scholarly journals Novel Lines of Evidence for the Asymmetric Strand Displacement Model of Mitochondrial DNA Replication

2018 ◽  
Vol 39 (2) ◽  
Author(s):  
Chih-Lin Hsieh
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Genome ◽  
Strand Displacement ◽  
Single Stranded Dna ◽  
Quantitative Evidence ◽  
Qualitative And Quantitative ◽  
Mtdna Replication ◽  
Displacement Model

ABSTRACT The mitochondrial genome, which consists of 16,569 bp of DNA with a cytosine-rich light (L) strand and a heavy (H) strand, exists as a multicopy closed circular genome within the mitochondrial matrix. The machinery for replication of the mammalian mitochondrial genome is distinct from that for replication of the nuclear genome. Three models have been proposed for mitochondrial DNA (mtDNA) replication, and one of the key differences among them is whether extensive single-stranded regions exist on the H strand. Here, three different methods that can detect single-stranded DNA (ssDNA) are utilized to identify the presence, location, and abundance of ssDNA on mtDNA. Importantly, none of these newly described methods involve the complication of prior mtDNA fractionation. The H strand was found to have extensive single-stranded regions with a profile consistent with the strand displacement model of mtDNA replication, whereas single strandedness was predominantly absent on the L strand. These findings are consistent with the in vivo occupancy of mitochondrial single-stranded DNA binding protein reported previously and provide strong new qualitative and quantitative evidence for the asymmetric strand displacement model of mtDNA replication.

scholarly journals Stress and corticosteroids regulate rat hippocampal mitochondrial DNA gene expression via the glucocorticoid receptor

2016 ◽  
Vol 113 (32) ◽  
pp. 9099-9104 ◽  
Author(s):  
Richard G. Hunter ◽  
Ma’ayan Seligsohn ◽  
Todd G. Rubin ◽  
Brian B. Griffiths ◽  
Yildirim Ozdemir ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Acute Stress ◽  
Nuclear Genome ◽  
Brain Mitochondria ◽  
Male Rats ◽  
Chip Sequencing ◽  
Corticosterone Treatment ◽  
Stress Dependent

Glucocorticoids (GCs) are involved in stress and circadian regulation, and produce many actions via the GC receptor (GR), which is classically understood to function as a nuclear transcription factor. However, the nuclear genome is not the only genome in eukaryotic cells. The mitochondria also contain a small circular genome, the mitochondrial DNA (mtDNA), that encodes 13 polypeptides. Recent work has established that, in the brain and other systems, the GR is translocated from the cytosol to the mitochondria and that stress and corticosteroids have a direct influence on mtDNA transcription and mitochondrial physiology. To determine if stress affects mitochondrially transcribed mRNA (mtRNA) expression, we exposed adult male rats to both acute and chronic immobilization stress and examined mtRNA expression using quantitative RT-PCR. We found that acute stress had a main effect on mtRNA expression and that expression of NADH dehydrogenase 1, 3, and 6 (ND-1, ND-3, ND-6) and ATP synthase 6 (ATP-6) genes was significantly down-regulated. Chronic stress induced a significant up-regulation of ND-6 expression. Adrenalectomy abolished acute stress-induced mtRNA regulation, demonstrating GC dependence. ChIP sequencing of GR showed that corticosterone treatment induced a dose-dependent association of the GR with the control region of the mitochondrial genome. These findings demonstrate GR and stress-dependent transcriptional regulation of the mitochondrial genome in vivo and are consistent with previous work linking stress and GCs with changes in the function of brain mitochondria.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

scholarly journals Mitochondrial DNA polymorphism and cardiovascular continuum diseases

2018 ◽  
pp. 9-13
Author(s):  
М.В. Голубенко ◽  
Р.Р. Салахов ◽  
Т.В. Шумакова ◽  
С.В. Буйкин ◽  
О.А. Макеева ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Cardiovascular Diseases ◽  
Mitochondrial Genome ◽  
Dna Polymorphism ◽  
Nuclear Genome ◽  
Published Data ◽  
Human Populations ◽  
Mitochondrial Dna Polymorphism ◽  
Polymorphism Level ◽  
Cardiovascular Continuum

