miRNA profiling of human naive CD4 T cells links miR-34c-5p to cell activation and HIV replication
Cell activation is a vital step for T-cell memory/effector differentiation as well as for productive HIV infection. To identify novel regulators of this process, we used next-generation sequencing to profile changes in microRNA expression occurring in purified human naive CD4 T cells in response to TCR stimulation and/or HIV infection. Our results demonstrate, for the first time, the transcriptional up-regulation of miR-34c-5p in response to TCR stimulation in naive CD4 T cells. The induction of this miR was further consistently found to be reduced by both HIV-1 and HIV-2 infections. Overexpression of miR-34c-5p led to cha...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Amaral, A. J., Andrade, J., Foxall, R. B., Matoso, P., Matos, A. M., Soares, R. S., Rocha, C., Ramos, C. G., Tendeiro, R., Serra-Caetano, A., Guerra-Assuncao, J. A., Santa-Marta, M., Goncalves, J., Gama-Carvalho, M., Sousa, A. E. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Hippo kinases maintain polarity during directional cell migration in Caenorhabditis elegans
Precise positioning of cells is crucial for metazoan development. Despite immense progress in the elucidation of the attractive cues of cell migration, the repulsive mechanisms that prevent the formation of secondary leading edges remain less investigated. Here, we demonstrate that Caenorhabditis elegans Hippo kinases promote cell migration along the anterior–posterior body axis via the inhibition of dorsal–ventral (DV) migration. Ectopic DV polarization was also demonstrated in gain-of-function mutant animals for C. elegans RhoG MIG-2. We identified serine 139 of MIG-2 as a novel conserved Hippo kinase ph...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Feng, G., Zhu, Z., Li, W.-J., Lin, Q., Chai, Y., Dong, M.-Q., Ou, G. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation Articles Source Type: research

An RNA-binding atypical tropomyosin recruits kinesin-1 dynamically to oskar mRNPs
Localization and local translation of oskar mRNA at the posterior pole of the Drosophila oocyte directs abdominal patterning and germline formation in the embryo. The process requires recruitment and precise regulation of motor proteins to form transport-competent mRNPs. We show that the posterior-targeting kinesin-1 is loaded upon nuclear export of oskar mRNPs, prior to their dynein-dependent transport from the nurse cells into the oocyte. We demonstrate that kinesin-1 recruitment requires the DmTropomyosin1-I/C isoform, an atypical RNA-binding tropomyosin that binds directly to dimerizing oskar 3'UTRs. Finally, we show t...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Gaspar, I., Sysoev, V., Komissarov, A., Ephrussi, A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Membrane & Intracellular Transport Articles Source Type: research

Replication fork passage drives asymmetric dynamics of a critical nucleoid-associated protein in Caulobacter
In bacteria, chromosome dynamics and gene expression are modulated by nucleoid-associated proteins (NAPs), but little is known about how NAP activity is coupled to cell cycle progression. Using genomic techniques, quantitative cell imaging, and mathematical modeling, our study in Caulobacter crescentus identifies a novel NAP (GapR) whose activity over the cell cycle is shaped by DNA replication. GapR activity is critical for cellular function, as loss of GapR causes severe, pleiotropic defects in growth, cell division, DNA replication, and chromosome segregation. GapR also affects global gene expression with a chromosomal ...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Arias-Cartin, R., Dobihal, G. S., Campos, M., Surovtsev, I. V., Parry, B., Jacobs-Wagner, C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode
Mitochondrial cytochrome c oxidase (CcO) transfers electrons from cytochrome c (Cyt.c) to O2 to generate H2O, a process coupled to proton pumping. To elucidate the mechanism of electron transfer, we determined the structure of the mammalian Cyt.c–CcO complex at 2.0-Å resolution and identified an electron transfer pathway from Cyt.c to CcO. The specific interaction between Cyt.c and CcO is stabilized by a few electrostatic interactions between side chains within a small contact surface area. Between the two proteins are three water layers with a long inter-molecular span, one of which lies between the other two ...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Shimada, S., Shinzawa-Itoh, K., Baba, J., Aoe, S., Shimada, A., Yamashita, E., Kang, J., Tateno, M., Yoshikawa, S., Tsukihara, T. Tags: Membrane & Intracellular Transport, Metabolism, Structural Biology Articles Source Type: research

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters
An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/TATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analy...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: de Jonge, W. J., O'Duibhir, E., Lijnzaad, P., van Leenen, D., Groot Koerkamp, M. J., Kemmeren, P., Holstege, F. C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

