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Journal articles on the topic 'Eukaryotic replication'

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Published: 4 June 2021

Last updated: 11 February 2022

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1

Villarreal, Luis P., and Victor R. DeFilippis. "A Hypothesis for DNA Viruses as the Origin of Eukaryotic Replication Proteins." Journal of Virology 74, no. 15 (August 1, 2000): 7079–84. http://dx.doi.org/10.1128/jvi.74.15.7079-7084.2000.

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ABSTRACT The eukaryotic replicative DNA polymerases are similar to those of large DNA viruses of eukaryotic and bacterial T4 phages but not to those of eubacteria. We develop and examine the hypothesis that DNA virus replication proteins gave rise to those of eukaryotes during evolution. We chose the DNA polymerase from phycodnavirus (which infects microalgae) as the basis of this analysis, as it represents a virus of a primitive eukaryote. We show that it has significant similarity with replicative DNA polymerases of eukaryotes and certain of their large DNA viruses. Sequence alignment confirms this similarity and establishes the presence of highly conserved domains in the polymerase amino terminus. Subsequent reconstruction of a phylogenetic tree indicates that these algal viral DNA polymerases are near the root of the clade containing all eukaryotic DNA polymerase delta members but that this clade does not contain the polymerases of other DNA viruses. We consider arguments for the polarity of this relationship and present the hypothesis that the replication genes of DNA viruses gave rise to those of eukaryotes and not the reverse direction.

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2

So, Antero G., and Kathleen M. Downey. "Eukaryotic DNA Replication." Critical Reviews in Biochemistry and Molecular Biology 27, no. 1-2 (January 1992): 129–55. http://dx.doi.org/10.3109/10409239209082561.

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3

Held, Paul G., and Nicholas H. Heintz. "Eukaryotic replication origins." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1130, no. 3 (April 1992): 235–46. http://dx.doi.org/10.1016/0167-4781(92)90435-3.

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4

Campbell, J. L. "Eukaryotic DNA Replication." Annual Review of Biochemistry 55, no. 1 (June 1986): 733–71. http://dx.doi.org/10.1146/annurev.bi.55.070186.003505.

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5

Zannis-Hadjopoulos, Maria, and Gerald B. Price. "Eukaryotic DNA replication." Journal of Cellular Biochemistry 75, S32 (1999): 1–14. http://dx.doi.org/10.1002/(sici)1097-4644(1999)75:32+<1::aid-jcb2>3.0.co;2-j.

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6

Diffley, John F. X. "Eukaryotic DNA replication." Current Opinion in Cell Biology 6, no. 3 (June 1994): 368–72. http://dx.doi.org/10.1016/0955-0674(94)90028-0.

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7

Wang, Thomas A., and Joachim J. Li. "Eukaryotic DNA replication." Current Opinion in Cell Biology 7, no. 3 (January 1995): 414–20. http://dx.doi.org/10.1016/0955-0674(95)80098-0.

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8

Denhardt, David T., and Emanuel A. Faust. "Eukaryotic DNA replication." BioEssays 2, no. 4 (April 1985): 148–54. http://dx.doi.org/10.1002/bies.950020403.

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9

DePamphilis, Melvin L. "Eukaryotic DNA Replication Origins." Cell 114, no. 3 (August 2003): 274–75. http://dx.doi.org/10.1016/s0092-8674(03)00604-4.

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10

Burgers, Peter M. J., and Thomas A. Kunkel. "Eukaryotic DNA Replication Fork." Annual Review of Biochemistry 86, no. 1 (June 20, 2017): 417–38. http://dx.doi.org/10.1146/annurev-biochem-061516-044709.

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11

Miller, Justin M., and Eric J. Enemark. "Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function." Archaea 2015 (2015): 1–14. http://dx.doi.org/10.1155/2015/305497.

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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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12

Kunkel, Thomas A. "Balancing eukaryotic replication asymmetry with replication fidelity." Current Opinion in Chemical Biology 15, no. 5 (October 2011): 620–26. http://dx.doi.org/10.1016/j.cbpa.2011.07.025.

