The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: Fact or farce?

Ishino, Yuji; Cann, Isaac

doi:10.1266/ggs.73.323

Cited by 42 publications

(26 citation statements)

References 73 publications

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“…However, many genes encoding proteins sharing sequence similarities with eukaryotic DNA replication proteins are present in all archaeal genomes (Olsen and Woese, 1997;Edgell and Doolittle, 1997;Ishino and Cann, 1998;Ishino, 1999, Leipe et al, 1999). Several proteins involved in homologous DNA recombination are also conserved between Eukarya and Archaea.…”

Section: Introductionmentioning

confidence: 99%

Novel endonuclease in Archaea cleaving DNA with various branched structure.

et al. 2002

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We identified a novel structure-specific endonuclease in Pyrococcus furiosus. This nuclease contains two distinct domains, which are similar to the DEAH helicase family at the N-terminal two-third and the XPF endonuclease superfamily at the C-terminal one-third of the protein, respectively. The C-terminal domain has an endonuclease activity cleaving the DNA strand at the 5'-side of nicked or flapped positions in the duplex DNA. The nuclease also incises in the proximity of the 5'-side of a branch point in the template strand for leading synthesis in the fork-structured DNA. The N-terminal helicase may work cooperatively to change the fork structure suitable for cleavage by the C-terminal endonuclease. This protein, designated as Hef (helicase-associated endonuclease for fork-structured DNA), may be a prototypical enzyme for resolving stalled forks during DNA replication, as well as working at nucleotide excision repair.

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Section: Introductionmentioning

confidence: 99%

Novel endonuclease in Archaea cleaving DNA with various branched structure.

et al. 2002

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“…Moreover, an understanding of how the hyperthermophilic Archaea maintain their genetic information systems in cells growing under conditions unfavorable to the stability of DNA is of particular interest to biologists. Several genes encoding eukaryotic-like DNA replication proteins are present in archaeal genomes (4,7,12,24). This has led to the proposal that the archaeal DNA replication mechanism is basically similar to that of Eucarya.…”

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“…This has led to the proposal that the archaeal DNA replication mechanism is basically similar to that of Eucarya. Except for the euryarchaeotic heterodimeric DNA polymerase (3,11,13,40), all archaeal DNA polymerases described to date are single subunit proteins with sequences similar to those of the family B (␣-like) DNA polymerases, which include the chromosomal DNA replicases of Eucarya (4,12,32). The archaeal family B DNA polymerases have low processivity in vitro, and their ability to replicate the genome has been questioned (29).…”

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“…Purified RFCS, RFCL, and PfuRFC were subjected to a gel filtration analysis using the SMART system (Amersham Pharmacia) to estimate the molecular mass of each molecule in the solution. Molecular standard markers containing thyroglobulin (670 kDa), bovine gamma globulin (158 kDa), chicken ovalbumin (44 kDa), equine myoglobin (17 kDa), and vitamin B 12 (1.35 kDa) (Bio-Rad) were used in a different run under the same conditions. N-terminal amino acid sequencing.…”

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Biochemical Analysis of Replication Factor C from the Hyperthermophilic ArchaeonPyrococcus furiosus

