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It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Sign In. Advanced Search. Search Menu. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents Abstract. Localization of the AT-rich regions within replication origin.
Structure of the AT-rich region. AT-rich region and repeated sequences — the essential elements of replication origins of bacterial replicons. Magdalena Rajewska , Magdalena Rajewska. Oxford Academic. Katarzyna Wegrzyn. Igor Konieczny. Select Format Select format. Permissions Icon Permissions. Abstract Repeated sequences are commonly present in the sites for DNA replication initiation in bacterial, archaeal, and eukaryotic replicons.
Figure 1. Open in new tab Download slide. Figure 2. Table 1 Repeated sequences within the AT-rich regions of selected replication origins. Open in new tab. Table 2 Proteins interacting or suspected to interact within the AT-rich regions.
DnaA V. DnaG primase E. SeqA E. IciA E. ArcA E. HobH E. DpiA E. CspA; CspE E. Google Scholar Crossref. Search ADS. P1 plasmid replication. Google Scholar PubMed. A single DnaA box is sufficient for initiation from the P1 plasmid origin. The AT richness and gid transcription determine the left border of the replication origin of the E. Mapping of the in vivo start site for leading strand DNA synthesis in plasmid R1.
An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. Duplex opening by DnaA protein at novel sequences in initiation of replication at the origin of the E. A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene.
A broad host range replicon with different requirements for replication initiation in three bacterial species. AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions.
The nucleotide sequence of replication and maintenance functions encoded by plasmid pSC Multiple replication origins of Halobacterium sp. Molecular cloning of replication and incompatibility regions from the R-plasmid R6K. Plasmid replication functions: two distinct segments of plasmid R1, RepA and RepD, express incompatibility and are capable of autonomous replication.
Mechanism of recruitment of DnaB helicase to the replication origin of the plasmid pSC Integration host factor of Escherichia coli reverses the inhibition of R6K plasmid replication by pi initiator protein. Replication of plasmid R6K gamma origin in vivo and in vitro : dependence on IHF binding to the ihf1 site.
The Chinese hamster dihydrofolate reductase origin consists of multiple potential nascent-strand start sites. Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda.
Replication origin of the broad host range plasmid RK2. Host-dependent requirement for specific DnaA boxes for plasmid RK2 replication. Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator. Distinct replication requirements for the two Vibrio cholerae chromosomes. The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation.
Replisome assembly at oriC, the replication origin of E. The integration host factor of Escherichia coli binds to multiple sites at plasmid R6K gamma origin and is essential for replication. Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. The dnaA protein complex with the E.
Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. DnaA protein is required for replication of the minimal replicon of the broad-host-range plasmid RK2 in Escherichia coli.
Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease. Localized DNA melting and structural pertubations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo. Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives. Differential binding of wild-type and a mutant RepA protein to oriR sequence suggests a model for the initiation of plasmid R1 replication.
Twenty years of the pPS10 replicon: insights on the molecular mechanism for the activation of DNA replication in iteron-containing bacterial plasmids. Initiation of heat-induced replication requires DnaA and the Lmer of oriC. A family of cold shock proteins in Bacillus subtilis is essential for cellular growth and for efficient protein synthesis at optimal and low temperatures. Insights into negative modulation of E.
Host participation in plasmid maintenance: dependence upon dnaA of replicons derived from P1 and F. Parental strand recognition of the DNA replication origin by the outer membrane in Escherichia coli.
Open complex formation by DnaA initiator protein at the Escherichia coli chromosomal origin requires the mer precisely spaced relative to the 9-mers. A novel protein binds a key origin sequence to block replication of an E.
Opposed actions of regulatory proteins, DnaA and IciA, in opening the replication origin of Escherichia coli. Replication of colicin E1 plasmid DNA in minicells from a unique replication initiation site. Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers initiator and dimers autogenous repressor.
DiaA, a novel DnaA-binding protein, ensures the timely initiation of Escherichia coli chromosome replication. Structural elements of the Streptomyces oriC region and their interactions with the DnaA protein. A multifunctional plasmid-encoded replication initiation protein both recruits and positions an active helicase at the replication origin. The initiator function of DnaA protein is negatively regulated by the sliding clamp of the E.
Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC. Activation in vivo of the minimal replication origin beta of plasmid R6K requires a small target sequence essential for DNA looping. Structural and functional analysis of a replication enhancer: separation of the enhancer activity from origin function by mutational dissection of the replication origin gamma of plasmid R6K.
DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading. Requirement of the Escherichia coli dnaA gene product for plasmid F maintenance. Replication of Vibrio cholerae chromosome I in Escherichia coli : dependence on dam methylation.
Construction of plasmid R6K derivatives in vitro : characterization of the R6K replication region. Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2. Helicase delivery and activation by DnaA and TrfA proteins during the initiation of replication of the broad host range plasmid RK2.
