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The “beautiful mechanism” by which an egg becomes an embryo

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From Phys.org:

The transition from an egg to a developing embryo is one of life’s most remarkable transformations. Yet little is known about it. Now Whitehead Institute researchers have deciphered how one aspect—control of the all-important translation of messenger RNAs (mRNAs) into proteins—switches as the egg becomes an embryo. That shift is controlled by a beautiful mechanism, which is triggered at a precise moment in development and automatically shuts itself off after a narrow window of 20 to 90 minutes.

As an egg develops, it stockpiles mRNAs from the mother because it will not have time to create new mRNAs during the rapid development of a very early embryo. When fertilized the egg becomes an embryo, the stashed maternal mRNAs are pressed into service for a brief window before the embryo starts transcribing its own mRNAs. This change occurs very early; in humans, only two to four cell divisions occur before this transition is executed. Whitehead Member Terry Orr-Weaver studies the control of translation of maternal mRNAs in the model organism Drosophila, or the fruit fly, because its developmental strategy offers experimental advantages. More.

A reader writes to note that the “beautiful mechanism” is described as a

negative feedback loop,” with the same function as those designed in engineering control systems: Furthermore, the activity of PNG kinase leads to the destruction of GNU, and this feedback loop limits this kinase’s activity to the narrow window of time in which it is needed.

“Active PNG leads to decreased GNU protein levels. This makes a negative feedback to shut down PNG kinase activity, thereby ensuring PNG kinase activity is constrained to the short developmental window of the oocyte-to-embryo transition

Another reader who forwarded this item points out that the authors let in the “d” word (and I don’t mean “Darwin”…. ):

The design of this transition could tell scientists more about how human cells work and embryos develop. For example, the switch could be a model for how cells massively and globally change mRNA translation. Also, similar kinase activity during early development has been noted in worms, which may mean that a comparable approach is used in other organisms, including humans.

Well, if the researchers’ careers take a beating for mentioning design, they will need to join the Free the Universities movement. After a while language Stalinism starts t collapse from its own uncommunicativeness and one must peak clearly again.

