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Coupling of replication and assembly

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https://www.readbyqxmd.com/read/29301493/pacbio-sequencing-of-copper-tolerant-xanthomonas-citri-reveals-presence-of-a-chimeric-plasmid-structure-and-provides-insights-into-reassortment-and-shuffling-of-transcription-activator-like-effectors-among-x-citri-strains
#1
Alberto M Gochez, Jose C Huguet-Tapia, Gerald V Minsavage, Deepak Shantaraj, Neha Jalan, Annett Strauß, Thomas Lahaye, Nian Wang, Blanca I Canteros, Jeffrey B Jones, Neha Potnis
BACKGROUND: Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains...
January 4, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29247059/rice-paddy-nitrospirae-encode-and-express-genes-related-to-sulfate-respiration-proposal-of-the-new-genus-candidatus-sulfobium
#2
Sarah Zecchin, Ralf C Mueller, Jana Seifert, Ulrich Stingl, Karthik Anantharaman, Martin von Bergen, Lucia Cavalca, Michael Pester
Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here, we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO4×2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression thereof in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics...
December 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29223786/the-eukaryotic-translation-initiation-factor-3-subunit-e-binds-to-classical-swine-fever-virus-ns5a-and-facilitates-viral-replication
#3
Xiaofeng Liu, Xiaoyu Wang, Qian Wang, Mingyang Luo, Huancheng Guo, Wenjie Gong, Changchun Tu, Jinfu Sun
Classical swine fever virus (CSFV) NS5A protein is a multifunctional protein, playing critical roles in viral RNA replication, translation and assembly. To further explore its functions in viral replication, interaction of NS5A with host factors was assayed using a his-tag "pull down" assay coupled with shotgun LC-MS/MS. Host protein translation initiation factor 3 subunit E was identified as a binding partner of NS5A, and confirmed by co-immunoprecipitation and co-localization analysis. Overexpression of eIF3E markedly enhanced CSFV genomic replication, viral protein expression and production of progeny virus, and downregulation of eIF3E by siRNA significantly decreased viral proliferation in PK-15 cells...
December 7, 2017: Virology
https://www.readbyqxmd.com/read/29199149/ultra-high-mass-multimer-analysis-of-protein-1a-capping-domains-by-a-silicon-nanomembrane-detector
#4
H C Shin, D Deterra, J Park, H Kim, M Nishikiori, Ch Uetrecht, P G Ahlquist, M Arbulu, R H Blick
Conventional time of flight ion detectors are based on secondary electron multipliers encountering a significant loss in detection efficiency, sensitivity and resolution with protein mass above 50kDa. In this work we employ a silicon nanomembrane detector in a Matrix-Assisted Laser Desorption/Ionization coupled to time of flight (MALDI-TOF) mass spectrometer. The operating principle relies on phonon-assisted field emission with excellent performance in the high mass range from 0.001-2MDa. In addition to the analysis of standard proteins the nanomembrane detector (NMD) has the potential for the detection and structural investigation of complex macromolecular assemblies through non-covalent interactions...
November 30, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29186822/venture-from-the-interior-herpesvirus-pul31-escorts-capsids-from-nucleoplasmic-replication-compartments-to-sites-of-primary-envelopment-at-the-inner-nuclear-membrane
#5
REVIEW
(no author information available yet)
Herpesviral capsid assembly is initiated in the nucleoplasm of the infected cell. Size constraints require that newly formed viral nucleocapsids leave the nucleus by an evolutionarily conserved vescular transport mechanism called nuclear egress. Mature capsids released from the nucleoplasm are engaged in a membrane-mediated budding process, composed of primary envelopment at the inner nuclear membrane and de-envelopment at the outer nuclear membrane. Once in the cytoplasm, the capsids receive their secondary envelope for maturation into infectious virions...
November 25, 2017: Cells
https://www.readbyqxmd.com/read/29167311/the-human-ctf4-orthologue-and-1-interacts-with-dna-polymerase-%C3%AE-primase-via-its-unique-c-terminal-hmg-box
#6
Mairi L Kilkenny, Aline C Simon, Jack Mainwaring, David Wirthensohn, Sandro Holzer, Luca Pellegrini
A dynamic multi-protein assembly known as the replisome is responsible for DNA synthesis in eukaryotic cells. In yeast, the hub protein Ctf4 bridges DNA helicase and DNA polymerase and recruits factors with roles in metabolic processes coupled to DNA replication. An important question in DNA replication is the extent to which the molecular architecture of the replisome is conserved between yeast and higher eukaryotes. Here, we describe the biochemical basis for the interaction of the human CTF4-orthologue AND-1 with DNA polymerase α (Pol α)/primase, the replicative polymerase that initiates DNA synthesis...