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13

Moreno, Sara Priego, and Agnieszka Gambus. "Mechanisms of eukaryotic replisome disassembly." Biochemical Society Transactions 48, no. 3 (June 3, 2020): 823–36. http://dx.doi.org/10.1042/bst20190363.

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DNA replication is a complex process that needs to be executed accurately before cell division in order to maintain genome integrity. DNA replication is divided into three main stages: initiation, elongation and termination. One of the key events during initiation is the assembly of the replicative helicase at origins of replication, and this mechanism has been very well described over the last decades. In the last six years however, researchers have also focused on deciphering the molecular mechanisms underlying the disassembly of the replicative helicase during termination. Similar to replisome assembly, the mechanism of replisome disassembly is strictly regulated and well conserved throughout evolution, although its complexity increases in higher eukaryotes. While budding yeast rely on just one pathway for replisome disassembly in S phase, higher eukaryotes evolved an additional mitotic pathway over and above the default S phase specific pathway. Moreover, replisome disassembly has been recently found to be a key event prior to the repair of certain DNA lesions, such as under-replicated DNA in mitosis and inter-strand cross-links (ICLs) in S phase. Although replisome disassembly in human cells has not been characterised yet, they possess all of the factors involved in these pathways in model organisms, and de-regulation of many of them are known to contribute to tumorigenesis and other pathological conditions.

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14

Walter, Johannes, and John Newport. "Initiation of Eukaryotic DNA Replication." Molecular Cell 5, no. 4 (April 2000): 617–27. http://dx.doi.org/10.1016/s1097-2765(00)80241-5.

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15

Makarova, K. S., and E. V. Koonin. "Archaeology of Eukaryotic DNA Replication." Cold Spring Harbor Perspectives in Biology 5, no. 11 (July 23, 2013): a012963. http://dx.doi.org/10.1101/cshperspect.a012963.

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16

Kearsey, Stephen E. "DNA replication in eukaryotic cells." Trends in Biochemical Sciences 22, no. 8 (August 1997): 323. http://dx.doi.org/10.1016/s0968-0004(97)82223-2.

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17

Coverley, D., and R. A. Laskey. "Regulation of Eukaryotic DNA Replication." Annual Review of Biochemistry 63, no. 1 (June 1994): 745–76. http://dx.doi.org/10.1146/annurev.bi.63.070194.003525.

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18

Bell, Stephen P., and Anindya Dutta. "DNA Replication in Eukaryotic Cells." Annual Review of Biochemistry 71, no. 1 (June 2002): 333–74. http://dx.doi.org/10.1146/annurev.biochem.71.110601.135425.

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19

Hubscher, U., and JM Sogo. "The Eukaryotic DNA Replication Fork." Physiology 12, no. 3 (June 1, 1997): 125–31. http://dx.doi.org/10.1152/physiologyonline.1997.12.3.125.

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Before a cell divides into two identical daughter cells, the entire genome must be replicated faithfully. The mechanistic details of this complex macromolecular process, called DNA replication, have recently been clarified. We focus on the current knowledge at the eukaryotic DNA replication fork at the levels of DNA and chromatin.

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20

Laskey, Ronald. "The Croonian Lecture 2001 Hunting the antisocial cancer cell: MCM proteins and their exploitation." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1458 (June 23, 2005): 1119–32. http://dx.doi.org/10.1098/rstb.2005.1656.

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Replicating large eukaryotic genomes presents the challenge of distinguishing replicated regions of DNA from unreplicated DNA. A heterohexamer of minichromosome maintenance (MCM) proteins is essential for the initiation of DNA replication. MCM proteins are loaded on to unreplicated DNA before replication begins and displaced progressively during replication. Thus, bound MCM proteins license DNA for one, and only one, round of replication and this licence is reissued each time a cell divides. MCM proteins are also the best candidates for the replicative helicases that unwind DNA during replication, but interesting questions arise about how they can perform this role, particularly as they are present on only unreplicated DNA, rather than clustered at replication forks. Although MCM proteins are bound and released cyclically from DNA during the cell cycle, higher eukaryotic cells retain them in the nucleus throughout the cell cycle. In contrast, MCMs are broken down when cells exit the cycle by quiescence or differentiation. We have exploited these observations to develop screening tests for the common carcinomas, starting with an attempt to improve the sensitivity of the smear test for cervical cancer. MCM proteins emerge as exceptionally promising markers for cancer screening and early diagnosis.

