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Wang X, Weidling I, Koppel S, Menta B, Perez Ortiz J, Kalani A, Wilkins HM, Swerdlow RH. Detection of mitochondria-pertinent components in exosomes. Mitochondrion 2020; 55:100-110. [PMID: 32980480 PMCID: PMC7669644 DOI: 10.1016/j.mito.2020.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/27/2020] [Accepted: 09/18/2020] [Indexed: 01/01/2023]
Abstract
We screened cell line and plasma-derived exosomes for molecules that localize to mitochondria or that reflect mitochondrial integrity. SH-SY5Y cell-derived exosomes contained humanin, citrate synthase, and fibroblast growth factor 21 protein, and plasma-derived exosomes contained humanin, voltage-dependent anion-selective channel 1, and transcription factor A protein. Nuclear mitochondrial (NUMT) DNA complicated analyses of mitochondrial DNA (mtDNA), which otherwise suggested exosomes contain at most very low amounts of extended mtDNA sequences but likely contain degraded pieces of mtDNA. Cell and plasma-derived exosomes contained several mtDNA-derived mRNA sequences, including those for ND2, CO2, and humanin. These results can guide exosome-focused, mitochondria-pertinent biomarker development.
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Affiliation(s)
- Xiaowan Wang
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Ian Weidling
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Scott Koppel
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Blaise Menta
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Judit Perez Ortiz
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Anuradha Kalani
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Heather M Wilkins
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Russell H Swerdlow
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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2
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Li W, Freudenberg J, Freudenberg J. Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome. Gene 2019; 691:141-152. [PMID: 30630097 DOI: 10.1016/j.gene.2018.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
Abstract
The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Jerome Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Jan Freudenberg
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
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3
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Benedict BD, Castellanos AA, Light JE. Phylogeographic assessment of the Heermann’s kangaroo rat (Dipodomys heermanni). J Mammal 2018. [DOI: 10.1093/jmammal/gyy166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Bridgett D Benedict
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Adrian A Castellanos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
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4
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Abstract
In recent years, a number of advancements have been made in the study of entire mitochondrial proteomes in both physiological and pathological conditions. Naturally occurring iodothyronines (i.e., T3 and T2) greatly influence mitochondrial oxidative capacity, directly or indirectly affecting the structure and function of the respiratory chain components. Blue native PAGE (BN-PAGE) can be used to isolate enzymatically active oxidative phosphorylation (OXPHOS) complexes in one step, allowing the clinical diagnosis of mitochondrial metabolism by monitoring OXPHOS catalytic and/or structural features. Protocols for isolating mammalian liver mitochondria and subsequent one-dimensional (1D) BN-PAGE will be described in relation to the impact of thyroid hormones on mitochondrial bioenergetics.
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5
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Xu J, Sheng Y, Xu F, Yu Y, Chen Y. Quantitative subcellular study of transferrin receptor-targeted doxorubicin and its metabolite in human breast cancer cells. Eur J Drug Metab Pharmacokinet 2013; 39:301-10. [PMID: 24363124 DOI: 10.1007/s13318-013-0165-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
Abstract
The extended use of doxorubicin (DOX) could be limited due to the emergence of drug resistance and cardiotoxicity associated with its treatment. Conjugates of DOX with transferrin (DOX-TRF) can effectively alleviate these side effects, thereby leading to a better treatment. The effectiveness of DOX-TRF could result from the enhancement of transferrin receptor (TfR)-mediated transportation. However, detailed TfR-mediated DOX delivery has not been fully elucidated thus far, which may rely on the quantitative subcellular study of DOX distribution and metabolism. In this study, an immunoisolation assay was developed to isolate the organelles with high purity, yield and integrity. Using this immunoisolation assay together with liquid chromatography-tandem mass spectrometry (LC/MS/MS), the subcellular distribution profiles of DOX and its main metabolite doxorubicinol (DOXol) in human breast cancer cells MCF-7/WT and MCF-7/ADR were determined and compared after the treatment of DOX and DOX-TRF. As expected, DOX-TRF treated cells have a higher drug accumulation compared to DOX treated cells. DOX-TRF was predominantly cytoplasmic. In addition, TfR-mediated transportation had a significant impact on the transformation of DOX to DOXol in the cells. This study provided the evidence that immunoisolation together with LC/MS/MS is an effective technique in subcellular investigations.
