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Coupling of replication and assembly

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https://www.readbyqxmd.com/read/28462924/identification-and-characterization-of-a-heterotrimeric-archaeal-dna-polymerase-holoenzyme
#1
Jiangyu Yan, Thomas R Beattie, Adriana L Rojas, Kelly Schermerhorn, Tamzin Gristwood, Jonathan C Trinidad, Sonja V Albers, Pietro Roversi, Andrew F Gardner, Nicola G A Abrescia, Stephen D Bell
Since their initial characterization over 30 years ago, it has been believed that the archaeal B-family DNA polymerases are single-subunit enzymes. This contrasts with the multi-subunit B-family replicative polymerases of eukaryotes. Here we reveal that the highly studied PolB1 from Sulfolobus solfataricus exists as a heterotrimeric complex in cell extracts. Two small subunits, PBP1 and PBP2, associate with distinct surfaces of the larger catalytic subunit and influence the enzymatic properties of the DNA polymerase...
May 2, 2017: Nature Communications
https://www.readbyqxmd.com/read/28448571/localization-of-adenovirus-morphogenesis-players-together-with-visualization-of-assembly-intermediates-and-failed-products-favor-a-model-where-assembly-and-packaging-occur-concurrently-at-the-periphery-of-the-replication-center
#2
Gabriela N Condezo, Carmen San Martín
Adenovirus (AdV) morphogenesis is a complex process, many aspects of which remain unclear. In particular, it is not settled where in the nucleus assembly and packaging occur, and whether these processes occur in a sequential or a concerted manner. Here we use immunofluorescence and immunoelectron microscopy (immunoEM) to trace packaging factors and structural proteins at late times post infection by either wildtype virus or a delayed packaging mutant. We show that representatives of all assembly factors are present in the previously recognized peripheral replicative zone, which therefore is the AdV assembly factory...
April 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28446668/serine-235-is-the-primary-ns5a-hyper-phosphorylation-site-responsible-for-hcv-replication
#3
Shih-Chin Hsu, Chieh-Wen Lo, Ting-Chun Pan, Kuan-Ying Lee, Ming-Jiun Yu
The non-structural protein 5A (NS5A) of the hepatitis C virus (HCV) is a phosphoprotein with two phosphorylation states: hypo- and hyper-phosphorylation. Genetic mutation studies have demonstrated a cluster of serine residues responsible for NS5A hyper-phosphorylation and functions in viral replication and assembly; however, the phosphorylation levels and potential interactions among the serine residues are unclear. We used three specific antibodies to measure NS5A phosphorylation at S222, S235, and S238 that were identified in our previous proteomics study...
April 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28418026/the-cac2-subunit-is-essential-for-productive-histone-binding-and-nucleosome-assembly-in-caf-1
#4
Francesca Mattiroli, Yajie Gu, Jeremy L Balsbaugh, Natalie G Ahn, Karolin Luger
Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28381790/the-wd40-domain-of-hira-is-essential-for-ri-nucleosome-assembly-in-xenopus-egg-extracts
#5
Ruibin Zhu, Mari Iwabuchi, Keita Ohsumi
Histone chaperones are a group of histone-binding proteins that facilitate the assembly of nucleosomes, the fundamental structural units of chromatin in eukaryotes. In nucleosome assembly, deposition of a histone H3-H4 tetramer onto DNA is the first and critical step, which is mediated by the histone chaperones HIRA and CAF-1. HIRA and CAF-1 are reportedly involved in DNA replication independent (RI) and replication coupled nucleosome assembly, respectively. However, the mechanisms by which they mediate histone deposition remain unclear...
