Browsing by Issue Date, starting with "2013-04"
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- Crystal structure of a poxvirus-like zalpha domain from cyprinid herpesvirus 3Publication . Tomé, Ana Rita; Kuś, Krzysztof; Correia, Silvia; Paulo, Lara Martins; Zacarias, Sónia; de Rosa, Matteo; Figueiredo, Delio; Parkhouse, R Michael E; Athanasiadis, AlekosZalpha domains are a subfamily of the winged helix-turn-helix domains sharing the unique ability to recognize CpG repeats in the left-handed Z-DNA conformation. In vertebrates, domains of this family are found exclusively in proteins that detect foreign nucleic acids and activate components of the antiviral interferon response. Moreover, poxviruses encode the Zalpha domain-containing protein E3L, a well-studied and potent inhibitor of interferon response. Here we describe a herpesvirus Zalpha-domain-containing protein (ORF112) from cyprinid herpesvirus 3. We demonstrate that ORF112 also binds CpG repeats in the left-handed conformation, and moreover, its structure at 1.75 Å reveals the Zalpha fold found in ADAR1, DAI, PKZ, and E3L. Unlike other Zalpha domains, however, ORF112 forms a dimer through a unique domain-swapping mechanism. Thus, ORF112 may be considered a new member of the Z-domain family having DNA binding properties similar to those of the poxvirus E3L inhibitor of interferon response.
- Basic properties of epigenetic systems: lessons from the centromerePublication . Gómez-Rodríguez, Mariluz; Jansen, Lars ETChromatin-based epigenetic inheritance cooperates with cis-acting DNA sequence information to propagate gene expression states and chromosome architecture across cell division cycles. Histone proteins and their modifications are central components of epigenetic systems but how, and to what extent, they are propagated is a matter of continued debate. Centromeric nucleosomes, marked by the histone H3 variant CENP-A, are stable across mitotic divisions and are assembled in a locus specific and cell cycle controlled manner. The mechanism of inheritance of this unique chromatin domain has important implications for how general nucleosome transmission is controlled in space and time.
- Assembly in G1 phase and long-term stability are unique intrinsic features of CENP-A nucleosomesPublication . Bodor, D. L.; Valente, L. P.; Mata, J. F.; Black, B. E.; Jansen, L. E. T.Centromeres are the site of kinetochore formation during mitosis. Centromere protein A (CENP-A), the centromere-specific histone H3 variant, is essential for the epigenetic maintenance of centromere position. Previously we showed that newly synthesized CENP-A is targeted to centromeres exclusively during early G1 phase and is subsequently maintained across mitotic divisions. Using SNAP-based fluorescent pulse labeling, we now demonstrate that cell cycle-restricted chromatin assembly at centromeres is unique to CENP-A nucleosomes and does not involve assembly of other H3 variants. Strikingly, stable retention is restricted to the CENP-A/H4 core of the nucleosome, which we find to outlast general chromatin across several cell divisions. We further show that cell cycle timing of CENP-A assembly is independent of centromeric DNA sequences and instead is mediated by the CENP-A targeting domain. Unexpectedly, this domain also induces stable transmission of centromeric nucleosomes, independent of the CENP-A deposition factor HJURP. This demonstrates that intrinsic properties of the CENP-A protein direct its cell cycle-restricted assembly and induces quantitative mitotic transmission of the CENP-A/H4 nucleosome core, ensuring long-term stability and epigenetic maintenance of centromere position.
- Q&A: Who needs a centrosome?Publication . Bettencourt-Dias, MónicaThe centrosome has several functions. The central one is as the major microtubule organizing center (MTOC) in proliferating animal cells: thus, it helps to organize the microtubules that form the mitotic spindle in dividing cells, and orchestrate a wide variety of cellular processes, including cell motility, signaling, adhesion, coordination of protein trafficking by the microtubule cytoskeleton and the acquisition of polarity. The centrosome has crucial links to the nucleus, the Golgi, cell to cell junctions and acto-myosin cytoskeleton that are very important in positioning it and thus shaping the microtubule cytoskeleton in relation to the cell and the organism (reviewed in [1]). The role of the centrosome in organizing cellular microtubules can differ from cell to cell and be regulated differently in different phases of the life of a cell.
- Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variantPublication . Earnshaw, W. C.; Allshire, R. C.; Black, B. E.; Bloom, K.; Brinkley, B. R.; Brown, W.; Cheeseman, I. M.; Choo, K. H. A.; Copenhaver, G. P.; DeLuca, J. G.; Desai, A.; Diekmann, S.; Erhardt, S.; Fitzgerald-Hayes, M.; Foltz, D.; Fukagawa, T.; Gassmann, R.; Gerlich, D. W.; Glover, D. M.; Gorbsky, G. J.; Harrison, S. C.; Heun, P.; Hirota, T.; Jansen, L. E. T.; Karpen, G.; Kops, G. J. P. L.; Lampson, M. A.; Lens, S. M.; Losada, A.; Luger, K.; Maiato, H.; Maddox, P. S.; Margolis, R. L.; Masumoto, H.; McAinsh, A. D.; Mellone, B. G.; Meraldi, P.; Musacchio, A.; Oegema, K.; O’Neill, R. J.; Salmon, E. D.; Scott, K. C.; Straight, A. F.; Stukenberg, P. T.; Sullivan, B. A.; Sullivan, K. F.; Sunkel, C. E.; Swedlow, J. R.; Walczak, C. E.; Warburton, P. E.; Westermann, S.; Willard, H. F.; Wordeman, L.; Yanagida, M.; Yen, T. J.; Yoda, K.; Cleveland, D. W.The first centromeric protein identified in any species was CENP-A, a divergent member of the histone H3 family that was recognised by autoantibodies from patients with scleroderma-spectrum disease. It has recently been suggested to rename this protein CenH3. Here, we argue that the original name should be maintained both because it is the basis of a long established nomenclature for centromere proteins and because it avoids confusion due to the presence of canonical histone H3 at centromeres.
- Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic DataPublication . Rasteiro, Rita; Chikhi, LounèsThe arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality.
- Comparative analysis of Streptococcus pneumoniae transmission in Portuguese and Finnish day-care centresPublication . Pessoa, Delphine; Hoti, Fabian; Syrjänen, Ritva; Sá-Leão, Raquel; Kaijalainen, Tarja; Gomes, M Gabriela M; Auranen, KariDay-care centre (DCC) attendees play a central role in maintaining the circulation of Streptococcus pneumoniae (pneumococcus) in the population. The prevalence of pneumococcal carriage is highest in DCC attendees but varies across countries and is found to be consistently lower in Finland than in Portugal. We compared key parameters underlying pneumococcal transmission in DCCs to understand which of these contributed to the observed differences in carriage prevalence.
- Atherogenesis May Involve the Prooxidant and Proinflammatory Effects of Ferryl HemoglobinPublication . Potor, László; Bányai, Emese; Becs, Gergely; Soares, Miguel P.; Balla, György; Balla, József; Jeney, ViktóriaOxidized cell-free hemoglobin (Hb), including covalently cross-linked Hb multimers, is present in advanced atherosclerotic lesions. Oxidation of Hb produces methemoglobin (Fe(3+)) and ferryl hemoglobin (Fe(4+) = O(2-)). Ferryl iron is unstable and can return to the Fe(3+) state by reacting with specific amino acids of the globin chains. In these reactions globin radicals are produced followed by termination reactions yielding covalently cross-linked Hb multimers. Despite the evanescent nature of the ferryl state, herein we refer to this oxidized Hb as "ferryl Hb." Our aim in this work was to study formation and biological effects of ferrylHb. We demonstrate that ferrylHb, like metHb, can release its heme group, leading to sensitization of endothelial cells (ECs) to oxidant-mediated killing and to oxidation of low-density lipoprotein (LDL). Furthermore, we observed that both oxidized LDL and lipids derived from human atherosclerotic lesions trigger Hb oxidation and subsequent production of covalently cross-linked ferrylHb multimers. Previously we showed that ferrylHb disrupts EC monolayer integrity and induces expression of inflammatory cell adhesion molecules. Here we show that when exposed to ferrylHb, EC monolayers exhibit increased permeability and enhanced monocyte adhesion. Taken together, interactions between cell-free Hb and atheroma lipids engage in a vicious cycle, amplifying oxidation of plaque lipids and Hb. These processes trigger EC activation and cytotoxicity.