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Affiliation(s)
- Jinhui Xu
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing, 211166, China
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6
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Lyons EA, Scheible MK, Sturk-Andreaggi K, Irwin JA, Just RS. A high-throughput Sanger strategy for human mitochondrial genome sequencing. BMC Genomics 2013; 14:881. [PMID: 24341507 PMCID: PMC3878621 DOI: 10.1186/1471-2164-14-881] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/19/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND A population reference database of complete human mitochondrial genome (mtGenome) sequences is needed to enable the use of mitochondrial DNA (mtDNA) coding region data in forensic casework applications. However, the development of entire mtGenome haplotypes to forensic data quality standards is difficult and laborious. A Sanger-based amplification and sequencing strategy that is designed for automated processing, yet routinely produces high quality sequences, is needed to facilitate high-volume production of these mtGenome data sets. RESULTS We developed a robust 8-amplicon Sanger sequencing strategy that regularly produces complete, forensic-quality mtGenome haplotypes in the first pass of data generation. The protocol works equally well on samples representing diverse mtDNA haplogroups and DNA input quantities ranging from 50 pg to 1 ng, and can be applied to specimens of varying DNA quality. The complete workflow was specifically designed for implementation on robotic instrumentation, which increases throughput and reduces both the opportunities for error inherent to manual processing and the cost of generating full mtGenome sequences. CONCLUSIONS The described strategy will assist efforts to generate complete mtGenome haplotypes which meet the highest data quality expectations for forensic genetic and other applications. Additionally, high-quality data produced using this protocol can be used to assess mtDNA data developed using newer technologies and chemistries. Further, the amplification strategy can be used to enrich for mtDNA as a first step in sample preparation for targeted next-generation sequencing.
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Affiliation(s)
| | | | | | | | - Rebecca S Just
- American Registry of Pathology, 120A Old Camden Rd,, Camden DE 19934, USA.
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Padrão AI, Vitorino R, Duarte JA, Ferreira R, Amado F. Unraveling the phosphoproteome dynamics in mammal mitochondria from a network perspective. J Proteome Res 2013; 12:4257-67. [PMID: 23964737 DOI: 10.1021/pr4003917] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With mitochondrion garnering more attention for its inextricable involvement in pathophysiological conditions, it seems imperative to understand the means by which the molecular pathways harbored in this organelle are regulated. Protein phosphorylation has been considered a central event in cellular signaling and, more recently, in the modulation of mitochondrial activity. Efforts have been made to understand the molecular mechanisms by which protein phosphorylation regulates mitochondrial signaling. With the advances in mass-spectrometry-based proteomics, there is a substantial hope and expectation in the increased knowledge of protein phosphorylation profile and its mode of regulation. On the basis of phosphorylation profiles, attempts have been made to disclose the kinases involved and how they control the molecular processes in mitochondria and, consequently, the cellular outcomes. Still, few studies have focused on mitochondrial phosphoproteome profiling, particularly in diseases. The present study reviews current data on protein phosphorylation profiling in mitochondria, the potential kinases involved and how pathophysiological conditions modulate the mitochondrial phosphoproteome. To integrate data from distinct research papers, we performed network analysis, with bioinformatic tools like Cytoscape, String, and PANTHER taking into consideration variables such as tissue specificity, biological processes, molecular functions, and pathophysiological conditions. For instance, data retrieved from these analyses evidence some homology in the mitochondrial phosphoproteome among liver and heart, with proteins from transport and oxidative phosphorylation clusters particularly susceptible to phosphorylation. A distinct profile was noticed for adipocytes, with proteins form metabolic processes, namely, triglycerides metabolism, as the main targets of phosphorylation. Regarding disease conditions, more phosphorylated proteins were observed in diabetics with some distinct phosphoproteins identified in type 2 prediabetic states and early type 2 diabetes mellitus. Heart-failure-related phosphorylated proteins are in much lower amount and are mainly involved in transport and metabolism. Nevertheless, technical considerations related to mitochondria isolation and protein separation should be considered in data comparison among different proteomic studies. Data from the present review will certainly open new perspectives of protein phosphorylation in mitochondria and will help to envisage future studies targeting the underlying regulatory mechanisms.
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Affiliation(s)
- Ana Isabel Padrão
- QOPNA, Department of Chemistry, University of Aveiro , 3810-193 Aveiro, Portugal
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8
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Kim SJ, Lee KY, Ju SJ. Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding. Mol Ecol Resour 2013; 13:781-7. [PMID: 23663201 DOI: 10.1111/1755-0998.12119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 11/30/2022]
Abstract
Members of the brachyuran crab family, Bythograeidae, are among the most abundant and common crabs in vent fields. However, their identification based on morphological characteristics often leads to incorrect species recognition due to a lack of taxonomic factors and the existence of sibling (or cryptic) species. For these reasons, we used DNA barcoding for vent crabs using mitochondrial cytochrome c oxidase subunit 1 (CO1). However, several nuclear mitochondrial pseudogenes (Numts) were amplified from Austinograea alayseae Guinot, 1990, using universal primers (Folmer primers). The Numts were characterized in six haplotypes, with 13.58-14.11% sequence divergence from A. alayseae, a higher nonsynonymous substitution ratio than true CO1, and the formation of an independent clade in bythograeids. In a neighbour-joining tree, the origin of the Numts would be expected to incorporate into the nucleus at an ancestral node of Austinograea, and they mutated more slowly in the nucleus than CO1 in the mitochondria. This evolutionary process may have resulted in the higher binding affinity of Numts for the Folmer primers than CO1. In the present study, we performed long PCR for the amplification of CO1 in A. alayseae. We also present evidence that Numts can introduce serious ambiguity into DNA barcoding, including overestimating the number of species in bythograeids. These results may help in conducting taxonomic studies using mitochondrial genes from organisms living in hydrothermal vent fields.