See also: Cells communicate to navigate a crowded embryo

Comments
Bacteria frequently need to adapt to altered environmental conditions. Adaptation requires changes in gene expression, often mediated by global regulators of transcription. The nucleoid-associated protein H-NS is a key global regulator in Gram-negative bacteria and is believed to be a crucial player in bacterial chromatin organization via its DNA-bridging activity. H-NS activity in vivo is modulated by physico-chemical factors (osmolarity, pH, temperature) and interaction partners. Mechanistically, it is unclear how functional modulation of H-NS by such factors is achieved.
Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity Ramon A van der Valk, Jocelyne Vreede, Liang Qin, Geri F Moolenaar, Andreas Hofmann, Nora Goosen, Remus T Dame Biophysics and Structural BiologyGenes and Chromosomes eLife 2017;6:e27369 doi: 10.7554/eLife.27369
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Sidechain dynamics represent an important functional component of protein behavior. Changes in ? for other peaks in our dataset may provide further insights into the regulation of different regions of the receptor by ligands, depending on assignment of the other Ile residues in our spectra.
Ligand modulation of sidechain dynamics in a wild-type human GPCR Lindsay D Clark, Igor Dikiy, Karen Chapman, Karin EJ Rödström, James Aramini, Michael V LeVine, George Khelashvili, Søren GF Rasmussen, Kevin H Gardner, Daniel M Rosenbaum eLife 2017;6:e28505 doi: 10.7554/eLife.28505
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[...] ligand-activated GPCRs are weakly coupled allosteric systems in which multiple energetic inputs (i.e. agonist and G protein binding) are required to predominantly populate the active conformation. [...] a set of loosely coupled microswitches connecting the orthosteric pocket and G protein binding site are activated by agonists in a non-concerted fashion, and stabilizing subsets of these rearrangements can lead to alternate overall conformations that have different signaling properties. These data represent an important first step towards understanding how agonists can activate the fast motions of specific sidechains to facilitate conformational changes of a GPCR.
Ligand modulation of sidechain dynamics in a wild-type human GPCR Lindsay D Clark, Igor Dikiy, Karen Chapman, Karin EJ Rödström, James Aramini, Michael V LeVine, George Khelashvili, Søren GF Rasmussen, Kevin H Gardner, Daniel M Rosenbaum eLife 2017;6:e28505 doi: 10.7554/eLife.28505
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October 21, 2017
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Our understanding of the molecular underpinnings of GPCR function has been greatly advanced over the past two decades through a combination of X-ray crystal structures, computational simulations, and spectroscopic studies of protein dynamics. How these diverse ligands activate signaling by a small number of G proteins and arrestins through a common structural scaffold remains a central problem for the GPCR field.
Ligand modulation of sidechain dynamics in a wild-type human GPCR Lindsay D Clark, Igor Dikiy, Karen Chapman, Karin EJ Rödström, James Aramini, Michael V LeVine, George Khelashvili, Søren GF Rasmussen, Kevin H Gardner, Daniel M Rosenbaum eLife 2017;6:e28505 doi: 10.7554/eLife.28505
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October 21, 2017
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Almost every aspect of the human body – from our senses to our moods – depends, in one way or another, on a large family of proteins called G-protein-coupled receptors. These receptor proteins, known as GPCRs for short, detect signals from outside the cell and trigger activity within the cell. This allows cells to gather information from their surroundings and to communicate with each other. Like all proteins, GPCRs are long chain-like molecules with a repetitive backbone and short branches called sidechains. Each sidechain has its own chemical properties and electrical charge, which can affect how different parts of the chain interact with each other and what shape the protein can adopt.
Ligand modulation of sidechain dynamics in a wild-type human GPCR Lindsay D Clark, Igor Dikiy, Karen Chapman, Karin EJ Rödström, James Aramini, Michael V LeVine, George Khelashvili, Søren GF Rasmussen, Kevin H Gardner, Daniel M Rosenbaum eLife 2017;6:e28505 doi: 10.7554/eLife.28505
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October 21, 2017