2017: Cell Structure and Function
https://www.readbyqxmd.com/read/28373564/cmg-pol-epsilon-dynamics-suggests-a-mechanism-for-the-establishment-of-leading-strand-synthesis-in-the-eukaryotic-replisome
#6
Jin Chuan Zhou, Agnieszka Janska, Panchali Goswami, Ludovic Renault, Ferdos Abid Ali, Abhay Kotecha, John F X Diffley, Alessandro Costa
The replisome unwinds and synthesizes DNA for genome duplication. In eukaryotes, the Cdc45-MCM-GINS (CMG) helicase and the leading-strand polymerase, Pol epsilon, form a stable assembly. The mechanism for coupling DNA unwinding with synthesis is starting to be elucidated, however the architecture and dynamics of the replication fork remain only partially understood, preventing a molecular understanding of chromosome replication. To address this issue, we conducted a systematic single-particle EM study on multiple permutations of the reconstituted CMG-Pol epsilon assembly...
April 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28335002/handcuffing-reversal-is-facilitated-by-proteases-and-replication-initiator-monomers
#7
Katarzyna Bury, Katarzyna Wegrzyn, Igor Konieczny
Specific nucleoprotein complexes are formed strictly to prevent over-initiation of DNA replication. An example of those is the so-called handcuff complex, in which two plasmid molecules are coupled together with plasmid-encoded replication initiation protein (Rep). In this work, we elucidate the mechanism of the handcuff complex disruption. In vitro tests, including dissociation progress analysis, demonstrate that the dimeric variants of plasmid RK2 replication initiation protein TrfA are involved in assembling the plasmid handcuff complex which, as we found, reveals high stability...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28322871/recurrent-emergence-of-structural-variants-of-ltr-retrotransposon-csrn1-evolving-novel-expression-strategy-and-their-selective-expansion-in-a-carcinogenic-liver-fluke-clonorchis-sinensis
#8
Seon-Hee Kim, Yoon Kong, Young-An Bae
Autonomous retrotransposons, in which replication and transcription are coupled, encode the essential gag and pol genes as a fusion or separate overlapping form(s) that are expressed in single transcripts regulated by a common upstream promoter. The element-specific expression strategies have driven development of relevant translational recoding mechanisms including ribosomal frameshifting to satisfy the protein stoichiometry critical for the assembly of infectious virus-like particles. Retrotransposons with different recoding strategies exhibit a mosaic distribution pattern across the diverse families of reverse transcribing elements, even though their respective distributions are substantially skewed towards certain family groups...
March 18, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28315525/insights-into-the-molecular-architecture-and-histone-h3-h4-deposition-mechanism-of-yeast-chromatin-assembly-factor-1
#9
Paul Victor Sauer, Jennifer Timm, Danni Liu, David Sitbon, Elisabetta Boeri-Erba, Christophe Velours, Norbert Mücke, Jörg Langowski, Françoise Ochsenbein, Geneviève Almouzni, Daniel Panne
How the very first step in nucleosome assembly, deposition of histone H3-H4 as tetramers or dimers on DNA, is accomplished remains largely unclear. Here, we report that yeast chromatin assembly factor 1 (CAF1), a conserved histone chaperone complex that deposits H3-H4 during DNA replication, binds a single H3-H4 heterodimer in solution. We identify a new DNA-binding domain in the large Cac1 subunit of CAF1, which is required for high-affinity DNA binding by the CAF1 three-subunit complex, and which is distinct from the previously described C-terminal winged-helix domain...
March 18, 2017: ELife
https://www.readbyqxmd.com/read/28246189/aee788-inhibits-basal-body-assembly-and-blocks-dna-replication-in-the-african-trypanosome
#10
Catherine Sullenberger, Daniel Piqué, Yuko Ogata, Kojo Mensa-Wilmot
Trypanosoma brucei causes human African trypanosomiasis (HAT). The pyrrolopyrimidine AEE788 (a hit for anti-HAT drug discovery) associates with three trypanosome protein kinases. Herein we delineate the effects of AEE788 on T. brucei using chemical biology strategies. AEE788 treatment inhibits DNA replication in the kinetoplast (mitochondrial nucleoid) and nucleus. In addition, AEE788 blocks duplication of the basal body and the bilobe without affecting mitosis. Thus, AEE788 prevents entry into the S-phase of the cell division cycle...
