Redox regulation of SUMO enzymes is required for ATM activity and survival in oxidative stress
To sense and defend against oxidative stress, cells depend on signal transduction cascades involving redox-sensitive proteins. We previously identified SUMO (small ubiquitin-related modifier) enzymes as downstream effectors of reactive oxygen species (ROS). Hydrogen peroxide transiently inactivates SUMO E1 and E2 enzymes by inducing a disulfide bond between their catalytic cysteines. How important their oxidation is in light of many other redox-regulated proteins has however been unclear. To selectively disrupt this redox switch, we identified a catalytically fully active SUMO E2 enzyme variant (Ubc9 D100A) with strongly r...
Source: EMBO Journal - June 13, 2016 Category: Molecular Biology Authors: Stankovic-Valentin, N., Drzewicka, K., König, C., Schiebel, E., Melchior, F. Tags: DNA Replication, Repair & Recombination, Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm
Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited differential DNA methylation affects de novo targeting of chromatin modifiers in the early endosperm. Our data reveal that polycomb-mediated H3 lysine 27 trimethylation (H3K27me3) is preferentially localized to regions that are targeted by the DNA glycosylase DEMETER (DME), mechanistically linking DNA hypomethy...
Source: EMBO Journal - June 13, 2016 Category: Molecular Biology Authors: Moreno-Romero, J., Jiang, H., Santos-Gonzalez, J., Köhler, C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology Articles Source Type: research

Loss of C9ORF72 impairs autophagy and synergizes with polyQ Ataxin-2 to induce motor neuron dysfunction and cell death
An intronic expansion of GGGGCC repeats within the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). Ataxin-2 with intermediate length of polyglutamine expansions (Ataxin-2 Q30x) is a genetic modifier of the disease. Here, we found that C9ORF72 forms a complex with the WDR41 and SMCR8 proteins to act as a GDP/GTP exchange factor for RAB8a and RAB39b and to thereby control autophagic flux. Depletion of C9orf72 in neurons partly impairs autophagy and leads to accumulation of aggregates of TDP-43 and P62 proteins, which are histopathological hallmarks of ALS-...
Source: EMBO Journal - June 13, 2016 Category: Molecular Biology Authors: Sellier, C., Campanari, M.-L., Julie Corbier, C., Gaucherot, A., Kolb-Cheynel, I., Oulad-Abdelghani, M., Ruffenach, F., Page, A., Ciura, S., Kabashi, E., Charlet-Berguerand, N. Tags: Neuroscience Articles Source Type: research

Higher-order oligomerization promotes localization of SPOP to liquid nuclear speckles
Membrane-less organelles in cells are large, dynamic protein/protein or protein/RNA assemblies that have been reported in some cases to have liquid droplet properties. However, the molecular interactions underlying the recruitment of components are not well understood. Herein, we study how the ability to form higher-order assemblies influences the recruitment of the speckle-type POZ protein (SPOP) to nuclear speckles. SPOP, a cullin-3-RING ubiquitin ligase (CRL3) substrate adaptor, self-associates into higher-order oligomers; that is, the number of monomers in an oligomer is broadly distributed and can be large. While wild...
Source: EMBO Journal - June 13, 2016 Category: Molecular Biology Authors: Marzahn, M. R., Marada, S., Lee, J., Nourse, A., Kenrick, S., Zhao, H., Ben-Nissan, G., Kolaitis, R.-M., Peters, J. L., Pounds, S., Errington, W. J., Prive, G. G., Taylor, J. P., Sharon, M., Schuck, P., Ogden, S. K., Mittag, T. Tags: Post-translational Modifications, Proteolysis & Proteomics, Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

Lost & found: C9ORF72 and the autophagy pathway in ALS/FTD
C9ORF72 expression is reduced in a substantial number of patients with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which may contribute to disease pathogenesis. However, its normal molecular function remains unknown. In this issue of The EMBO Journal, Sellier et al (2016) identified a novel protein complex consisting of C9ORF72, WDR41, and SMCR8 that acts as a GDP-GTP exchange factor (GEF) for RAB8a and RAB39b and is regulated by TBK1, whose partial loss of function also causes ALS and FTD. They further reveal a potential modulatory role for this novel complex in macroautophagy (autophagy), ...
Source: EMBO Journal - June 13, 2016 Category: Molecular Biology Authors: Almeida, S., Gao, F.-B. Tags: Neuroscience News [amp ] Views Source Type: research