Митохондриальный геном кодирует жизненно важные белки субъединиц дыхательной цепи и характеризуется высоким уровнем полиморфизма в популяциях человека. Однако работы по поиску генов предрасположенности к многофакторным заболеваниям, в том числе сердечно-сосудистым, часто ограничиваются анализом ядерного генома. В то же время показано, что отдельные генотипы мтДНК могут отличаться более высокой или низкой эффективностью окислительного фосфорилирования. Выявлены ассоциации популяционного полиморфизма мтДНК с сердечно-сосудистыми заболеваниями. Согласно результатам наших исследований, а также опубликованных другими авторами результатам ассоциативных и функциональных исследований, можно говорить о том, что эффект полиморфизма мтДНК проявляется чаще не в предрасположенности к сердечно-сосудистым заболеваниям в целом, а в риске развития осложнений и коморбидных фенотипов в пределах синтропии сердечно-сосудистого континуума. Mitochondrial genome, encoding respiratory chain subunits, is characterized by high polymorphism level in human populations. In most studies for susceptibility genes for common diseases, including cardiovascular diseases, the analysis is limited to the nuclear genome. It was shown that particular mtDNA genotypes may differ by oxidative phosphorylation efficiency. Some associations of mtDNA polymorphisms with cardiovascular diseases have been found. According to our results and published data, we suggest that mtDNA effect on cardiovascular system does not manifest in predisposition to cardiovascular diseases themselves but rather in risk of complications and comorbidities in the cardiovascular continuum.

scholarly journals Mitochondrial Development during Life Cycle Differentiation of African Trypanosomes: Evidence for a Kinetoplast-dependent Differentiation Control Point

2002 ◽  
Vol 13 (10) ◽  
pp. 3747-3759 ◽  
Author(s):  
Mark W. Timms ◽  
Frederick J. van Deursen ◽  
Edward F. Hendriks ◽  
Keith R. Matthews
Keyword(s):  
Life Cycle ◽  
Rna Interference ◽  
Mitochondrial Genome ◽  
Topoisomerase Ii ◽  
Developmental Regulation ◽  
Control Point ◽  
Nuclear Genome ◽  
Mitochondrial Activity ◽  
African Trypanosomes

Life cycle differentiation of African trypanosomes entails developmental regulation of mitochondrial activity. This requires regulation of the nuclear genome and the kinetoplast, the trypanosome's unusual mitochondrial genome. To investigate the potential cross talk between the nuclear and mitochondrial genome during the events of differentiation, we have 1) disrupted expression of a nuclear-encoded component of the cytochrome oxidase (COX) complex; and 2) generated dyskinetoplastid cells, which lack a mitochondrial genome. Using RNA interference (RNAi) and by disrupting the nuclear COX VI gene, we demonstrate independent regulation of COX component mRNAs encoded in the nucleus and kinetoplast. However, two independent approaches (acriflavine treatment and RNA interference ablation of mitochondrial topoisomerase II) failed to establish clonal lines of dyskinetoplastid bloodstream forms. Nevertheless, dyskinetoplastid forms generated in vivo could undergo two life cycle differentiation events: transition from bloodstream slender to stumpy forms and the initiation of transformation to procyclic forms. However, they subsequently arrested at a specific point in this developmental program before cell cycle reentry. These results provide strong evidence for a requirement for kinetoplast DNA in the bloodstream and for a kinetoplast-dependent control point during differentiation to procyclic forms.

Bioresorbable Glass Fibres Facilitate Peripheral Nerve Regeneration

2005 ◽  
Vol 30 (3) ◽  
pp. 242-247 ◽  
Author(s):  
S. BUNTING ◽  
L. DI SILVIO ◽  
S. DEB ◽  
S. HALL
Keyword(s):  
Axonal Regeneration ◽  
Peripheral Nerve Regeneration ◽  
Adult Rats ◽  
Quantitative Evidence ◽  
Qualitative And Quantitative ◽  
Axonal Regrowth ◽  
Sciatic Nerves ◽  
Proof Of Principle

This is a proof of principle report showing that fibres of Bioglass® 45S5 can form a biocompatible scaffold to guide regrowing peripheral axons in vivo. We demonstrate that cultured rat Schwann cells and fibroblasts grow on Bioglass® fibres in vitro using SEM and immunohistochemistry, and provide qualitative and quantitative evidence of axonal regeneration through a Silastic conduit filled with Bioglass® fibres in vivo (across a 0.5 cm interstump gap in the sciatic nerves of adult rats). Axonal regrowth at 4 weeks is indistinguishable from that which occurs across an autograft. Bioglass® fibres are not only biocompatible and bioresorbable, which are absolute requirements of successful devices, but are also amenable to bioengineering, and therefore have the potential for use in the most challenging clinical cases, where there are long inter-stump gaps to be bridged.