November 2017: Open Biology
https://www.readbyqxmd.com/read/29163571/setting-up-shop-the-formation-and-function-of-the-viral-factories-of-cauliflower-mosaic-virus
#7
REVIEW
James E Schoelz, Scott Leisner
Similar to cells, viruses often compartmentalize specific functions such as genome replication or particle assembly. Viral compartments may contain host organelle membranes or they may be mainly composed of viral proteins. These compartments are often termed: inclusion bodies (IBs), viroplasms or viral factories. The same virus may form more than one type of IB, each with different functions, as illustrated by the plant pararetrovirus, Cauliflower mosaic virus (CaMV). CaMV forms two distinct types of IBs in infected plant cells, those composed mainly of the viral proteins P2 (which are responsible for transmission of CaMV by insect vectors) and P6 (required for viral intra-and inter-cellular infection), respectively...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29151691/parallel-mrna-proteomics-and-mirna-expression-analysis-in-cell-line-models-of-the-intestine
#8
Finbarr O'Sullivan, Joanne Keenan, Sinead Aherne, Fiona O'Neill, Colin Clarke, Michael Henry, Paula Meleady, Laura Breen, Niall Barron, Martin Clynes, Karina Horgan, Padraig Doolan, Richard Murphy
AIM: To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. METHODS: Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array...
November 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29149077/rna-virus-evolution-via-a-quasispecies-based-model-reveals-a-drug-target-with-a-high-barrier-to-resistance
#9
Richard J Bingham, Eric C Dykeman, Reidun Twarock
The rapid occurrence of therapy-resistant mutant strains provides a challenge for anti-viral therapy. An ideal drug target would be a highly conserved molecular feature in the viral life cycle, such as the packaging signals in the genomes of RNA viruses that encode an instruction manual for their efficient assembly. The ubiquity of this assembly code in RNA viruses, including major human pathogens, suggests that it confers selective advantages. However, their impact on viral evolution cannot be assessed in current models of viral infection that lack molecular details of virus assembly...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29106372/53bp1-and-brca1-control-pathway-choice-for-stalled-replication-restart
#10
Yixi Xu, Shaokai Ning, Zheng Wei, Ran Xu, Xinlin Xu, Mengtan Xing, Rong Guo, Dongyi Xu
The cellular pathways that restart stalled replication forks are essential for genome stability and tumor prevention. However, how many of these pathways exist in cells and how these pathways are selectively activated remain unclear. Here, we describe two major fork restart pathways, and demonstrate that their selection is governed by 53BP1 and BRCA1, which are known to control the pathway choice to repair double-strand DNA breaks (DSBs). Specifically, 53BP1 promotes a fork cleavage-free pathway, whereas BRCA1 facilitates a break-induced replication (BIR) pathway coupled with SLX-MUS complex-mediated fork cleavage...
November 6, 2017: ELife
https://www.readbyqxmd.com/read/29070793/cellular-splicing-factor-uap56-stimulates-trimeric-np-formation-for-assembly-of-functional-influenza-viral-ribonucleoprotein-complexes
#11
Yifan Hu, Vishal Gor, Kazuya Morikawa, Kyosuke Nagata, Atsushi Kawaguchi
The influenza virus RNA genome exists as a ribonucleoprotein (RNP) complex by interacting with NP, one of virus-encoded RNA binding proteins. It is proposed that trimeric NP is a functional form, but it is not clear how trimeric NP is formed and transferred to RNA. UAP56, a cellular splicing factor, functions as a molecular chaperone for NP and is required for the replication-coupled RNP formation of newly synthesized viral genome, but the details of NP transfer to viral RNA by UAP56 is unclear. Here we found that UAP56 is complexed with trimeric NP, but not monomeric NP...
October 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28959049/continual-reproduction-of-self-assembling-oligotriazole-peptide-nanomaterials
#12
Roberto J Brea, Neal K Devaraj
Autocatalytic chemical reactions, whereby a molecule is able to catalyze its own formation from a set of precursors, mimic nature's ability to generate identical copies of relevant biomolecules, and are thought to have been crucial for the origin of life. While several molecular autocatalysts have been previously reported, coupling autocatalytic behavior to macromolecular self-assembly has been challenging. Here, we report a non-enzymatic and chemoselective methodology capable of autocatalytically producing triskelion peptides that self-associate into spherical bioinspired nanostructures...
September 28, 2017: Nature Communications
https://www.readbyqxmd.com/read/28921953/new-antimony-selenide-nickel-oxide-photocathode-boosts-the-efficiency-of-graphene-quantum-dot-co-sensitized-solar-cells
#13
Ankita Kolay, Ramesh K Kokal, Ankarao Kalluri, Isaac Macwan, Prabir K Patra, Partha Ghosal, Melepurath Deepa
A novel assembly of a photocathode and a 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 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...
October 11, 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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