TY - JOUR AB - Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry. AU - Qu, Kun AU - Glass, Bärbel AU - Doležal, Michal AU - Schur, Florian AU - Murciano, Brice AU - Rein, Alan AU - Rumlová, Michaela AU - Ruml, Tomáš AU - Kräusslich, Hans-Georg AU - Briggs, John A. G. ID - 5770 IS - 50 JF - Proceedings of the National Academy of Sciences SN - 00278424 TI - Structure and architecture of immature and mature murine leukemia virus capsids VL - 115 ER - TY - JOUR AB - Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game. AU - Avni, Guy AU - Kupferman, Orna ID - 608 JF - Theoretical Computer Science TI - Synthesis from component libraries with costs VL - 712 ER - TY - JOUR AB - Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins. AU - Miklosi, Andras AU - Del Favero, Giorgia AU - Bulat, Tanja AU - Höger, Harald AU - Shigemoto, Ryuichi AU - Marko, Doris AU - Lubec, Gert ID - 705 IS - 6 JF - Molecular Neurobiology TI - Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes VL - 55 ER - TY - JOUR AB - Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote. AU - Nishiyama, Tomoaki AU - Sakayama, Hidetoshi AU - De Vries, Jan AU - Buschmann, Henrik AU - Saint Marcoux, Denis AU - Ullrich, Kristian AU - Haas, Fabian AU - Vanderstraeten, Lisa AU - Becker, Dirk AU - Lang, Daniel AU - Vosolsobě, Stanislav AU - Rombauts, Stephane AU - Wilhelmsson, Per AU - Janitza, Philipp AU - Kern, Ramona AU - Heyl, Alexander AU - Rümpler, Florian AU - Calderón Villalobos, Luz AU - Clay, John AU - Skokan, Roman AU - Toyoda, Atsushi AU - Suzuki, Yutaka AU - Kagoshima, Hiroshi AU - Schijlen, Elio AU - Tajeshwar, Navindra AU - Catarino, Bruno AU - Hetherington, Alexander AU - Saltykova, Assia AU - Bonnot, Clemence AU - Breuninger, Holger AU - Symeonidi, Aikaterini AU - Radhakrishnan, Guru AU - Van Nieuwerburgh, Filip AU - Deforce, Dieter AU - Chang, Caren AU - Karol, Kenneth AU - Hedrich, Rainer AU - Ulvskov, Peter AU - Glöckner, Gernot AU - Delwiche, Charles AU - Petrášek, Jan AU - Van De Peer, Yves AU - Friml, Jirí AU - Beilby, Mary AU - Dolan, Liam AU - Kohara, Yuji AU - Sugano, Sumio AU - Fujiyama, Asao AU - Delaux, Pierre Marc AU - Quint, Marcel AU - Theissen, Gunter AU - Hagemann, Martin AU - Harholt, Jesper AU - Dunand, Christophe AU - Zachgo, Sabine AU - Langdale, Jane AU - Maumus, Florian AU - Van Der Straeten, Dominique AU - Gould, Sven B AU - Rensing, Stefan ID - 148 IS - 2 JF - Cell TI - The Chara genome: Secondary complexity and implications for plant terrestrialization VL - 174 ER - TY - JOUR AB - The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved. AU - Cavallari, Nicola AU - Nibau, Candida AU - Fuchs, Armin AU - Dadarou, Despoina AU - Barta, Andrea AU - Doonan, John ID - 403 IS - 6 JF - The Plant Journal TI - The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A VL - 94 ER -