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21

Walters, Alison D., and James P. J. Chong. "Methanococcus maripaludis: an archaeon with multiple functional MCM proteins?" Biochemical Society Transactions 37, no. 1 (January 20, 2009): 1–6. http://dx.doi.org/10.1042/bst0370001.

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There are a large number of proteins involved in the control of eukaryotic DNA replication, which act together to ensure DNA is replicated only once every cell cycle. Key proteins involved in the initiation and elongation phases of DNA replication include the MCM (minchromosome maintenance) proteins, MCM2–MCM7, a family of six related proteins believed to act as the replicative helicase. Genome sequencing has revealed that the archaea possess a simplified set of eukaryotic replication homologues. The complexity of the DNA replication machinery in eukaryotes has led to a number of archaeal species being adapted as model organisms for the study of the DNA replication process. Most archaea sequenced to date possess a single MCM homologue that forms a hexameric complex. Recombinant MCMs from several archaea have been used in the biochemical characterization of the protein, revealing that the MCM complex has ATPase, DNA-binding and -unwinding activities. Unusually, the genome of the methanogenic archaeon Methanococcus maripaludis contains four MCM homologues, all of which contain the conserved motifs required for function. The availability of a wide range of genetic tools for the manipulation of M. maripaludis and the relative ease of growth of this organism in the laboratory makes it a good potential model for studying the role of multiple MCMs in DNA replication.

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22

Mirkin, Ekaterina V., and Sergei M. Mirkin. "Replication Fork Stalling at Natural Impediments." Microbiology and Molecular Biology Reviews 71, no. 1 (March 2007): 13–35. http://dx.doi.org/10.1128/mmbr.00030-06.

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SUMMARY Accurate and complete replication of the genome in every cell division is a prerequisite of genomic stability. Thus, both prokaryotic and eukaryotic replication forks are extremely precise and robust molecular machines that have evolved to be up to the task. However, it has recently become clear that the replication fork is more of a hurdler than a runner: it must overcome various obstacles present on its way. Such obstacles can be called natural impediments to DNA replication, as opposed to external and genetic factors. Natural impediments to DNA replication are particular DNA binding proteins, unusual secondary structures in DNA, and transcription complexes that occasionally (in eukaryotes) or constantly (in prokaryotes) operate on replicating templates. This review describes the mechanisms and consequences of replication stalling at various natural impediments, with an emphasis on the role of replication stalling in genomic instability.

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23

Dionne, I., N. P. Robinson, A. T. McGeoch, V. L. Marsh, A. Reddish, and S. D. Bell. "DNA replication in the hyperthermophilic archaeon Sulfolobus solfataricus." Biochemical Society Transactions 31, no. 3 (June 1, 2003): 674–76. http://dx.doi.org/10.1042/bst0310674.

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Studies of the DNA-replication machinery of Archaea have revealed striking similarities to that of eukaryotes. Indeed, it appears that in most cases Archaea possess a simplified version of the eukaryotic replication apparatus. Studies of Archaea are therefore shedding light on the fundamental processes of DNA replication in both domains of life.

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24

MacNeill, Stuart A. "Protein–protein interactions in the archaeal core replisome." Biochemical Society Transactions 39, no. 1 (January 19, 2011): 163–68. http://dx.doi.org/10.1042/bst0390163.

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Most of the core components of the archaeal chromosomal DNA replication apparatus share significant protein sequence similarity with eukaryotic replication factors, making the Archaea an excellent model system for understanding the biology of chromosome replication in eukaryotes. The present review summarizes current knowledge of how the core components of the archaeal chromosome replication apparatus interact with one another to perform their essential functions.

