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Genes & Development Jun 2017DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork.... (Review)
Review
DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2-7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability.
Topics: Animals; Chromatin; DNA Helicases; DNA Replication; Evolution, Molecular; Genomic Instability; Humans; Minichromosome Maintenance Proteins; Replication Origin
PubMed: 28717046
DOI: 10.1101/gad.298232.117 -
Robust linear DNA degradation supports replication-initiation-defective mutants in Escherichia coli.G3 (Bethesda, Md.) Nov 2022RecBCD helicase/nuclease supports replication fork progress via recombinational repair or linear DNA degradation, explaining recBC mutant synthetic lethality with...
RecBCD helicase/nuclease supports replication fork progress via recombinational repair or linear DNA degradation, explaining recBC mutant synthetic lethality with replication elongation defects. Since replication initiation defects leave chromosomes without replication forks, these should be insensitive to the recBCD status. Surprisingly, we found that both Escherichia coli dnaA46(Ts) and dnaC2(Ts) initiation mutants at semi-permissive temperatures are also recBC-colethal. Interestingly, dnaA46 recBC lethality suppressors suggest underinitiation as the problem, while dnaC2 recBC suppressors signal overintiation. Using genetic and physical approaches, we studied the dnaA46 recBC synthetic lethality, for the possibility that RecBCD participates in replication initiation. Overproduced DnaA46 mutant protein interferes with growth of dnaA+ cells, while the residual viability of the dnaA46 recBC mutant depends on the auxiliary replicative helicase Rep, suggesting replication fork inhibition by the DnaA46 mutant protein. The dnaA46 mutant depends on linear DNA degradation by RecBCD, rather than on recombinational repair. At the same time, the dnaA46 defect also interacts with Holliday junction-moving defects, suggesting reversal of inhibited forks. However, in contrast to all known recBC-colethals, which fragment their chromosomes, the dnaA46 recBC mutant develops no chromosome fragmentation, indicating that its inhibited replication forks are stable. Physical measurements confirm replication inhibition in the dnaA46 mutant shifted to semi-permissive temperatures, both at the level of elongation and initiation, while RecBCD gradually restores elongation and then initiation. We propose that RecBCD-catalyzed resetting of inhibited replication forks allows replication to displace the "sticky" DnaA46(Ts) protein from the chromosomal DNA, mustering enough DnaA for new initiations.
Topics: Escherichia coli; Escherichia coli Proteins; DNA Replication; DNA Helicases; DNA; Mutant Proteins; DNA, Bacterial; Mutation; Bacterial Proteins; Chromosomes, Bacterial
PubMed: 36165702
DOI: 10.1093/g3journal/jkac228 -
Initiation of chromosome replication: structure and function of oriC and DnaA protein in eubacteria.Research in Microbiology 1991Recent advances in DNA technology have made it possible to analyse the structure and function of the replication origin region of the chromosomes of various bacteria.... (Comparative Study)
Comparative Study Review
Recent advances in DNA technology have made it possible to analyse the structure and function of the replication origin region of the chromosomes of various bacteria. Comparative studies have shown that 2 basic elements, the replicator and initiator, involved in initiation of chromosome replication are common to most eubacteria but with differences in the fine organization of these elements. In this article, we first review studies of the structural analysis of the origin regions of bacterial chromosomes, and then we summarize our recent work on the function of the 2 elements in Bacillus subtilis as compared to Escherichia coli, in order to show how organization of the elements is related to the differences in regulation of the initiation of replication in the 2 bacteria. Remarkable conservation of genes and their organization in the replication origin region was found in 5 bacteria representative of 3 major branches of the bacterial phylogenic tree. It was concluded that the conserved region containing the dnaA gene is the replication origin of the ancestral bacterium. Conservation of DnaA protein and its binding sequence (DnaA box) is remarkable, suggesting that they are the initiator and replicator of the chromosomes of most eubacteria. We have recently isolated an autonomously replicating sequence (ars) from B. subtilis. The essential features of ars, the presence of DnaA boxes and repeats of an AT rich 15-mer, are the same as E. coli oriC. However, 2 DnaA-box regions flanking the dnaA gene are both required for B. subtilis ars. The function of DnaA protein in vivo was studied in detail using a temperature-sensitive dnaA mutant in B. subtilis.(ABSTRACT TRUNCATED AT 250 WORDS)
Topics: Bacillus subtilis; Chromosome Mapping; DNA Replication; DNA, Bacterial; DNA-Binding Proteins; Escherichia coli; Gene Expression Regulation, Bacterial; In Vitro Techniques; Transcription, Genetic
PubMed: 1784823
DOI: 10.1016/0923-2508(91)90065-i -
Critical Reviews in Biochemistry and... Aug 2017Break-induced replication (BIR) is an important pathway specializing in repair of one-ended double-strand DNA breaks (DSBs). This type of DSB break typically arises at... (Review)
Review
Break-induced replication (BIR) is an important pathway specializing in repair of one-ended double-strand DNA breaks (DSBs). This type of DSB break typically arises at collapsed replication forks or at eroded telomeres. BIR initiates by invasion of a broken DNA end into a homologous template followed by initiation of DNA synthesis that can proceed for hundreds of kilobases. This synthesis is drastically different from S-phase replication in that instead of a replication fork, BIR proceeds via a migrating bubble and is associated with conservative inheritance of newly synthesized DNA. This unusual mode of DNA replication is responsible for frequent genetic instabilities associated with BIR, including hyper-mutagenesis, which can lead to the formation of mutation clusters, extensive loss of heterozygosity, chromosomal translocations, copy-number variations and complex genomic rearrangements. In addition to budding yeast experimental systems that were initially employed to investigate eukaryotic BIR, recent studies in different organisms including humans, have provided multiple examples of BIR initiated within different cellular contexts, including collapsed replication fork and telomere maintenance in the absence of telomerase. In addition, significant progress has been made towards understanding microhomology-mediated BIR (MMBIR) that can promote complex chromosomal rearrangements, including those associated with cancer and those leading to a number of neurological disorders in humans.
