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Trends in Biochemical Sciences Apr 2000Replication arrests are associated with genome rearrangements, which result from either homologous or non-homologous recombination. Interestingly, proteins involved in... (Review)
Review
Replication arrests are associated with genome rearrangements, which result from either homologous or non-homologous recombination. Interestingly, proteins involved in homologous recombination are able to convert an arrested replication fork into a recombination intermediate, which promotes replication restart and thus presumably prevents genome rearrangements.
Topics: DNA Helicases; DNA Replication; Recombination, Genetic
PubMed: 10754549
DOI: 10.1016/s0968-0004(00)01560-7 -
Cold Spring Harbor Perspectives in... Oct 2014The links between recombination and replication have been appreciated for decades and it is now generally accepted that these two fundamental aspects of DNA metabolism... (Review)
Review
The links between recombination and replication have been appreciated for decades and it is now generally accepted that these two fundamental aspects of DNA metabolism are inseparable: Homologous recombination is essential for completion of DNA replication and vice versa. This review focuses on the roles that recombination enzymes play in underpinning genome duplication, aiding replication fork movement in the face of the many replisome barriers that challenge genome stability. These links have many conserved features across all domains of life, reflecting the conserved nature of the substrate for these reactions, DNA.
Topics: DNA; DNA Replication; Genomic Instability; Homologous Recombination; Models, Genetic; Recombination, Genetic
PubMed: 25341919
DOI: 10.1101/cshperspect.a016550 -
International Journal of Molecular... Jan 2022DNA helicase and polymerase work cooperatively at the replication fork to perform leading-strand DNA synthesis. It was believed that the helicase migrates to the...
DNA helicase and polymerase work cooperatively at the replication fork to perform leading-strand DNA synthesis. It was believed that the helicase migrates to the forefront of the replication fork where it unwinds the duplex to provide templates for DNA polymerases. However, the molecular basis of the helicase-polymerase coupling is not fully understood. The recently elucidated T7 replisome structure suggests that the helicase and polymerase sandwich parental DNA and each enzyme pulls a daughter strand in opposite directions. Interestingly, the T7 polymerase, but not the helicase, carries the parental DNA with a positively charged cleft and stacks at the fork opening using a β-hairpin loop. Here, we created and characterized T7 polymerases each with a perturbed β-hairpin loop and positively charged cleft. Mutations on both structural elements significantly reduced the strand-displacement synthesis by T7 polymerase but had only a minor effect on DNA synthesis performed against a linear DNA substrate. Moreover, the aforementioned mutations eliminated synergistic helicase-polymerase binding and unwinding at the DNA fork and processive fork progressions. Thus, our data suggested that T7 polymerase plays a dominant role in helicase-polymerase coupling and replisome progression.
Topics: Bacteriophage T7; DNA Helicases; DNA Replication; DNA, Viral; DNA-Directed DNA Polymerase; Viral Proteins
PubMed: 35163266
DOI: 10.3390/ijms23031342 -
Current Opinion in Structural Biology Oct 2013Recent advances in the development of single-molecule approaches have made it possible to study the dynamics of biomolecular systems in great detail. More recently, such... (Review)
Review
Recent advances in the development of single-molecule approaches have made it possible to study the dynamics of biomolecular systems in great detail. More recently, such tools have been applied to study the dynamic nature of large multi-protein complexes that support multiple enzymatic activities. In this review, we will discuss single-molecule studies of the replisome, the protein complex responsible for the coordinated replication of double-stranded DNA. In particular, we will focus on new insights obtained into the dynamic nature of the composition of the DNA-replication machinery and how the dynamic replacement of components plays a role in the regulation of the DNA-replication process.
