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Coupling of replication and assembly

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 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
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 17, 2017: Genesis: the Journal of Genetics and Development
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 11, 2017: Nanoscale
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
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
G Margaris, M Vasilakaki, D Peddis, K N Trohidou, S Laureti, C Binns, E Agostinelli, D Rinaldi, R Mathieu, D Fiorani
In nanoparticle systems consisting of two magnetic materials (bi-magnetic nanoparticles or nanoparticles embedded in a magnetic matrix), there is a constantly growing interest in the investigation of the interplay between interparticle interactions and the nanoparticle-matrix interface exchange coupling, because of its enormous impact on a number of technological applications. The understanding of the mechanisms of such interplay is a great challenge, as it would allow controlling equilibrium and non-equilibrium magnetization dynamics of exchange coupled nanoparticles systems and finely tuning their anisotropy...
January 20, 2017: Nanotechnology
Paul B Talbert, Steven Henikoff
Most histones are assembled into nucleosomes behind the replication fork to package newly synthesized DNA. By contrast, histone variants, which are encoded by separate genes, are typically incorporated throughout the cell cycle. Histone variants can profoundly change chromatin properties, which in turn affect DNA replication and repair, transcription, and chromosome packaging and segregation. Recent advances in the study of histone replacement have elucidated the dynamic processes by which particular histone variants become substrates of histone chaperones, ATP-dependent chromatin remodellers and histone-modifying enzymes...
December 7, 2016: Nature Reviews. Molecular Cell Biology
Vanessa Menil-Philippot, Christophe Thiriet
Histone modifications have been widely correlated with genetic activities. However, how these posttranslational modifications affect the dynamics and the structure of chromatin is poorly understood. Here, we describe the incorporation of the exogenous histone proteins into the slime mold Physarum polycephalum, which has been revealed to be a valuable tool for examining different facets of the function histones in chromatin dynamics like replication-coupled chromatin assembly, histone exchange, and nucleosome turnover...
2017: Methods in Molecular Biology
Grasiella Angelina Andriani, Vinnycius Pereira Almeida, Francesca Faggioli, Maurizio Mauro, Wanxia Li Tsai, Laura Santambrogio, Alexander Maslov, Massimo Gadina, Judith Campisi, Jan Vijg, Cristina Montagna
Age-related accumulation of ploidy changes is associated with decreased expression of genes controlling chromosome segregation and cohesin functions. To determine the consequences of whole chromosome instability (W-CIN) we down-regulated the spindle assembly checkpoint component BUB1 and the mitotic cohesin SMC1A, and used four-color-interphase-FISH coupled with BrdU incorporation and analyses of senescence features to reveal the fate of W-CIN cells. We observed significant correlations between levels of not-diploid cells and senescence-associated features (SAFs)...
October 12, 2016: Scientific Reports
Wallace H Liu, Sarah C Roemer, Yeyun Zhou, Zih-Jie Shen, Briana K Dennehey, Jeremy L Balsbaugh, Jennifer C Liddle, Travis Nemkov, Natalie G Ahn, Kirk C Hansen, Jessica K Tyler, Mair Ea Churchill
The histone chaperone Chromatin Assembly Factor 1 (CAF-1) deposits tetrameric (H3/H4)2 histones onto newly-synthesized DNA during DNA replication. To understand the mechanism of the tri-subunit CAF-1 complex in this process, we investigated the protein-protein interactions within the CAF-1-H3/H4 architecture using biophysical and biochemical approaches. Hydrogen/deuterium exchange and chemical cross-linking coupled to mass spectrometry reveal interactions that are essential for CAF-1 function in budding yeast, and importantly indicate that the Cac1 subunit functions as a scaffold within the CAF-1-H3/H4 complex...
September 30, 2016: ELife
Sou Nobukawa, Haruhiko Nishimura
It is well known that cerebellar motor control is fine-tuned by the learning process adjusted according to rich error signals from inferior olive (IO) neurons. Schweighofer and colleagues proposed that these signals can be produced by chaotic irregular firing in the IO neuron assembly; such chaotic resonance (CR) was replicated in their computer demonstration of a Hodgkin-Huxley (HH)-type compartment model. In this study, we examined the response of CR to a periodic signal in the IO neuron assembly comprising the Llinás approach IO neuron model...
September 14, 2016: Neural Computation
Namrata Gupta, Suhani Thakker, Subhash C Verma
The establishment of latency is an essential for lifelong persistence and pathogenesis of Kaposi's sarcoma-associated herpesvirus (KSHV). Latency-associated nuclear antigen (LANA) is the most abundantly expressed protein during latency and is important for viral genome replication and transcription. Replication-coupled nucleosome assembly is a major step in packaging the newly synthesized DNA into chromatin, but the mechanism of KSHV genome chromatinization post-replication is not understood. Here, we show that nucleosome assembly protein 1-like protein 1 (NAP1L1) associates with LANA...
September 7, 2016: Scientific Reports
F Meyer
Eukaryotic genes are often interrupted by stretches of sequence with no protein coding potential or obvious function. After transcription, these interrupting sequences must be removed to give rise to the mature messenger RNA. This fundamental process is called RNA splicing and is achieved by complicated machinery made of protein and RNA that assembles around the RNA to be edited. Viruses also use RNA splicing to maximize their coding potential and economize on genetic space, and use clever strategies to manipulate the splicing machinery to their advantage...