Presynaptic inhibition upon CB1 or mGlu2/3 receptor activation requires ERK/MAPK phosphorylation of Munc18-1
Presynaptic cannabinoid (CB1R) and metabotropic glutamate receptors (mGluR2/3) regulate synaptic strength by inhibiting secretion. Here, we reveal a presynaptic inhibitory pathway activated by extracellular signal-regulated kinase (ERK) that mediates CB1R- and mGluR2/3-induced secretion inhibition. This pathway is triggered by a variety of events, from foot shock-induced stress to intense neuronal activity, and induces phosphorylation of the presynaptic protein Munc18-1. Mimicking constitutive phosphorylation of Munc18-1 results in a drastic decrease in synaptic transmission. ERK-mediated phosphorylation of Munc18-1 ultima...
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: Schmitz, S. K., King, C., Kortleven, C., Huson, V., Kroon, T., Kevenaar, J. T., Schut, D., Saarloos, I., Hoetjes, J. P., de Wit, H., Stiedl, O., Spijker, S., Li, K. W., Mansvelder, H. D., Smit, A. B., Cornelisse, L. N., Verhage, M., Toonen, R. F. Tags: Neuroscience Articles Source Type: research

The retinal pigment epithelium as a gateway for monocyte trafficking into the eye
The choroid plexus epithelium within the brain ventricles orchestrates blood-derived monocyte entry to the central nervous system under injurious conditions, including when the primary injury site is remote from the brain. Here, we hypothesized that the retinal pigment epithelium (RPE) serves a parallel role, as a gateway for monocyte trafficking to the retina following direct or remote injury. We found elevated expression of genes encoding leukocyte trafficking determinants in mouse RPE as a consequence of retinal glutamate intoxication or optic nerve crush (ONC). Blocking VCAM-1 after ONC interfered with monocyte infiltr...
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: Benhar, I., Reemst, K., Kalchenko, V., Schwartz, M. Tags: Neuroscience Articles Source Type: research

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity
TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N-terminal portion which comprises a canonical RING domain, one or two B-box domains and a coiled-coil region that mediates ligase dimerization. Self-association via the coiled-coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and sh...
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: Koliopoulos, M. G., Esposito, D., Christodoulou, E., Taylor, I. A., Rittinger, K. Tags: Post-translational Modifications, Proteolysis & Proteomics, Structural Biology Articles Source Type: research

miRISC and the CCR4-NOT complex silence mRNA targets independently of 43S ribosomal scanning
miRNAs associate with Argonaute (AGO) proteins to silence the expression of mRNA targets by inhibiting translation and promoting deadenylation, decapping, and mRNA degradation. A current model for silencing suggests that AGOs mediate these effects through the sequential recruitment of GW182 proteins, the CCR4–NOT deadenylase complex and the translational repressor and decapping activator DDX6. An alternative model posits that AGOs repress translation by interfering with eIF4A function during 43S ribosomal scanning and that this mechanism is independent of GW182 and the CCR4–NOT complex in Drosophila melanogaste...
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: Kuzuoglu-Öztürk, D., Bhandari, D., Huntzinger, E., Fauser, M., Helms, S., Izaurralde, E. Tags: Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Tyrosination of {alpha}-tubulin controls the initiation of processive dynein-dynactin motility
Post-translational modifications (PTMs) of α/β-tubulin are believed to regulate interactions with microtubule-binding proteins. A well-characterized PTM involves in the removal and re-ligation of the C-terminal tyrosine on α-tubulin, but the purpose of this tyrosination–detyrosination cycle remains elusive. Here, we examined the processive motility of mammalian dynein complexed with dynactin and BicD2 (DDB) on tyrosinated versus detyrosinated microtubules. Motility was decreased ~fourfold on detyrosinated microtubules, constituting the largest effect of a tubulin PTM on motor function observed to dat...
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: McKenney, R. J., Huynh, W., Vale, R. D., Sirajuddin, M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

Rac1-Rab11-FIP3 regulatory hub coordinates vesicle traffic with actin remodeling and T-cell activation
The immunological synapse generation and function is the result of a T-cell polarization process that depends on the orchestrated action of the actin and microtubule cytoskeleton and of intracellular vesicle traffic. However, how these events are coordinated is ill defined. Since Rab and Rho families of GTPases control intracellular vesicle traffic and cytoskeleton reorganization, respectively, we investigated their possible interplay. We show here that a significant fraction of Rac1 is associated with Rab11-positive recycling endosomes. Moreover, the Rab11 effector FIP3 controls Rac1 intracellular localization and Rac1 ta...
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: Bouchet, J., del Rio-Iniguez, I., Lasserre, R., Agüera-Gonzalez, S., Cuche, C., Danckaert, A., McCaffrey, M. W., Di Bartolo, V., Alcover, A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Immunology, Membrane & Intracellular Transport Articles Source Type: research