The pseudophosphatase STYX targets the F-box of FBXW7 and inhibits SCFFBXW7 function
The F-box protein FBXW7 is the substrate-recruiting subunit of an SCF ubiquitin ligase and a major tumor-suppressor protein that is altered in several human malignancies. Loss of function of FBXW7 results in the stabilization of numerous proteins that orchestrate cell proliferation and survival. Little is known about proteins that directly regulate the function of this protein. In the current work, we have mapped the interactome of the enigmatic pseudophosphatase STYX. We reasoned that a catalytically inactive phosphatase might have adopted novel mechanisms of action. The STYX interactome contained several F-box proteins, ...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Reiterer, V., Figueras-Puig, C., Le Guerroue, F., Confalonieri, S., Vecchi, M., Jalapothu, D., Kanse, S. M., Deshaies, R. J., Di Fiore, P. P., Behrends, C., Farhan, H. Tags: Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Hypoxia-inducible factors: coupling glucose metabolism and redox regulation with induction of the breast cancer stem cell phenotype
Reduced oxygen availability (hypoxia) leads to increased production of reactive oxygen species (ROS) by the electron transport chain. Here, I review recent work delineating mechanisms by which hypoxia-inducible factor 1 (HIF-1) mediates adaptive metabolic responses to hypoxia, including increased flux through the glycolytic pathway and decreased flux through the tricarboxylic acid cycle, in order to decrease mitochondrial ROS production. HIF-1 also mediates increased flux through the serine synthesis pathway and mitochondrial one-carbon (folate cycle) metabolism to increase mitochondrial antioxidant production (NADPH and g...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Semenza, G. L. Tags: Cancer, Metabolism Review Source Type: research

Brief encounters of cytochrome c
Transient protein interactions are paramount to life where fast and efficient transfer of information and cargo are often integral to pathways and networks. However, complexes formed by transient protein interactions are often times resistant to direct structural characterization due to their inherent, dynamic nature, so our knowledge to date typically derives from biochemical, biophysical and computational methods. In this issue, Shimada and co-authors present the crystal structure of the mammalian cytochrome c oxidase in complex with its electron donor cytochrome c, identifying a new class of protein–protein intera...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Lyons, J. A., Nissen, P. Tags: Membrane & Intracellular Transport, Metabolism, Structural Biology News [amp ] Views Source Type: research

TFIID or not TFIID, a continuing transcriptional SAGA
Eukaryotic protein-coding genes are typically classified into two groups: those with expression regulated by specific signals versus the relatively constant "housekeeping" genes. Although these differences are associated with alternative modes of RNA polymerase II (RNAP II) pre-initiation complex (PIC) assembly, a role for gene-specific activators in controlling "regulatability" has been difficult to rule out. To address this question, de Jonge et al (2017) studied a group of genes controlled by a common activator but dependent on either TFIID or SAGA and found that the magnitude of regulation stro...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Kubik, S., Bruzzone, M. J., Shore, D. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription News [amp ] Views Source Type: research

Global snapshots of bacterial RNA networks
While bacteria were long thought to rely primarily on transcriptional control, it is now well established that they also use numerous small RNAs to regulate mRNA translation and stability. There has recently been a surge in studies, including one by Waters et al (2017) in this issue of The EMBO Journal, that have used clever variations of the RNA-seq technique to comprehensively map small RNA–target networks. (Source: EMBO Journal)
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Hör, J., Vogel, J. Tags: Methods & Resources, Microbiology, Virology & Host Pathogen Interaction, RNA Biology News [amp ] Views Source Type: research

mGluR long-term depression regulates GluA2 association with COPII vesicles and exit from the endoplasmic reticulum
mGluR long-term depression (mGluR-LTD) is a form of synaptic plasticity induced at excitatory synapses by metabotropic glutamate receptors (mGluRs). mGluR-LTD reduces synaptic strength and is relevant to learning and memory, autism, and sensitization to cocaine; however, the mechanism is not known. Here we show that activation of Group I mGluRs in medium spiny neurons induces trafficking of GluA2 from the endoplasmic reticulum (ER) to the synapse by enhancing GluA2 binding to essential COPII vesicle proteins, Sec23 and Sec13. GluA2 exit from the ER further depends on IP3 and Ryanodine receptor-controlled Ca2+ release as we...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Pick, J. E., Khatri, L., Sathler, M. F., Ziff, E. B. Tags: Neuroscience Articles Source Type: research