2016: Progress in Molecular Biology and Translational Science
Mireia Ferrer, Simon Henriet, Célia Chamontin, Sébastien Lainé, Marylène Mougel
In cells, positive strand RNA viruses, such as Retroviridae, must selectively recognize their full-length RNA genome among abundant cellular RNAs to assemble and release particles. How viruses coordinate the intracellular trafficking of both RNA and protein components to the assembly sites of infectious particles at the cell surface remains a long-standing question. The mechanisms ensuring packaging of genomic RNA are essential for viral infectivity. Since RNA packaging impacts on several essential functions of retroviral replication such as RNA dimerization, translation and recombination events, there are many studies that require the determination of RNA packaging efficiency and/or RNA packaging ability...
2016: Viruses
Luca Pellegrini, Alessandro Costa
The DNA replication machinery, or replisome, is a macromolecular complex that combines DNA unwinding, priming and synthesis activities. In eukaryotic cells, the helicase and polymerases are multi-subunit, highly-dynamic assemblies whose structural characterization requires an integrated approach. Recent studies have combined single-particle electron cryo-microscopy and protein crystallography to gain insights into the mechanism of DNA duplication by the eukaryotic replisome. We review current understanding of how replication fork unwinding by the CMG helicase is coupled to leading-strand synthesis by polymerase (Pol) ɛ and lagging-strand priming by Pol α/primase, and discuss emerging principles of replisome organization...
October 2016: Trends in Biochemical Sciences
Yandong Yin, Eli Rothenberg
Super-resolution microscopy coupled with multiplexing techniques can resolve specific spatial arrangements of different components within molecular complexes. However, reliable quantification and analysis of such specific organization is extremely problematic because it is frequently obstructed by random co-localization incidents between crowded molecular species and the intrinsic heterogeneity of molecular complexes. To address this, we present a Triple-Pair-Correlation (TPC) analysis approach for unbiased interpretation of the spatial organization of molecular assemblies in crowded three-color super-resolution (SR) images...
2016: Scientific Reports
Samantha C Lewis, Lauren F Uchiyama, Jodi Nunnari
Mitochondrial DNA (mtDNA) encodes RNAs and proteins critical for cell function. In human cells, hundreds to thousands of mtDNA copies are replicated asynchronously, packaged into protein-DNA nucleoids, and distributed within a dynamic mitochondrial network. The mechanisms that govern how nucleoids are chosen for replication and distribution are not understood. Mitochondrial distribution depends on division, which occurs at endoplasmic reticulum (ER)-mitochondria contact sites. These sites were spatially linked to a subset of nucleoids selectively marked by mtDNA polymerase and engaged in mtDNA synthesis--events that occurred upstream of mitochondrial constriction and division machine assembly...
July 15, 2016: Science
Fabrizio Villa, Aline C Simon, Maria Angeles Ortiz Bazan, Mairi L Kilkenny, David Wirthensohn, Mel Wightman, Dijana Matak-Vinkovíc, Luca Pellegrini, Karim Labib
Replisome assembly at eukaryotic replication forks connects the DNA helicase to DNA polymerases and many other factors. The helicase binds the leading-strand polymerase directly, but is connected to the Pol α lagging-strand polymerase by the trimeric adaptor Ctf4. Here, we identify new Ctf4 partners in addition to Pol α and helicase, all of which contain a "Ctf4-interacting-peptide" or CIP-box. Crystallographic analysis classifies CIP-boxes into two related groups that target different sites on Ctf4. Mutations in the CIP-box motifs of the Dna2 nuclease or the rDNA-associated protein Tof2 do not perturb DNA synthesis genome-wide, but instead lead to a dramatic shortening of chromosome 12 that contains the large array of rDNA repeats...
August 4, 2016: Molecular Cell
Shan Dong, Long Liu, Weining Wu, Stuart D Armstrong, Dong Xia, Hao Nan, Julian A Hiscox, Hongying Chen
UNLABELLED: Porcine reproductive and respiratory syndrome virus (PRRSV) has caused tremendous economic losses and continues to be a serious problem to the swine industry worldwide. Although extensive research has been focused on PRRSV, the structure and function of some viral proteins like nonstructural protein12 (NSP12), which may play important roles in viral replication and production, still remain unknown. In order to better understand the function of NSP12, we investigated the interaction of NSP12 with cellular proteins using quantitative proteomics coupled with an immune-precipitation strategy based on the over expression of an NSP12-EGFP fusion protein in 293T cells...
September 2, 2016: Journal of Proteomics
Iris V Hood, James M Berger
Replisome assembly requires the loading of replicative hexameric helicases onto origins by AAA+ ATPases. How loader activity is appropriately controlled remains unclear. Here, we use structural and biochemical analyses to establish how an antimicrobial phage protein interferes with the function of the Staphylococcus aureus replicative helicase loader, DnaI. The viral protein binds to the loader's AAA+ ATPase domain, allowing binding of the host replicative helicase but impeding loader self-assembly and ATPase activity...
2016: ELife
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