Scanning for a unified model for translational repression by microRNAs
MicroRNAs (miRNAs) silence target mRNAs by inhibiting translation and subsequently initiating mRNA decay. The mechanism by which miRNAs silence translation is still poorly understood, with a number of competing models proposed. In this issue of The EMBO Journal, Kuzuoğlu-Öztürk et al (2016) investigated miRNA silencing in human and insect cells. Their data support a model whereby miRNAs inhibit translation initiation. However, in contrast to several recent reports, their data suggest that translational inhibition is independent of 43S ribosomal subunit scanning, eIF4A translation factor activity, and 5'UTR second...
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: Nishimura, T., Fabian, M. R. Tags: Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research

A tale of two {alpha}-tubulin tails
Post-translational modifications of tubulin, such as the removal of the C-terminal tyrosine of α-tubulin, have long been proposed to influence the ability of microtubule motors to walk along the microtubule surface. This hypothesis has now been tested for cytoplasmic dynein-1 (dynein), revealing that active dynein–dynactin–adaptor complexes prefer to start moving on tyrosinated microtubules. This choice is governed by the p150 subunit of dynactin. Once moving, however, dynein is not choosy about whether the microtubule is tyrosinated or not. (Source: EMBO Journal)
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: Allan, V. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport News [amp ] Views Source Type: research

Considerations for a European animal welfare standard to evaluate adverse phenotypes in teleost fish
(Source: EMBO Journal)
Source: EMBO Journal - May 30, 2016 Category: Molecular Biology Authors: Bert, B., Chmielewska, J., Bergmann, S., Busch, M., Driever, W., Finger-Baier, K., Hössler, J., Köhler, A., Leich, N., Misgeld, T., Nöldner, T., Reiher, A., Schartl, M., Seebach-Sproedt, A., Thumberger, T., Schönfelder, G., Tags: Commentary Source Type: research

Regulators of complement activity mediate inhibitory mechanisms through a common C3b-binding mode
We present crystal structures of human RCA (MCP, DAF, and CR1) and a smallpox virus homolog (SPICE) bound to complement component C3b. Our structural data reveal that up to four consecutive homologous CCP domains (i–iv), responsible for inhibition, bind in the same orientation and extended arrangement at a shared binding platform on C3b. Large sequence variations in CCP domains explain the diverse C3b-binding patterns, with limited or no contribution of some individual domains, while all regulators show extensive contacts with C3b for the domains at the third site. A variation of ~100° rotation around the lo...
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Forneris, F., Wu, J., Xue, X., Ricklin, D., Lin, Z., Sfyroera, G., Tzekou, A., Volokhina, E., Granneman, J. C., Hauhart, R., Bertram, P., Liszewski, M. K., Atkinson, J. P., Lambris, J. D., Gros, P. Tags: Immunology, Structural Biology Articles Source Type: research

Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers
The existence of a 30-nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg2+-dependent self-association of linear 12-mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call "oligomers", are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10-nm fibers, rather than folded 3...
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Maeshima, K., Rogge, R., Tamura, S., Joti, Y., Hikima, T., Szerlong, H., Krause, C., Herman, J., Seidel, E., DeLuca, J., Ishikawa, T., Hansen, J. C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics Articles Source Type: research

How to make a synaptic ribbon: RIBEYE deletion abolishes ribbons in retinal synapses and disrupts neurotransmitter release
Synaptic ribbons are large proteinaceous scaffolds at the active zone of ribbon synapses that are specialized for rapid sustained synaptic vesicles exocytosis. A single ribbon-specific protein is known, RIBEYE, suggesting that ribbons may be constructed from RIBEYE protein. RIBEYE knockdown in zebrafish, however, only reduced but did not eliminate ribbons, indicating a more ancillary role. Here, we show in mice that full deletion of RIBEYE abolishes all presynaptic ribbons in retina synapses. Using paired recordings in acute retina slices, we demonstrate that deletion of RIBEYE severely impaired fast and sustained neurotra...
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Maxeiner, S., Luo, F., Tan, A., Schmitz, F., Südhof, T. C. Tags: Neuroscience Articles Source Type: research

Toxic gain of function from mutant FUS protein is crucial to trigger cell autonomous motor neuron loss
FUS is an RNA-binding protein involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS-containing aggregates are often associated with concomitant loss of nuclear FUS. Whether loss of nuclear FUS function, gain of a cytoplasmic function, or a combination of both lead to neurodegeneration remains elusive. To address this question, we generated knockin mice expressing mislocalized cytoplasmic FUS and complete FUS knockout mice. Both mouse models display similar perinatal lethality with respiratory insufficiency, reduced body weight and length, and largely similar alterations in gene ...
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Scekic-Zahirovic, J., Sendscheid, O., El Oussini, H., Jambeau, M., Sun, Y., Mersmann, S., Wagner, M., Dieterle, S., Sinniger, J., Dirrig-Grosch, S., Drenner, K., Birling, M.-C., Qiu, J., Zhou, Y., Li, H., Fu, X.-D., Rouaux, C., Shelkovnikova, T., Witting, Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

eIF4A inactivates TORC1 in response to amino acid starvation
This study identifies specific components of the translation machinery as important mediators of TORC1 inactivation upon amino acid removal. (Source: EMBO Journal)
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Tsokanos, F.-F., Albert, M.-A., Demetriades, C., Spirohn, K., Boutros, M., Teleman, A. A. Tags: Metabolism, Protein Biosynthesis & Quality Control, Signal Transduction Articles Source Type: research