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GPCRs regulate all aspects of human physiology, and biophysical studies have deepened our understanding of GPCR conformational regulation by different ligands. Yet there is no experimental evidence for how sidechain dynamics control allosteric transitions between GPCR conformations. To address this deficit, we generated samples of a wild-type GPCR (A2AR) that are deuterated apart from (1)H/(13)C NMR probes at isoleucine ?1 methyl groups, which facilitated (1)H/(13)C methyl TROSY NMR measurements with opposing ligands. Our data indicate that low [Na(+)] is required to allow large agonist-induced structural changes in A2AR, and that patterns of sidechain dynamics substantially differ between agonist (NECA) and inverse agonist (ZM241385) bound receptors, with the inverse agonist suppressing fast ps-ns timescale motions at the G protein binding site. Our approach to GPCR NMR creates a framework for exploring how different regions of a receptor respond to different ligands or signaling proteins through modulation of fast ps-ns sidechain dynamics.
Ligand modulation of sidechain dynamics in a wild-type human GPCR Lindsay D Clark, Igor Dikiy, Karen Chapman, Karin EJ Rödström, James Aramini, Michael V LeVine, George Khelashvili, Søren GF Rasmussen, Kevin H Gardner, Daniel M Rosenbaum eLife 2017;6:e28505 doi: 10.7554/eLife.28505
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October 21, 2017
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We discovered that in budding yeast, kinetochore inactivation occurs by reducing the abundance of a limiting subunit, Ndc80. Furthermore, we uncovered an integrated mechanism that acts at the transcriptional and translational level to repress NDC80 expression. Central to this mechanism is the developmentally controlled transcription of an alternate NDC80 mRNA isoform, which itself cannot produce protein due to regulatory upstream ORFs in its extended 5' leader. Instead, transcription of this isoform represses the canonical NDC80 mRNA expression in cis, thereby inhibiting Ndc80 protein synthesis. This model of gene regulation raises the intriguing notion that transcription of an mRNA, despite carrying a canonical coding sequence, can directly cause gene repression.
Kinetochore inactivation by expression of a repressive mRNA Jingxun Chen, Amy Tresenrider, Minghao Chia, David T McSwiggen, Gianpiero Spedale, Victoria Jorgensen, Hanna Liao, Folkert Jacobus van Werven, Elcin Unal eLife 2017;6:e27417 doi: 10.7554/eLife.27417
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October 21, 2017
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Differentiation programs such as meiosis depend on extensive gene regulation to mediate cellular morphogenesis. Meiosis requires transient removal of the outer kinetochore, the complex that connects microtubules to chromosomes. How the meiotic gene expression program temporally restricts kinetochore function is unknown.
Kinetochore inactivation by expression of a repressive mRNA Jingxun Chen, Amy Tresenrider, Minghao Chia, David T McSwiggen, Gianpiero Spedale, Victoria Jorgensen, Hanna Liao, Folkert Jacobus van Werven, Elcin Unal eLife 2017;6:e27417 doi: 10.7554/eLife.27417
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October 21, 2017
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Cell differentiation programs require dynamic regulation of gene expression. During meiotic prophase in Saccharomyces cerevisiae, expression of the kinetochore complex subunit Ndc80 is downregulated by a 5' extended long undecoded NDC80 transcript isoform. Transcription from a distal NDC80 promoter directs Set1-dependent histone H3K4 dimethylation and Set2-dependent H3K36 trimethylation to establish a repressive chromatin state in the downstream canonical NDC80 promoter. As a consequence, NDC80 expression is repressed during meiotic prophase. The transcriptional mechanism described here is rapidly reversible, adaptable to fine-tune gene expression, and relies on Set2 and the Set3 histone deacetylase complex. Thus, expression of a 5' extended mRNA isoform causes transcriptional interference at the downstream promoter. [...] this is an effective mechanism to promote dynamic changes in gene expression during cell differentiation.
Transcription of a 5' extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter Minghao Chia, Amy Tresenrider, Jingxun Chen, Gianpiero Spedale, Victoria Jorgensen, Elçin Ünal, Folkert Jacobus van Werven eLife 2017;6:e27420 doi: 10.7554/eLife.27420
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October 20, 2017
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In eukaryotic cells, RNA binding proteins (RBPs) play critical roles in regulating almost every aspect of gene expression, often shuttling between the nucleus and the cytoplasm. They are also key determinants in cell fate via controlling the target mRNAs under the regulation of various signaling pathways in response to environmental stresses. Therefore, understanding the mechanisms that couple the location of mRNA and RBPs is a major challenge in the field of gene expression and signal responses.
Rae1-mediated nuclear export of Rnc1 is an important determinant in controlling MAPK signaling Ryosuke Satoh, Kanako Hagihara, Reiko Sugiura Curr Genet (2017). https://doi.org/10.1007/s00294-017-0732-5