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Affiliation(s)
- Se-Joo Kim
- Deep-sea and Seabed Resources Research Division, Korea Institute of Ocean Science & Technology, Gyeonggi-do, 426-744, Korea
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9
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Glutaminase immunoreactivity and enzyme activity is increased in the rat dorsal root ganglion following peripheral inflammation. PAIN RESEARCH AND TREATMENT 2011; 2012:414697. [PMID: 22229088 PMCID: PMC3250962 DOI: 10.1155/2012/414697] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/29/2011] [Accepted: 09/08/2011] [Indexed: 01/16/2023]
Abstract
Following inflammation, primary sensory neurons in the dorsal root ganglion (DRG) alter the production of several proteins. Most DRG neurons are glutamatergic, using glutaminase as the enzyme for glutamate production, but little is known about glutaminase following inflammation. In the present study, adjuvant-induced arthritis (AIA) was produced in rats with complete Freund's adjuvant into the hindpaw. At 7 days of AIA, DRG were examined with glutaminase immunohistochemistry, Western blot immunoreactivity, and enzyme activity. Image analysis revealed that glutaminase was elevated most in small-sized neurons (21%) (P < 0.05). Western blot analysis revealed a 19% increase (P < 0.05) in total glutaminase and 21% in mitochondrial glutaminase (P < 0.05). Glutaminase enzyme activity was elevated 29% (P < 0.001) from 2.20 to 2.83 moles/kg/hr. Elevated glutaminase in primary sensory neurons could lead to increased glutamate production in spinal primary afferent terminals contributing to central sensitization or in the peripheral process contributing to peripheral sensitization.
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10
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Ovchinnikov IV, Kholina OI. Genome digging: insight into the mitochondrial genome of Homo. PLoS One 2010; 5:e14278. [PMID: 21151557 PMCID: PMC3000329 DOI: 10.1371/journal.pone.0014278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 11/17/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt) on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1) into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split. PRINCIPAL FINDINGS Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2) with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively. CONCLUSIONS This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N)/d(S) dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective population size and possessed genetic diversity comparable with those of chimpanzee and gorilla.
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Affiliation(s)
- Igor V Ovchinnikov
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, United States of America.
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11
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Erpenbeck D, Voigt O, Adamski M, Woodcroft BJ, Hooper JNA, Worheide G, Degnan BM. NUMTs in the Sponge Genome Reveal Conserved Transposition Mechanisms in Metazoans. Mol Biol Evol 2010; 28:1-5. [DOI: 10.1093/molbev/msq217] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Ruiz-Romero C, Blanco FJ. Mitochondrial proteomics and its application in biomedical research. MOLECULAR BIOSYSTEMS 2009; 5:1130-42. [DOI: 10.1039/b906296n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Magda D, Lecane P, Prescott J, Thiemann P, Ma X, Dranchak PK, Toleno DM, Ramaswamy K, Siegmund KD, Hacia JG. mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft. BMC Genomics 2008; 9:521. [PMID: 18980691 PMCID: PMC2612029 DOI: 10.1186/1471-2164-9-521] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 11/03/2008] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in eukaryotic cellular function. However, the effects mitochondrial DNA (mtDNA) levels have on the nuclear transcriptome have not been defined under physiological conditions. In order to address this issue, we characterized the gene expression profiles of A549 lung cancer cells and their mtDNA-depleted rho0 counterparts grown in culture and as tumor xenografts in immune-deficient mice. RESULTS Cultured A549 rho0 cells were respiration-deficient and showed enhanced levels of transcripts relevant to metal homeostasis, initiation of the epithelial-mesenchymal transition, and glucuronidation pathways. Several well-established HIF-regulated transcripts showed increased or decreased abundance relative to the parental cell line. Furthermore, growth in culture versus xenograft has a significantly greater influence on expression profiles, including transcripts involved in mitochondrial structure and both aerobic and anaerobic energy metabolism. However, both in vitro and in vivo, mtDNA levels explained the majority of the variance observed in the expression of transcripts in glucuronidation, tRNA synthetase, and immune surveillance related pathways. mtDNA levels in A549 xenografts also affected the expression of genes, such as AMACR and PHYH, involved in peroxisomal lipid metabolic pathways. CONCLUSION We have identified mtDNA-dependent gene expression profiles that are shared in cultured cells and in xenografts. These profiles indicate that mtDNA-depleted cells could provide informative model systems for the testing the efficacy of select classes of therapeutics, such as anti-angiogenesis agents. Furthermore, mtDNA-depleted cells grown culture and in xenografts provide a powerful means to investigate possible relationships between mitochondrial activity and gene expression profiles in normal and pathological cells.