The mitochondrial outer membrane protein MDI promotes local protein synthesis and mtDNA replication
Early embryonic development features rapid nuclear DNA replication cycles, but lacks mtDNA replication. To meet the high-energy demands of embryogenesis, mature oocytes are furnished with vast amounts of mitochondria and mtDNA. However, the cellular machinery driving massive mtDNA replication in ovaries remains unknown. Here, we describe a Drosophila AKAP protein, MDI that recruits a translation stimulator, La-related protein (Larp), to the mitochondrial outer membrane in ovaries. The MDI-Larp complex promotes the synthesis of a subset of nuclear-encoded mitochondrial proteins by cytosolic ribosomes on the mitochondrial su...
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Zhang, Y., Chen, Y., Gucek, M., Xu, H. Tags: Development & Differentiation, DNA Replication, Repair & Recombination, Protein Biosynthesis & Quality Control Articles Source Type: research

Cerebral cortex expansion and folding: what have we learned?
One of the most prominent features of the human brain is the fabulous size of the cerebral cortex and its intricate folding. Cortical folding takes place during embryonic development and is important to optimize the functional organization and wiring of the brain, as well as to allow fitting a large cortex in a limited cranial volume. Pathological alterations in size or folding of the human cortex lead to severe intellectual disability and intractable epilepsy. Hence, cortical expansion and folding are viewed as key processes in mammalian brain development and evolution, ultimately leading to increased intellectual perform...
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Fernandez, V., Llinares-Benadero, C., Borrell, V. Tags: Neuroscience Review Source Type: research

Eyes without a ribbon
Eye and ear employ specialized glutamatergic synapses that feature an elaborate electron-dense projection—the synaptic ribbon. Despite major efforts, the function of the synaptic ribbon has remained enigmatic, because its brick-stone-like core-component RIBEYE has remained hard to crack genetically. In an elegant study, Maxeiner et al (2016) genetically deleted RIBEYE in mice. This abolished retinal ribbons and impaired exocytosis at the presynaptic active zone of bipolar cells. (Source: EMBO Journal)
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Moser, T. Tags: Neuroscience News [amp ] Views Source Type: research

FUScinating insights into motor neuron degeneration
Point mutations in FUS cause amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease—but do they do that by a loss of the protein's normal function, or by endowing it with novel toxic functions, or both? In this issue of The EMBO Journal, Scekic-Zahirovic et al (2016) report that mutant FUS, but not the complete loss of FUS, triggers motor neuron degeneration in mice, arguing for a toxic gain-of-function mechanism. (Source: EMBO Journal)
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Dormann, D. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

eIF4A moonlights as an off switch for TORC1
TORC1 is actively inhibited upon amino acid withdrawal. Tsokanos et al (2016) shed light on the underlying molecular mechanism. They demonstrate that upon removal of exogenous amino acids, eIF4A inhibits TORC1 via TSC2. Thus, whereas it is well known that TORC1 regulates the translation machinery, we now know the inverse is also true. (Source: EMBO Journal)
Source: EMBO Journal - May 15, 2016 Category: Molecular Biology Authors: Swierczynska, M. M., Hall, M. N. Tags: Metabolism, Protein Biosynthesis & Quality Control, Signal Transduction News [amp ] Views Source Type: research

Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
The molecular roles of many RNA-binding proteins in bacterial post-transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP-seq) have begun to revolutionize the transcriptome-wide mapping of eukaryotic RNA-binding protein target sites. We have applied CLIP-seq to chart the target landscape of two major bacterial post-transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single-nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during thei...
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Holmqvist, E., Wright, P. R., Li, L., Bischler, T., Barquist, L., Reinhardt, R., Backofen, R., Vogel, J. Tags: Methods & Resources, Microbiology, Virology & Host Pathogen Interaction, RNA Biology Source Type: research