scholarly journals Proofreading deficiency in mitochondrial DNA polymerase does not affect total dNTP pools in mouse embryos

2020 ◽  
Author(s):  
Sushma Sharma ◽  
Camilla Koolmeister ◽  
Phong Tran ◽  
Anna Karin Nilsson ◽  
Nils-Göran Larsson ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Genome ◽  
Living Organism ◽  
Mouse Embryos ◽  
Premature Aging ◽  
Genome Replication ◽  
Dntp Pool ◽  
Mtdna Replication ◽  
Induced Pluripotent ◽  
Mitochondrial Dna Polymerase

AbstractMitochondrial DNA (mtDNA) mutator mice express proofreading-deficient mtDNA polymerase gamma (PolgD257A) and age prematurely1,2, whereas mice with other mitochondrial defects do not show global signs of early aging. The reason for this discrepancy is not completely understood. Hämäläinen et al. recently reported that both induced pluripotent stem cells (iPSCs) and primary mutator embryonic fibroblasts harboring PolgD257A demonstrate increased mtDNA replication frequency leading to depletion of the total cellular dNTP pool3. The authors proposed that the decreased availability of cellular dNTPs for nuclear genome replication leads to compromised nuclear genome maintenance and premature aging. Here we report that total cellular dNTP pools are normal in mtDNA mutator mouse embryos (genotype: PolgD257A/D257A), which shows that a living organism exclusively expressing PolgD257A has normal total dNTP pools despite ubiquitous rapid cell division.

scholarly journals Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia Magna

2020 ◽  
Author(s):  
Krzysztof Kowal ◽  
Angelika Tkaczyk ◽  
Mariusz Pierzchała ◽  
Adam Bownik ◽  
Brygida Ślaska
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Daphnia Magna ◽  
Sequence Homology ◽  
Nuclear Genome ◽  
Complete Information ◽  
Trna Genes ◽  
Entire Genome ◽  
Mtdna Sequence ◽  
D Loop

Abstract Background: This is the first study in which the Daphnia magna (D. magna) nuclear genome deposited in the GenBank data-base was analyzed for pseudogene sequences of mitochondrial origin. The first complete information about the genome of D. magna was published by Lee et al. in 2019. To date, there is no information about pseudogenes localized in the genome of D. magna . The aim of the present study was to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome analyses.Results: Bioinformatic analysis showed 1909 fragments of the mitochondrial genome of D. magna , of which 1630 fragments were located in ten linkage groups (LG) of the nuclear genome (nDNA). The most frequently occurring fragments of the mtDNA sequence in the nuclear genome included ND2 (115), ND3 (113), and TRNA-CYS (110)). However, the highest number of NUMTs was observed for the D-loop (147). 253 fragments showed 100% homology (from 16 to 46 bp) with mtDNA gene sequences. The sequence homology for TRNA-MET was 100% for all 6 NUMTs (from 16 to 18 bp). The overall length of NUMTs in the nDNA was 44.391 bp (from 16 to 182 bp), which accounted for 0.042% of the entire genome.Conclusions: The best-matched NUMTs covering more than 90% of the mtDNA gene sequence have been identified for the TRNA-ARG (95%), TRNA-GLU (97%), and TRNA-THR (95%) genes, and they may be included in the functional nuclear tRNA genes. Using the product of total DNA isolation in mtDNA studies, coamplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes and the D-loop with a length exceeding 200 bp. It was observed that TRNA-MET fragments had the highest level of sequence homology, which means that they could be evolutionarily the youngest. The lowest degree of homology was found in the pseudogene derived from the mtDNA D-loop sequence. It may probably be the oldest element of mitochondrial DNA incorporated into the nuclear genome; however, further analysis is necessary.

scholarly journals Mitochondrial sequences or Numts – By-catch differs between sequencing methods

2019 ◽  
Author(s):  
Hannes Becher ◽  
Richard A Nichols
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Genome ◽  
Short Read ◽  
Ancestral Sequences ◽  
Mtdna Sequence ◽  
Long Read ◽  
Data Yield ◽  
By Catch ◽  
Numt Sequence

