Rolling-Circle Replication in Mitochondrial DNA Inheritance: Scientific Evidence and Significance from Yeast to Human Cells

Studies of mitochondrial (mt)DNA replication, which forms the basis of mitochondrial inheritance, have demonstrated that a rolling-circle replication mode exists in yeasts and human cells. In yeast, rolling-circle mtDNA replication mediated by homologous recombination is the predominant pathway for replication of wild-type mtDNA. In human cells, reactive oxygen species (ROS) induce rolling-circle replication to produce concatemers, linear tandem multimers linked by head-to-tail unit-sized mtDNA that promote restoration of homoplasmy from heteroplasmy. The event occurs ahead of mtDNA replication mechanisms observed in mammalian cells, especially under higher ROS load, as newly synthesized mtDNA is concatemeric in hydrogen peroxide-treated human cells. Rolling-circle replication holds promise for treatment of mtDNA heteroplasmy-attributed diseases, which are regarded as incurable. This review highlights the potential therapeutic value of rolling-circle mtDNA replication.

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Reactive oxygen species stimulate mitochondrial allele segregation toward homoplasmy in human cells

Molecular Biology of the Cell ◽

10.1091/mbc.e15-10-0690 ◽

2016 ◽

Vol 27 (10) ◽

pp. 1684-1693 ◽

Cited By ~ 7

Author(s):

Feng Ling ◽

Rong Niu ◽

Hideyuki Hatakeyama ◽

Yu-ichi Goto ◽

Takehiko Shibata ◽

...

Keyword(s):

Reactive Oxygen Species ◽

Reactive Oxygen ◽

Oxygen Species ◽

Rolling Circle Replication ◽

Wild Type ◽

Mt Dna ◽

Primary Fibroblast ◽

Rolling Circle ◽

Allele Segregation ◽

Mother Cells

Mitochondria that contain a mixture of mutant and wild-type mitochondrial (mt) DNA copies are heteroplasmic. In humans, homoplasmy is restored during early oogenesis and reprogramming of somatic cells, but the mechanism of mt-allele segregation remains unknown. In budding yeast, homoplasmy is restored by head-to-tail concatemer formation in mother cells by reactive oxygen species (ROS)–induced rolling-circle replication and selective transmission of concatemers to daughter cells, but this mechanism is not obvious in higher eukaryotes. Here, using heteroplasmic m.3243A > G primary fibroblast cells derived from MELAS patients treated with hydrogen peroxide (H2O2), we show that an optimal ROS level promotes mt-allele segregation toward wild-type and mutant mtDNA homoplasmy. Enhanced ROS level reduced the amount of intact mtDNA replication templates but increased linear tandem multimers linked by head-to-tail unit-sized mtDNA (mtDNA concatemers). ROS-triggered mt-allele segregation correlated with mtDNA-concatemer production and enabled transmission of multiple identical mt-genome copies as a single unit. Our results support a mechanism by which mt-allele segregation toward mt-homoplasmy is mediated by concatemers.

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Mechanisms of Recombination between Diverged Sequences in Wild-Type and BLM-Deficient Mouse and Human Cells

Molecular and Cellular Biology ◽

10.1128/mcb.01553-09 ◽

2010 ◽

Vol 30 (8) ◽

pp. 1887-1897 ◽

Cited By ~ 40

Author(s):

Jeannine R. LaRocque ◽

Maria Jasin

Keyword(s):

Gene Conversion ◽

Mammalian Cells ◽

Sequence Divergence ◽

Dna Lesions ◽

Human Cells ◽

Deficient Mouse ◽

Wild Type ◽

Strand Breaks ◽

Major Mechanism ◽

Homeologous Recombination

ABSTRACT Double-strand breaks (DSBs) are particularly deleterious DNA lesions for which cells have developed multiple mechanisms of repair. One major mechanism of DSB repair in mammalian cells is homologous recombination (HR), whereby a homologous donor sequence is used as a template for repair. For this reason, HR repair of DSBs is also being exploited for gene modification in possible therapeutic approaches. HR is sensitive to sequence divergence, such that the cell has developed ways to suppress recombination between diverged (“homeologous”) sequences. In this report, we have examined several aspects of HR between homeologous sequences in mouse and human cells. We found that gene conversion tracts are similar for mouse and human cells and are generally ≤100 bp, even in Msh2 − / − cells which fail to suppress homeologous recombination. Gene conversion tracts are mostly unidirectional, with no observed mutations. Additionally, no alterations were observed in the donor sequences. While both mouse and human cells suppress homeologous recombination, the suppression is substantially less in the transformed human cells, despite similarities in the gene conversion tracts. BLM-deficient mouse and human cells suppress homeologous recombination to a similar extent as wild-type cells, unlike Sgs1-deficient Saccharomyces cerevisiae.