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25

Bielinsky, A. K., and S. A. Gerbi. "Where it all starts: eukaryotic origins of DNA replication." Journal of Cell Science 114, no. 4 (February 15, 2001): 643–51. http://dx.doi.org/10.1242/jcs.114.4.643.

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Chromosomal origins of DNA replication in eukaryotic cells not only are crucial for understanding the basic process of DNA duplication but also provide a tool to analyze how cell cycle regulators are linked to the replication machinery. During the past decade much progress has been made in identifying replication origins in eukaryotic genomes. More recently, replication initiation point (RIP) mapping has allowed us to detect start sites for DNA synthesis at the nucleotide level and thus to monitor replication initiation events at the origin very precisely. Beyond giving us the precise positions of start sites, the application of RIP mapping in yeast and human cells has revealed a single, defined start point at which replication initiates, a scenario very reminiscent of transcription initiation. More importantly, studies in yeast have shown that the binding site for the initiator, the origin recognition complex (ORC), lies immediately adjacent to the replication start point, which suggests that ORC directs the initiation machinery to a distinct site. Therefore, in our pursuit of identifying ORC-binding sites in higher eukaryotes, RIP mapping may lead the way.

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26

MacNeill, Stuart A. "Structure and function of the GINS complex, a key component of the eukaryotic replisome." Biochemical Journal 425, no. 3 (January 15, 2010): 489–500. http://dx.doi.org/10.1042/bj20091531.

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High-fidelity chromosomal DNA replication is fundamental to all forms of cellular life and requires the complex interplay of a wide variety of essential and non-essential protein factors in a spatially and temporally co-ordinated manner. In eukaryotes, the GINS complex (from the Japanese go-ichi-ni-san meaning 5-1-2-3, after the four related subunits of the complex Sld5, Psf1, Psf2 and Psf3) was recently identified as a novel factor essential for both the initiation and elongation stages of the replication process. Biochemical analysis has placed GINS at the heart of the eukaryotic replication apparatus as a component of the CMG [Cdc45–MCM (minichromosome maintenance) helicase–GINS] complex that most likely serves as the replicative helicase, unwinding duplex DNA ahead of the moving replication fork. GINS homologues are found in the archaea and have been shown to interact directly with the MCM helicase and with primase, suggesting a central role for the complex in archaeal chromosome replication also. The present review summarizes current knowledge of the structure, function and evolution of the GINS complex in eukaryotes and archaea, discusses possible functions of the GINS complex and highlights recent results that point to possible regulation of GINS function in response to DNA damage.

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27

Majerník, A. I., E. R. Jenkinson, and J. P. J. Chong. "DNA replication in thermophiles." Biochemical Society Transactions 32, no. 2 (April 1, 2004): 236–39. http://dx.doi.org/10.1042/bst0320236.

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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.

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28

Vengrova, Sonya, Sandra Codlin, and Jacob Z. Dalgaard. "RTS1—an eukaryotic terminator of replication." International Journal of Biochemistry & Cell Biology 34, no. 9 (September 2002): 1031–34. http://dx.doi.org/10.1016/s1357-2725(02)00040-7.

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29

Kumar, Charanya, and Dirk Remus. "Eukaryotic replication origins: Strength in flexibility." Nucleus 7, no. 3 (May 3, 2016): 292–300. http://dx.doi.org/10.1080/19491034.2016.1187353.

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30

Forsburg, Susan L. "Eukaryotic MCM Proteins: Beyond Replication Initiation." Microbiology and Molecular Biology Reviews 68, no. 1 (March 2004): 109–31. http://dx.doi.org/10.1128/mmbr.68.1.109-131.2004.

