scholarly journals DNA Helicase–Polymerase Coupling in Bacteriophage DNA Replication

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1739
Author(s):  
Chen-Yu Lo ◽  
Yang Gao
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Molecular Mechanisms ◽  
Bacteriophage T4 ◽  
Dna Helicase ◽  
Model Systems ◽  
Genome Replication ◽  
Template Strand ◽  
Replication Systems ◽  
Mechanistic Basis

Bacteriophages have long been model systems to study the molecular mechanisms of DNA replication. During DNA replication, a DNA helicase and a DNA polymerase cooperatively unwind the parental DNA. By surveying recent data from three bacteriophage replication systems, we summarized the mechanistic basis of DNA replication by helicases and polymerases. Kinetic data have suggested that a polymerase or a helicase alone is a passive motor that is sensitive to the base-pairing energy of the DNA. When coupled together, the helicase–polymerase complex is able to unwind DNA actively. In bacteriophage T7, helicase and polymerase reside right at the replication fork where the parental DNA is separated into two daughter strands. The two motors pull the two daughter strands to opposite directions, while the polymerase provides a separation pin to split the fork. Although independently evolved and containing different replisome components, bacteriophage T4 replisome shares mechanistic features of Hel–Pol coupling that are similar to T7. Interestingly, in bacteriophages with a limited size of genome like Φ29, DNA polymerase itself can form a tunnel-like structure, which encircles the DNA template strand and facilitates strand displacement synthesis in the absence of a helicase. Studies on bacteriophage replication provide implications for the more complicated replication systems in bacteria, archaeal, and eukaryotic systems, as well as the RNA genome replication in RNA viruses.

scholarly journals Initiating DNA replication: a matter of prime importance

2019 ◽  
Vol 47 (1) ◽  
pp. 351-356 ◽  
Author(s):  
Stephen D. Bell
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
De Novo ◽  
Broad Class ◽  
Genome Replication ◽  
Extrachromosomal Element ◽  
Replication Systems ◽  
Dna Chain ◽  
Mechanistic Basis ◽  
Cellular Dna

Abstract It has been known for decades that the principal replicative DNA polymerases that effect genome replication are incapable of starting DNA synthesis de novo. Rather, they require a 3′-OH group from which to extend a DNA chain. Cellular DNA replication systems exploit a dedicated, limited processivity RNA polymerase, termed primase, that synthesizes a short oligoribonucleotide primer which is then extended by a DNA polymerase. Thus, primases can initiate synthesis, proceed with primer elongation for a short distance then transfer the primer to a DNA polymerase. Despite these well-established properties, the mechanistic basis of these dynamic behaviours has only recently been established. In the following, the author will describe recent insights from studies of the related eukaryotic and archaeal DNA primases. Significantly, the general conclusions from these studies likely extend to a broad class of extrachromosomal element-associated primases as well as the human primase-related DNA repair enzyme, PrimPol.

scholarly journals Archaeal DNA polymerases: new frontiers in DNA replication and repair

2018 ◽  
Vol 2 (4) ◽  
pp. 503-516 ◽  
Author(s):  
Christopher D.O. Cooper
Keyword(s):  
Dna Repair ◽  
Dna Replication ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Dna Amplification ◽  
Model Systems ◽  
Genome Replication ◽  
Sequencing Technologies ◽  
Dna Replication And Repair ◽  
Polymerase Chain

Archaeal DNA polymerases have long been studied due to their superior properties for DNA amplification in the polymerase chain reaction and DNA sequencing technologies. However, a full comprehension of their functions, recruitment and regulation as part of the replisome during genome replication and DNA repair lags behind well-established bacterial and eukaryotic model systems. The archaea are evolutionarily very broad, but many studies in the major model systems of both Crenarchaeota and Euryarchaeota are starting to yield significant increases in understanding of the functions of DNA polymerases in the respective phyla. Recent advances in biochemical approaches and in archaeal genetic models allowing knockout and epitope tagging have led to significant increases in our understanding, including DNA polymerase roles in Okazaki fragment maturation on the lagging strand, towards reconstitution of the replisome itself. Furthermore, poorly characterised DNA polymerase paralogues are finding roles in DNA repair and CRISPR immunity. This review attempts to provide a current update on the roles of archaeal DNA polymerases in both DNA replication and repair, addressing significant questions that remain for this field.