May 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/28196962/spatial-and-temporal-analysis-of-alphavirus-replication-and-assembly-in-mammalian-and-mosquito-cells
#11
Joyce Jose, Aaron B Taylor, Richard J Kuhn
Sindbis virus (SINV [genus Alphavirus, family Togaviridae]) is an enveloped, mosquito-borne virus. Alphaviruses cause cytolytic infections in mammalian cells while establishing noncytopathic, persistent infections in mosquito cells. Mosquito vector adaptation of alphaviruses is a major factor in the transmission of epidemic strains of alphaviruses. Though extensive studies have been performed on infected mammalian cells, the morphological and structural elements of alphavirus replication and assembly remain poorly understood in mosquito cells...
February 14, 2017: MBio
https://www.readbyqxmd.com/read/28188349/on-line-dynamic-extraction-system-hyphenated-to-inductively-coupled-plasma-optical-emission-spectrometry-for-automatic-determination-of-oral-bioaccessible-trace-metal-fractions-in-airborne-particulate-matter
#12
Victoria Mohr, Manuel Miró, Andreas Limbeck
For a realistic evaluation of the potential hazard emanating from airborne particulate matter (APM), the determination of the total inhaled metal amounts associated with APM is insufficient in risk assessment. Additional information about metal fractions that can be mobilized by the human body is necessary, because only those soluble (also called bioaccessible) fractions can be absorbed by the human body, and thus potentially cause adverse health effects. In the present study, a dynamic flow-through approach as a front end to inductively coupled plasma optical emission spectrometry (ICP-OES) exploiting advanced flow analysis is employed for on-line handling of multiple APM samples and determination of bioaccessible trace metals under worst case extraction scenarios...
February 10, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28141856/transcriptional-profiling-in-experimental-visceral-leishmaniasis-reveals-a-broad-splenic-inflammatory-environment-that-conditions-macrophages-toward-a-disease-promoting-phenotype
#13
Fanping Kong, Omar A Saldarriaga, Heidi Spratt, E Yaneth Osorio, Bruno L Travi, Bruce A Luxon, Peter C Melby
Visceral Leishmaniasis (VL), caused by the intracellular protozoan Leishmania donovani, is characterized by relentlessly increasing visceral parasite replication, cachexia, massive splenomegaly, pancytopenia and ultimately death. Progressive disease is considered to be due to impaired effector T cell function and/or failure of macrophages to be activated to kill the intracellular parasite. In previous studies, we used the Syrian hamster (Mesocricetus auratus) as a model because it mimics the progressive nature of active human VL...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28134787/control-of-genome-integrity-by-rfc-complexes-conductors-of-pcna-loading-onto-and-unloading-from-chromatin-during-dna-replication
#14
REVIEW
Yasushi Shiomi, Hideo Nishitani
During cell division, genome integrity is maintained by faithful DNA replication during S phase, followed by accurate segregation in mitosis. Many DNA metabolic events linked with DNA replication are also regulated throughout the cell cycle. In eukaryotes, the DNA sliding clamp, proliferating cell nuclear antigen (PCNA), acts on chromatin as a processivity factor for DNA polymerases. Since its discovery, many other PCNA binding partners have been identified that function during DNA replication, repair, recombination, chromatin remodeling, cohesion, and proteolysis in cell-cycle progression...
January 26, 2017: Genes
https://www.readbyqxmd.com/read/28125036/regulation-of-replication-fork-advance-and-stability-by-nucleosome-assembly
#15
REVIEW
Felix Prado, Douglas Maya
The advance of replication forks to duplicate chromosomes in dividing cells requires the disassembly of nucleosomes ahead of the fork and the rapid assembly of parental and de novo histones at the newly synthesized strands behind the fork. Replication-coupled chromatin assembly provides a unique opportunity to regulate fork advance and stability. Through post-translational histone modifications and tightly regulated physical and genetic interactions between chromatin assembly factors and replisome components, chromatin assembly: (1) controls the rate of DNA synthesis and adjusts it to histone availability; (2) provides a mechanism to protect the integrity of the advancing fork; and (3) regulates the mechanisms of DNA damage tolerance in response to replication-blocking lesions...