Distinct modes of recruitment of the CCR4-NOT complex by Drosophila and vertebrate Nanos
Nanos proteins repress the expression of target mRNAs by recruiting effector complexes through non-conserved N-terminal regions. In vertebrates, Nanos proteins interact with the NOT1 subunit of the CCR4–NOT effector complex through a NOT1 interacting motif (NIM), which is absent in Nanos orthologs from several invertebrate species. Therefore, it has remained unclear whether the Nanos repressive mechanism is conserved and whether it also involves direct interactions with the CCR4–NOT deadenylase complex in invertebrates. Here, we identify an effector domain (NED) that is necessary for the Drosophila melanogaster...
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Raisch, T., Bhandari, D., Sabath, K., Helms, S., Valkov, E., Weichenrieder, O., Izaurralde, E. Tags: RNA Biology, Structural Biology Articles Source Type: research

Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation
The initiation of eukaryotic DNA replication requires the assembly of active CMG (Cdc45-MCM-GINS) helicases at replication origins by a set of conserved and essential firing factors. This process is controlled during the cell cycle by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), and in response to DNA damage by the checkpoint kinase Rad53/Chk1. Here we show that Sld3, previously shown to be an essential CDK and Rad53 substrate, is recruited to the inactive MCM double hexamer in a DDK-dependent manner. Sld3 binds specifically to DDK-phosphorylated peptides from two MCM subunits (Mcm4, 6) and then recruits ...
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Deegan, T. D., Yeeles, J. T., Diffley, J. F. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

GEMC1 is a critical regulator of multiciliated cell differentiation
The generation of multiciliated cells (MCCs) is required for the proper function of many tissues, including the respiratory tract, brain, and germline. Defects in MCC development have been demonstrated to cause a subclass of mucociliary clearance disorders termed reduced generation of multiple motile cilia (RGMC). To date, only two genes, Multicilin (MCIDAS) and cyclin O (CCNO) have been identified in this disorder in humans. Here, we describe mice lacking GEMC1 (GMNC), a protein with a similar domain organization as Multicilin that has been implicated in DNA replication control. We have found that GEMC1-deficient mice are...
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Terre, B., Piergiovanni, G., Segura-Bayona, S., Gil-Gomez, G., Youssef, S. A., Attolini, C. S.-O., Wilsch-Bräuninger, M., Jung, C., Rojas, A. M., Marjanovic, M., Knobel, P. A., Palenzuela, L., Lopez-Rovira, T., Forrow, S., Huttner, W. B., Valverde Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation Articles Source Type: research

Relief of hypoxia by angiogenesis promotes neural stem cell differentiation by targeting glycolysis
Blood vessels are part of the stem cell niche in the developing cerebral cortex, but their in vivo role in controlling the expansion and differentiation of neural stem cells (NSCs) in development has not been studied. Here, we report that relief of hypoxia in the developing cerebral cortex by ingrowth of blood vessels temporo-spatially coincided with NSC differentiation. Selective perturbation of brain angiogenesis in vessel-specific Gpr124 null embryos, which prevented the relief from hypoxia, increased NSC expansion at the expense of differentiation. Conversely, exposure to increased oxygen levels rescued NSC differ...
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Lange, C., Turrero Garcia, M., Decimo, I., Bifari, F., Eelen, G., Quaegebeur, A., Boon, R., Zhao, H., Boeckx, B., Chang, J., Wu, C., Le Noble, F., Lambrechts, D., Dewerchin, M., Kuo, C. J., Huttner, W. B., Carmeliet, P. Tags: Neuroscience, Vascular Biology & Angiogenesis Articles Source Type: research

Interplay between Fanconi anemia and homologous recombination pathways in genome integrity
The Fanconi anemia (FA) pathway plays a central role in the repair of DNA interstrand crosslinks (ICLs) and regulates cellular responses to replication stress. Homologous recombination (HR), the error-free pathway for double-strand break (DSB) repair, is required during physiological cell cycle progression for the repair of replication-associated DNA damage and protection of stalled replication forks. Substantial crosstalk between the two pathways has recently been unravelled, in that key HR proteins such as the RAD51 recombinase and the tumour suppressors BRCA1 and BRCA2 also play important roles in ICL repair. Consistent...
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Michl, J., Zimmer, J., Tarsounas, M. Tags: Cancer, DNA Replication, Repair & Recombination, Molecular Biology of Disease Reviews Source Type: research

Elucidating the DDK-dependent step in replication initiation
By phosphorylating specific replication factors, cell cycle kinases ensure that eukaryotic DNA replication is initiated once and only once per mitotic cell division. New work in The EMBO Journal now reveals how DDK-mediated phosphorylation of Mcm2-7 helicase subunits is read out by Sld3, which provides further integration with CDK phosphorylation. (Source: EMBO Journal)
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Araki, H. Tags: DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