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Morphogens regulate tissue patterning through their distribution in concentration gradients. Emerging research establishes a role for specialized signalling filopodia, or cytonemes, in morphogen dispersion and signalling. Hedgehog (Hh) morphogen is transported via vesicles along cytonemes emanating from signal-producing cells to form a gradient in Drosophila epithelia. However, the mechanisms for signal reception and transfer are still undefined.
Cytoneme-mediated cell-cell contacts for Hedgehog reception. González-Méndez L1, Seijo-Barandiarán I1, Guerrero I1. Elife. 6. pii: e24045. doi: 10.7554/eLife.24045.
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Further insights into the tissue specificity of underreplicated domains and the mechanisms of their designation will be critical to our understanding of how chromatin configuration can affect the elongation phase of DNA replication.
DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression Brian L. Hua and Terry L. Orr-Weaver Genetics vol. 207 no. 1 29-47; https://doi.org/10.1534/genetics.115.186627
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October 19, 2017
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A crucial question to be solved is how genomic regions are established that lack ORC binding. Another is whether genomic rearrangements resulting from underreplication serve biological functions.
DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression Brian L. Hua and Terry L. Orr-Weaver Genetics vol. 207 no. 1 29-47; https://doi.org/10.1534/genetics.115.186627
Work in progress... stay tuned. Complex functionally specified informational complexityDionisio
October 19, 2017
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The tools in Drosophila will permit identification of the state of chromatin modifications and associated proteins at origins and correlation with origin activity as well as contacts between origins and other chromosomal sequences.
DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression Brian L. Hua and Terry L. Orr-Weaver Genetics vol. 207 no. 1 29-47; https://doi.org/10.1534/genetics.115.186627
Work in progress... stay tuned. Complex functionally specified informational complexityDionisio
October 19, 2017
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The ability to track the activation of specific origins during gene amplification revealed at least three distinct mechanisms of origin activation, including the possibility of ORC-independent initiation. Analyzing whether these mechanisms operate at origins during a canonical S phase and whether the other amplicon origins utilize additional activation mechanisms will be important.
DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression Brian L. Hua and Terry L. Orr-Weaver Genetics vol. 207 no. 1 29-47; https://doi.org/10.1534/genetics.115.186627
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A key future direction will be to decipher the chromatin configurations and chromosome conformation that designate origin and ORC positioning.
DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression Brian L. Hua and Terry L. Orr-Weaver Genetics vol. 207 no. 1 29-47; https://doi.org/10.1534/genetics.115.186627
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Proper control of DNA replication is critical to ensure genomic integrity during cell proliferation. In addition, differential regulation of the DNA replication program during development can change gene copy number to influence cell size and gene expression. The ability to identify ORC binding sites in a variety of differentiated cell types has revealed a high degree of tissue specificity of origin positioning within the genome. Both the mechanism that dictates when origins become active and the biological significance of replication timing remain to be determined [...]
DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression Brian L. Hua and Terry L. Orr-Weaver Genetics vol. 207 no. 1 29-47; https://doi.org/10.1534/genetics.115.186627
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October 18, 2017
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Morphogen concentration gradients that extend across developmental fields form by dispersion from source cells. In the Drosophila wing disc, Hedgehog (Hh) produced by posterior compartment cells distributes in a concentration gradient to adjacent cells of the anterior compartment. [...] in the wing disc, Hh distributions and signaling are dependent upon basal release and uptake, and on cytoneme-mediated movement.
Essential basal cytonemes take up Hedgehog in the Drosophila wing imaginal disc Weitao Chen, Hai Huang, Ryo Hatori, Thomas B. Kornberg Development 2017 144: 3134-3144; doi: 10.1242/dev.149856
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October 17, 2017