January 24, 2017: Genes
https://www.readbyqxmd.com/read/28096365/unlocking-tn3-family-transposase-activity-in-vitro-unveils-an-asymetric-pathway-for-transposome-assembly
#16
Emilien Nicolas, Cédric A Oger, Nathan Nguyen, Michaël Lambin, Amandine Draime, Sébastien C Leterme, Michael Chandler, Bernard F J Hallet
The Tn3 family is a widespread group of replicative transposons that are notorious for their contribution to the dissemination of antibiotic resistance and the emergence of multiresistant pathogens worldwide. The TnpA transposase of these elements catalyzes DNA breakage and rejoining reactions required for transposition. It also is responsible for target immunity, a phenomenon that prevents multiple insertions of the transposon into the same genomic region. However, the molecular mechanisms whereby TnpA acts in both processes remain unknown...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095613/xenopus-egg-extract-to-study-regulation-of-genome-wide-and-locus-specific-dna-replication
#17
REVIEW
Erica Raspelli, Lucia Falbo, Vincenzo Costanzo
Faithful DNA replication, coupled with accurate repair of DNA damage, is essential to maintain genome stability and relies on different DNA metabolism genes. Many of these genes are involved in the assembly of replication origins, in the coordination of DNA repair to protect replication forks progression in the presence of DNA damage and in the replication of repetitive chromatin regions. Some DNA metabolism genes are essential in higher eukaryotes, suggesting the existence of specialized mechanisms of repair and replication in organisms with complex genomes...
January 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28074956/tunable-superapolar-lotus-to-rose-hierarchical-nanosurfaces-via-vertical-carbon-nanotubes-driven-electrohydrodynamic-lithography
#18
Chiara Busà, Jonathan James Stanley Rickard, Eugene Chun, Yaw Chong, Viroshan Navaratnam, Pola Goldberg Oppenheimer
The development of a robust, cost-effective, scalable and simple technique that enables the design and construction of well-controlled large area superhydrophobic surface structures which can be easily tuned from lotus-leaf to rose-petal state is essential to enable progress in realising the full applied potential of such surfaces. In this study, we introduce the tuneable carbon nanotubes-based electrohydrodynamic lithography (CNT-EHL) to fabricate unique multiscale structured cones and nanohair-like architectures with various periodicities and dimensions, successfully enabling surface energy minimization...
January 26, 2017: Nanoscale
https://www.readbyqxmd.com/read/28059623/coordinating-cell-cycle-regulated-histone-gene-expression-through-assembly-and-function-of-the-histone-locus-body
#19
Robert J Duronio, William F Marzluff
Metazoan replication-dependent (RD) histone genes encode the only known cellular mRNAs that are not polyadenylated. These mRNAs end instead in a conserved stem-loop, which is formed by an endonucleolytic cleavage of the pre-mRNA. The genes for all 5 histone proteins are clustered in all metazoans and coordinately regulated with high levels of expression during S phase. Production of histone mRNAs occurs in a nuclear body called the Histone Locus Body (HLB), a subdomain of the nucleus defined by a concentration of factors necessary for histone gene transcription and pre-mRNA processing...
January 6, 2017: RNA Biology
https://www.readbyqxmd.com/read/28000624/plant-leaves-as-natural-green-scaffolds-for-palladium-catalyzed-suzuki-miyaura-coupling-reactions
#20
Vipul Sharma, Suneel Kumar, Ashish Bahuguna, Diksha Gambhir, Prateep Singh Sagara, Venkata Krishnan
This work presents a novel approach of using natural plant leaf surfaces having intricate hierarchical structures as scaffolds for Pd nanoparticles and demonstrated it as a Green dip catalyst for Suzuki-Miyaura coupling reactions in water. The influence of the topographical texture of the plant leaves on the deposition and catalytic properties of Pd nanoparticles are presented and discussed. The catalytic activity can be correlated to the surface texture of the leaves, wherein it has been found that the micro/nanostructures present on the surface strongly influence the assembly and entrapment of the nanoparticles, and thereby control aggregation and leaching of the catalysts...
December 21, 2016: Bioinspiration & Biomimetics
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