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Abstract
Physiological and pathological roles for R-loop structures continue to be discovered, and studies suggest that R-loops could contribute to human disease. R-loops are nucleic acid structures characterized by a DNA:RNA hybrid and displaced single-stranded DNA that occur in connection with transcription. R-loops form naturally and have been shown to be important for a number of physiological processes such as mitochondrial replication initiation, class switch recombination, DNA repair, modulating DNA topology, and regulation of gene expression. However, subsets of R-loops or persistent R-loops lead to DNA breaks, chromosome rearrangement, and genome instability. In addition, R-loops have been linked to human diseases, specifically neurological disorders and cancer. Of the large amount of research produced recently on R-loops, this review covers evidence for R-loop involvement in normal cellular physiology and pathophysiology, as well as describing factors that contribute to R-loop regulation.
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Affiliation(s)
- Ryan Patrick Mackay
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Qinqin Xu
- Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Paul M Weinberger
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA.,Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
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2
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Yeast mitochondrial HMG proteins: DNA-binding properties of the most evolutionarily divergent component of mitochondrial nucleoids. Biosci Rep 2015; 36:e00288. [PMID: 26647378 PMCID: PMC4725248 DOI: 10.1042/bsr20150275] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/01/2015] [Indexed: 02/07/2023] Open
Abstract
Comparative biochemical analysis of mtHMG proteins from distantly related yeast species revealed that they exhibit a preference for recombination/replication intermediates. We discuss how these biochemical characteristics relate to the role of mtHMG proteins in mtDNA compaction and evolution. Yeast mtDNA is compacted into nucleoprotein structures called mitochondrial nucleoids (mt-nucleoids). The principal mediators of nucleoid formation are mitochondrial high-mobility group (HMG)-box containing (mtHMG) proteins. Although these proteins are some of the fastest evolving components of mt-nucleoids, it is not known whether the divergence of mtHMG proteins on the level of their amino acid sequences is accompanied by diversification of their biochemical properties. In the present study we performed a comparative biochemical analysis of yeast mtHMG proteins from Saccharomyces cerevisiae (ScAbf2p), Yarrowia lipolytica (YlMhb1p) and Candida parapsilosis (CpGcf1p). We found that all three proteins exhibit relatively weak binding to intact dsDNA. In fact, ScAbf2p and YlMhb1p bind quantitatively to this substrate only at very high protein to DNA ratios and CpGcf1p shows only negligible binding to dsDNA. In contrast, the proteins exhibit much higher preference for recombination intermediates such as Holliday junctions (HJ) and replication forks (RF). Therefore, we hypothesize that the roles of the yeast mtHMG proteins in maintenance and compaction of mtDNA in vivo are in large part mediated by their binding to recombination/replication intermediates. We also speculate that the distinct biochemical properties of CpGcf1p may represent one of the prerequisites for frequent evolutionary tinkering with the form of the mitochondrial genome in the CTG-clade of hemiascomycetous yeast species.
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Zheng KW, Wu RY, He YD, Xiao S, Zhang JY, Liu JQ, Hao YH, Tan Z. A competitive formation of DNA:RNA hybrid G-quadruplex is responsible to the mitochondrial transcription termination at the DNA replication priming site. Nucleic Acids Res 2014; 42:10832-44. [PMID: 25140009 PMCID: PMC4176368 DOI: 10.1093/nar/gku764] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Human mitochondrial DNA contains a distinctive guanine-rich motif denoted conserved sequence block II (CSB II) that stops RNA transcription, producing prematurely terminated transcripts to prime mitochondrial DNA replication. Recently, we reported a general phenomenon that DNA:RNA hybrid G-quadruplexes (HQs) readily form during transcription when the non-template DNA strand is guanine-rich and such HQs in turn regulate transcription. In this work, we show that transcription of mitochondrial DNA leads to the formation of a stable HQ or alternatively an unstable intramolecular DNA G-quadruplex (DQ) at the CSB II. The HQ is the dominant species and contributes to the majority of the premature transcription termination. Manipulating the stability of the DQ has little effect on the termination even in the absence of HQ; however, abolishing the formation of HQs by preventing the participation of either DNA or RNA abolishes the vast majority of the termination. These results demonstrate that the type of G-quadruplexes (HQ or DQ) is a crucial determinant in directing the transcription termination at the CSB II and suggest a potential functionality of the co-transcriptionally formed HQ in DNA replication initiation. They also suggest that the competition/conversion between an HQ and a DQ may regulate the function of a G-quadruplex-forming sequence.
