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Coupling of replication and assembly

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https://www.readbyqxmd.com/read/28921953/new-antimony-selenide-nickel-oxide-photocathode-boosts-the-efficiency-of-graphene-quantum-dots-co-sensitized-solar-cell
#1
Ankita Kolay, Ramesh K Kokal, Ankarao Kalluri, Isaac Macwan, Prabir K Patra, Partha Ghosal, Melepurath Deepa
A novel assembly of a photocathode and photoanode is investigated to explore their complementary effects in enhancing the photovoltaic performance of a quantum dot solar cell (QDSC). While p-type nickel oxide (NiO) has been used previously, antimony selenide (Sb2Se3) has not been used in a QDSC, especially as a component of a counter electrode (CE) architecture that doubles up as the photocathode. Here, near infrared (NIR) light absorbing Sb2Se3 nanoparticles (NPs) coated over electrodeposited NiO nanofibers on a carbon (C)-fabric substrate was employed as the highly efficient photocathode...
September 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28840236/quantitative-microscopy-reveals-centromeric-chromatin-stability-size-and-cell-cycle-mechanisms-to-maintain-centromere-homeostasis
#2
Ana Stankovic, Lars E T Jansen
Centromeres are chromatin domains specified by nucleosomes containing the histone H3 variant, CENP-A. This unique centromeric structure is at the heart of a strong self-templating epigenetic mechanism that renders centromeres heritable. We review how specific quantitative microscopy approaches have contributed to the determination of the copy number, architecture, size, and dynamics of centromeric chromatin and its associated centromere complex and kinetochore. These efforts revealed that the key to long-term centromere maintenance is the slow turnover of CENP-A nucleosomes, a critical size of the chromatin domain and its cell cycle-coupled replication...
2017: Progress in Molecular and Subcellular Biology
https://www.readbyqxmd.com/read/28807089/supramolecular-based-ultrasonic-assisted-dispersion-solidification-liquid-liquid-microextraction-of-copper-and-cobalt-prior-to-their-flame-atomic-absorption-spectrometry-determination
#3
Ardeshir Shokrollahi, Foroogh Ebrahimi
In the present work, a simple, efficient, and environmentally friendly method was proposed for the simultaneous preconcentration and determination of minute quantities of copper and cobalt in water samples and serum by a supramolecular-based ultrasonic-assisted dispersion solidification liquid–liquid microextraction (DSLLME) procedure coupled with flame atomic absorption spectrometry. The procedure is based on the DSLLME of copper and cobalt with decanoic acid–tetrahydrofuran supramolecular solvent (SUPRAS) in the presence of sodium diethyldithiocarbamate, as the complexing agent...
August 15, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28696003/relative-abundance-of-candidatus-tenderia-electrophaga-is-linked-to-cathodic-current-in-an-aerobic-biocathode-community
#4
Anthony P Malanoski, Baochuan Lin, Brian J Eddie, Zheng Wang, W Judson Hervey, Sarah M Glaven
Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture-independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO2 fixation to extracellular electron transfer and O2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes...
July 11, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28666361/identification-of-multiple-roles-for-histone-acetyltransferase-1-in-replication-coupled-chromatin-assembly
#5
Paula A Agudelo Garcia, Michael E Hoover, Pei Zhang, Prabakaran Nagarajan, Michael A Freitas, Mark R Parthun
Histone acetyltransferase 1 (Hat1) catalyzes the acetylation of newly synthesized histone H4 at lysines 5 and 12 that accompanies replication-coupled chromatin assembly. The acetylation of newly synthesized H4 occurs in the cytoplasm and the function of this acetylation is typically ascribed to roles in either histone nuclear import or deposition. Using cell lines from Hat1+/+ and Hat1-/- mouse embryos, we demonstrate that Hat1 is not required for either histone nuclear import or deposition. We employed quantitative proteomics to characterize Hat1-dependent changes in the composition of nascent chromatin structure...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28615292/rtt101-mms1-mms22-coordinates-replication-coupled-sister-chromatid-cohesion-and-nucleosome-assembly
#6
Jingjing Zhang, Di Shi, Xiaoli Li, Lin Ding, Jun Tang, Cong Liu, Katsuhiko Shirahige, Qinhong Cao, Huiqiang Lou
Two sister chromatids must be held together by a cohesion process from their synthesis during S phase to segregation in anaphase. Despite its pivotal role in accurate chromosome segregation, how cohesion is established remains elusive. Here, we demonstrate that yeast Rtt101-Mms1, Cul4 family E3 ubiquitin ligases are stronger dosage suppressors of loss-of-function eco1 mutants than PCNA The essential cohesion reaction, Eco1-catalyzed Smc3 acetylation is reduced in the absence of Rtt101-Mms1. One of the adaptor subunits, Mms22, associates directly with Eco1...
August 2017: EMBO Reports
https://www.readbyqxmd.com/read/28600325/hira-deficiency-in-muscle-fibers-causes-hypertrophy-and-susceptibility-to-oxidative-stress
#7
Nicolas Valenzuela, Benjamin Soibam, Lerong Li, Jing Wang, Lauren A Byers, Yu Liu, Robert J Schwartz, M David Stewart
Nucleosome assembly proceeds through DNA replication-coupled or replication-independent mechanisms. For skeletal myocytes, whose nuclei have permanently exited the cell cycle, replication-independent assembly is the only mode available for chromatin remodeling. For this reason, any nucleosome composition alterations accompanying transcriptional responses to physiological signals must occur through a DNA replication-independent pathway. HIRA is the histone chaperone primarily responsible for replication-independent incorporation of histone variant H3...
June 9, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28596587/histones-h3-and-h4-require-their-relevant-amino-tails-for-efficient-nuclear-import-and-replication-coupled-chromatin-assembly-in-vivo
#8
Aïda Ejlassi, Vanessa Menil-Philippot, Angélique Galvani, Christophe Thiriet
Concomitant chromatin assembly and DNA duplication is essential for cell survival and genome integrity, and requires newly synthesized histones. Although the N-terminal domains of newly synthesized H3 and H4 present critical functions, their requirement for replication-coupled chromatin assembly is controversial. Using the unique capability of the spontaneous internalization of exogenous proteins in Physarum, we showed that H3 and H4 N-tails present critical functions in nuclear import during the S-phase, but are dispensable for assembly into nucleosomes...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28462924/identification-and-characterization-of-a-heterotrimeric-archaeal-dna-polymerase-holoenzyme
#9
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
#10
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-hyperphosphorylation-site-responsible-for-hepatitis-c-virus-replication
#11
Shih-Chin Hsu, Chieh-Wen Lo, Ting-Chun Pan, Kuan-Ying Lee, Ming-Jiun Yu
The nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) is a phosphoprotein with two phosphorylation states: hypo- and hyperphosphorylation. Genetic mutation studies have demonstrated a cluster of serine residues responsible for NS5A hyperphosphorylation 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...
July 15, 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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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