Unloading of homologous recombination factors is required for restoring double-stranded DNA at damage repair loci
Cells use homology-dependent DNA repair to mend chromosome breaks and restore broken replication forks, thereby ensuring genome stability and cell survival. DNA break repair via homology-based mechanisms involves nuclease-dependent DNA end resection, which generates long tracts of single-stranded DNA required for checkpoint activation and loading of homologous recombination proteins Rad52/51/55/57. While recruitment of the homologous recombination machinery is well characterized, it is not known how its presence at repair loci is coordinated with downstream re-synthesis of resected DNA. We show that Rad51 inhibits recruitm...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Vasianovich, Y., Altmannova, V., Kotenko, O., Newton, M. D., Krejci, L., Makovets, S. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Negative regulation of type I IFN signaling by phosphorylation of STAT2 on T387
The transcription factor ISGF3, comprised of IRF9 and tyrosine-phosphorylated STATs 1 and 2, transmits the signal from the type I interferon receptor to the genome. We have discovered a novel phosphorylation of STAT2 on T387 that negatively regulates this response. In most untreated cell types, the majority of STAT2 is phosphorylated on T387 constitutively. In response to interferon-β, the T387A mutant of STAT2 is much more effective than wild-type STAT2 in mediating the expression of many interferon-stimulated genes, in protecting cells against virus infection, and in inhibiting cell growth. Interferon-β-tr...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Wang, Y., Nan, J., Willard, B., Wang, X., Yang, J., Stark, G. R. Tags: Signal Transduction Articles Source Type: research

Endothelial basement membrane laminin 511 is essential for shear stress response
Shear detection and mechanotransduction by arterial endothelium requires junctional complexes containing PECAM-1 and VE-cadherin, as well as firm anchorage to the underlying basement membrane. While considerable information is available for junctional complexes in these processes, gained largely from in vitro studies, little is known about the contribution of the endothelial basement membrane. Using resistance artery explants, we show that the integral endothelial basement membrane component, laminin 511 (laminin α5), is central to shear detection and mechanotransduction and its elimination at this site results ...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Di Russo, J., Luik, A.-L., Yousif, L., Budny, S., Oberleithner, H., Hofschröer, V., Klingauf, J., van Bavel, E., Bakker, E. N., Hellstrand, P., Bhattachariya, A., Albinsson, S., Pincet, F., Hallmann, R., Sorokin, L. M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Vascular Biology & Angiogenesis Articles Source Type: research

Hair follicle stem cell cultures reveal self-organizing plasticity of stem cells and their progeny
Understanding how complex tissues are formed, maintained, and regenerated through local growth, differentiation, and remodeling requires knowledge on how single-cell behaviors are coordinated on the population level. The self-renewing hair follicle, maintained by a distinct stem cell population, represents an excellent paradigm to address this question. A major obstacle in mechanistic understanding of hair follicle stem cell (HFSC) regulation has been the lack of a culture system that recapitulates HFSC behavior while allowing their precise monitoring and manipulation. Here, we establish an in vitro culture system bas...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Chacon-Martinez, C. A., Klose, M., Niemann, C., Glauche, I., Wickström, S. A. Tags: Development & Differentiation, Stem Cells, Systems & Computational Biology Articles Source Type: research

VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy
Rupture of endosomes and lysosomes is a major cellular stress condition leading to cell death and degeneration. Here, we identified an essential role for the ubiquitin-directed AAA-ATPase, p97, in the clearance of damaged lysosomes by autophagy. Upon damage, p97 translocates to lysosomes and there cooperates with a distinct set of cofactors including UBXD1, PLAA, and the deubiquitinating enzyme YOD1, which we term ELDR components for Endo-Lysosomal Damage Response. Together, they act downstream of K63-linked ubiquitination and p62 recruitment, and selectively remove K48-linked ubiquitin conjugates from a subpopulation of d...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Papadopoulos, C., Kirchner, P., Bug, M., Grum, D., Koerver, L., Schulze, N., Poehler, R., Dressler, A., Fengler, S., Arhzaouy, K., Lux, V., Ehrmann, M., Weihl, C. C., Meyer, H. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Maintaining hair follicle stem cell identity in a dish
Identifying and mimicking the signals that regulate stem cell self-renewal, differentiation and maintenance in a petri dish is crucial to faithfully recapitulate stem cell behaviour in vitro. In this issue, Chacón-Martínez et al (2017) describe novel culture conditions that allow the long-term expansion and maintenance of functional murine hair follicle stem cells. This exciting discovery provides a faithful platform to study hair follicle stem cells in vitro and potentially perform drug screening for skin and hair follicle disorders. (Source: EMBO Journal)
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Sanchez-Danes, A., Blanpain, C. Tags: Development & Differentiation, Stem Cells, Systems & Computational Biology News [amp ] Views Source Type: research