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Affiliation(s)
- Darren Magda
- Department of Biochemistry and Molecular Biology, University of Southern California, 2250 Alcazar Street, IGM 240, Los Angeles, CA 90089, USA.
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15
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Gherman A, Chen PE, Teslovich TM, Stankiewicz P, Withers M, Kashuk CS, Chakravarti A, Lupski JR, Cutler DJ, Katsanis N. Population bottlenecks as a potential major shaping force of human genome architecture. PLoS Genet 2008; 3:e119. [PMID: 17658953 PMCID: PMC1925129 DOI: 10.1371/journal.pgen.0030119] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 06/04/2007] [Indexed: 11/24/2022] Open
Abstract
The modern synthetic view of human evolution proposes that the fixation of novel mutations is driven by the balance among selective advantage, selective disadvantage, and genetic drift. When considering the global architecture of the human genome, the same model can be applied to understanding the rapid acquisition and proliferation of exogenous DNA. To explore the evolutionary forces that might have morphed human genome architecture, we investigated the origin, composition, and functional potential of numts (nuclear mitochondrial pseudogenes), partial copies of the mitochondrial genome found abundantly in chromosomal DNA. Our data indicate that these elements are unlikely to be advantageous, since they possess no gross positional, transcriptional, or translational features that might indicate beneficial functionality subsequent to integration. Using sequence analysis and fossil dating, we also show a probable burst of integration of numts in the primate lineage that centers on the prosimian–anthropoid split, mimics closely the temporal distribution of Alu and processed pseudogene acquisition, and coincides with the major climatic change at the Paleocene–Eocene boundary. We therefore propose a model according to which the gross architecture and repeat distribution of the human genome can be largely accounted for by a population bottleneck early in the anthropoid lineage and subsequent effectively neutral fixation of repetitive DNA, rather than positive selection or unusual insertion pressures. Throughout evolutionary history, fragments of the mitochondrial genome, known as numts (for nuclear mitochondrial sequences), have been inserted into the nuclear genome. These fragments are distinct from all other classes of repetitive DNA found in nuclear genomes, not least because they are incapable of mediating their own proliferation. Taking advantage of their unique evolutionary properties, we have used numts to improve our understanding of the architecture of the human genome with special emphasis on the mechanism of acquisition and retention of repeat sequences, which comprise the bulk of nuclear DNA. We find that numts are unlikely to have any evolutionary benefit driving their retention. Moreover, numts are not acquired randomly during evolutionary time. Instead, their rate of acquisition spikes dramatically around pronounced population bottlenecks, in a manner reminiscent of other repeat classes. Therefore, we propose that the primary driving force of repeat acquisition in the genome is not selection, but random genetic drift, whose force becomes pronounced during profound reductions of population size. Our findings support the theory of neutral evolution, according to which random genetic drift exerts an influence on the acquisition of DNA changes that far outweighs the power of positive selection.
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MESH Headings
- Alu Elements
- Animals
- Cell Line
- Chromosome Mapping
- DNA/genetics
- DNA, Mitochondrial/genetics
- Evolution, Molecular
- Genetic Drift
- Genetics, Population
- Genome, Human
- Genome, Mitochondrial
- Humans
- In Situ Hybridization, Fluorescence
- Models, Genetic
- Primates/genetics
- Protein Biosynthesis
- Pseudogenes
- Repetitive Sequences, Nucleic Acid
- Selection, Genetic
- Time Factors
- Transcription, Genetic
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Affiliation(s)
- Adrian Gherman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Peter E Chen
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tanya M Teslovich
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marjorie Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Carl S Kashuk
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - David J Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail: (DJC); (NK)
| | - Nicholas Katsanis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail: (DJC); (NK)
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16
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Jeon JP, Shim SM, Nam HY, Baik SY, Kim JW, Han BG. Copy number increase of 1p36.33 and mitochondrial genome amplification in Epstein-Barr virus-transformed lymphoblastoid cell lines. ACTA ACUST UNITED AC 2007; 173:122-30. [PMID: 17321327 DOI: 10.1016/j.cancergencyto.2006.10.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 10/17/2006] [Accepted: 10/19/2006] [Indexed: 11/22/2022]
Abstract
Array CGH has been applied to detect chromosomal aberrations in cancer and genetic diseases. Epstein-Barr virus (EBV)-infected B lymphocytes are transformed to continuously proliferating lymphoblastoid cell lines (LCLs), which are a very common genome resource for human genetic studies. We used bacterial artificial chromosome (BAC) array CGH to assess a chromosomal aberration of LCLs in EBV-induced B-cell transformation. At early passages, LCLs exhibited a greater copy number variation in 1p36.33 compared to primary B-cells. Quantitative polymerase chain reaction (PCR) confirmed the increase in the copy number in 1p36.33. Because a segment of 1p36.33 is nearly identical to a part of the mitochondrial DNA, this increase was attributed to an increase in the copy number of mitochondrial DNA. The expression levels of mitochondrial biogenesis-related genes were elevated in the LCLs, which is consistent with the increased copy numbers of mitochondrial DNA, suggesting that increased mitochondrial biogenesis is indicative of the progression of EBV-mediated B-cell transformation. In addition, our array CGH of LCLs revealed potential copy number polymorphisms of chromosomal segments among Korean populations. Taken together, these findings suggest that LCLs in the early passages preserve the chromosomal integrity of primary B-cells at the cytogenetic level during EBV-transformed B-cell immortalization, except for a copy number variation in 1p36.33 due to increased mitochondrial DNA copy numbers. Thus, analyses of array CGH profiles of diseases should take into account the potential for copy number variation of 1p36.33.