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Cell culture systems have the potential to accelerate studies addressing provocative questions about cytoneme biology, including how morphogens are gated into cytonemes, how cytoneme-localized proteins are appropriately trafficked within the structures, and how cytoneme directionality and length are controlled to assure morphogens reach their desired targets. Answering such questions will be essential to advance our understanding of how morphogen gradients are generated and reinforced during tissue development.
A fixation method to preserve cultured cell cytonemes facilitates mechanistic interrogation of morphogen transport William J. Bodeen, Suresh Marada, Ashley Truong, Stacey K. Ogden Development 2017 144: 3612-3624; doi: 10.1242/dev.152736
Work in progress… stay tuned. Complex functionally specified informational complexityDionisio
October 17, 2017
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Elucidation of the precise mechanism by which Disp expression alters cytoneme behavior to increase occurrence rates requires further study. It is unlikely that Disp functions in isolation to modulate cytoneme behavior. [...] multiple signals sent and received between neighboring cells probably converge to direct cytoneme function during tissue development. Future mechanistic studies using cultured cell cytonemes will be directed at defining this biology, and identifying mechanisms by which Disp might help to integrate such signals and promote function of Hh-containing cytonemes.
A fixation method to preserve cultured cell cytonemes facilitates mechanistic interrogation of morphogen transport William J. Bodeen, Suresh Marada, Ashley Truong, Stacey K. Ogden Development 2017 144: 3612-3624; doi: 10.1242/dev.152736
Work in progress... stay tuned. Complex functionally specified informational complexityDionisio
October 17, 2017
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During development, tissue patterning occurs as a consequence of morphogenetic signaling. Morphogens are produced in and deployed from cells localized to discrete domains of developing tissues, and spread from their source to provide instructional cues to signal-receiving cells. Morphogens signal short-range to adjacent cells, and long-range to targets situated at significant distances from the source (Tabata and Takei, 2004). The exact processes facilitating morphogen transport and distribution are not yet fully established. However, several models have been proposed, including free or hindered diffusion, transcytosis, exovesicle shuttling and direct delivery through specialized filopodia called cytonemes (Muller et al., 2013).
A fixation method to preserve cultured cell cytonemes facilitates mechanistic interrogation of morphogen transport William J. Bodeen, Suresh Marada, Ashley Truong, Stacey K. Ogden Development 2017 144: 3612-3624; doi: 10.1242/dev.152736
The authors of this paper should have consulted a biochemistry professor who a couple of years ago in this website claimed to know exactly how to cook the whole enchilada. :) But they should have asked “honest questions” (whatever that means) lest he won’t share his secret recipe. :) Complex functionally specified informational complexityDionisio
October 17, 2017
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[...] Hedgehog and Dispatched colocalize in cytonemes [...] [...] cholesterol-modified Hedgehog acts through Dispatched to increase cytoneme occurrence. [...] this occurs through Dispatched-mediated slowing of cytoneme retraction rates.
A fixation method to preserve cultured cell cytonemes facilitates mechanistic interrogation of morphogen transport William J. Bodeen, Suresh Marada, Ashley Truong, Stacey K. Ogden Development 2017 144: 3612-3624; doi: 10.1242/dev.152736
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October 17, 2017
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During development, extracellular cues guiding cell fate determination are provided by morphogens. One mechanism by which morphogens are proposed to traverse extracellular space is by traveling along specialized filopodia called cytonemes. These cellular highways extend between signal-producing and -receiving cells to enable direct morphogen delivery. Although genetic studies support cytoneme involvement in morphogen transport, mechanistic insight into how they are regulated is limited owing to technical challenges associated with performing cell biological analysis of the delicate filopodial structures.
A fixation method to preserve cultured cell cytonemes facilitates mechanistic interrogation of morphogen transport William J. Bodeen, Suresh Marada, Ashley Truong, Stacey K. Ogden Development 2017 144: 3612-3624; doi: 10.1242/dev.152736
The authors of this paper should have consulted a biochemistry professor who a couple of years ago in this website claimed to know exactly how to cook the whole enchilada. :) But they should have asked "honest questions" (whatever that means) lest he won't share his secret recipe. :) Complex functionally specified informational complexityDionisio
October 17, 2017