Removing the waste bags: how p97 drives autophagy of lysosomes
Removal of ruptured lysosomes by autophagy is one of the mechanisms by which cells alleviate detrimental consequences of lysosome leakage and may prevent the initiation of signaling cascades that lead to cell death. In this issue of The EMBO Journal, Papadopoulos et al (2017) report an essential role of p97 and its cofactors in autophagic clearance of damaged lysosomes and provide evidences for the relevance of p97 in neurodegenerative conditions. (Source: EMBO Journal)
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Seczynska, M., Dikic, I. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Aryl hydrocarbon receptor is required for optimal B-cell proliferation
The aryl hydrocarbon receptor (AhR), a transcription factor known for mediating xenobiotic toxicity, is expressed in B cells, which are known targets for environmental pollutants. However, it is unclear what the physiological functions of AhR in B cells are. We show here that expression of Ahr in B cells is up-regulated upon B-cell receptor (BCR) engagement and IL-4 treatment. Addition of a natural ligand of AhR, FICZ, induces AhR translocation to the nucleus and transcription of the AhR target gene Cyp1a1, showing that the AhR pathway is functional in B cells. AhR-deficient (Ahr–/–) B cells proliferate less th...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Villa, M., Gialitakis, M., Tolaini, M., Ahlfors, H., Henderson, C. J., Wolf, C. R., Brink, R., Stockinger, B. Tags: Immunology Articles Source Type: research

IL-1 signaling is critical for expansion but not generation of autoreactive GM-CSF+ Th17 cells
Interleukin-1 (IL-1) is implicated in numerous pathologies, including multiple sclerosis and its animal model experimental autoimmune encephalomyelitis (EAE). However, the exact mechanism by which IL-1 is involved in the generation of pathogenic T cells and in disease development remains largely unknown. We found that following EAE induction, pertussis toxin administration leads to IL-1 receptor type 1 (IL-1R1)-dependent IL-1β expression by myeloid cells in the draining lymph nodes. This myeloid-derived IL-1β did not vitally contribute to the generation and plasticity of Th17 cells, but rather promoted the expans...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Mufazalov, I. A., Schelmbauer, C., Regen, T., Kuschmann, J., Wanke, F., Gabriel, L. A., Hauptmann, J., Müller, W., Pinteaux, E., Kurschus, F. C., Waisman, A. Tags: Immunology Articles Source Type: research

Stabilization of the metaphase spindle by Cdc14 is required for recombinational DNA repair
Cells are constantly threatened by multiple sources of genotoxic stress that cause DNA damage. To maintain genome integrity, cells have developed a coordinated signalling network called DNA damage response (DDR). While multiple kinases have been thoroughly studied during DDR activation, the role of protein dephosphorylation in the damage response remains elusive. Here, we show that the phosphatase Cdc14 is essential to fulfil recombinational DNA repair in budding yeast. After DNA double-strand break (DSB) generation, Cdc14 is transiently released from the nucleolus and activated. In this state, Cdc14 targets the spindle po...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Villoria, M. T., Ramos, F., Duenas, E., Faull, P., Cutillas, P. R., Clemente-Blanco, A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

Gata6 promotes hair follicle progenitor cell renewal by genome maintenance during proliferation
Cell proliferation is essential to rapid tissue growth and repair, but can result in replication-associated genome damage. Here, we implicate the transcription factor Gata6 in adult mouse hair follicle regeneration where it controls the renewal of rapidly proliferating epithelial (matrix) progenitors and hence the extent of production of terminally differentiated lineages. We find that Gata6 protects against DNA damage associated with proliferation, thus preventing cell cycle arrest and apoptosis. Furthermore, we show that in vivo Gata6 stimulates EDA-receptor signaling adaptor Edaradd level and NF-B pathway activatio...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Wang, A. B., Zhang, Y. V., Tumbar, T. Tags: Development & Differentiation, DNA Replication, Repair & Recombination, Stem Cells Articles Source Type: research