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SUMMARY The minichromosome maintenance (or MCM) protein family is composed of six related proteins that are conserved in all eukaryotes. They were first identified by genetic screens in yeast and subsequently analyzed in other experimental systems using molecular and biochemical methods. Early data led to the identification of MCMs as central players in the initiation of DNA replication. More recent studies have shown that MCM proteins also function in replication elongation, probably as a DNA helicase. This is consistent with structural analysis showing that the proteins interact together in a heterohexameric ring. However, MCMs are strikingly abundant and far exceed the stoichiometry of replication origins; they are widely distributed on unreplicated chromatin. Analysis of mcm mutant phenotypes and interactions with other factors have now implicated the MCM proteins in other chromosome transactions including damage response, transcription, and chromatin structure. These experiments indicate that the MCMs are central players in many aspects of genome stability.

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31

Diffley, John F. X. "Early events in eukaryotic DNA replication." Trends in Cell Biology 2, no. 10 (October 1992): 298–303. http://dx.doi.org/10.1016/0962-8924(92)90119-8.

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32

Kearsey, Stephen. "Eukaryotic DNA Replication — A Practical Approach." Heredity 83, no. 2 (August 1999): 219–20. http://dx.doi.org/10.1046/j.1365-2540.1999.0609b.x.

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33

Li, Huilin, and Michael E. O’Donnell. "Mathematical description of eukaryotic chromosome replication." Proceedings of the National Academy of Sciences 116, no. 11 (February 19, 2019): 4776–78. http://dx.doi.org/10.1073/pnas.1900968116.

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34

Hyrien, Olivier, and Arach Goldar. "Mathematical modelling of eukaryotic DNA replication." Chromosome Research 18, no. 1 (November 20, 2009): 147–61. http://dx.doi.org/10.1007/s10577-009-9092-4.

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35

Yuan, Zuanning, and Huilin Li. "Molecular mechanisms of eukaryotic origin initiation, replication fork progression, and chromatin maintenance." Biochemical Journal 477, no. 18 (September 24, 2020): 3499–525. http://dx.doi.org/10.1042/bcj20200065.

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Eukaryotic DNA replication is a highly dynamic and tightly regulated process. Replication involves several dozens of replication proteins, including the initiators ORC and Cdc6, replicative CMG helicase, DNA polymerase α-primase, leading-strand DNA polymerase ε, and lagging-strand DNA polymerase δ. These proteins work together in a spatially and temporally controlled manner to synthesize new DNA from the parental DNA templates. During DNA replication, epigenetic information imprinted on DNA and histone proteins is also copied to the daughter DNA to maintain the chromatin status. DNA methyltransferase 1 is primarily responsible for copying the parental DNA methylation pattern into the nascent DNA. Epigenetic information encoded in histones is transferred via a more complex and less well-understood process termed replication-couple nucleosome assembly. Here, we summarize the most recent structural and biochemical insights into DNA replication initiation, replication fork elongation, chromatin assembly and maintenance, and related regulatory mechanisms.

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36

Hyrien, Olivier. "How MCM loading and spreading specify eukaryotic DNA replication initiation sites." F1000Research 5 (August 24, 2016): 2063. http://dx.doi.org/10.12688/f1000research.9008.1.

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DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb) non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs), the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC), they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.

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Feng, Gang, Yue Yuan, Zeyang Li, Lu Wang, Bo Zhang, Jiechen Luo, Jianguo Ji, and Daochun Kong. "Replication fork stalling elicits chromatin compaction for the stability of stalling replication forks." Proceedings of the National Academy of Sciences 116, no. 29 (July 1, 2019): 14563–72. http://dx.doi.org/10.1073/pnas.1821475116.

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DNA replication forks in eukaryotic cells stall at a variety of replication barriers. Stalling forks require strict cellular regulations to prevent fork collapse. However, the mechanism underlying these cellular regulations is poorly understood. In this study, a cellular mechanism was uncovered that regulates chromatin structures to stabilize stalling forks. When replication forks stall, H2BK33, a newly identified acetylation site, is deacetylated and H3K9 trimethylated in the nucleosomes surrounding stalling forks, which results in chromatin compaction around forks. Acetylation-mimic H2BK33Q and its deacetylase clr6-1 mutations compromise this fork stalling-induced chromatin compaction, cause physical separation of replicative helicase and DNA polymerases, and significantly increase the frequency of stalling fork collapse. Furthermore, this fork stalling-induced H2BK33 deacetylation is independent of checkpoint. In summary, these results suggest that eukaryotic cells have developed a cellular mechanism that stabilizes stalling forks by targeting nucleosomes and inducing chromatin compaction around stalling forks. This mechanism is named the “Chromsfork” control: Chromatin Compaction Stabilizes Stalling Replication Forks.