DNA replication in thermophiles

2004 ◽  
Vol 32 (2) ◽  
pp. 236-239 ◽  
Author(s):  
A.I. Majerník ◽  
E.R. Jenkinson ◽  
J.P.J. Chong
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Molecular Mechanisms ◽  
Pyrococcus Furiosus ◽  
Model Systems ◽  
Eukaryotic Cells ◽  
Dna Manipulation ◽  
Processing Enzymes ◽  
The Many ◽  
Thermophilic Archaea

DNA replication enzymes in the thermophilic Archaea have previously attracted attention due to their obvious use in methods such as PCR. The proofreading ability of the Pyrococcus furiosus DNA polymerase has resulted in a commercially successful product (Pfu polymerase). One of the many notable features of the Archaea is the fact that their DNA processing enzymes appear on the whole to be more like those found in eukaryotes than bacteria. These proteins also appear to be simpler versions of those found in eukaryotes. For these reasons, archaeal organisms make potentially interesting model systems to explore the molecular mechanisms of processes such as DNA replication, repair and recombination. Why archaeal DNA-manipulation systems were adopted over bacterial systems by eukaryotic cells remains a most interesting question that we suggest may be linked to thermophily.

Prokaryotic DNA replication mechanisms

1987 ◽  
Vol 317 (1187) ◽  
pp. 395-420 ◽  
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Replication Fork ◽  
Kinetic Studies ◽  
Dna Helicase ◽  
Gene 32 ◽  
Dna Template ◽  
Lagging Strand

The three different prokaryotic replication systems that have been most extensively studied use the same basic components for moving a DNA replication fork, even though the individual proteins are different and lack extensive amino acid sequence homology. In the T4 bacteriophage system, the components of the DNA replication complex can be grouped into functional classes as follows: DNA polymerase (gene 43 protein), helix-destabilizing protein (gene 32 protein), polymerase accessory proteins (gene 44/62 and 45 proteins), and primosome proteins (gene 41 DNA helicase and gene 61 RNA primase). DNA synthesis in the in vitro system starts by covalent addition onto the 3'OH end at a random nick on a double-stranded DNA template and proceeds to generate a replication fork that moves at about the in vivo rate, and with approximately the in vivo base-pairing fidelity. DNA is synthesized at the fork in a continuous fashion on the leading strand and in a discontinuous fashion on the lagging strand (generating short Okazaki fragments with 5'-linked pppApCpXpYpZ pentaribonucleotide primers). Kinetic studies reveal that the DNA polymerase molecule on the lagging strand stays associated with the fork as it moves. Therefore the DNA template on the lagging strand must be folded so that the stop site for the synthesis of one Okazaki fragment is adjacent to the start site for the next such fragment, allowing the polymerase and other replication proteins on the lagging strand to recycle.

PolA2 is required for embryo development in ArabidopsisThis paper is one of a selection of papers published in a Special Issue from the National Research Council of Canada – Plant Biotechnology Institute.

Botany ◽  
2009 ◽  
Vol 87 (6) ◽  
pp. 626-634 ◽  
Author(s):  
Hui Yang ◽  
Daoquan Xiang ◽  
Sathya Prakash Venglat ◽  
Yongguo Cao ◽  
Edwin Wang ◽  
...  
Keyword(s):  
Dna Replication ◽  
Embryo Development ◽  
Dna Polymerase ◽  
Apical Cell ◽  
National Research Council ◽  
Model Systems ◽  
Proper Function ◽  
Dna Polymerase Α ◽  
Insertional Inactivation ◽  
Embryo Lethality

DNA replication machinery is highly conserved in eukaryotes. DNA polymerase is essential for the synthesis of new DNA strands and for DNA repair. Despite the significant progress in the understanding of these processes in yeast and animal model systems, there is only scant information available for their counterparts in plants. Among different multisubunit-containing DNA polymerases, DNA polymerase α (POLA complex) is composed of four subunits. In this study, we report on the characterization of PolA2, which encodes the putative B subunit of DNA polymerase α in Arabidopsis thaliana (L.) Heynh. PolA2 is a single copy gene in Arabidopsis and shows highly conserved regions with putative homologs in other plant species. Insertional inactivation of PolA2 in Arabidopsis leads to embryo lethality, with developmental arrest at or before the four-cell stage during embryogenesis. The apical cell lineage is strongly affected in the mutant embryos and the endosperm initial cell fails to divide. PolA2 is expressed broadly in the early phases of embryo development during the period of active cell divisions, while during the later stages of development expression is reduced and more localized. Ectopic overexpression of PolA2 produced dominant negative phenotypes with gametic and embryo lethality suggesting that coordinated and parallel expression with other subunits is critical for its proper function in DNA replication and plant development.

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