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Affiliation(s)
- Ke-wei Zheng
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Ren-yi Wu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yi-de He
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Shan Xiao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Jia-yu Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Jia-quan Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yu-hua Hao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Zheng Tan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
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Shen Y, Nandi P, Taylor MB, Stuckey S, Bhadsavle HP, Weiss B, Storici F. RNA-driven genetic changes in bacteria and in human cells. Mutat Res 2011; 717:91-8. [PMID: 21515292 DOI: 10.1016/j.mrfmmm.2011.03.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 03/20/2011] [Accepted: 03/31/2011] [Indexed: 11/16/2022]
Abstract
As recently demonstrated in the yeast Saccharomyces cerevisiae model organism using synthetic RNA-containing oligonucleotides (oligos), RNA can serve as a template for DNA synthesis at the chromosomal level during the process of double-strand break (DSB) repair. Herein we show that the phenomenon of RNA-mediated DNA modification and repair is not limited to yeast cells. A tract of six ribonucleotides embedded in single-strand DNA oligos corresponding to either lagging or leading strand sequences could serve as a template to correct a defective lacZ marker gene in the chromosome of the bacterium Escherichia coli. In order to test the capacity of RNA to modify DNA in mammalian cells, we utilized DNA oligos containing an embedded tract of six ribonucleotides, as well as oligos mostly made of RNA. These oligos were designed to repair a chromosomal break generated within a copy of the green fluorescent protein (GFP) gene randomly integrated into the genome of human HEK-293 cells. We show that these RNA-containing oligos can serve as templates to repair a DSB in human cells and can introduce base changes into genomic or plasmid DNA. In both E. coli and human cells, the strand bias of chromosomal gene correction by the single-strand RNA-containing oligos was the same as that obtained for the corresponding DNA molecules. Therefore, the RNA-containing oligos are not converted into a cDNA before annealing with complementary DNA. Overall, we demonstrate that in both bacterial and human cells, as in yeast, RNA sequences can have a direct role in DNA genetic modification and remodeling.
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Affiliation(s)
- Ying Shen
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
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5
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Fukuoh A, Ohgaki K, Hatae H, Kuraoka I, Aoki Y, Uchiumi T, Jacobs HT, Kang D. DNA conformation-dependent activities of human mitochondrial RNA polymerase. Genes Cells 2009; 14:1029-42. [PMID: 19624753 DOI: 10.1111/j.1365-2443.2009.01328.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Mitochondrial RNA polymerase (POLRMT) is a core protein for mitochondrial DNA (mtDNA) transcription. In addition, POLRMT is assumed to be involved in replication, although its exact role is not yet clearly elucidated. We have found novel properties of human POLRMT using a reconstituted transcription system. Various lengths of RNA molecules were synthesized from templates even without a defined promoter sequence, when we used supercoiled circular double-stranded DNA as a template. This promoter-independent activity was as strong as the promoter-dependent one. Promoter-independent DNA conformation-dependent transcription required TFB2M. On supercoiled templates, the promoter-independent activity was strongly suppressed by a putatively physiological amount of TFAM, while promoter-dependent transcription was inhibited to a lesser extent. These different inhibition patterns by TFAM may be important for prevention of random RNA synthesis in vivo. Promoter-independent activity was also observed on relaxed circular single-stranded DNA, where its activity no longer required TFB2M. RNA synthesis on single-stranded DNA was weakly suppressed by a putatively physiological amount of TFAM but restored by the addition of mitochondrial single-stranded DNA binding protein. We suggest that these properties of POLRMT could explain the characteristic features of mammalian mtDNA transcription and replication.