Topics: DNA Replication; Models, Biological; Multiprotein Complexes; Protein Binding
PubMed: 23890728
DOI: 10.1016/j.sbi.2013.06.018 -
Plant Molecular Biology Dec 2011Mini-chromosome maintenance (MCM) proteins form heterohexameric complex (MCM2-7) to serve as licensing factor for DNA replication to make sure that genomic DNA is... (Review)
Review
Mini-chromosome maintenance (MCM) proteins form heterohexameric complex (MCM2-7) to serve as licensing factor for DNA replication to make sure that genomic DNA is replicated completely and accurately once during S phase in a single cell cycle. MCMs were initially identified in yeast for their role in plasmid replication or cell cycle progression. Each of six MCM contains highly conserved sequence called "MCM box", which contains two ATPase consensus Walker A and Walker B motifs. Studies on MCM proteins showed that (a) the replication origins are licensed by stable binding of MCM2-7 to form pre-RC (pre-replicative complex) during G1 phase of the cell cycle, (b) the activation of MCM proteins by CDKs (cyclin-dependent kinases) and DDKs (Dbf4-dependent kinases) and their helicase activity are important for pre-RC to initiate the DNA replication, and (c) the release of MCMs from chromatin renders the origins "unlicensed". DNA replication licensing in plant is, in general, less characterized. The MCMs have been reported from Arabidopsis, maize, tobacco, pea and rice, where they are found to be highly expressed in dividing tissues such as shoot apex and root tips, localized in nucleus and cytosol and play important role in DNA replication, megagametophyte and embryo development. The identification of six MCM coding genes from pea and Arabidopsis suggest six distinct classes of MCM protein in higher plant, and the conserved function right across the eukaryotes. This overview of MCMs contains an emphasis on MCMs from plants and the novel role of MCM6 in abiotic stress tolerance.
Topics: Cell Cycle; Cell Cycle Proteins; DNA Replication; Plant Proteins
PubMed: 22038093
DOI: 10.1007/s11103-011-9836-3 -
Seminars in Cancer Biology Apr 2013Normal cellular division requires that the genome be faithfully replicated to ensure that unaltered genomic information is passed from one generation to the next. DNA... (Review)
Review
Normal cellular division requires that the genome be faithfully replicated to ensure that unaltered genomic information is passed from one generation to the next. DNA replication initiates from thousands of origins scattered throughout the genome every cell cycle; however, not all origins initiate replication at the same time. A vast amount of work over the years indicates that different origins along each eukaryotic chromosome are activated in early, middle or late S phase. This temporal control of DNA replication is referred to as the replication-timing program. The replication-timing program represents a very stable epigenetic feature of chromosomes. Recent evidence has indicated that the replication-timing program can influence the spatial distribution of mutagenic events such that certain regions of the genome experience increased spontaneous mutagenesis compared to surrounding regions. This influence has helped shape the genomes of humans and other multicellular organisms and can affect the distribution of mutations in somatic cells. It is also becoming clear that the replication-timing program is deregulated in many disease states, including cancer. Aberrant DNA replication timing is associated with changes in gene expression, changes in epigenetic modifications and an increased frequency of structural rearrangements. Furthermore, certain replication timing changes can directly lead to overt genomic instability and may explain unique mutational signatures that are present in cells that have undergone the recently described processes of "chromothripsis" and "kataegis". In this review, we will discuss how the normal replication timing program, as well as how alterations to this program, can contribute to the evolution of the genomic landscape in normal and cancerous cells.
Topics: Animals; DNA Replication; DNA Replication Timing; Epigenesis, Genetic; Gene Expression Regulation, Neoplastic; Genomic Instability; Humans; Models, Biological; Neoplasms; Time Factors
PubMed: 23327985
DOI: 10.1016/j.semcancer.2013.01.001 -
Trends in Cell Biology Nov 2002To ensure the fidelity of DNA replication, cells activate a stress-response pathway when DNA replication is perturbed. This pathway regulates not only progress through... (Review)
Review
To ensure the fidelity of DNA replication, cells activate a stress-response pathway when DNA replication is perturbed. This pathway regulates not only progress through the cell cycle but also transcription, apoptosis, DNA repair/recombination and DNA replication itself. Mounting evidence has suggested that this pathway is important for the maintenance of genomic integrity. Here, we discuss recent findings about how this pathway is activated by replication stress and how it regulates the DNA-replication machinery to alleviate the stress.