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MESH Headings
- Aneuploidy
- Cell Line, Transformed
- Cell Transformation, Viral/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Human, Pair 1/genetics
- DNA, Mitochondrial/genetics
- Gene Amplification
- Gene Expression
- Genome, Human/genetics
- Herpesvirus 4, Human/physiology
- Humans
- Lymphocytes/metabolism
- Lymphocytes/pathology
- Lymphocytes/virology
- Microarray Analysis/methods
- Mitochondrial Proteins/genetics
- Nucleic Acid Hybridization/methods
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
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Affiliation(s)
- Jae-Pil Jeon
- BioBank for Health Sciences, Center for Genome Science, National Institute of Health, Korea Center for Disease Control and Prevention, 5 Nokbun, Eunpyung-Gu, Seoul 122-701, Republic of Korea
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17
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Abstract
The HapMap data are being widely used in human genetic studies. We show by direct resequencing of a approximately 6-kb region of chromosome 1 that the HapMap data are unreliable for this region. This region contains a recent mitochondrial (mt) DNA insertion. The HapMap data report the corresponding mtDNA variation and not the nuclear DNA variation. In view of mtDNA insertions of varying lengths throughout the human genome and considerable segmental duplications, it is necessary to use the HapMap data cautiously.
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Affiliation(s)
- Nidhan K Biswas
- Human Genetics Unit, Indian Statistical Institute, Kolkata, West Bengal, India
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Hazkani-Covo E, Graur D. A Comparative Analysis of numt Evolution in Human and Chimpanzee. Mol Biol Evol 2006; 24:13-8. [PMID: 17056643 DOI: 10.1093/molbev/msl149] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial DNA sequences are frequently transferred into the nuclear genome, giving rise to numts (nuclear DNA sequences of mitochondrial origin). So far, the evolutionary history of numts has largely been studied by using single genomes. Here, we present the first attempt to study numt evolution in a comparative manner by using a pairwise genomic alignment. The total number of numts was estimated to be 452 in human and 469 in chimpanzee. numts that were found in both genomes at identical loci were deemed to be orthologous; 391 numts (>80%) were classified as such. The preponderance of orthologous numts is due to the very short divergence time between the 2 hominoids. The rest of numts were deemed to be nonorthologous. Nonorthologous numts were subdivided into 1) ancestral numts that have lost an ortholog in one species through deletion (12 in human and 11 in chimpanzee), 2) new numts acquired by the insertion of a mitochondrial sequence after the divergence of the 2 species (34 in human and 46 in chimpanzee), and 3) paralogous numts created by the tandem duplication of a preexisting numt (2 in human). This approach also enabled us to reconstruct the numt repertoire in the common ancestor of humans and chimpanzees (409 numts). Our comparative approach is also useful in identifying the exact boundaries of numts.
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Parr RL, Maki J, Reguly B, Dakubo GD, Aguirre A, Wittock R, Robinson K, Jakupciak JP, Thayer RE. The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation. BMC Genomics 2006; 7:185. [PMID: 16859552 PMCID: PMC1538596 DOI: 10.1186/1471-2164-7-185] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 07/21/2006] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Nuclear mitochondrial pseudogenes (numts) are a potential source of contamination during mitochondrial DNA PCR amplification. This possibility warrants careful experimental design and cautious interpretation of heteroplasmic results. RESULTS Here we report the cloning and sequencing of numts loci, amplified from human tissue and rho-zero (rho0) cells (control) with primers known to amplify the mitochondrial genome. This paper is the first to fully sequence 46 paralogous nuclear DNA fragments that represent the entire mitochondrial genome. This is a surprisingly small number due primarily to the primer sets used in this study, because prior to this, BLAST searches have suggested that nuclear DNA harbors between 400 to 1,500 paralogous mitochondrial DNA fragments. Our results indicate that multiple numts were amplified simultaneously with the mitochondrial genome and increased the load of pseudogene signal in PCR reactions. Further, the entire mitochondrial genome was represented by multiple copies of paralogous nuclear sequences. CONCLUSION These findings suggest that mitochondrial genome disease-associated biomarkers must be rigorously authenticated to preclude any affiliation with paralogous nuclear pseudogenes. Importantly, the common perception that mitochondrial template "swamps" numts loci precluding detectable amplification, depends on the region of the mitochondrial genome targeted by the PCR reaction and the number of pseudogene loci that may co-amplify. Cloning and relevant sequencing data will facilitate the correct interpretation. This is the first complete, wet-lab characterization of numts that represent the entire mitochondrial genome.