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Affiliation(s)
- Atsushi Fukuoh
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
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6
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Hybridization between mitochondrial heavy strand tDNA and expressed light strand tRNA modulates the function of heavy strand tDNA as light strand replication origin. J Mol Biol 2008; 379:188-99. [DOI: 10.1016/j.jmb.2008.03.066] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2007] [Revised: 03/23/2008] [Accepted: 03/31/2008] [Indexed: 11/24/2022]
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7
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Epstein-Barr virus immediate-early protein Zta co-opts mitochondrial single-stranded DNA binding protein to promote viral and inhibit mitochondrial DNA replication. J Virol 2008; 82:4647-55. [PMID: 18305033 DOI: 10.1128/jvi.02198-07] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Disruption of cellular metabolic processes and usurpation of host proteins are hallmarks of herpesvirus lytic infection. Epstein-Barr virus (EBV) lytic replication is initiated by the immediate-early protein Zta. Zta is a multifunctional DNA binding protein that stimulates viral gene transcription, nucleates a replication complex at the viral origin of lytic replication, and inhibits cell cycle proliferation. To better understand these functions and identify cellular collaborators of Zta, we purified an epitope-tagged version of Zta in cells capable of supporting lytic replication. FLAG-tagged Zta was purified from a nuclear fraction using FLAG antibody immunopurification and peptide elution. Zta-associated proteins were isolated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and identified by mass spectrometry. The Zta-associated proteins included members of the HSP70 family and various single-stranded DNA and RNA binding proteins. The nuclear replication protein A subunits (RPA70 and RPA32) and the human mitochondrial single-stranded DNA binding protein (mtSSB) were confirmed by Western blotting to be specifically enriched in the FLAG-Zta immunopurified complex. mtSSB coimmunoprecipitated with endogenous Zta during reactivation of EBV-positive Burkitt lymphoma and lymphoblastoid cell lines. Small interfering RNA depletion of mtSSB reduced Zta-induced lytic replication of EBV but had only a modest effect on transcription activation function. A point mutation in the Zta DNA binding domain (C189S), which is known to reduce lytic cycle replication, eliminated mtSSB association with Zta. The predominantly mitochondrial localization of mtSSB was shifted to partly nuclear localization in cells expressing Zta. Mitochondrial DNA synthesis and genome copy number were reduced by Zta-induced EBV lytic replication. We conclude that Zta interaction with mtSSB serves the dual function of facilitating viral and blocking mitochondrial DNA replication.
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Slocum SL, Buss JA, Kimura Y, Bianco PR. Characterization of the ATPase activity of the Escherichia coli RecG protein reveals that the preferred cofactor is negatively supercoiled DNA. J Mol Biol 2007; 367:647-64. [PMID: 17292398 PMCID: PMC1913479 DOI: 10.1016/j.jmb.2007.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2006] [Revised: 12/29/2006] [Accepted: 01/02/2007] [Indexed: 02/07/2023]
Abstract
RecG is a member of the superfamily 2 helicase family. Its possible role in vivo is ATP hydrolysis driven regression of stalled replication forks. To gain mechanistic insight into how this is achieved, a coupled spectrophotometric assay was utilized to characterize the ATPase activity of RecG in vitro. The results demonstrate an overwhelming preference for negatively supercoiled DNA ((-)scDNA) as a cofactor for the hydrolysis of ATP. In the presence of (-)scDNA the catalytic efficiency of RecG and the processivity (as revealed through heparin trapping), were higher than on any other cofactor examined. The activity of RecG on (-)scDNA was not due to the presence of single-stranded regions functioning as loading sites for the enzyme as relaxed circular DNA treated with DNA gyrase, resulted in the highest levels of ATPase activity. Relaxation of (-)scDNA by a topoisomerase resulted in a 12-fold decrease in ATPase activity, comparable to that observed on both linear double-stranded (ds)DNA and (+)scDNA. In addition to the elevated activity in the presence of (-)scDNA, RecG also has high activity on model 4Y-substrates (i.e. chicken foot structures). This is due largely to the high apparent affinity of the enzyme for this DNA substrate, which is 46-fold higher than a 2Y-substrate (i.e. a three-way with two single-stranded (ss)DNA arms). Finally, the enzyme exhibited significant, but lower activity on ssDNA. This activity was enhanced by the Escherichia coli stranded DNA-binding protein (SSB) protein, which occurs through stabilizing of the binding of RecG to ssDNA. Stabilization is not afforded by the bacteriophage gene 32 protein, indicating a species specific, protein-protein interaction is involved. These results combine to provide significant insight into the manner and timing of the interaction of RecG with DNA at stalled replication forks.