Topics: Animals; DNA Replication; Genes, cdc; S Phase; Signal Transduction; Yeasts
PubMed: 12446112
DOI: 10.1016/s0962-8924(02)02380-2 -
ACS Synthetic Biology Jul 2018The yeast cytoplasmically localized pGKL1/TP-DNAP1 plasmid/DNA polymerase pair forms an orthogonal DNA replication system whose mutation rate can be drastically...
The yeast cytoplasmically localized pGKL1/TP-DNAP1 plasmid/DNA polymerase pair forms an orthogonal DNA replication system whose mutation rate can be drastically increased without influencing genomic replication, thereby supporting in vivo continuous evolution. Here, we report that the pGKL2/TP-DNAP2 plasmid/DNA polymerase pair forms a second orthogonal replication system. We show that custom genes can be encoded and expressed from pGKL2, that error-prone TP-DNAP2s can be engineered, and that pGKL2 replication by TP-DNAP2 is both orthogonal to genomic replication in Saccharomyces cerevisiae and mutually orthogonal with pGKL1 replication by TP-DNAP1. This demonstration of two mutually orthogonal DNA replication systems with tunable error rates and properties should enable new applications in cell-based continuous evolution, genetic recording, and synthetic biology at large.
Topics: DNA Replication; DNA-Directed DNA Polymerase; Metabolic Engineering; Plasmids
PubMed: 29969238
DOI: 10.1021/acssynbio.8b00195 -
Methods in Cell Biology 2024DNA replication is a complex and tightly regulated process that must proceed accurately and completely if the cell is to faithfully transmit genetic material to its...
DNA replication is a complex and tightly regulated process that must proceed accurately and completely if the cell is to faithfully transmit genetic material to its progeny. Organisms have thus evolved complex mechanisms to deal with the myriad exogenous and endogenous sources of replication impediments to which the cell is subject. These mechanisms are of particular relevance to cancer biology, given that such "replication stress" frequently foreshadows genome instability during cancer pathogenesis, and that many traditional chemotherapies and a number of precision medicines function by interfering with the progress of DNA replication. Visualization of the progress and dynamics of DNA replication in living cells was historically a major challenge, neatly surmounted by the development of DNA fiber assays that utilize the fluorescent detection of halogenated nucleotides to track replication forks at single-molecule resolution. This methodology has been widely applied to study the dynamics of unperturbed DNA replication, as well as the cellular responses to various replication stress scenarios. In recent years, subtle modifications to DNA fiber assays have facilitated assessment of the stability of nascent DNA at stalled replication forks, as well as the detection of single-stranded DNA gaps and their subsequent filling by error-prone polymerases. Here, we present and discuss several iterations of the fiber assay and suggest methodologies for the analysis of the data obtained.
Topics: Humans; DNA Replication; DNA; Genomic Instability; Neoplasms; DNA Repair
PubMed: 38359983
DOI: 10.1016/bs.mcb.2023.02.007 -
Current Opinion in Genetics &... Apr 2004Recombination plays a crucial role in underpinning genome duplication, ensuring that replication blocks are removed or bypassed, and that the replication machinery is... (Review)
Review
Recombination plays a crucial role in underpinning genome duplication, ensuring that replication blocks are removed or bypassed, and that the replication machinery is subsequently reloaded back onto the DNA. Recent studies have identified a surprising variety of ways in which damaged replication forks are repaired and have shown that the mechanism used depends on the nature of the original blocking lesion. Indeed, an emerging theme is that a single recombination enzyme or complex can perform highly varied tasks, depending on the context of the recombination reaction.
Topics: Archaea; Bacteria; DNA Damage; DNA Repair; DNA Replication; Enzymes; Recombination, Genetic
PubMed: 15196455
DOI: 10.1016/j.gde.2004.01.001