Cann¹,

Ishino²,

Yuasa³

et al. 2001

J Bacteriol

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Replication factor C (RFC) and proliferating cell nuclear antigen (PCNA) are accessory proteins essential for processive DNA synthesis in the domain Eucarya. The function of RFC is to load PCNA, a processivity factor of eukaryotic DNA polymerases ␦ and , onto primed DNA templates. RFC-like genes, arranged in tandem in the Pyrococcus furiosus genome, were cloned and expressed individually in Escherichia coli cells to determine their roles in DNA synthesis. The P. furiosus RFC (PfuRFC) consists of a small subunit (RFCS) and a large subunit (RFCL). Highly purified RFCS possesses an ATPase activity, which was stimulated up to twofold in the presence of both single-stranded DNA (ssDNA) and P. furiosus PCNA (PfuPCNA). The ATPase activity of PfuRFC itself was as strong as that of RFCS. However, in the presence of PfuPCNA and ssDNA, PfuRFC exhibited a 10-fold increase in ATPase activity under the same conditions. RFCL formed very large complexes by itself and had an extremely weak ATPase activity, which was not stimulated by PfuPCNA and DNA. The PfuRFC stimulated PfuPCNA-dependent DNA synthesis by both polymerase I and polymerase II from P. furiosus. We propose that PfuRFC is required for efficient loading of PfuPCNA and that the role of RFC in processive DNA synthesis is conserved in Archaea and Eucarya.In the eukaryotic DNA replication system, replication factor C (RFC) and proliferating cell nuclear antigen (PCNA) are DNA polymerase auxiliary proteins implicated in replicative and repair DNA synthesis (reviewed in reference 42). The replicative DNA polymerases (pol␦ and polε) in Eucarya are highly processive, i.e., they can polymerize long stretches of DNA without dissociating from the template. This property is conferred upon both DNA polymerases by PCNA, a ringshaped homotrimeric protein capable of encircling and sliding along duplex DNA. PCNA works as an elongation factor for DNA polymerases by tethering the polymerases to the DNA template. For the loading of PCNA onto DNA, a clamp loader consisting of four distinct small subunits and one large subunit is required. The clamp loader, commonly known as RFC, performs this function in an ATP-dependent manner by (i) recognizing the primer terminus, (ii) binding to and opening the donut-shaped PCNA, and (iii) linking the opened PCNA topologically to the DNA. In the bacteria and bacteriophage systems, the replicative DNA polymerases also require the clamp molecule for their processive DNA synthesis. The molecular mechanisms of the clamp-loading process have been basically conserved, although the amino acid sequences of each molecule are distinctly different from those of eukaryotic proteins. Escherichia coli DNA polymerase III (Pol III) ␥-subunit and T4 gp44/gp62 are well known as the clamp loaders for their sliding clamps, Pol III ␤-subunit and T4 gp45, respectively (20,44).Since the discovery of Archaea, the third domain of life, the molecular mechanisms of their DNA transactions have become a very interesting subject. However, the current knowledge of the archaeal DNA...

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“…An understanding of how the hyperthermophilic archaea maintain their genetic information systems in cells growing under conditions unfavorable to the stability of DNA is of particular interest. The archaeal replication systems are more similar to those in Eucarya than those in Bacteria (Edgell and Doolittle, 1997;Ishino and Cann, 1998). The large subunit (RFCL, 55kDa) and the small subunit (RFCS, 37kDa), which jointly constitute, in the ratio of one to four, the clamp loader RFC complex from Pyrococcus furiosus , share significant sequence identity with their eukaryotic homologs Cann et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Identification of the critical region in Replication factor C from Pyrococcus furiosus for the stable complex formation with Proliferating cell nuclear antigen and DNA

Nishida¹,

Ishino²,

Miyata³

et al. 2005

Genes Genet. Syst.

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Replication factor C (RFC) and proliferating cell nuclear antigen (PCNA) are accessory proteins essential for processive DNA synthesis. The function of RFC is to load PCNA, a processivity factor of replicative DNA polymerases, onto primed DNA templates. The central hole of the PCNA homo-trimeric ring encircles doublestranded DNA, so that DNA polymerases can operate for DNA synthesis with PCNA along a DNA template. The Pyrococcus furiosus RFC ( Pfu RFC) consists of a small subunit (RFCS, 37kDa) and a large subunit (RFCL, 55kDa), which show significant sequence identity to the eukaryotic homologs. The C-terminal region of RFCL has an acidic cluster of about 30 amino acids, which consists mainly of glutamic acid residues, and a following basic cluster of 10 amino acids, which consists mainly of lysine residues. These clusters of charged amino acids, which precede the C-terminal consensus sequence, PIP (PCNA interacting protein)-box, are conserved in several archaeal RFCLs. The series of mutant Pfu RFC containing the C-terminal deletions in RFCL were constructed. The mutational analyses showed that the charged cluster is not essential for loading of PCNA onto DNA. However, the region containing the basic cluster is important for the stable ternary (RFC-PCNA-DNA) complex formation.

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The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: Fact or farce?

Cited by 42 publications

References 73 publications

Novel endonuclease in Archaea cleaving DNA with various branched structure.

Novel endonuclease in Archaea cleaving DNA with various branched structure.

Biochemical Analysis of Replication Factor C from the Hyperthermophilic ArchaeonPyrococcus furiosus

Identification of the critical region in Replication factor C from Pyrococcus furiosus for the stable complex formation with Proliferating cell nuclear antigen and DNA

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