The archaeal DNA replication machinery: past, present and future

Ishino, Sonoko; Kelman, Lori M.; Kelman, Zvi; Ishino, Yuji

doi:10.1266/ggs.88.315

Cited by 10 publications

(8 citation statements)

References 30 publications

(31 reference statements)

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“…The replisome composition is dynamic; some components involved in lagging-strand synthesis only transiently associate with the replisome, whereas others require long-lived stable interactions for activity (1)(2)(3). Although sequence conservation and homology modeling have identified many components of the archaeal replisome, archaeon-specific replication factors have also been isolated from complexes formed with established components of the replication machinery (4)(5)(6)(7)(8)(9)(10). One such factor, encoded by TK1252 in Thermococcus kodakarensis and designated GAN (GINS-associated nuclease), shares sequence and structural similarities with the bacterial RecJ and eukaryotic Cdc45 proteins (11,12).…”

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The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis

et al. 2017

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Many aspects of and factors required for DNA replication are conserved across all three domains of life, but there are some significant differences surrounding lagging-strand synthesis. In Archaea, a 5=-to-3= exonuclease, related to both bacterial RecJ and eukaryotic Cdc45, that associates with the replisome specifically through interactions with GINS was identified and designated GAN (for GINS-associated nuclease). Despite the presence of a well-characterized flap endonuclease (Fen1), it was hypothesized that GAN might participate in primer removal during Okazaki fragment maturation, and as a Cdc45 homologue, GAN might also be a structural component of an archaeal CMG (Cdc45, MCM, and GINS) replication complex. We demonstrate here that, individually, either Fen1 or GAN can be deleted, with no discernible effects on viability and growth. However, deletion of both Fen1 and GAN was not possible, consistent with both enzymes catalyzing the same step in primer removal from Okazaki fragments in vivo. RNase HII has also been proposed to participate in primer processing during Okazaki fragment maturation. Strains with both Fen1 and RNase HII deleted grew well. GAN activity is therefore sufficient for viability in the absence of both RNase HII and Fen1, but it was not possible to construct a strain with both RNase HII and GAN deleted. Fen1 alone is therefore insufficient for viability in the absence of both RNase HII and GAN. The ability to delete GAN demonstrates that GAN is not required for the activation or stability of the archaeal MCM replicative helicase. IMPORTANCEThe mechanisms used to remove primer sequences from Okazaki fragments during lagging-strand DNA replication differ in the biological domains. Bacteria use the exonuclease activity of DNA polymerase I, whereas eukaryotes and archaea encode a flap endonuclease (Fen1) that cleaves displaced primer sequences. RNase HII and the GINS-associated exonuclease GAN have also been hypothesized to assist in primer removal in Archaea. Here we demonstrate that in Thermococcus kodakarensis, either Fen1 or GAN activity is sufficient for viability. Furthermore, GAN can support growth in the absence of both Fen1 and RNase HII, but Fen1 and RNase HII are required for viability in the absence of GAN.KEYWORDS Archaea, CMG complex, DNA replication, GINS-associated nuclease GAN, Okazaki fragment, RNase HII, flap endonuclease Fen1 D NA replication is catalyzed by a protein complex, designated the replisome, with structural and catalytic components tightly regulated, intertwined, and coordinated to facilitate both leading-and lagging-strand synthesis. The replisome composition is

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confidence: 99%

The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis

et al. 2017

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“…In archaea, DNA replication and responses to DNA damage occur in the context of a relatively simple prokaryotic cell, yet these processes involve proteins and other molecular features homologous to those of eukaryotic cells, rather than bacteria (Ishino et al 2013). This situation makes archaea strategic for understanding the diversity and evolution of mechanisms that preserve genome integrity, but the archaeal mechanisms remain largely unexplored in their cellular context.…”

Section: Discussionmentioning

confidence: 99%

“…As the third, deeply diverging, lineage of cellular organisms distinct from bacteria and eukaryotes, archaea provide a unique perspective on the diversity and evolution of DNA replication and damage-coping mechanisms. The scheme of DNA replication in archaea incorporates many eukaryotic features but is simpler than that of eukaryotes (Ishino et al 2013). Archaeal replication origins are recognized by Cdc6/ Orc1 homologs, and the replicative helicase is an MCM homolog that moves 39 to 59 on the leading-strand template (Barry and Bell 2006;Li et al 2013).…”

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Lesion-Induced Mutation in the Hyperthermophilic Archaeon Sulfolobus acidocaldarius and Its Avoidance by the Y-Family DNA Polymerase Dbh