Topics: DNA Copy Number Variations; DNA Damage; DNA Repair; DNA Replication; Eukaryotic Cells; Humans
PubMed: 28427283
DOI: 10.1080/10409238.2017.1314444 -
Research in Microbiology May 2012DNA replication in eukaryotes initiates at specific sites known as origins of replication, or replicators. These replication origins occur throughout the genome, though... (Review)
Review
DNA replication in eukaryotes initiates at specific sites known as origins of replication, or replicators. These replication origins occur throughout the genome, though the propensity of their occurrence depends on the type of organism. In eukaryotes, zones of initiation of replication spanning from about 100 to 50,000 base pairs have been reported. The characteristics of eukaryotic replication origins are best understood in the budding yeast Saccharomyces cerevisiae, where some autonomously replicating sequences, or ARS elements, confer origin activity. ARS elements are short DNA sequences of a few hundred base pairs, identified by their efficiency at initiating a replication event when cloned in a plasmid. ARS elements, although structurally diverse, maintain a basic structure composed of three domains, A, B and C. Domain A is comprised of a consensus sequence designated ACS (ARS consensus sequence), while the B domain has the DNA unwinding element and the C domain is important for DNA-protein interactions. Although there are ∼400 ARS elements in the yeast genome, not all of them are active origins of replication. Different groups within the genus Saccharomyces have ARS elements as components of replication origin. The present paper provides a comprehensive review of various aspects of ARSs, starting from their structural conservation to sequence thermodynamics. All significant and conserved functional sequence motifs within different types of ARS elements have been extensively described. Issues like silencing at ARSs, their inherent fragility and factors governing their replication efficiency have also been addressed. Progress in understanding crucial components associated with the replication machinery and timing at these ARS elements is discussed in the section entitled "The replicon revisited".
Topics: Base Sequence; Conserved Sequence; DNA Replication; DNA, Fungal; Molecular Sequence Data; Nucleic Acid Conformation; Replication Origin; Saccharomyces cerevisiae
PubMed: 22504206
DOI: 10.1016/j.resmic.2012.03.003 -
FEBS Letters Aug 2012DNA replication is precisely regulated in time and space, thereby safeguarding genomic integrity. In eukaryotes, replication initiates from multiple sites along the... (Review)
Review
DNA replication is precisely regulated in time and space, thereby safeguarding genomic integrity. In eukaryotes, replication initiates from multiple sites along the genome, termed origins of replication, and propagates bidirectionally. Dynamic origin bound complexes dictate where and when replication should initiate. During late mitosis and G1 phase, putative origins are recognized and become "licensed" through the assembly of pre-replicative complexes (pre-RCs) that include the MCM2-7 helicases. Subsequently, at the G1/S phase transition, a fraction of pre-RCs are activated giving rise to the establishment of replication forks. Origin location is influenced by chromatin and nuclear organization and origin selection exhibits stochastic features. The regulatory mechanisms that govern these cell cycle events rely on the periodic fluctuation of cyclin dependent kinase (CDK) activity through the cell cycle.
Topics: Cell Nucleus; Cyclin-Dependent Kinases; DNA Replication; G1 Phase; S Phase; Stochastic Processes
PubMed: 22841721
DOI: 10.1016/j.febslet.2012.07.042 -
Trends in Cell Biology Mar 2011Mutations in DNA replication initiator genes in both prokaryotes and eukaryotes lead to a pleiotropic array of phenotypes, including defects in chromosome segregation,... (Review)
Review
Mutations in DNA replication initiator genes in both prokaryotes and eukaryotes lead to a pleiotropic array of phenotypes, including defects in chromosome segregation, cytokinesis, cell cycle regulation and gene expression. For years, it was not clear whether these diverse effects were indirect consequences of perturbed DNA replication, or whether they indicated that DNA replication initiator proteins had roles beyond their activity in initiating DNA synthesis. Recent work from a range of organisms has demonstrated that DNA replication initiator proteins play direct roles in many cellular processes, often functioning to coordinate the initiation of DNA replication with essential cell-cycle activities. The aim of this review is to highlight these new findings, focusing on the pathways and mechanisms utilized by DNA replication initiator proteins to carry out a diverse array of cellular functions.