AbstractNuclear inserts derived from mitochondrial DNA (Numts) encode valuable information. Being mostly non-functional, and accumulating mutations more slowly than mitochondrial sequence, they act like molecular fossils – they preserve information on the ancestral sequences of the mitochondrial DNA. In addition, changes to the Numt sequence since their insertion into the nuclear genome carry information about the nuclear phylogeny. These attributes cannot be reliably exploited if Numt sequence is confused with the mitochondrial genome (mtDNA). The analysis of mtDNA would be similarly compromised by any confusion, for example producing misleading results in DNA barcoding that used mtDNA sequence. We propose a method to distinguish Numts from mtDNA, without the need for comprehensive assembly of the nuclear genome or the physical separation of organelles and nuclei. It exploits the different biases of long and short-read sequencing. We find that short-read data yield mainly mtDNA sequences, whereas long-read sequencing strongly enriches for Numt sequences. We demonstrate the method using genome-skimming (coverage < 1x) data obtained on Illumina short-read and PacBio long-read technology from DNA extracted from six grasshopper individuals. The mitochondrial genome sequences were assembled from the short-read data despite the presence of Numts. The PacBio data contained a much higher proportion of Numt reads (over 16-fold), making us caution against the use of long-read methods for studies using mitochondrial loci. We obtained two estimates of the genomic proportion of Numts. Finally, we introduce “tangle plots”, a way of visualising Numt structural rearrangements and comparing them between samples.

A study of mitochondrial DNA mutations in peripheral lymphocytes in an aging cohort

2003 ◽  
Vol 31 (2) ◽  
pp. 444-446 ◽  
Author(s):  
B. Zhang ◽  
S. Ye ◽  
A.A. Sayer ◽  
S.R. Hammans ◽  
S. Adio ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Somatic Mutation ◽  
Large Scale ◽  
Nuclear Genome ◽  
Epidemiological Studies ◽  
Elderly Subjects ◽  
Long Pcr ◽  
Peripheral Lymphocytes ◽  
Wide Range

Somatic mutation in the mitochondrial genome occurs much more rapidly than in the nuclear genome and is a feature, possibly contributory, of the aging of cells and tissues. Identifying mitochondrial sequence changes in blood DNA of elderly subjects may provide a maker for the epigenetic changes of mitochondrial DNA known to occur in tissues with lower cellular turnover, and would also have implications for immunosenescence. No large-scale epidemiological studies have been reported previously. In this study we have established long-PCR banks of the mitochondrial genome from peripheral lymphocytes for an elderly cohort of 716 individuals with a range of measured aging phenotypes, and we have established assays for three widely reported mutations: the 4977 bp and 8048 bp deletions and point mutation A3243G. No individuals were identified with detectable heteroplasmy for these changes. Implications for tissue and population prevalence are discussed. The mitochondrial long-PCR DNA banks established will be useful for a wide range of studies of somatic mutation and of germline haplotypes in relation to aging.

scholarly journals Mitochondrial Fostering: The Mitochondrial Genome May Play a Role in Plant Orphan Gene Evolution

2020 ◽  
Vol 11 ◽  
Author(s):  
Seth O’Conner ◽  
Ling Li
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Gene Evolution ◽  
Nuclear Genome ◽  
Bioinformatic Analysis ◽  
Land Plants ◽  
Mitochondrial Genomes ◽  
Recombination Rates ◽  
Orphan Genes ◽  
Orphan Gene

Plant mitochondrial genomes exhibit unique evolutionary patterns. They have a high rearrangement but low mutation rate, and a large size. Based on massive mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique evolutionary traits, we propose a “Mitochondrial Fostering” theory where the organelle genome plays an integral role in the arrival and development of orphan genes (genes with no homologs in other lineages). Two approaches were used to test this theory: (1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial originating DNA that migrated to the nucleus) at the genome level, and (2) bioinformatic analysis of particular orphan sequences present in both the mitochondrial genome and the nuclear genome of Arabidopsis thaliana. One study example is given about one orphan sequence that codes for two unique orphan genes: one in the mitochondrial genome and another one in the nuclear genome. DNA alignments show regions of this A. thaliana orphan sequence exist scattered throughout other land plant mitochondrial genomes. This is consistent with the high recombination rates of mitochondrial genomes in land plants. This may also enable the creation of novel coding sequences within the orphan loci, which can then be transferred to the nuclear genome and become exposed to new evolutionary pressures. Our study also reveals a high correlation between the amount of mitochondrial DNA transferred to the nuclear genome and the number of orphan genes in land plants. All the data suggests the mitochondrial genome may play a role in nuclear orphan gene evolution in land plants.

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