Dedicated SNAREs and specialized TRIM cargo receptors mediate secretory autophagy
Autophagy is a process delivering cytoplasmic components to lysosomes for degradation. Autophagy may, however, play a role in unconventional secretion of leaderless cytosolic proteins. How secretory autophagy diverges from degradative autophagy remains unclear. Here we show that in response to lysosomal damage, the prototypical cytosolic secretory autophagy cargo IL-1β is recognized by specialized secretory autophagy cargo receptor TRIM16 and that this receptor interacts with the R-SNARE Sec22b to recruit cargo to the LC3-II+ sequestration membranes. Cargo secretion is unaffected by downregulation of syntaxin 17, a SN...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Kimura, T., Jia, J., Kumar, S., Choi, S. W., Gu, Y., Mudd, M., Dupont, N., Jiang, S., Peters, R., Farzam, F., Jain, A., Lidke, K. A., Adams, C. M., Johansen, T., Deretic, V. Tags: Autophagy & Cell Death, Immunology, Membrane & Intracellular Transport Articles Source Type: research

Polarized cortical tension drives zebrafish epiboly movements
The principles underlying the biomechanics of morphogenesis are largely unknown. Epiboly is an essential embryonic event in which three tissues coordinate to direct the expansion of the blastoderm. How and where forces are generated during epiboly, and how these are globally coupled remains elusive. Here we developed a method, hydrodynamic regression (HR), to infer 3D pressure fields, mechanical power, and cortical surface tension profiles. HR is based on velocity measurements retrieved from 2D+T microscopy and their hydrodynamic modeling. We applied HR to identify biomechanically active structures and changes in cortex lo...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Hernandez-Vega, A., Marsal, M., Pouille, P.-A., Tosi, S., Colombelli, J., Luque, T., Navajas, D., Pagonabarraga, I., Martin-Blanco, E. Tags: Development & Differentiation, Systems & Computational Biology Articles Source Type: research

Prostaglandin E2 promotes intestinal repair through an adaptive cellular response of the epithelium
Adaptive cellular responses are often required during wound repair. Following disruption of the intestinal epithelium, wound-associated epithelial (WAE) cells form the initial barrier over the wound. Our goal was to determine the critical factor that promotes WAE cell differentiation. Using an adaptation of our in vitro primary epithelial cell culture system, we found that prostaglandin E2 (PGE2) signaling through one of its receptors, Ptger4, was sufficient to drive a differentiation state morphologically and transcriptionally similar to in vivo WAE cells. WAE cell differentiation was a permanent state and domin...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Miyoshi, H., VanDussen, K. L., Malvin, N. P., Ryu, S. H., Wang, Y., Sonnek, N. M., Lai, C.-W., Stappenbeck, T. S. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells Articles Source Type: research

The Wae to repair: prostaglandin E2 (PGE2) triggers intestinal wound repair
Accurate wound repair is a crucial step to protect organisms from environmental damage, for example infection and toxin exposure. In this issue of The EMBO Journal, Miyoshi et al (2017) have elucidated a new mechanism underpinning this process within the intestine where mesenchymal prostaglandin E2 produced following damage drives intestinal regeneration. (Source: EMBO Journal)
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Jackstadt, R., Sansom, O. J. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells News [amp ] Views Source Type: research

Stefan Jentsch (1955-2016)--Maestro of the ubiquitin family
(Source: EMBO Journal)
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Hoppe, T., Branzei, D. Tags: Obituary Source Type: research

Seipin regulates ER-lipid droplet contacts and cargo delivery
Seipin is an endoplasmic reticulum (ER) membrane protein implicated in lipid droplet (LD) biogenesis and mutated in severe congenital lipodystrophy (BSCL2). Here, we show that seipin is stably associated with nascent ER–LD contacts in human cells, typically via one mobile focal point per LD. Seipin appears critical for such contacts since ER–LD contacts were completely missing or morphologically aberrant in seipin knockout and BSCL2 patient cells. In parallel, LD mobility was increased and protein delivery from the ER to LDs to promote LD growth was decreased. Moreover, while growing LDs normally acquire lipid ...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Salo, V. T., Belevich, I., Li, S., Karhinen, L., Vihinen, H., Vigouroux, C., Magre, J., Thiele, C., Hölttä-Vuori, M., Jokitalo, E., Ikonen, E. Tags: Membrane & Intracellular Transport Articles Source Type: research

