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Coupling of replication and assembly

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https://www.readbyqxmd.com/read/29751847/asf1-is-required-to-load-histones-on-the-hira-complex-in-preparation-of-paternal-chromatin-assembly-at-fertilization
#1
Béatrice Horard, Laure Sapey-Triomphe, Emilie Bonnefoy, Benjamin Loppin
BACKGROUND: Anti-Silencing Factor 1 (ASF1) is a conserved H3-H4 histone chaperone involved in both Replication-Coupled and Replication-Independent (RI) nucleosome assembly pathways. At DNA replication forks, ASF1 plays an important role in regulating the supply of H3.1/2 and H4 to the CAF-1 chromatin assembly complex. ASF1 also provides H3.3-H4 dimers to HIRA and DAXX chaperones for RI nucleosome assembly. The early Drosophila embryo is an attractive system to study chromatin assembly in a developmental context...
May 11, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29743356/the-hiv-1-tat-protein-enhances-splicing-at-the-major-splice-donor-site
#2
Nancy Mueller, Alexander O Pasternak, Bep Klaver, Marion Cornelissen, Ben Berkhout, Atze T Das
Transcription of the HIV-1 proviral DNA and subsequent processing of the primary transcript results in the production of a large set of unspliced and differentially spliced viral RNAs. The major splice donor site (5'ss) that is located in the untranslated leader of the HIV-1 transcript is used for the production of all spliced RNAs and splicing at this site has to be tightly regulated to allow the balanced production of all viral RNAs and proteins. We demonstrate that the viral Tat protein, which is known to activate viral transcription, also stimulates splicing at the major 5'ss...
May 9, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29611806/mcm2-7-dependent-cohesin-loading-during-s-phase-promotes-sister-chromatid-cohesion
#3
Ge Zheng, Mohammed Kanchwala, Chao Xing, Hongtao Yu
DNA replication transforms cohesin rings dynamically associated with chromatin into the cohesive form to establish sister-chromatid cohesion. Here, we show that, in human cells, cohesin loading onto chromosomes during early S phase requires the replicative helicase MCM2-7 and the kinase DDK. Cohesin and its loader SCC2/4 (NIPBL/MAU2 in humans) associate with DDK and phosphorylated MCM2-7. This binding does not require MCM2-7 activation by CDC45 and GINS, but its persistence on activated MCM2-7 requires fork-stabilizing replisome components...
April 3, 2018: ELife
https://www.readbyqxmd.com/read/29545586/stimulation-of-alpha2-adrenergic-receptors-impairs-influenza-virus-infection
#4
Ken Matsui, Makoto Ozawa, Maki Kiso, Makoto Yamashita, Toshihiko Maekawa, Minoru Kubota, Sumio Sugano, Yoshihiro Kawaoka
Influenza A viruses cause seasonal epidemics and occasional pandemics. The emergence of viruses resistant to neuraminidase (NA) inhibitors and M2 ion channel inhibitors underlines the need for alternate anti-influenza drugs with novel mechanisms of action. Here, we report the discovery of a host factor as a potential target of anti-influenza drugs. By using cell-based virus replication screening of a chemical library and several additional assays, we identified clonidine as a new anti-influenza agent in vitro...
March 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29525670/cellular-hsp27-interacts-with-classical-swine-fever-virus-ns5a-protein-and-negatively-regulates-viral-replication-by-the-nf-%C3%AE%C2%BAb-signaling-pathway
#5
Shifeng Ling, Mingyang Luo, Shengnan Jiang, Jiayu Liu, Chunying Ding, Qinghuan Zhang, Huancheng Guo, Wenjie Gong, Changchun Tu, Jinfu Sun
Classical swine fever virus (CSFV) nonstructural protein NS5A is a multifunctional protein functioning in regulation of viral genome replication, protein translation and assembly by interaction with viral or host proteins. Here, heat shock protein 27 (Hsp27) has been identified as a novel binding partner of NS5A by using His tag "pull down" coupled with shotgun LC-MS/MS, with interaction of both proteins further confirmed by co-immunoprecipitation and laser confocal assays. In PK-15 cells, silencing of Hsp27 expression by siRNA enhanced CSFV replication, and upregulation of Hsp27 inhibited viral proliferation...