It's a family act: the geminin triplets take center stage in motile ciliogenesis
The balance between proliferation and differentiation is a fundamental aspect of multicellular life. Perhaps nowhere is this delicate balance more palpable than in the multiciliated cells (MCCs) that line the respiratory tract, the ependyma, and the oviduct. These cells contain dozens to hundreds of motile cilia that beat in a concerted fashion to generate directed fluid flow over the tissue surface. Although MCCs have exited the cell cycle, remarkably, they retain the ability to duplicate their centrioles and to mature those centrioles into ciliary basal bodies—two features, which are known to be normally under stri...
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Vladar, E. K., Mitchell, B. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation News [amp ] Views Source Type: research

Fetal neurogenesis: breathe HIF you can
Microvascular circulation creates a supporting niche for neurogenesis through the secretion of angiocrine factors. The emerging concept that energy balance and metabolic status play a role in the modulation of stem cells suggests that oxygen delivery by nearby capillary vascular beds could also regulate neurogenesis. Blood vessel formation and neuron production proceed in a coordinated fashion in the developing cerebral cortex, providing a unique opportunity to test the possibility that oxygen supply regulates cell fate decisions in neurogenic niches. The interesting study by the Carmeliet laboratory yields evidence that t...
Source: EMBO Journal - May 1, 2016 Category: Molecular Biology Authors: Morante-Redolat, J. M., Farinas, I. Tags: Neuroscience, Vascular Biology & Angiogenesis News [amp ] Views Source Type: research

UCP2 regulates energy metabolism and differentiation potential of human pluripotent stem cells
(Source: EMBO Journal)
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Zhang, J., Khvorostov, I., Hong, J. S., Oktay, Y., Vergnes, L., Nuebel, E., Wahjudi, P. N., Setoguchi, K., Wang, G., Do, A., Jung, H.-J., McCaffery, J. M., Kurland, I. J., Reue, K., Lee, W.-N. P., Koehler, C. M., Teitell, M. A. Tags: Corrigendum Source Type: research

The transcriptional coactivator Bob1 promotes the development of follicular T helper cells via Bcl6
Follicular T helper (Tfh) cells are key regulators of the germinal center reaction and long-term humoral immunity. Tfh cell differentiation requires the sustained expression of the transcriptional repressor Bcl6; however, its regulation in CD4+ T cells is incompletely understood. Here, we report that the transcriptional coactivator Bob1, encoded by the Pou2af1 gene, promotes Bcl6 expression and Tfh cell development. We found that Bob1 together with the octamer transcription factors Oct1/Oct2 can directly bind to and transactivate the Bcl6 and Btla promoters. Mixed bone marrow chimeras revealed that Bob1 is required for the...
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Stauss, D., Brunner, C., Berberich-Siebelt, F., Höpken, U. E., Lipp, M., Müller, G. Tags: Immunology Articles Source Type: research

USP19 modulates autophagy and antiviral immune responses by deubiquitinating Beclin-1
Autophagy, mediated by a number of autophagy-related (ATG) proteins, plays an important role in the bulk degradation of cellular constituents. Beclin-1 (also known as Atg6 in yeast) is a core protein essential for autophagic initiation and other biological processes. The activity of Beclin-1 is tightly regulated by multiple post-translational modifications, including ubiquitination, yet the molecular mechanism underpinning its reversible deubiquitination remains poorly defined. Here, we identified ubiquitin-specific protease 19 (USP19) as a positive regulator of autophagy, but a negative regulator of type I interferon (IFN...
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Jin, S., Tian, S., Chen, Y., Zhang, C., Xie, W., Xia, X., Cui, J., Wang, R.-F. Tags: Autophagy & Cell Death, Immunology, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

ALS-linked protein disulfide isomerase variants cause motor dysfunction
This study identifies ER proteostasis imbalance as a risk factor for ALS, driving initial stages of the disease. (Source: EMBO Journal)
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Woehlbier, U., Colombo, A., Saaranen, M. J., Perez, V., Ojeda, J., Bustos, F. J., Andreu, C. I., Torres, M., Valenzuela, V., Medinas, D. B., Rozas, P., Vidal, R. L., Lopez-Gonzalez, R., Salameh, J., Fernandez-Collemann, S., Munoz, N., Matus, S., Armisen, Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Ribonuclease H2 mutations induce a cGAS/STING-dependent innate immune response
Aicardi–Goutières syndrome (AGS) provides a monogenic model of nucleic acid-mediated inflammation relevant to the pathogenesis of systemic autoimmunity. Mutations that impair ribonuclease (RNase) H2 enzyme function are the most frequent cause of this autoinflammatory disorder of childhood and are also associated with systemic lupus erythematosus. Reduced processing of either RNA:DNA hybrid or genome-embedded ribonucleotide substrates is thought to lead to activation of a yet undefined nucleic acid-sensing pathway. Here, we establish Rnaseh2bA174T/A174T knock-in mice as a subclinical model of disease, identifyi...
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Mackenzie, K. J., Carroll, P., Lettice, L., Tarnauskaite, Z., Reddy, K., Dix, F., Revuelta, A., Abbondati, E., Rigby, R. E., Rabe, B., Kilanowski, F., Grimes, G., Fluteau, A., Devenney, P. S., Hill, R. E., Reijns, M. A., Jackson, A. P. Tags: Immunology Articles Source Type: research