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Eukaryotic PrimPol is a recently discovered DNA-dependent DNA primase and translesion synthesis DNA polymerase found in the nucleus and mitochondria. Although PrimPol has been shown to be required for repriming of stalled replication forks in the nucleus, its role in mitochondria has remained unresolved. Our results not only help in the understanding of how mitochondria cope with replicative stress but can also explain some controversial features of the lagging-strand replication.
PrimPol is required for replication reinitiation after mtDNA damage Rubén Torregrosa-Muñumera,1, Josefin M. E. Forslundb,1, Steffi Goffarta, Annika Pfeifferb, Gorazd Stojkovi?b, Gustavo Carvalhoc, Natalie Al-Furoukhb, Luis Blancoc, Sjoerd Wanrooijb,2,3, and Jaakko L. O. Pohjoismäki doi: 10.1073/pnas.1705367114 PNAS
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October 16, 2017
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Human PrimPol is a DNA primase/polymerase involved in DNA damage tolerance and prevents nuclear genome instability. PrimPol is also localized to the mitochondria, but its precise function in mitochondrial DNA maintenance has remained elusive. PrimPol from human cell lines might be preferred for more complex studies including analysis of its interactions with various partner proteins.
Boldinova EO, Stojkovi? G, Khairullin R, Wanrooij S, Makarova AV (2017) Optimization of the expression, purification and polymerase activity reaction conditions of recombinant human PrimPol. PLoS ONE12(9): e0184489. https://doi.org/10.1371/journal.pone.0184489
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October 16, 2017
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DNA damage tolerance (DDT) enables bypassing of DNA lesions during replication, thereby preventing fork stalling, replication stress, and secondary DNA damage related to fork stalling. Three modes of DDT have been documented: translesion synthesis (TLS), template switching (TS), and repriming. TLS and TS depend on site-specific PCNA K164 monoubiquitination and polyubiquitination, respectively.
DNA damage tolerance in hematopoietic stem and progenitor cells in mice Bas Pilzeckera,1, Olimpia Alessandra Buoninfantea,1, Paul van den Berka,1, Cesare Lancinib, Ji-Ying Songc, Elisabetta Citteriob, and Heinz Jacobs PNAS vol. 114 no. 33 E6875–E6883, doi: 10.1073/pnas.1706508114
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October 16, 2017
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The enhancement of PrimPol polymerase activity by RPA on a long ssDNA template may be due to different reasons [...] [...] PrimPol finds the opportunity to bind in proximity to the stalling site, probably by an specific interaction with RPA that reinforces its avidity for ssDNA, synthesizing a new primer to restart leading strand synthesis and re-establishing normal fork progression [...]
Human PrimPol activity is enhanced by RPA María I. Martínez-Jiménez, Antonio Lahera & Luis Blanco Scientific Reports 7, Article number: 783 (2017) doi:10.1038/s41598-017-00958-3
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[...] it is likely that RPA binds the template strands used in our polymerases assays (14 and 49?nt, respectively) with a higher affinity than PrimPol. It is also possible that the unwinding activity of RPA melts the primer, precluding PrimPol extension.
Human PrimPol activity is enhanced by RPA María I. Martínez-Jiménez, Antonio Lahera & Luis Blanco Scientific Reports 7, Article number: 783 (2017) doi:10.1038/s41598-017-00958-3
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DNA polymerases are the enzymes responsible for making and repairing the DNA to ensure cell viability. Strikingly, although PrimPol recruitment to stalled forks seems to be mediated by RPA, it was proposed that RPA elicits an inhibitory effect on PrimPol activities in order to limit error-prone synthesis
Human PrimPol activity is enhanced by RPA María I. Martínez-Jiménez, Antonio Lahera & Luis Blanco Scientific Reports 7, Article number: 783 (2017) doi:10.1038/s41598-017-00958-3
Did somebody say 'Strikingly'? Complex functionally specified informational complexityDionisio
October 16, 2017
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Human PrimPol is a primase belonging to the AEP superfamily with the unique ability to synthesize DNA primers de novo, and a non-processive DNA polymerase able to bypass certain DNA lesions. PrimPol facilitates both mitochondrial and nuclear replication fork progression either acting as a conventional TLS polymerase, or repriming downstream of blocking lesions. These new findings supports the existence of a functional PrimPol/RPA association that allows repriming at the exposed ssDNA regions formed in the leading strand upon replicase stalling.
Human PrimPol activity is enhanced by RPA María I. Martínez-Jiménez, Antonio Lahera & Luis Blanco Scientific Reports 7, Article number: 783 (2017) doi:10.1038/s41598-017-00958-3
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