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Affiliation(s)
- Ryan L Parr
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Jennifer Maki
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Brian Reguly
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Gabriel D Dakubo
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Andrea Aguirre
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Roy Wittock
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Kerry Robinson
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - John P Jakupciak
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Robert E Thayer
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
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20
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Kim JH, Antunes A, Luo SJ, Menninger J, Nash WG, O’Brien SJ, Johnson WE. Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species. Gene 2005; 366:292-302. [PMID: 16380222 PMCID: PMC1592465 DOI: 10.1016/j.gene.2005.08.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 08/03/2005] [Accepted: 08/30/2005] [Indexed: 10/25/2022]
Abstract
Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondrial genome, is one of the largest to be reported in eukaryotes. The Panthera genus numt differs from the numt previously described in the Felis genus in: (1) chromosomal location (F2-telomeric region vs. D2-centromeric region), (2) gene make up (from the ND5 to the ATP8 vs. from the CR to the COII), (3) size (12.5 vs. 7.9 kb), and (4) structure (single monomer vs. tandemly repeated in Felis). These distinctions indicate that the origin of this large numt fragment in the nuclear genome of the Panthera species is an independent insertion from that of the domestic cat lineage, which has been further supported by phylogenetic analyses. The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species.
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Affiliation(s)
- Jae-Heup Kim
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick Cancer Research and Development Center (NCI-FCRDC), Frederick, MD 21702-1201, USA
| | - Agostinho Antunes
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick Cancer Research and Development Center (NCI-FCRDC), Frederick, MD 21702-1201, USA
- REQUIMTE, Grupo de Química Teórica e Computacional – Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Shu-Jin Luo
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick Cancer Research and Development Center (NCI-FCRDC), Frederick, MD 21702-1201, USA
| | - Joan Menninger
- Basic Research Program, SAIC-Frederick, Inc., NCI Frederick, Frederick, MD, USA
| | | | - Stephen J. O’Brien
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick Cancer Research and Development Center (NCI-FCRDC), Frederick, MD 21702-1201, USA
| | - Warren E. Johnson
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick Cancer Research and Development Center (NCI-FCRDC), Frederick, MD 21702-1201, USA
- * Corresponding author. Tel.: 301-846-7483; fax: 301-846-6327. E-mail: (W.E. Johnson)
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21
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Binder DR, Dunn WH, Swerdlow RH. Molecular characterization of mtDNA depleted and repleted NT2 cell lines. Mitochondrion 2005; 5:255-65. [PMID: 16050988 DOI: 10.1016/j.mito.2005.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2005] [Revised: 04/25/2005] [Accepted: 04/26/2005] [Indexed: 10/25/2022]
Abstract
Transmitochondrial cytoplasmic hybrids (cybrids) enable functional assessment of mitochondrial DNA (mtDNA)-encoded proteins. Cybrid production often utilizes cell lines depleted of endogenous mtDNA (rho0 cells), and a number of suitable rho0 cell lines exist for this purpose. We now provide molecular data characterizing an NT2 human teratocarcinoma rho0 cell line, as well as NT2 cybrid derivatives. NT2 rho0 cells contained no detectable mtDNA on a sensitive PCR assay. Eight weeks after exogenous mtDNA transfer cybrids showed no evidence of endogenous mtDNA reversion, and heteroplasmic ratios of a single nucleotide substitution roughly reflected that of the blood samples used to repopulate their mtDNA.
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Affiliation(s)
- Daniel R Binder
- Department of Neurology, University of Virginia Health System, 1 Hospital Drive, Charlottesville, VA 22908, USA
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22
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Swerdlow RH, Redpath GT, Binder DR, Davis JN, VandenBerg SR. Mitochondrial DNA depletion analysis by pseudogene ratioing. J Neurosci Methods 2005; 150:265-71. [PMID: 16118020 DOI: 10.1016/j.jneumeth.2005.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 06/21/2005] [Accepted: 06/28/2005] [Indexed: 11/20/2022]
Abstract
The mitochondrial DNA (mtDNA) depletion status of rho(0) cell lines is typically assessed by hybridization or polymerase chain reaction (PCR) experiments, in which the failure to hybridize mtDNA or amplify mtDNA using mtDNA-directed primers suggests thorough mitochondrial genome removal. Here, we report the use of an mtDNA pseudogene ratioing technique for the additional confirmation of rho0 status. Total genomic DNA from a U251 human glioma cell line treated with ethidium bromide was amplified using primers designed to anneal either mtDNA or a previously described nuclear DNA-embedded mtDNA pseudogene (mtDNApsi). The resultant PCR product was used to generate plasmid clones. Sixty-two plasmid clones were genotyped, and all arose from mtDNApsi template. These data allowed us to determine with 95% confidence that the resultant mtDNA-depleted cell line contains less than one copy of mtDNA per 10 cells. Unlike previous hybridization or PCR-based analyses of mtDNA depletion, this mtDNApsi ratioing technique does not rely on interpretation of a negative result, and may prove useful as an adjunct for the determination of rho0 status or mtDNA copy number.