May 2018: Virology
https://www.readbyqxmd.com/read/29499038/crystal-structures-of-pcna-mutant-proteins-defective-in-gene-silencing-suggest-a-novel-interaction-site-on-the-front-face-of-the-pcna-ring
#6
Christine M Kondratick, Jacob M Litman, Kurt V Shaffer, M Todd Washington, Lynne M Dieckman
Proliferating cell nuclear antigen (PCNA), a homotrimeric protein, is the eukaryotic sliding clamp that functions as a processivity factor for polymerases during DNA replication. Chromatin association factor 1 (CAF-1) is a heterotrimeric histone chaperone protein that is required for coupling chromatin assembly with DNA replication in eukaryotes. CAF-1 association with replicating DNA, and the targeting of newly synthesized histones to sites of DNA replication and repair requires its interaction with PCNA. Genetic studies have identified three mutant forms of PCNA in yeast that cause defects in gene silencing and exhibit altered association of CAF-1 to chromatin in vivo, as well as inhibit binding to CAF-1 in vitro...
2018: PloS One
https://www.readbyqxmd.com/read/29487689/cdk1-and-plk1-coordinate-the-disassembly-and-reassembly-of-the-nuclear-envelope-in-vertebrate-mitosis
#7
Ines J de Castro, Raquel Sales Gil, Lorena Ligammari, Maria Laura Di Giacinto, Paola Vagnarelli
Micronuclei (MN) arise from chromosomes or fragments that fail to be incorporated into the primary nucleus after cell division. These structures are a major source of genetic instability caused by DNA repair and replication defects coupled to aberrant Nuclear Envelope (NE). These problems ultimately lead to a spectrum of chromosome rearrangements called chromothripsis, a phenomenon that is a hallmark of several cancers. Despite its importance, the molecular mechanism at the origin of this instability is still not understood...
January 30, 2018: Oncotarget
https://www.readbyqxmd.com/read/29474959/alpha-gamma-phase-amplitude-coupling-subserves-information-transfer-during-perceptual-sequence-learning
#8
Elinor Tzvi, Leon J Bauhaus, Till U Kessler, Matthias Liebrand, Malte Wöstmann, Ulrike M Krämer
Cross-frequency coupling is suggested to serve transfer of information between wide-spread neuronal assemblies and has been shown to underlie many cognitive functions including learning and memory. In previous work, we found that alpha (8-13 Hz) - gamma (30-48 Hz) phase amplitude coupling (αγPAC) is decreased during sequence learning in bilateral frontal cortex and right parietal cortex. We interpreted this to reflect decreased demands for visuo-motor mapping once the sequence has been encoded. In the present study, we put this hypothesis to the test by adding a "simple" condition to the standard serial reaction time task (SRTT) with minimal needs for visuo-motor mapping...
March 2018: Neurobiology of Learning and Memory
https://www.readbyqxmd.com/read/29444942/a-functional-link-between-rna-replication-and-virion-assembly-in-the-potyvirus-plum-pox-virus
#9
Araiz Gallo, Adrian Valli, María Calvo, Juan Antonio García
Accurate assembly of viral particles in the potyvirus Plum pox virus (PPV) has been shown to depend on the contribution of the multifunctional viral protein HCPro. In this study, we show that other viral factors, in addition to the capsid protein (CP) and HCPro, are necessary for the formation of stable PPV virions. The CP produced in Nicotiana benthamiana leaves from a subviral RNA termed LONG, which expresses a truncated polyprotein that lacks P1 and HCPro, together with HCPro supplied in trans , was assembled into virus-like particles and remained stable after in vitro incubation...
May 1, 2018: Journal of Virology
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
#10
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-carry-and-express-genes-related-to-sulfate-respiration-proposal-of-the-new-genus-candidatus-sulfobium
#11
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 ·2H2 O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression of this pathway in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics...
March 1, 2018: 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
#12
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...
February 2018: Virology
https://www.readbyqxmd.com/read/29199149/ultra-high-mass-multimer-analysis-of-protein-1a-capping-domains-by-a-silicon-nanomembrane-detector
#13
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...
March 20, 2018: 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
#14
REVIEW
Susanne M. Bailer
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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