Positioning and the specific sequence of each mer motif are critical for activity of the plasmid RK2 replication origin. The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. Complexes at the replication origin of Bacillus subtilis with homologous and heterologous DnaA protein. Binding modes of the initiator and inhibitor forms of the replication protein pi to the gamma ori iteron of plasmid R6K.
Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein. Study of plasmid replication in Escherichia coli with a combination of 2D gel electrophoresis and electron microscopy. Okazaki fragments are named after the Japanese research team and married couple Reiji and Tsuneko Okazaki , who first discovered them in The strand with the Okazaki fragments is known as the lagging strand , and its synthesis is said to be discontinuous. The leading strand can be extended from one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments.
A protein called the sliding clamp holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. Beyond its role in initiation, topoisomerase also prevents the overwinding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it.
The primers are removed by the exonuclease activity of DNA polymerase I, and the gaps are filled in. Figure 4. Click for a larger image. At the origin of replication, topoisomerase II relaxes the supercoiled chromosome. Two replication forks are formed by the opening of the double-stranded DNA at the origin, and helicase separates the DNA strands, which are coated by single-stranded binding proteins to keep the strands separated.
DNA replication occurs in both directions. On the leading strand, DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches called Okazaki fragments.
Once the complete chromosome has been replicated, termination of DNA replication must occur. Although much is known about initiation of replication, less is known about the termination process. Following replication, the resulting complete circular genomes of prokaryotes are concatenated, meaning that the circular DNA chromosomes are interlocked and must be separated from each other. This is accomplished through the activity of bacterial topoisomerase IV, which introduces double-stranded breaks into DNA molecules, allowing them to separate from each other; the enzyme then reseals the circular chromosomes.
The resolution of concatemers is an issue unique to prokaryotic DNA replication because of their circular chromosomes. Because both bacterial DNA gyrase and topoisomerase IV are distinct from their eukaryotic counterparts, these enzymes serve as targets for a class of antimicrobial drugs called quinolones. Eukaryotic genomes are much more complex and larger than prokaryotic genomes and are typically composed of multiple linear chromosomes Table 2. The human genome , for example, has 3 billion base pairs per haploid set of chromosomes, and 6 billion base pairs are inserted during replication.
There are multiple origins of replication on each eukaryotic chromosome Figure 5 ; the human genome has 30, to 50, origins of replication.
The rate of replication is approximately nucleotides per second—10 times slower than prokaryotic replication. Figure 5. Eukaryotic chromosomes are typically linear, and each contains multiple origins of replication. The essential steps of replication in eukaryotes are the same as in prokaryotes. Before replication can start, the DNA has to be made available as a template.
Eukaryotic DNA is highly supercoiled and packaged, which is facilitated by many proteins, including histones see Structure and Function of Cellular Genomes.
At the origin of replication , a prereplication complex composed of several proteins, including helicase , forms and recruits other enzymes involved in the initiation of replication, including topoisomerase to relax supercoiling, single-stranded binding protein, RNA primase , and DNA polymerase. Following initiation of replication, in a process similar to that found in prokaryotes, elongation is facilitated by eukaryotic DNA polymerases.
The gaps that remain are sealed by DNA ligase. Because eukaryotic chromosomes are linear, one might expect that their replication would be more straightforward. In the leading strand, synthesis continues until it reaches either the end of the chromosome or another replication fork progressing in the opposite direction. On the lagging strand, DNA is synthesized in short stretches, each of which is initiated by a separate primer. When the replication fork reaches the end of the linear chromosome, there is no place to make a primer for the DNA fragment to be copied at the end of the chromosome.
These ends thus remain unpaired and, over time, they may get progressively shorter as cells continue to divide. The ends of the linear chromosomes are known as telomeres and consist of noncoding repetitive sequences. The telomeres protect coding sequences from being lost as cells continue to divide. The discovery of the enzyme telomerase Figure 6 clarified our understanding of how chromosome ends are maintained.
Telomerase contains a catalytic part and a built-in RNA template. In this way, the ends of the chromosomes are replicated. In humans, telomerase is typically active in germ cells and adult stem cells; it is not active in adult somatic cells and may be associated with the aging of these cells. Eukaryotic microbes including fungi and protozoans also produce telomerase to maintain chromosomal integrity.
For her discovery of telomerase and its action, Elizabeth Blackburn — received the Nobel Prize for Medicine or Physiology in Figure 6. In eukaryotes, the ends of the linear chromosomes are maintained by the action of the telomerase enzyme. To copy their nucleic acids, plasmids and viruses frequently use variations on the pattern of DNA replication described for prokaryote genomes. Digestion 2.
The Blood System 3. Disease Defences 4. Gas Exchange 5. Homeostasis Higher Level 7: Nucleic Acids 1. DNA Structure 2. Transcription 3. Translation 8: Metabolism 1. Metabolism 2. Cell Respiration 3. Photosynthesis 9: Plant Biology 1. Xylem Transport 2. Phloem Transport 3. Plant Growth 4. Plant Reproduction Genetics 1. Meiosis 2. Inheritance 3.
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