Cohesin acetylation and Wapl-Pds5 oppositely regulate translocation of cohesin along DNA
This study provides insight into the nature of individual cohesin dynamics and the mechanisms by which cohesin achieves cohesion in different chromatin contexts. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Kanke, M., Tahara, E., Huis in't Veld, P. J., Nishiyama, T. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

Rapid movement and transcriptional re-localization of human cohesin on DNA
The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA. It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three-dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown. Here, we used single-molecule imaging to show that cohesin can diffuse rapidly on DNA i...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Davidson, I. F., Goetz, D., Zaczek, M. P., Molodtsov, M. I., Huis in 't Veld, P. J., Weissmann, F., Litos, G., Cisneros, D. A., Ocampo-Hafalla, M., Ladurner, R., Uhlmann, F., Vaziri, A., Peters, J.-M. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

Bimodal behaviour of interfollicular epidermal progenitors regulated by hair follicle position and cycling
Interfollicular epidermal (IFE) homeostasis is a major physiological process allowing maintenance of the skin barrier function. Despite progress in our understanding of stem cell populations in different hair follicle compartments, cellular mechanisms of IFE maintenance, in particular, whether a hierarchy of progenitors exists within this compartment, have remained controversial. We here used multicolour lineage tracing with Brainbow transgenic labels activated in the epidermis to track individual keratinocyte clones. Two modes of clonal progression could be observed in the adult murine dorsal skin. Clones attached to hair...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Roy, E., Neufeld, Z., Cerone, L., Wong, H. Y., Hodgson, S., Livet, J., Khosrotehrani, K. Tags: Development & Differentiation, Stem Cells, Systems & Computational Biology Articles Source Type: research

The diverse and expanding role of mass spectrometry in structural and molecular biology
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen–deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology in...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Lössl, P., van de Waterbeemd, M., Heck, A. J. Tags: Methods & Resources, Post-translational Modifications, Proteolysis & Proteomics, Transcription Review Source Type: research

Zika virus NS1, a pathogenicity factor with many faces
Recent publications in The EMBO Journal (Xu et al, 2016) and in Nature Structural & Molecular Biology (Brown et al, 2016) report crystal structures of the Zika virus (ZIKV) NS1 protein. The structures reveal unique surface properties that help explain the specificity of anti-ZIKV NS1 antibodies. Possible functions of this multifaceted pathogenicity factor are discussed here on the basis of the structures and cautious extrapolation from other flaviviruses. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Hilgenfeld, R. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology News [amp ] Views Source Type: research

Bimodal skin progenitors--a matter of place and time
The skin carries out specialist functions such as barrier formation and thermoregulation. The mode of cellular replenishment of the surface epithelium that forms the outermost layer during steady-state homeostasis is a subject of intensive investigations. A detailed analysis of the interfollicular epidermis reported in this issue of The EMBO Journal (Roy et al, 2016) reveals that hair follicles in their growth phase influence cellular behaviour of epithelial cells in their immediate proximity. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Ulyanchenko, S., Jensen, K. B. Tags: Development & Differentiation, Stem Cells, Systems & Computational Biology News [amp ] Views Source Type: research

Susan Lee Lindquist (1949-2016)--pioneer in the study of cellular protein folding and disease
(Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Hartl, F.-U. Tags: Obituary Source Type: research

Preprint Deja Vu
Twenty-five years ago, in August 1991, I spent a couple of afternoons at Los Alamos National Laboratory writing some simple software that enabled a small group of physicists to share drafts of their articles via automated email transactions with a central repository. Within a few years, the site migrated to the nascent WorldWideWeb as arXiv.org, and experienced both expansion in coverage and heavy growth in usage that continues to this day. In 1998, I gave a talk to a group of biologists—including David Lipman, Pat Brown, and Michael Eisen—at a meeting at Cold Spring Harbor Laboratory (CSHL) to describe th...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Ginsparg, P. Tags: Commentary Source Type: research

Preparing for Preprints
Preprints reduce delays in sharing research results and increase the amount and diversity of data available to the scientific community. Support of this communication mechanism through appropriate policies by journals, funders and institutions will encourage community engagement. Widespread adoption would benefit both individual scientists and research, and it might improve publishing in scientific journals. Preprints are one step towards an Open Science future. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Pulverer, B. Tags: Editorial Source Type: research