Topics: Animals; Bacterial Proteins; Cell Cycle; DNA; DNA Replication; DNA-Binding Proteins; Humans; Origin Recognition Complex
PubMed: 21123069
DOI: 10.1016/j.tcb.2010.10.006 -
Genome Research Feb 2017Eukaryotic cells initiate DNA synthesis by sequential firing of hundreds of origins. This ordered replication is described by replication profiles, which measure the DNA...
Eukaryotic cells initiate DNA synthesis by sequential firing of hundreds of origins. This ordered replication is described by replication profiles, which measure the DNA content within a cell population. Here, we show that replication dynamics can be deduced from replication profiles of free-cycling cells. While such profiles lack explicit temporal information, they are sensitive to fork velocity and initiation capacity through the passive replication pattern, namely the replication of origins by forks emanating elsewhere. We apply our model-based approach to a compendium of profiles that include most viable budding yeast mutants implicated in replication. Predicted changes in fork velocity or initiation capacity are verified by profiling synchronously replicating cells. Notably, most mutants implicated in late (or early) origin effects are explained by global modulation of fork velocity or initiation capacity. Our approach provides a rigorous framework for analyzing DNA replication profiles of free-cycling cells.
Topics: Chromosome Structures; DNA Replication; Genome, Fungal; Models, Genetic; Replication Origin; Saccharomyces cerevisiae
PubMed: 28028072
DOI: 10.1101/gr.205849.116 -
Microbiology and Molecular Biology... Dec 1997Many bacterial plasmids replicate by a rolling-circle (RC) mechanism. Their replication properties have many similarities to as well as significant differences from... (Review)
Review
Many bacterial plasmids replicate by a rolling-circle (RC) mechanism. Their replication properties have many similarities to as well as significant differences from those of single-stranded DNA (ssDNA) coliphages, which also replicate by an RC mechanism. Studies on a large number of RC plasmids have revealed that they fall into several families based on homology in their initiator proteins and leading-strand origins. The leading-strand origins contain distinct sequences that are required for binding and nicking by the Rep proteins. Leading-strand origins also contain domains that are required for the initiation and termination of replication. RC plasmids generate ssDNA intermediates during replication, since their lagging-strand synthesis does not usually initiate until the leading strand has been almost fully synthesized. The leading- and lagging-strand origins are distinct, and the displaced leading-strand DNA is converted to the double-stranded form by using solely the host proteins. The Rep proteins encoded by RC plasmids contain specific domains that are involved in their origin binding and nicking activities. The replication and copy number of RC plasmids, in general, are regulated at the level of synthesis of their Rep proteins, which are usually rate limiting for replication. Some RC Rep proteins are known to be inactivated after supporting one round of replication. A number of in vitro replication systems have been developed for RC plasmids and have provided insight into the mechanism of plasmid RC replication.
Topics: Amino Acid Sequence; Bacteria; Bacterial Proteins; Base Sequence; DNA Replication; DNA, Bacterial; DNA, Circular; Molecular Sequence Data; Plasmids
PubMed: 9409148
DOI: 10.1128/mmbr.61.4.442-455.1997 -
Annual Review of Genetics 2007Eukaryotic DNA replication is regulated to ensure all chromosomes replicate once and only once per cell cycle. Replication begins at many origins scattered along each... (Review)
Review
Eukaryotic DNA replication is regulated to ensure all chromosomes replicate once and only once per cell cycle. Replication begins at many origins scattered along each chromosome. Except for budding yeast, origins are not defined DNA sequences and probably are inherited by epigenetic mechanisms. Initiation at origins occurs throughout the S phase according to a temporal program that is important in regulating gene expression during development. Most replication proteins are conserved in evolution in eukaryotes and archaea, but not in bacteria. However, the mechanism of initiation is conserved and consists of origin recognition, assembly of prereplication (pre-RC) initiative complexes, helicase activation, and replisome loading. Cell cycle regulation by protein phosphorylation ensures that pre-RC assembly can only occur in G1 phase, whereas helicase activation and loading can only occur in S phase. Checkpoint regulation maintains high fidelity by stabilizing replication forks and preventing cell cycle progression during replication stress or damage.
Topics: Animals; Cell Cycle; Chromosomes; DNA Replication
PubMed: 17630848
DOI: 10.1146/annurev.genet.41.110306.130308