Diversity of the DNA Replication System in the<i>Archaea</i>Domain

Sarmiento, Felipe; Long, Feng; Cann, Isaac; Whitman, William B.

doi:10.1155/2014/675946

Cited by 18 publications

(14 citation statements)

References 158 publications

(202 reference statements)

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“…Due to the strong functional and sequence conservation, archaeal MCM proteins have proven to be powerful tools for elucidating essential features of MCM function. The MCM complexes of many archaea form homohexamers from a single gene product [ 27 ]. As such, these archaeal MCM complexes represent simplified versions of the eukaryotic Mcm2–7 complex and can serve as a model, both structurally and biochemically.…”

Section: Archaeal MCM As a Model For Eukaryotic Mcm2–7mentioning

confidence: 99%

Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function

Miller

Enemark

2015

Archaea

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In eukaryotes, the replicative helicase is the large multisubunit CMG complex consisting of the Mcm2–7 hexameric ring, Cdc45, and the tetrameric GINS complex. The Mcm2–7 ring assembles from six different, related proteins and forms the core of this complex. In archaea, a homologous MCM hexameric ring functions as the replicative helicase at the replication fork. Archaeal MCM proteins form thermostable homohexamers, facilitating their use as models of the eukaryotic Mcm2–7 helicase. Here we review archaeal MCM helicase structure and function and how the archaeal findings relate to the eukaryotic Mcm2–7 ring.

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Section: Archaeal MCM As a Model For Eukaryotic Mcm2–7mentioning

confidence: 99%

Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function

Miller

Enemark

2015

Archaea

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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: 93%

<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 partner brings proteins with the histone-fold, from which eukaryotic histones, nucleosomes, and the substrate for epigenetic control of gene expression evolved [58][59][60]. The multiple-origin nature of archaeal DNA replication is also essential in the propagation of large amounts of DNA, which was necessary to replicate chromosomes of eukaryotic size [80,81].…”

Section: Energy and Information: A Good Recipe For Complexitymentioning

confidence: 99%

“…The compaction of eukaryotic DNA into nucleosomes allowed the nascent eukaryotic lineage to store and manage vastly more information than was possible in prokaryotes, and thus to express a dramatically larger number of different proteins than were expressed in prokaryotes. At the same time, the multiple replication origins germane to archaeal DNA [80,81] allowed eukaryotic chromosomes to expand to the size range now characteristic of eukaryotic cells. Through acetylation and methylation, histones also provided a simple mechanism of information transfer about the nutrient and energetic state of the nascent eukaryotic cell into chromatin condensation and activity.…”

Section: Trends Trends In In Microbiology Microbiologymentioning

confidence: 99%

Archaeal Histone Contributions to the Origin of Eukaryotes

Brunk

Martin

2019

Trends in Microbiology

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The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells. Eukaryotes from Prokaryotes: Symbiotic Contributions HighlightsThe last common ancestor of eukaryotes had mitochondria, pointing to hostsymbiont interactions at eukaryote origin. Mitochondria contributed energy, genes, and membranes to the eukaryotic lineage. What did the archaeal host contribute?Recent metagenomic studies propose that close relatives of the archaeal host exist that are 'complex' (phagocytosing) and that the archaeal host brought that complexity to eukaryotes.Yet complex archaea have not been found, and there are doubts that the metagenomic archaeal data represent truly complex archaea.Alternatively, histones could have been the key archaeal contribution to eukaryote complexity.In eukaryotes, histone modifications link gene expression to the physiological state of the cell via carbon-, energy-, and nitrogen-sensing through regulators such as AMPK, GCN2, and TOR. The Archaeal ContributionSince their discovery, archaea have been implicated as relatives of the host lineage at the origin of eukaryogenesis and mitochondria [18,19]. There is now much discussion about the possibility that complex, phagocytosing archaea might be yet discovered in nature, based on metagenomic data [20][21][22]. In that view, the contribution of archaea is unequivocal: the archaeal host brought preformed complexity to the eukaryotic lineage. Indeed, the possibility that some archaea or archaeal relatives might possess a primitive cytoskeleton has been discussed for decades [23][24][25][26].

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Diversity of the DNA Replication System in theArchaeaDomain

Cited by 18 publications

References 158 publications

Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function

Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function

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

Archaeal Histone Contributions to the Origin of Eukaryotes

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