Molecular basis of ion permeability in a voltage-gated sodium channel
Voltage-gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na+  Li+ >> K+, Ca2+, ...
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Naylor, C. E., Bagneris, C., DeCaen, P. G., Sula, A., Scaglione, A., Clapham, D. E., Wallace, B. Tags: Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

CPAP promotes timely cilium disassembly to maintain neural progenitor pool
A mutation in the centrosomal-P4.1-associated protein (CPAP) causes Seckel syndrome with microcephaly, which is suggested to arise from a decline in neural progenitor cells (NPCs) during development. However, mechanisms of NPCs maintenance remain unclear. Here, we report an unexpected role for the cilium in NPCs maintenance and identify CPAP as a negative regulator of ciliary length independent of its role in centrosome biogenesis. At the onset of cilium disassembly, CPAP provides a scaffold for the cilium disassembly complex (CDC), which includes Nde1, Aurora A, and OFD1, recruited to the ciliary base for timely cilium di...
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Gabriel, E., Wason, A., Ramani, A., Gooi, L. M., Keller, P., Pozniakovsky, A., Poser, I., Noack, F., Telugu, N. S., Calegari, F., Saric, T., Hescheler, J., Hyman, A. A., Gottardo, M., Callaini, G., Alkuraya, F. S., Gopalakrishnan, J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Molecular Biology of Disease Articles Source Type: research

When Myc's asleep, embryonic stem cells are dormant
Myc is one of the original reprogramming factors used to produce induced pluripotent stem cells. However, it is not necessary, instead its main role is to increase the efficiency of the reprogramming. The article by Scognamiglio et al (2016) helps clarify how. The authors show that Myc depletion leads to a reversible dormant state consistent with diapause. In this state, the cell sees its proliferation potential diminished but its pluripotency unchanged. The ability to coordinate the induction of this state should have important implications in cell differentiation. (Source: EMBO Journal)
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Nakagawa, M., Karagiannis, P., Yamanaka, S. Tags: Development & Differentiation, Stem Cells News [amp ] Views Source Type: research

ER strikes again: Proteostasis Dysfunction In ALS
The precise contribution of endoplasmic reticulum (ER) chaperone protein disulfide isomerase (PDI) variants in human amyotrophic lateral sclerosis (ALS) patients to the pathogenesis of ALS remained unclear. In the present study, Woehlbier et al (2016) demonstrated that these PDI variants are capable of altering motor neuron morphology, impairing the expression of synaptic proteins, and compromising neuromuscular junction (NMJ) integrity. (Source: EMBO Journal)
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Maharjan, N., Saxena, S. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

cGAS-STING do it again: pivotal role in RNase H2 genetic disease
RNase H2 is a susceptibility gene for the Aicardi–Goutières syndrome (AGS), a genetic auto-inflammatory disease. Mackenzie and colleagues now report a tractable mouse model for the disease, implicating the cGAS-STING pathway. (Source: EMBO Journal)
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Gentili, M., Manel, N. Tags: Immunology News [amp ] Views Source Type: research

Three in a row--how sodium ions cross the channel
Sodium channels are central to a host of fundamental cellular processes, including sensory perception, pain, and muscle contraction. In order to understand any of these processes in detail, it is necessary to know the atomic structure of the channel proteins both with and without bound sodium ions. In this issue, Naylor et al (2016) present the structure of a bacterial sodium channel tetramer. The three bound, partially hydrated sodium ions line up neatly in a row inside the selectivity filter, providing us with the first detailed insights into ion conduction in sodium channels, and the mechanisms by which sodium and ...
Source: EMBO Journal - April 14, 2016 Category: Molecular Biology Authors: Kühlbrandt, W. Tags: Membrane & Intracellular Transport, Structural Biology News [amp ] Views Source Type: research

ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling
(Source: EMBO Journal)
Source: EMBO Journal - March 30, 2016 Category: Molecular Biology Authors: Deshpande, R. A., Williams, G. J., Limbo, O., Williams, R. S., Kuhnlein, J., Lee, J.-H., Classen, S., Guenther, G., Russell, P., Tainer, J. A., Paull, T. T. Tags: Corrigendum Source Type: research