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Studies on the late replication of phage lambda: Rolling-circle replication of the wild type and a partially suppressed strain, Oam29 Pam80

Journal of Molecular Biology ◽

10.1016/s0022-2836(75)80120-3 ◽

1975 ◽

Vol 98 (2) ◽

pp. 305-320 ◽

Cited By ~ 36

Author(s):

Deepak Bastia ◽

Noboru Sueoka ◽

Edward C. Cox

Keyword(s):

Late Replication ◽

Rolling Circle Replication ◽

Phage Lambda ◽

Wild Type ◽

Rolling Circle

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Rolling-Circle Replication of an Animal Circovirus Genome in a Theta-Replicating Bacterial Plasmid in Escherichia coli

Journal of Virology ◽

10.1128/jvi.00655-06 ◽

2006 ◽

Vol 80 (17) ◽

pp. 8686-8694 ◽

Cited By ~ 39

Author(s):

Andrew K. Cheung

Keyword(s):

Escherichia Coli ◽

Dna Replication ◽

Mammalian Cells ◽

Unit Length ◽

Release Mechanism ◽

Rolling Circle Replication ◽

Replication Process ◽

Rolling Circle ◽

Rep Protein ◽

Bacterial Plasmid

ABSTRACT A bacterial plasmid containing 1.75 copies of double-stranded porcine circovirus (PCV) DNA in tandem (0.8 copy of PCV type 1 [PCV1], 0.95 copy of PCV2) with two origins of DNA replication (Ori) yielded three different DNA species when transformed into Escherichia coli: the input construct, a unit-length chimeric PCV1Rep/PCV2Cap genome with a composite Ori but lacking the plasmid vector, and a molecule consisting of the remaining 0.75 copy PCV1Cap/PCV2Rep genome with a different composite Ori together with the bacterial plasmid. Replication of the input construct was presumably via the theta replication mechanism utilizing the ColE1 Ori, while characteristics of the other two DNA species, including a requirement of two PCV Oris and the virus-encoded replication initiator Rep protein, suggest they were generated via the rolling-circle copy-release mechanism. Interestingly, the PCV-encoded Rep′ protein essential for PCV DNA replication in mammalian cells was not required in bacteria. The fact that the Rep′ protein function(s) can be compensated by the bacterial replication machinery to support the PCV DNA replication process echoes previous suggestions that circular single-stranded DNA animal circoviruses, plant geminiviruses, and nanoviruses may have evolved from prokaryotic episomal replicons.

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DNA Recombination-Initiation Plays a Role in the Extremely Biased Inheritance of Yeast [rho−] Mitochondrial DNA That Contains the Replication Origin ori5

Molecular and Cellular Biology ◽

10.1128/mcb.00770-06 ◽

2006 ◽

Vol 27 (3) ◽

pp. 1133-1145 ◽

Cited By ~ 37

Author(s):

Feng Ling ◽

Akiko Hori ◽

Takehiko Shibata

Keyword(s):

Mitochondrial Dna ◽

Replication Origin ◽

Excision Repair ◽

Dna Recombination ◽

Strand Break ◽

Yeast Cells ◽

Rolling Circle Replication ◽

Rolling Circle ◽

Mtdna Replication ◽

Base Excision

ABSTRACT Hypersuppressiveness, as observed in Saccharomyces cerevisiae, is an extremely biased inheritance of a small mitochondrial DNA (mtDNA) fragment that contains a replication origin (HS [rho −] mtDNA). Our previous studies showed that concatemers (linear head-to-tail multimers) are obligatory intermediates for mtDNA partitioning and are primarily formed by rolling-circle replication mediated by Mhr1, a protein required for homologous mtDNA recombination. In this study, we found that Mhr1 is required for the hypersuppressiveness of HS [ori5] [rho −] mtDNA harboring ori5, one of the replication origins of normal ([rho +]) mtDNA. In addition, we detected an Ntg1-stimulated double-strand break at the ori5 locus. Purified Ntg1, a base excision repair enzyme, introduced a double-stranded break by itself into HS [ori5] [rho −] mtDNA at ori5 isolated from yeast cells. Both hypersuppressiveness and concatemer formation of HS [ori5] [rho −] mtDNA are simultaneously suppressed by the ntg1 null mutation. These results support a model in which, like homologous recombination, rolling-circle HS [ori5] [rho −] mtDNA replication is initiated by double-stranded breakage in ori5, followed by Mhr1-mediated homologous pairing of the processed nascent DNA ends with circular mtDNA. The hypersuppressiveness of HS [ori5] [rho −] mtDNA depends on a replication advantage furnished by the higher density of ori5 sequences and on a segregation advantage furnished by the higher genome copy number on transmitted concatemers.