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Takisawa, Haruhiko, Satoru Mimura, and Yumiko Kubota. "Eukaryotic DNA replication: from pre-replication complex to initiation complex." Current Opinion in Cell Biology 12, no. 6 (December 2000): 690–96. http://dx.doi.org/10.1016/s0955-0674(00)00153-8.

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39

Kelly, Thomas, and A. John Callegari. "Dynamics of DNA replication in a eukaryotic cell." Proceedings of the National Academy of Sciences 116, no. 11 (February 4, 2019): 4973–82. http://dx.doi.org/10.1073/pnas.1818680116.

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Each genomic locus in a eukaryotic cell has a distinct average time of replication during S phase that depends on the spatial and temporal pattern of replication initiation events. Replication timing can affect genomic integrity because late replication is associated with an increased mutation rate. For most eukaryotes, the features of the genome that specify the location and timing of initiation events are unknown. To investigate these features for the fission yeast, Schizosaccharomyces pombe, we developed an integrative model to analyze large single-molecule and global genomic datasets. The model provides an accurate description of the complex dynamics of S. pombe DNA replication at high resolution. We present evidence that there are many more potential initiation sites in the S. pombe genome than previously identified and that the distribution of these sites is primarily determined by two factors: the sequence preferences of the origin recognition complex (ORC), and the interference of transcription with the assembly or stability of prereplication complexes (pre-RCs). We suggest that in addition to directly interfering with initiation, transcription has driven the evolution of the binding properties of ORC in S. pombe and other eukaryotic species to target pre-RC assembly to regions of the genome that are less likely to be transcribed.

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40

Cavalier-Smith, Thomas. "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree." Biology Letters 6, no. 3 (December 23, 2009): 342–45. http://dx.doi.org/10.1098/rsbl.2009.0948.

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I discuss eukaryotic deep phylogeny and reclassify the basal eukaryotic kingdom Protozoa and derived kingdom Chromista in the light of multigene trees. I transfer the formerly protozoan Heliozoa and infrakingdoms Alveolata and Rhizaria into Chromista, which is sister to kingdom Plantae and arguably originated by synergistic double internal enslavement of green algal and red algal cells. I establish new subkingdoms (Harosa; Hacrobia) for the expanded Chromista. The protozoan phylum Euglenozoa differs immensely from other eukaryotes in its nuclear genome organization (trans-spliced multicistronic transcripts), mitochondrial DNA organization, cytochrome c -type biogenesis, cell structure and arguably primitive mitochondrial protein-import and nuclear DNA prereplication machineries. The bacteria-like absence of mitochondrial outer-membrane channel Tom40 and DNA replication origin-recognition complexes from trypanosomatid Euglenozoa roots the eukaryotic tree between Euglenozoa and all other eukaryotes (neokaryotes), or within Euglenozoa. Given their unique properties, I segregate Euglenozoa from infrakingdom Excavata (now comprising only phyla Percolozoa, Loukozoa, Metamonada), grouping infrakingdoms Euglenozoa and Excavata as the ancestral protozoan subkingdom Eozoa. I place phylum Apusozoa within the derived protozoan subkingdom Sarcomastigota. Clarifying early eukaryote evolution requires intensive study of properties distinguishing Euglenozoa from neokaryotes and Eozoa from neozoa (eukaryotes except Eozoa; ancestrally defined by haem lyase).

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41

Das, Mitali, Sunita Singh, Satyajit Pradhan, and Gopeshwar Narayan. "MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity." Molecular Biology International 2014 (October 19, 2014): 1–11. http://dx.doi.org/10.1155/2014/574850.