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Affiliation(s)
- Stephen L. Slocum
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14214 USA
| | - Jackson A. Buss
- Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY 14214 USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214 USA
| | - Yuji Kimura
- Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY 14214 USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214 USA
| | - Piero R. Bianco
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14214 USA
- Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY 14214 USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214 USA
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Kang D, Hamasaki N. Mitochondrial Transcription Factor A in the Maintenance of Mitochondrial DNA. Ann N Y Acad Sci 2006; 1042:101-8. [PMID: 15965051 DOI: 10.1196/annals.1338.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mitochondria have their own genome, which is essential for proper oxidative phosphorylation needed for a large part of ATP production in a cell. Although mitochondrial DNA-less (rho0) cells can survive under special conditions, the integrity of the mitochondrial genome is critical for survival of multicellular organisms. Mitochondrial transcription factor A (TFAM), originally cloned as transcription factor, is essential for the maintenance of mtDNA. Recently, it has become known that TFAM plays critical roles in multiple aspects to maintain the integrity of mitochondrial DNA: transcription, replication, nucleoid formation, damage sensing, and DNA repair. The effects of TFAM in these aspects are intimately related to each other and to function as a whole for the purpose of maintenance of mtDNA.
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Affiliation(s)
- Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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10
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Taanman JW, Llewelyn Williams S. The Human Mitochondrial Genome. OXIDATIVE STRESS AND DISEASE 2005. [DOI: 10.1201/9781420028843.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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11
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Fish J, Raule N, Attardi G. Discovery of a major D-loop replication origin reveals two modes of human mtDNA synthesis. Science 2005; 306:2098-101. [PMID: 15604407 DOI: 10.1126/science.1102077] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mammalian mitochondrial DNA (mtDNA) replication has long been considered to occur by asymmetric synthesis of the two strands, starting at the multiple origins of the strand-displacement loop (D-loop). We report the discovery of a major replication origin at position 57 in the D-loop of several human cell lines (HeLa, A549, and 143B.TK-) and immortalized lymphocytes. The nascent chains starting at this origin, in contrast to those initiated at the previously described origins, do not terminate prematurely at the 3' end of the D-loop but proceed well beyond this control point, behaving as "true" replicating strands. This origin is mainly responsible for mtDNA maintenance under steady-state conditions, whereas mtDNA synthesis from the formerly identified D-loop origins may be more important for recovery after mtDNA depletion and for accelerating mtDNA replication in response to physiological demands.
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Affiliation(s)
- Jennifer Fish
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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12
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Abstract
Several questions in our understanding of mitochondria are unanswered. These include how the ratio of mitochondrial (mt)DNA to mitochondria is maintained, how the accumulation of defective, rapidly replicating mitochondrial DNA is avoided, how the ratio of mitochondria to cells is adjusted to fit cellular needs, and why any proteins are synthesized in mitochondria rather than simply imported. In bacteria, large hyperstructures or assemblies of proteins, mRNA, lipids and ions have been proposed to constitute a level of organization intermediate between macromolecules and whole cells. Here, we suggest how the concept of hyperstructures together with other concepts developed for bacteria such as transcriptional sensing and spontaneous segregation may provide answers to mitochondrial problems. In doing this, we show how the problem of the very existence of mtDNA brings its own solution.
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Affiliation(s)
- Mirella Trinei
- Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy
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Ohsato T, Ishihara N, Muta T, Umeda S, Ikeda S, Mihara K, Hamasaki N, Kang D. Mammalian mitochondrial endonuclease G. Digestion of R-loops and localization in intermembrane space. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:5765-70. [PMID: 12444964 DOI: 10.1046/j.1432-1033.2002.03238.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mammalian mitochondria contain strong nuclease activity. Endonuclease G (endoG), which predominantly resides in mitochondria, accounts for a large part of this nuclease activity. It has been proposed to act as an RNase H-like nuclease on RNA.DNA hybrids (R-loops) in the D-loop region where the origins of mitochondrial replication are mapped, providing RNA primers for mtDNA replication. However, in contrast with this proposed activity, endoG has recently been shown to translocate to nuclei on apoptotic stimulation and act as a nuclease without sequence specificity. To clarify the role of endoG in mtDNA replication, we examined its submitochondrial localization and its ability to cleave R-loops. At low concentration, it preferentially produces double-stranded breaks in R-loops, but does not act as an RNase H-like nuclease. In addition, it exists in the mitochondrial intermembrane space, but not in the matrix where mtDNA replication occurs. These results do not support the involvement of endoG in mtDNA replication. Based on the fact that guanine tracts, which are preferential targets of endoG, tend to form triplex structures and that endoG produces double-stranded breaks in R-loops, we propose that three-stranded DNA may be the preferred substrate of endoG.