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Rapid host adaptation by extensive recombination

Journal of General Virology ◽

10.1099/vir.0.007724-0 ◽

2009 ◽

Vol 90 (3) ◽

pp. 734-746 ◽

Cited By ~ 62

Author(s):

Eric van der Walt ◽

Edward P. Rybicki ◽

Arvind Varsani ◽

J. E. Polston ◽

Rosalind Billharz ◽

...

Keyword(s):

Recombination Breakpoint ◽

Experimental Investigations ◽

Streak Virus ◽

Rolling Circle Replication ◽

Wild Type ◽

Rolling Circle ◽

Experimental Scheme ◽

Fundamental Biological Process ◽

Biochemical Mechanisms ◽

Recombination Breakpoints

Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature.

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Gene amplification: mechanisms and involvement in cancer

BioMolecular Concepts ◽

10.1515/bmc-2013-0026 ◽

2013 ◽

Vol 4 (6) ◽

pp. 567-582 ◽

Cited By ~ 29

Author(s):

Atsuka Matsui ◽

Tatsuya Ihara ◽

Hiraku Suda ◽

Hirofumi Mikami ◽

Kentaro Semba

Keyword(s):

Drosophila Melanogaster ◽

Gene Amplification ◽

Dihydrofolate Reductase ◽

Mammalian Cells ◽

Replication Fork ◽

Template Switching ◽

Rolling Circle Replication ◽

Rolling Circle ◽

Reductase Gene ◽

Fork Stalling

AbstractGene amplification was recognized as a physiological process during the development of Drosophila melanogaster. Intriguingly, mammalian cells use this mechanism to overexpress particular genes for survival under stress, such as during exposure to cytotoxic drugs. One well-known example is the amplification of the dihydrofolate reductase gene observed in methotrexate-resistant cells. Four models have been proposed for the generation of amplifications: extrareplication and recombination, the breakage-fusion-bridge cycle, double rolling-circle replication, and replication fork stalling and template switching. Gene amplification is a typical genetic alteration in cancer, and historically many oncogenes have been identified in the amplified regions. In this regard, novel cancer-associated genes may remain to be identified in the amplified regions. Recent comprehensive approaches have further revealed that co-amplified genes also contribute to tumorigenesis in concert with known oncogenes in the same amplicons. Considering that cancer develops through the alteration of multiple genes, gene amplification is an effective acceleration machinery to promote tumorigenesis. Identification of cancer-associated genes could provide novel and effective therapeutic targets.

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Nuclease-Deficient FEN-1 Blocks Rad51/BRCA1-Mediated Repair and Causes Trinucleotide Repeat Instability

Molecular and Cellular Biology ◽

10.1128/mcb.23.17.6063-6074.2003 ◽

2003 ◽

Vol 23 (17) ◽

pp. 6063-6074 ◽

Cited By ~ 56

Author(s):

Craig Spiro ◽

Cynthia T. McMurray

Keyword(s):

Dna Repair ◽

Huntington's Disease ◽

Huntington’S Disease ◽

Mammalian Cells ◽

Direct Evidence ◽

Trinucleotide Repeat ◽

Human Cells ◽

Wild Type ◽

Repeat Instability ◽

In Cells

ABSTRACT Previous studies have shown that expansion-prone repeats form structures that inhibit human flap endonuclease (FEN-1). We report here that faulty processing by FEN-1 initiates repeat instability in mammalian cells. Disease-length CAG tracts in Huntington's disease mice heterozygous for FEN-1 display a tendency toward expansions over contractions during intergenerational inheritance compared to those in homozygous wild-type mice. Further, with regard to human cells expressing a nuclease-defective FEN-1, we provide direct evidence that an unprocessed FEN-1 substrate is a precursor to instability. In cells with no endogenous defects in DNA repair, exogenous nuclease-defective FEN-1 causes repeat instability and aberrant DNA repair. Inefficient flap processing blocks the formation of Rad51/BRCA1 complexes but invokes repair by other pathways.

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