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Affiliation(s)
- Russell H Swerdlow
- Department of Neurology, University of Virginia Health System, Box 394, Charlottesville, VA 22908, USA.
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23
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Armand R, Channon JY, Kintner J, White KA, Miselis KA, Perez RP, Lewis LD. The effects of ethidium bromide induced loss of mitochondrial DNA on mitochondrial phenotype and ultrastructure in a human leukemia T-cell line (MOLT-4 cells). Toxicol Appl Pharmacol 2004; 196:68-79. [PMID: 15050409 DOI: 10.1016/j.taap.2003.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2003] [Accepted: 12/11/2003] [Indexed: 11/26/2022]
Abstract
Mitochondrial DNA-deficient (rho(0)) cells were generated following a 26-day incubation of MOLT-4 lymphoblastoid T cells in ethidium bromide (3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide). The absence of mitochondrial DNA (mtDNA) in the resultant MOLT-4 rho(0) cells was confirmed by Southern analysis and quantitative polymerase chain reaction (PCR). MOLT-4 rho(0) cells proliferated more slowly than parental cells (wild type) and produced significantly more lactate (approximately fourfold increase; P < 0.001) with concomitantly reduced oxygen consumption (12.3% vs. 100%; P < 0.001) compared with the wild type. MOLT-4 rho(0) cells also showed reduced cytochrome c oxidase activity and a reduced cytochrome c oxidase/citrate synthase activity ratio compared to parental wild-type MOLT-4 cells (P < 10(-11)). Electron microscopy showed elongated mitochondria with parallel cristae in MOLT-4 cells although the mitochondria in MOLT-4 rho(0) cells appeared enlarged, some were vacuolated with either an absent or a grossly distorted cristae pattern. Vital staining with 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolyl-carbocyanine iodide (JC-1) was used to image mitochondria in intact cells and study mitochondrial transmembrane potential (Deltapsi(m)). Flow cytometry using JC-1 indicated that MOLT-4 rho(0) had a lower Deltapsi(m) than MOLT-4. Sodium fluoride (an inhibitor of the glycolytic pathway) at a concentration of 20 mM further reduced the Deltapsi(m) in MOLT-4-rho(0) cells. This data suggested that a glycolytic pathway product, possibly ATP, was required for the maintenance of Deltapsi(m) in MOLT-4 rho(0) cells.
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Affiliation(s)
- Ray Armand
- Section of Clinical Pharmacology, Department of Medicine, Dartmouth Medical School and Dartmouth Hitchcock Medical Center, Lebanon, NH 03756, USA
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24
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Jensen-Seaman MI, Sarmiento EE, Deinard AS, Kidd KK. Nuclear integrations of mitochondrial DNA in gorillas. Am J Primatol 2004; 63:139-47. [PMID: 15258958 DOI: 10.1002/ajp.20047] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Great ape systematics, particularly at the species level and below, is currently under debate, due in part to the recent influx of molecular data. The phylogenies of previously published mitochondrial control region (or D-loop) DNA sequences in gorillas show deep splits within West African gorillas (Gorilla gorilla gorilla), and very high levels of nucleotide diversity in this subspecies. Here we demonstrate that several previously reported D-loop haplotypes from West African gorillas are in all likelihood nuclear integrations of mitochondrial DNA. Revised estimates of the amount and pattern of mitochondrial DNA diversity in gorillas are provided, revealing two reciprocally monophyletic and highly divergent groups of gorillas, concurrent with their geographic distribution.
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25
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Marchbanks RM, Ryan M, Day INM, Owen M, McGuffin P, Whatley SA. A mitochondrial DNA sequence variant associated with schizophrenia and oxidative stress. Schizophr Res 2003; 65:33-8. [PMID: 14623372 DOI: 10.1016/s0920-9964(03)00011-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have previously reported a changed mitochondrial (mt) gene expression in brain from patients with schizophrenia [Schizophr. Res. 14 (1995) 203]; now, we describe the distribution in the mtDNA from lymphocytes of a heteroplasmic sequence variation that was originally found in the mtDNA from the postmortem brain of a patient with schizophrenia. The variant is m.12027T>C and results in the change from isoleucine to threonine at position 423 of the ND4 subunit of NADH-ubiquinone reductase. Using a PCR-RFLP method, we have determined the heteroplasmy as the ratio of variant to total (variant ratio) at m.12027 in 184 controls and 181 patients with schizophrenia as well as 24 postmortem brain samples. The distribution of variants is bimodal having peaks at variant ratios of 0.262 and 0.732. The variant-rich fraction is very significantly associated with schizophrenia in males (47%), while there is only 18% in control males. There are significantly more variant-rich control females (36%) than control males (18%), suggesting that the female population is less sensitive to the presence of a variant in terms of liability to schizophrenia. In variant-rich samples from postmortem brain originating from both sexes, there is an increased superoxide production, suggesting that the variation contributes to oxidative stress. Antioxidant glycosides, such as quercetin rutoside, quench the superoxide production without (in contrast to neuroleptic drugs) interfering with the electron transfer activity of the reductase.