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Affiliation(s)
- Takashi Ohsato
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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Iwaasa M, Umeda S, Ohsato T, Takamatsu C, Fukuoh A, Iwasaki H, Shinagawa H, Hamasaki N, Kang D. 1-Methyl-4-phenylpyridinium ion, a toxin that can cause parkinsonism, alters branched structures of DNA. J Neurochem 2002; 82:30-7. [PMID: 12091462 DOI: 10.1046/j.1471-4159.2002.00996.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
During replication, human mitochondrial DNA (mtDNA) takes on a triple-stranded structure known as a D-loop, which is implicated in replication and transcription. 1-Methyl-4-phenylpyridinium ion (MPP+), a toxin inducing parkinsonism, inhibits mtDNA replication, possibly by resolving the D-loops. For initiation of mtDNA replication, mitochondria are thought to have another triple-stranded structure, an R-loop. The R-loop, which is resolved by a bacterial junction-specific helicase, RecG, is also resolved by MPP+. Because mitochondrial D-loops are likewise resolved by RecG, the D- and R-loops may share a similar branched structure. MPP+ resolves cruciform DNA in supercoiled DNA. MPP+ converts a stacked conformation to an extended conformation in a synthetic Holliday junction. This conversion is reversed by 1 mM Mg(2+), as is the resolution of the D-loops or cruciform DNA. These observations suggest that the junction structure of mitochondrial D- and R-loops is affected by MPP+.
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Affiliation(s)
- Mitsutoshi Iwaasa
- Department of Neurosurgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
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Takamatsu C, Umeda S, Ohsato T, Ohno T, Abe Y, Fukuoh A, Shinagawa H, Hamasaki N, Kang D. Regulation of mitochondrial D-loops by transcription factor A and single-stranded DNA-binding protein. EMBO Rep 2002; 3:451-6. [PMID: 11964388 PMCID: PMC1084112 DOI: 10.1093/embo-reports/kvf099] [Citation(s) in RCA: 168] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During replication, mitochondrial DNA (mtDNA) takes on a triple-stranded structure called a D-loop. Although their physiological roles are not understood, D-loops are implicated in replication and transcription of mtDNA. Little is known about the turnover of D-loops. We investigated the effects of mitochondrial transcription factor A (TFAM) and single-stranded DNA-binding protein (mtSSB) on D-loops. In human HeLa cells, TFAM and mtSSB are, respectively, 1700- and 3000-fold more abundant than mtDNA. This level of TFAM is two orders of magnitude higher than reported previously and is sufficient to wrap human mtDNA entirely. TFAM resolves D-loops in vitro if added in similar stoichiometries. mtSSB inhibits the resolution of mtDNA by TFAM but enhances resolution by RecG, a junction-specific helicase from Escherichia coli. Hence, mtSSB functions in both stabilization and resolution. We propose that TFAM and mtSSB are cooperatively involved in stabilizing D-loops and in the maintenance of mtDNA.
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Affiliation(s)
- Chihiro Takamatsu
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
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16
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Dudas KC, Kreuzer KN. UvsW protein regulates bacteriophage T4 origin-dependent replication by unwinding R-loops. Mol Cell Biol 2001; 21:2706-15. [PMID: 11283250 PMCID: PMC86901 DOI: 10.1128/mcb.21.8.2706-2715.2001] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The UvsW protein of bacteriophage T4 is involved in many aspects of phage DNA metabolism, including repair, recombination, and recombination-dependent replication. UvsW has also been implicated in the repression of origin-dependent replication at late times of infection, when UvsW is normally synthesized. Two well-characterized T4 origins, ori(uvsY) and ori(34), are believed to initiate replication through an R-loop mechanism. Here we provide both in vivo and in vitro evidence that UvsW is an RNA-DNA helicase that catalyzes the dissociation of RNA from origin R-loops. Two-dimensional gel analyses show that the replicative intermediates formed at ori(uvsY) persist longer in a uvsW mutant infection than in a wild-type infection. In addition, the inappropriate early expression of UvsW protein results in the loss of these replicative intermediates. Using a synthetic origin R-loop, we also demonstrate that purified UvsW functions as a helicase that efficiently dissociates RNA from R-loops. These and previous results from a number of studies provide strong evidence that UvsW is a molecular switch that allows T4 replication to progress from a mode that initiates from R-loops at origins to a mode that initiates from D-loops formed by recombination proteins.