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As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM) 2–7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the “MCM paradox.” Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

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Pavlov, Youri I., Anna S. Zhuk, and Elena I. Stepchenkova. "DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer." Cancers 12, no. 12 (November 24, 2020): 3489. http://dx.doi.org/10.3390/cancers12123489.

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Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. The principal idea of participation of different polymerases in specific transactions at the fork proposed by Morrison and coauthors 30 years ago and later named “division of labor,” remains standing, with an amendment of the broader role of polymerase δ in the replication of both the lagging and leading DNA strands. However, cancer-associated mutations predominantly affect the catalytic subunit of polymerase ε that participates in leading strand DNA synthesis. We analyze how new findings in the DNA replication field help elucidate the polymerase variants’ effects on cancer.

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Parker, Richard P., Alison D. Walters, and James P. J. Chong. "Bacterial and eukaryotic systems collide in the three Rs of Methanococcus." Biochemical Society Transactions 39, no. 1 (January 19, 2011): 111–15. http://dx.doi.org/10.1042/bst0390111.

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Methanococcus maripaludis S2 is a methanogenic archaeon with a well-developed genetic system. Its mesophilic nature offers a simple system in which to perform complementation using bacterial and eukaryotic genes. Although information-processing systems in archaea are generally more similar to those in eukaryotes than those in bacteria, the order Methanococcales has a unique complement of DNA replication proteins, with multiple MCM (minichromosome maintenance) proteins and no obvious originbinding protein. A search for homologues of recombination and repair proteins in M. maripaludis has revealed a mixture of bacterial, eukaryotic and some archaeal-specific homologues. Some repair pathways appear to be completely absent, but it is possible that archaeal-specific proteins could carry out these functions. The replication, recombination and repair systems in M. maripaludis are an interesting mixture of eukaryotic and bacterial homologues and could provide a system for uncovering novel interactions between proteins from different domains of life.

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Eydmann, T., E. Sommariva, T. Inagawa, S. Mian, A. J. S. Klar, and J. Z. Dalgaard. "Rtf1-Mediated Eukaryotic Site-Specific Replication Termination." Genetics 180, no. 1 (August 24, 2008): 27–39. http://dx.doi.org/10.1534/genetics.108.089243.

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Saugar, Irene, María Ángeles Ortiz-Bazán, and José Antonio Tercero. "Tolerating DNA damage during eukaryotic chromosome replication." Experimental Cell Research 329, no. 1 (November 2014): 170–77. http://dx.doi.org/10.1016/j.yexcr.2014.07.009.

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Balakrishnan, Lata, Jason W. Gloor, and Robert A. Bambara. "Reconstitution of eukaryotic lagging strand DNA replication." Methods 51, no. 3 (July 2010): 347–57. http://dx.doi.org/10.1016/j.ymeth.2010.02.017.

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Schwob, Etienne. "Flexibility and governance in eukaryotic DNA replication." Current Opinion in Microbiology 7, no. 6 (December 2004): 680–90. http://dx.doi.org/10.1016/j.mib.2004.10.017.

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Kearsey, Stephen E., Karim Labib, and Domenico Maiorano. "Cell cycle control of eukaryotic DNA replication." Current Opinion in Genetics & Development 6, no. 2 (April 1996): 208–14. http://dx.doi.org/10.1016/s0959-437x(96)80052-9.

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Leatherwood, Janet. "Emerging mechanisms of eukaryotic DNA replication initiation." Current Opinion in Cell Biology 10, no. 6 (December 1998): 742–48. http://dx.doi.org/10.1016/s0955-0674(98)80117-8.

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Iftode, Cristina, Yaron Daniely, and James A. Borowiec. "Replication Protein A (RPA): The Eukaryotic SSB." Critical Reviews in Biochemistry and Molecular Biology 34, no. 3 (January 1999): 141–80. http://dx.doi.org/10.1080/10409239991209255.

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