Sakofsky

Grogan

2015

Genetics

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Hyperthermophilic archaea offer certain advantages as models of genome replication, and Sulfolobus Y-family polymerases Dpo4 (S. solfataricus) and Dbh (S. acidocaldarius) have been studied intensively in vitro as biochemical and structural models of trans-lesion DNA synthesis (TLS). However, the genetic functions of these enzymes have not been determined in the native context of living cells. We developed the first quantitative genetic assays of replication past defined DNA lesions and error-prone motifs in Sulfolobus chromosomes and used them to measure the efficiency and accuracy of bypass in normal and dbh 2 strains of Sulfolobus acidocaldarius. Oligonucleotide-mediated transformation allowed low levels of abasic-site bypass to be observed in S. acidocaldarius and demonstrated that the local sequence context affected bypass specificity; in addition, most erroneous TLS did not require Dbh function. Applying the technique to another common lesion, 7,8-dihydro-8-oxo-deoxyguanosine (8-oxo-dG), revealed an antimutagenic role of Dbh. The efficiency and accuracy of replication past 8-oxo-dG was higher in the presence of Dbh, and up to 90% of the Dbh-dependent events inserted dC. A third set of assays, based on phenotypic reversion, showed no effect of Dbh function on spontaneous 21 frameshifts in mononucleotide tracts in vivo, despite the extremely frequent slippage at these motifs documented in vitro. Taken together, the results indicate that a primary genetic role of Dbh is to avoid mutations at 8-oxo-dG that occur when other Sulfolobus enzymes replicate past this lesion. The genetic evidence that Dbh is recruited to 8-oxo-dG raises questions regarding the mechanism of recruitment, since Sulfolobus spp. have eukaryotic-like replisomes but no ubiquitin.KEYWORDS trans-lesion DNA synthesis (TLS); abasic site; 7,8-dihydro-8-oxo-deoxyguanosine; oligonucleotide-mediated transformation T HE fact that DNA damage occurs in all living cells poses a threat to the accurate replication and partitioning of their genomes. Cells counter this threat with an array of diverse damage-coping systems, some of which repair the DNA, whereas others enable replication to continue past persistent lesions. Lesion bypass, also termed "damage tolerance," can follow various alternatives, which are broadly distinguished as error-free vs. error-prone (Lehmann et al. 2007). The error-free pathways generally use recombinationassociated functions to pair a strand, newly synthesized on intact template, to the damaged DNA strand; the mechanisms for this include transient reversal of the replication fork and strand exchange at gaps left behind the fork (Sale 2012). These mechanisms bypass lesions accurately, although they can promote other forms of genetic instability, such as ectopic recombination between dispersed repeats (Izhar et al. 2013).Error-prone mechanisms of lesion bypass, in contrast, use specialized, trans-lesion synthesis (TLS) polymerases to continue strand elongation using the damaged template; most of these enzymes belong to t...

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“…This domain can be taxonomically divided into five Phyla. Crenarchaeota and Euryarchaeota are best characterized, and this taxonomic division is strongly supported by comparative genomics (Ishino, Kelman, Kelman, & Ishino, 2013;Sarmiento, Long, Cann, & Whitman, 2014). These five Phyla have 163 genomes that have already been revealed with 50 genomes from Crenarchaeota and 113 from Euryarchaeota (Jozwiakowski, Gholami, & Doherty, 2015).…”

Section: Introductionmentioning

confidence: 94%

“…In addition, that mechanism has some archaeal-specific particularities, instead of being a simpler version of the eukaryotic replication machinery (Kelman & Kelman, 2014). The study of archaeal DNA replication was initiated shortly after the recognition of Archaea as the third domain of life (Ishino et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

<b>Prediction of mutations on structure primase of the archaeon <i>Sulfolobus solfataricus

Souza

Diniz

2017

Acta Sci. Biol. Sci.

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ABSTRACT. All living organisms need a DNA replication mechanism and it has been conserved in the three domains of life throughout evolutionary process. Primase is the enzyme responsible for synthesizing de novo RNA primers in DNA replication. Archaeo-Eukaryotic Primase (AEP) is the superfamily that typically forms a heterodimeric complex containing both a small catalytic subunit (PriS) and a large accessory noncatalytic subunit (PriL). Sulfolobus solfataricus is a model organism for research on the Genetics field. The aim of this work was to evaluate, via Bioinformatics tools, three mutations in the large subunit (PriL) of the archaeon Sulfolobus solfataricus. The aspartic acid residue in the positions (Asp) 62, (Asp) 235, (Asp) 241 have been substituted by glutamic acid (Glu). The highest positive free energy variation of the three substitutions analyzed occurred with the mutation at the (Asp) 241 site. The in silico analysis suggested that these mutations in PriL may destabilize its tridimensional structure interfering with replication mechanisms of Sulfolobus solfataricus. Moreover, it may also alter interactions with other molecules, making salt bridges, for instance.Keywords: in silico, PriL, 3D structure, DNA replication, primer, mutations.Predição de mutações na estrutura da primase da arquea Sulfolobus solfataricus RESUMO. Todos os organismos vivos necessitam de um eficiente mecanismo de replicação de DNA. Ao longo da evolução biológica foi observado que esse mecanismo é conservado nos três domínios da vida. Uma enzima importante que participa desse mecanismo é a RNA primase, a qual é responsável pela síntese de novo de iniciadores de RNA na replicação do DNA. Em Arquea-Eucariota, RNA Primase (AEP) tipicamente forma um complexo heterodimérico, que contém uma pequena subunidade catalítica (PriS) e uma subunidade maior não catalítica acessória (PriL). Sulfolobus solfataricus é um organismo modelo de Arquea para a pesquisa no campo da genética. O objetivo deste trabalho foi avaliar, por meio de ferramentas de bioinformática, três mutações pontuais na subunidade maior (PriL) de Sulfolobus solfataricus. Nas sequências mutantes, os resíduos de ácido aspártico nas posições (Asp) 62, (Asp) 235, (Asp) 241 foram substituídos por ácido glutâmico (Glu). A maior variação de energia livre positiva das três mutações analisadas ocorreu no sítio (Asp) 241. A análise in silico sugeriu que essas mutações em PriL podem desestabilizar sua estrutura tridimensional, interferindo com os mecanismos de replicação de Sulfolobus solfataricus. Além disso, podem alterar interações com outras moléculas, formando pontes salinas.Palavras-chave: in silico, PriL, estrutura 3D, Replicação de DNA, iniciador, mutações.

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The archaeal DNA replication machinery: past, present and future

Cited by 10 publications

References 30 publications

The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis

The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis

Lesion-Induced Mutation in the Hyperthermophilic Archaeon Sulfolobus acidocaldarius and Its Avoidance by the Y-Family DNA Polymerase Dbh

<b>Prediction of mutations on structure primase of the archaeon <i>Sulfolobus solfataricus

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