Intraflagellar transport proteins 172, 80, 57, 54, 38, and 20 form a stable tubulin-binding IFT-B2 complex
Intraflagellar transport (IFT) relies on the IFT complex and is required for ciliogenesis. The IFT-B complex consists of 9–10 stably associated core subunits and six "peripheral" subunits that were shown to dissociate from the core structure at moderate salt concentration. We purified the six "peripheral" IFT-B subunits of Chlamydomonas reinhardtii as recombinant proteins and show that they form a stable complex independently of the IFT-B core. We suggest a nomenclature of IFT-B1 (core) and IFT-B2 (peripheral) for the two IFT-B subcomplexes. We demonstrate that IFT88, together with the N-terminal ...
Source: EMBO Journal - March 30, 2016 Category: Molecular Biology Authors: Taschner, M., Weber, K., Mourao, A., Vetter, M., Awasthi, M., Stiegler, M., Bhogaraju, S., Lorentzen, E. Tags: Cell Adhesion, Polarity & Cytoskeleton Articles Source Type: research

Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50
The Mre11–Rad50–Nbs1 (MRN) complex is a central factor in the repair of DNA double-strand breaks (DSBs). The ATP-dependent mechanisms of how MRN detects and endonucleolytically processes DNA ends for the repair by microhomology-mediated end-joining or further resection in homologous recombination are still unclear. Here, we report the crystal structures of the ATPS-bound dimer of the Rad50NBD (nucleotide-binding domain) from the thermophilic eukaryote Chaetomium thermophilum (Ct) in complex with either DNA or CtMre11RBD (Rad50-binding domain) along with small-angle X-ray scattering and cross-linking studies. Th...
Source: EMBO Journal - March 30, 2016 Category: Molecular Biology Authors: Seifert, F. U., Lammens, K., Stoehr, G., Kessler, B., Hopfner, K.-P. Tags: DNA Replication, Repair & Recombination, Structural Biology Articles Source Type: research

ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex
ATP-dependent DNA end recognition and nucleolytic processing are central functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair. However, it is still unclear how ATP binding and hydrolysis primes the MR function and regulates repair pathway choice in cells. Here, Methanococcus jannaschii MR-ATPS-DNA structure reveals that the partly deformed DNA runs symmetrically across central groove between two ATPS-bound Rad50 nucleotide-binding domains. Duplex DNA cannot access the Mre11 active site in the ATP-free full-length MR complex. ATP hydrolysis drives rotation of the nucleotide-binding domain and induces ...
Source: EMBO Journal - March 30, 2016 Category: Molecular Biology Authors: Liu, Y., Sung, S., Kim, Y., Li, F., Gwon, G., Jo, A., Kim, A.-K., Kim, T., Song, O.-k., Lee, S. E., Cho, Y. Tags: DNA Replication, Repair & Recombination, Structural Biology Articles Source Type: research

Mitochondria are required for pro-ageing features of the senescent phenotype
Cell senescence is an important tumour suppressor mechanism and driver of ageing. Both functions are dependent on the development of the senescent phenotype, which involves an overproduction of pro-inflammatory and pro-oxidant signals. However, the exact mechanisms regulating these phenotypes remain poorly understood. Here, we show the critical role of mitochondria in cellular senescence. In multiple models of senescence, absence of mitochondria reduced a spectrum of senescence effectors and phenotypes while preserving ATP production via enhanced glycolysis. Global transcriptomic analysis by RNA sequencing revealed that a ...
Source: EMBO Journal - March 30, 2016 Category: Molecular Biology Authors: Correia-Melo, C., Marques, F. D., Anderson, R., Hewitt, G., Hewitt, R., Cole, J., Carroll, B. M., Miwa, S., Birch, J., Merz, A., Rushton, M. D., Charles, M., Jurk, D., Tait, S. W., Czapiewski, R., Greaves, L., Nelson, G., Bohlooly-Y, M., Rodriguez-Cuenca, Tags: Ageing, Cell Cycle, Metabolism Articles Source Type: research

Upstream ORFs are prevalent translational repressors in vertebrates
Regulation of gene expression is fundamental in establishing cellular diversity and a target of natural selection. Untranslated mRNA regions (UTRs) are key mediators of post-transcriptional regulation. Previous studies have predicted thousands of ORFs in 5' UTRs, the vast majority of which have unknown function. Here, we present a systematic analysis of the translation and function of upstream open reading frames (uORFs) across vertebrates. Using high-resolution ribosome footprinting, we find that (i) uORFs are prevalent within vertebrate transcriptomes, (ii) the majority show signatures of active translation, and (iii) uO...
Source: EMBO Journal - March 30, 2016 Category: Molecular Biology Authors: Johnstone, T. G., Bazzini, A. A., Giraldez, A. J. Tags: Protein Biosynthesis & Quality Control, RNA Biology, Systems & Computational Biology Articles Source Type: research