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Affiliation(s)
- K C Dudas
- Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
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17
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Ohno T, Umeda S, Hamasaki N, Kang D. Binding of human mitochondrial transcription factor A, an HMG box protein, to a four-way DNA junction. Biochem Biophys Res Commun 2000; 271:492-8. [PMID: 10799324 DOI: 10.1006/bbrc.2000.2656] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondrial transcription factor A (mtTFA), the only known transcription factor in mitochondria, is also implicated in maintenance of mitochondrial genome although little is elucidated about its molecular basis. mtTFA is a member of HMG box proteins family. Some HMG proteins bind with high affinity to four-way DNA junctions that mimic a Holliday structure, a putative intermediate in DNA recombination. To explore possible involvement of a Holliday-like structure in the maintenance of mitochondrial genome, we examine the binding of recombinant human mtTFA to a synthetic four-way DNA junction. The human mtTFA binds to the four-way DNA junction with an approximately 10-fold higher affinity than to the corresponding linear duplex DNA and with essentially the same affinity as to a 40-mer DNA containing the human mitochondrial light strand promoter sequence. The mtTFA binds to the four-way as a monomer. Both of the two HMG box domains of human mtTFA are required for the high affinity binding to the four-way junction.
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Affiliation(s)
- T Ohno
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
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18
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Umeda S, Muta T, Ohsato T, Takamatsu C, Hamasaki N, Kang D. The D-loop structure of human mtDNA is destabilized directly by 1-methyl-4-phenylpyridinium ion (MPP+), a parkinsonism-causing toxin. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:200-6. [PMID: 10601867 DOI: 10.1046/j.1432-1327.2000.00990.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine has been reported to cause parkinsonism via its neurotoxic form, 1-methyl-4-phenylpyridinium ion (MPP+), which inhibits complex I of the mitochondrial respiratory chain. Its parkinsonism-causing mechanisms attract a great deal of interest as a model of the disease. Recently, we reported that MPP+ strongly decreases the amount of mtDNA independent of the inhibition of complex I. Maintenance of a proper amount of mtDNA is essential for the normal function of mitochondria as exemplified in many mitochondrial diseases. The most characteristic feature in vertebral mtDNA replication is that H-strand synthesis proceeds displacing the parental H-strand as a long single strand. It forms the D-loop, a triplex replication intermediate composed of the parental L-strand, nascent H-strand and displaced H-strand. Here we show that MPP+ does not inhibit DNA synthesis by DNA polymerase gamma, but rather releases the nascent H-strands from mtDNA both in organello and in vitro. This indicates that MPP+ directly destabilizes the D-loop structure, thereby inhibiting replication. This study raises a new mechanism, i.e. destabilization of replication intermediates, for depletion of mtDNA.
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MESH Headings
- 1-Methyl-4-phenylpyridinium/pharmacology
- DNA Polymerase gamma
- DNA Replication/drug effects
- DNA Replication/genetics
- DNA, Mitochondrial/biosynthesis
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Single-Stranded/biosynthesis
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA-Directed DNA Polymerase/metabolism
- HeLa Cells
- Hot Temperature
- Humans
- Hydrogen-Ion Concentration
- Kinetics
- Mitochondria/drug effects
- Mitochondria/enzymology
- Mitochondria/genetics
- Nucleic Acid Conformation/drug effects
- Nucleic Acid Denaturation/drug effects
- Parkinson Disease, Secondary/chemically induced
- Parkinson Disease, Secondary/genetics
- Potassium Iodide/pharmacology
- Recombinant Proteins/metabolism
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Affiliation(s)
- S Umeda
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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