Sulfatase modifying factor 1 trafficking through the cells: from endoplasmic reticulum to the endoplasmic reticulum
(Source: EMBO Journal)
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Zito, E., Buono, M., Pepe, S., Settembre, C., Annunziata, I., Surace, E. M., Dierks, T., Monti, M., Cozzolino, M., Pucci, P., Ballabio, A., Cosma, M. P. Tags: Corrigendum Source Type: research

A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit {beta}5i
Inhibition of the immunoproteasome subunit β5i alleviates autoimmune diseases in preclinical studies and represents a promising new anti-inflammatory therapy. However, the lack of structural data on the human immunoproteasome still hampers drug design. Here, we systematically determined the potency of seven α' β' epoxyketone inhibitors with varying N-caps and P3-stereochemistry for mouse/human β5c/β5i and found pronounced differences in their subunit and species selectivity. Using X-ray crystallography, the compounds were analyzed for their modes of binding to chimeric yeast proteasomes that incor...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Huber, E. M., Heinemeyer, W., de Bruin, G., Overkleeft, H. S., Groll, M. Tags: Chemical Biology, Post-translational Modifications, Proteolysis & Proteomics Resource Source Type: research

The MMS22L-TONSL heterodimer directly promotes RAD51-dependent recombination upon replication stress
Homologous recombination (HR) is a key pathway that repairs DNA double-strand breaks (DSBs) and helps to restart stalled or collapsed replication forks. How HR supports replication upon genotoxic stress is not understood. Using in vivo and in vitro approaches, we show that the MMS22L–TONSL heterodimer localizes to replication forks under unperturbed conditions and its recruitment is increased during replication stress in human cells. MMS22L–TONSL associates with replication protein A (RPA)-coated ssDNA, and the MMS22L subunit directly interacts with the strand exchange protein RAD51. MMS22L is require...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Piwko, W., Mlejnkova, L. J., Mutreja, K., Ranjha, L., Stafa, D., Smirnov, A., Brodersen, M. M., Zellweger, R., Sturzenegger, A., Janscak, P., Lopes, M., Peter, M., Cejka, P. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

CLPP coordinates mitoribosomal assembly through the regulation of ERAL1 levels
Despite being one of the most studied proteases in bacteria, very little is known about the role of ClpXP in mitochondria. We now present evidence that mammalian CLPP has an essential role in determining the rate of mitochondrial protein synthesis by regulating the level of mitoribosome assembly. Through a proteomic approach and the use of a catalytically inactive CLPP, we produced the first comprehensive list of possible mammalian ClpXP substrates involved in the regulation of mitochondrial translation, oxidative phosphorylation, and a number of metabolic pathways. We further show that the defect in mitoribosomal assembly...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Szczepanowska, K., Maiti, P., Kukat, A., Hofsetz, E., Nolte, H., Senft, K., Becker, C., Ruzzenente, B., Hornig-Do, H.-T., Wibom, R., Wiesner, R. J., Krüger, M., Trifunovic, A. Tags: Metabolism, Post-translational Modifications, Proteolysis & Proteomics, Protein Biosynthesis & Quality Control Articles Source Type: research

RKIP and TBK1 form a positive feedback loop to promote type I interferon production in innate immunity
This study reveals a previously unrecognized positive feedback loop between RKIP and TBK1 that is essential for type I interferon production in anti-viral innate immunity. (Source: EMBO Journal)
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Gu, M., Liu, Z., Lai, R., Liu, S., Lin, W., Ouyang, C., Ye, S., Huang, H., Wang, X. Tags: Immunology Articles Source Type: research

Hair cell synaptic dysfunction, auditory fatigue and thermal sensitivity in otoferlin Ile515Thr mutants
The multi-C2 domain protein otoferlin is required for hearing and mutated in human deafness. Some OTOF mutations cause a mild elevation of auditory thresholds but strong impairment of speech perception. At elevated body temperature, hearing is lost. Mice homozygous for one of these mutations, OtofI515T/I515T, exhibit a moderate hearing impairment involving enhanced adaptation to continuous or repetitive sound stimulation. In OtofI515T/I515T inner hair cells (IHCs), otoferlin levels are diminished by 65%, and synaptic vesicles are enlarged. Exocytosis during prolonged stimulation is strongly reduced. This indicates that oto...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Strenzke, N., Chakrabarti, R., Al-Moyed, H., Müller, A., Hoch, G., Pangrsic, T., Yamanbaeva, G., Lenz, C., Pan, K.-T., Auge, E., Geiss-Friedlander, R., Urlaub, H., Brose, N., Wichmann, C., Reisinger, E. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Inactivation of the type I interferon pathway reveals long double-stranded RNA-mediated RNA interference in mammalian cells
RNA interference (RNAi) elicited by long double-stranded (ds) or base-paired viral RNA constitutes the major mechanism of antiviral defence in plants and invertebrates. In contrast, it is controversial whether it acts in chordates. Rather, in vertebrates, viral RNAs induce a distinct defence system known as the interferon (IFN) response. Here, we tested the possibility that the IFN response masks or inhibits antiviral RNAi in mammalian cells. Consistent with that notion, we find that sequence-specific gene silencing can be triggered by long dsRNAs in differentiated mouse cells rendered deficient in components of the IFN pa...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Maillard, P. V., Van der Veen, A. G., Deddouche-Grass, S., Rogers, N. C., Merits, A., Reis e Sousa, C. Tags: Immunology, RNA Biology Articles Source Type: research