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Affiliation(s)
- R M Marchbanks
- Human Genetics Division, Southhampton University Hospital, Duthie Building (Mailpoint 808), SO16 6YD, UK.
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van den Heuvel APJ, de Vries-Smits AMM, van Weeren PC, Dijkers PF, de Bruyn KMT, Riedl JA, Burgering BMT. Binding of protein kinase B to the plakin family member periplakin. J Cell Sci 2003; 115:3957-66. [PMID: 12244133 DOI: 10.1242/jcs.00069] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The serine/threonine kinase protein kinase B (PKB/c-Akt) acts downstream of the lipid kinase phosphoinositide 3-kinase (PI3K) and functions as an essential mediator in many growth-factor-induced cellular responses such as cell cycle regulation, cell survival and transcriptional regulation. PI3K activation generates 3'-phosphorylated phosphatidylinositol lipids (PtdIns3P) and PKB activation requires PtdIns3P-dependent membrane translocation and phosphorylation by upstream kinases. However PKB activation and function is also regulated by interaction with other proteins. Here we show binding of PKB to periplakin, a member of the plakin family of cytolinker proteins. Interaction between PKB and periplakin was mapped to part of the pleckstrin homology (PH) domain of PKB, which is probably not involved in lipid binding, and indeed binding to periplakin did not affect PKB activation. We therefore investigated the possibility that periplakin may act as a scaffold or localization signal for PKB. In cells endogenous periplakin localizes to different cellular compartments, including plasma membrane, intermediate filament structures, the nucleus and mitochondria. Overexpression of the C-terminal part of periplakin, encompassing the PKB binding region, results in predominant intermediate filament localization and little nuclear staining. This also resulted in inhibition of nuclear PKB signalling as indicated by inhibition of PKB-dependent Forkhead transcription factor regulation. These results suggest a possible role for periplakin as a localization signal in PKB-mediated signalling.
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Affiliation(s)
- A Pieter J van den Heuvel
- Laboratory of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Center Utrecht, Stratenum, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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Tourmen Y, Baris O, Dessen P, Jacques C, Malthièry Y, Reynier P. Structure and chromosomal distribution of human mitochondrial pseudogenes. Genomics 2002; 80:71-7. [PMID: 12079285 DOI: 10.1006/geno.2002.6798] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear mitochondrial pseudogenes (Numts) have been found in the genome of many eukaryote species, including humans. Using a BLAST approach, we found 1105 DNA sequences homologous to mitochondrial DNA (mtDNA) in the August 2001 Goldenpath human genome database. We assembled these sequences manually into 286 pseudogenes on the basis of single insertion events and constructed a chromosomal map of these Numts. Some pseudogenes appeared highly modified, containing inversions, deletions, duplications, and displaced sequences. In the case of four randomly selected Numts, we used PCR tests on cells lacking mtDNA to ensure that our technique was free from genome-sequencing artifacts. Furthermore, phylogenetic investigation suggested that one Numt, apparently inserted into the nuclear genome 25-30 million years ago, had been duplicated at least 10 times in various chromosomes during the course of evolution. Thus, these pseudogenes should be very useful in the study of ancient mtDNA and nuclear genome evolution.
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Affiliation(s)
- Yves Tourmen
- INSERM EMI-U 00-18, Laboratoire de Biochimie et Biologie Moléculaire, CHU d'Angers, Angers, F-49033, France.
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28
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Correction. Proc Natl Acad Sci U S A 2001. [DOI: 10.1073/pnas.98.22.12854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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29
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Mourier T, Hansen AJ, Willerslev E, Arctander P. The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Mol Biol Evol 2001; 18:1833-7. [PMID: 11504863 DOI: 10.1093/oxfordjournals.molbev.a003971] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Abstract
Pseudogenes are commonly encountered during investigation of the genomes of a wide range of life forms. This review concentrates on vertebrate, and in particular mammalian, pseudogenes and describes their origin and subsequent evolution. Consideration is also given to pseudogenes that are transcribed and to the unusual group of genes that exist at the interface between functional genes and non-functional pseudogenes. As the sequences of different genomes are characterised, the recognition and interpretation of pseudogene sequences will become more important and have a greater impact in the field of molecular genetics.
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Affiliation(s)
- A J Mighell
- Molecular Medicine Unit, The University of Leeds, Clinical Sciences Building, St. James's University Hospital, Leeds, UK.
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