected to rapid change. Here, we assess the different models and the prospects for preventing the accumulation of deleterious mitochondrial DNA variants with time.
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Affiliation(s)
- Ian J Holt
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Thomas B L Kirkwood
- Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
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15
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Busch KB, Kowald A, Spelbrink JN. Quality matters: how does mitochondrial network dynamics and quality control impact on mtDNA integrity? Philos Trans R Soc Lond B Biol Sci 2015; 369:20130442. [PMID: 24864312 DOI: 10.1098/rstb.2013.0442] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Mammalian mtDNA encodes for 13 core proteins of oxidative phosphorylation. Mitochondrial DNA mutations and deletions cause severe myopathies and neuromuscular diseases. Thus, the integrity of mtDNA is pivotal for cell survival and health of the organism. We here discuss the possible impact of mitochondrial fusion and fission on mtDNA maintenance as well as positive and negative selection processes. Our focus is centred on the important question of how the quality of mtDNA nucleoids can be assured when selection and mitochondrial quality control works on functional and physiological phenotypes constituted by oxidative phosphorylation proteins. The organelle control theory suggests a link between phenotype and nucleoid genotype. This is discussed in the light of new results presented here showing that mitochondrial transcription factor A/nucleoids are restricted in their intramitochondrial mobility and probably have a limited sphere of influence. Together with recent published work on mitochondrial and mtDNA heteroplasmy dynamics, these data suggest first, that single mitochondria might well be internally heterogeneous and second, that nucleoid genotypes might be linked to local phenotypes (although the link might often be leaky). We discuss how random or site-specific mitochondrial fission can isolate dysfunctional parts and enable their elimination by mitophagy, stressing the importance of fission in the process of mtDNA quality control. The role of fusion is more multifaceted and less understood in this context, but the mixing and equilibration of matrix content might be one of its important functions.
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Affiliation(s)
- Karin B Busch
- Division of Mitochondrial Dynamics, School of Biology and Chemistry, University of Osnabrück, 49069 Osnabrück, Germany
| | - Axel Kowald
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
| | - Johannes N Spelbrink
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, PO Box 9101, 6500 HB Nijmegen, The Netherlands FinMIT Centre of Excellence, Institute of Biomedical Technology and Tampere University Hospital, Pirkanmaa Hospital District, 33014 Tampere, Finland
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16
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Szklarczyk R, Nooteboom M, Osiewacz HD. Control of mitochondrial integrity in ageing and disease. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130439. [PMID: 24864310 DOI: 10.1098/rstb.2013.0439] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Various molecular and cellular pathways are active in eukaryotes to control the quality and integrity of mitochondria. These pathways are involved in keeping a 'healthy' population of this essential organelle during the lifetime of the organism. Quality control (QC) systems counteract processes that lead to organellar dysfunction manifesting as degenerative diseases and ageing. We discuss disease- and ageing-related pathways involved in mitochondrial QC: mtDNA repair and reorganization, regeneration of oxidized amino acids, refolding and degradation of severely damaged proteins, degradation of whole mitochondria by mitophagy and finally programmed cell death. The control of the integrity of mtDNA and regulation of its expression is essential to remodel single proteins as well as mitochondrial complexes that determine mitochondrial functions. The redundancy of components, such as proteases, and the hierarchies of the QC raise questions about crosstalk between systems and their precise regulation. The understanding of the underlying mechanisms on the genomic, proteomic, organellar and cellular levels holds the key for the development of interventions for mitochondrial dysfunctions, degenerative processes, ageing and age-related diseases resulting from impairments of mitochondria.
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Affiliation(s)
- Radek Szklarczyk
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands Department of Clinical Genetics, Unit Clinical Genomics, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Marco Nooteboom
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Heinz D Osiewacz
- Faculty for Biosciences and Cluster of Excellence 'Macromolecular Complexes', Goethe University, Molecular Developmental Biology, 60438 Frankfurt am Main, Germany
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Transcription could be the key to the selection advantage of mitochondrial deletion mutants in aging. Proc Natl Acad Sci U S A 2014; 111:2972-7. [PMID: 24569805 DOI: 10.1073/pnas.1314970111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The mitochondrial theory of aging is widely popular but confronted by several apparent inconsistencies. On the one hand, mitochondrial energy production is of central importance to the health and proper functioning of cells, and single-cell studies have shown that mtDNA deletion mutants accumulate in a clonal fashion in various mammalian species, displacing the wild-type mtDNAs. On the other hand, no explanation exists yet for the clonal expansion of mtDNA mutants that is compatible with experimental observations. We present here a new idea based on the distinctive connection between transcription and replication of metazoan mtDNA. Bioinformatic analysis of mtDNA deletion spectra strongly supports the predictions of this hypothesis and identifies specific candidates for proteins involved in transcriptional control of mtDNA replication. Computer simulations show the mechanism to be compatible with the available data from short- and long-lived mammalian species.
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Khrapko K, Turnbull D. Mitochondrial DNA mutations in aging. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 127:29-62. [PMID: 25149213 DOI: 10.1016/b978-0-12-394625-6.00002-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The relationship of mitochondrial DNA mutations to aging is still debated. Most mtDNA mutations are recessive: there are multiple copies per cell and mutation needs to clonally expand to cause respiratory deficiency. Overall mtDNA mutant loads are low, so effects of mutations are limited to critical areas where mutations locally reach high fractions. This includes respiratory chain deficient zones in muscle fibers, respiratory-deficient crypts in colon, and massive expansions of deleted mtDNA in substantia nigra neurons. mtDNA "mutator" mouse with increased rate of mtDNA mutations is a useful model, although rates and distribution of mutations may significantly deviate from what is observed in human aging. Comparison of species with different longevity reveals intriguing longevity-related traits in mtDNA sequence, although their significance is yet to be evaluated. The impact of somatic mtDNA mutations rapidly increases with age, so their importance is expected to grow as human life expectancy increases.
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Affiliation(s)
- Konstantin Khrapko
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Doug Turnbull
- LLHW Centre for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
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Kowald A, Klipp E. Mathematical models of mitochondrial aging and dynamics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 127:63-92. [PMID: 25149214 DOI: 10.1016/b978-0-12-394625-6.00003-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Research on the role of mitochondria in aging and disease is rapidly growing. Furthermore, in recent years, it also became clear that mitochondria are dynamic structures undergoing constant and rapid cycles of fusion and fission. The involvement of mitochondria in multiple complex processes makes them a prime target for mathematical and computational modeling. This review consists of two parts. In the first (Section 2), we provide a detailed introduction to the underlying concepts of mathematical modeling to help the reader who is not so familiar with these techniques to judge the requirements and results that can be obtained through modeling. In the second part (Section 3), we review existing mathematical and computational models that investigate mitochondrial dynamics and the role of mitochondria for the aging process.
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Affiliation(s)
- Axel Kowald
- Theoretical Biophysics, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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