What's hot about otoferlin
Mutations in the otoferlin (OTOF) gene lead to profound hearing loss in humans. Interestingly, a number of missense otoferlin mutations cause hearing defects but only at higher body temperature, and the reasons for this have been elusive until now. A study published in this issue of The EMBO Journal (Strenzke et al, 2016) adds insight into the underlying mechanisms for this heat-dependent hearing loss. (Source: EMBO Journal)
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Avraham, K. B. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

Present and not reporting for duty: dsRNAi in mammalian cells
Double-stranded RNA interference (dsRNAi) represents a primary means of anti-viral defense in plants, worms, and insects, yet appears mostly supplanted by the protein-based interferon (IFN) response in vertebrates such as mammals. The degree to which dsRNAi is anti-viral in mammals has been contentious. Maillard et al (2016) find that dsRNAi retains sequence-specific silencing in mammalian cells incapable of triggering an IFN response, suggesting that dsRNAi is inhibited by the action of interferon-stimulated genes. Importantly, they observe that while dsRNA can "vaccinate" against the incoming cognate ...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Luna, J. M., Wu, X., Rice, C. M. Tags: Immunology, RNA Biology News [amp ] Views Source Type: research

A pH- and ionic strength-dependent conformational change in the neck region regulates DNGR-1 function in dendritic cells
DNGR-1 is receptor expressed by certain dendritic cell (DC) subsets and by DC precursors in mouse. It possesses a C-type lectin-like domain (CTLD) followed by a poorly characterized neck region coupled to a transmembrane region and short intracellular tail. The CTLD of DNGR-1 binds F-actin exposed by dead cell corpses and causes the receptor to signal and potentiate cross-presentation of dead cell-associated antigens by DCs. Here, we describe a conformational change that occurs in the neck region of DNGR-1 in a pH- and ionic strength-dependent manner and that controls cross-presentation of dead cell-associated antigens. We...
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Hanc, P., Schulz, O., Fischbach, H., Martin, S. R., Kjaer, S., Reis e Sousa, C. Tags: Immunology Articles Source Type: research

Chm7 and Heh1 collaborate to link nuclear pore complex quality control with nuclear envelope sealing
The integrity of the nuclear envelope barrier relies on membrane remodeling by the ESCRTs, which seal nuclear envelope holes and contribute to the quality control of nuclear pore complexes (NPCs); whether these processes are mechanistically related remains poorly defined. Here, we show that the ESCRT-II/III chimera, Chm7, is recruited to a nuclear envelope subdomain that expands upon inhibition of NPC assembly and is required for the formation of the storage of improperly assembled NPCs (SINC) compartment. Recruitment to sites of NPC assembly is mediated by its ESCRT-II domain and the LAP2-emerin-MAN1 (LEM) family of integ...
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Webster, B. M., Thaller, D. J., Jäger, J., Ochmann, S. E., Borah, S., Lusk, C. P. Tags: Membrane & Intracellular Transport Articles Source Type: research

Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters
Mediator is a conserved, essential transcriptional coactivator complex, but its in vivo functions have remained unclear due to conflicting data regarding its genome-wide binding pattern obtained by genome-wide ChIP. Here, we used ChEC-seq, a method orthogonal to ChIP, to generate a high-resolution map of Mediator binding to the yeast genome. We find that Mediator associates with upstream activating sequences (UASs) rather than the core promoter or gene body under all conditions tested. Mediator occupancy is surprisingly correlated with transcription levels at only a small fraction of genes. Using the same approach to ...
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Grünberg, S., Henikoff, S., Hahn, S., Zentner, G. E. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research