Transcriptome-based profiling of yolk sac-derived macrophages reveals a role for Irf8 in macrophage maturation
Recent studies have shown that tissue macrophages (M) arise from embryonic progenitors of the yolk sac (YS) and fetal liver and colonize tissues before birth. Further studies have proposed that developmentally distinct tissue M can be identified based on the differential expression of F4/80 and CD11b, but whether a characteristic transcriptional profile exists is largely unknown. Here, we took advantage of an inducible fate-mapping system that facilitated the identification of CD45+c-kit–CX3CR1+F4/80+ (A2) progenitors of the YS as the source of F4/80hi but not CD11bhi M. Large-scale transcriptional profiling of ...
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Hagemeyer, N., Kierdorf, K., Frenzel, K., Xue, J., Ringelhan, M., Abdullah, Z., Godin, I., Wieghofer, P., Costa Jordao, M. J., Ulas, T., Yorgancioglu, G., Rosenbauer, F., Knolle, P. A., Heikenwalder, M., Schultze, J. L., Prinz, M. Tags: Immunology Articles Source Type: research

Statistical relevance--relevant statistics, part II: presenting experimental data
(Source: EMBO Journal)
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Klaus, B. Tags: Commentary Source Type: research

Cloud storage for endosomes
Coordinated regulation of vesicle trafficking is critical for the proper functioning of a cell. The bulk of cellular transport vesicles are sequestered in a "perinuclear cloud", with only a small fraction released to the cell periphery. Jongsma et al (2016) found that the ER-associated E3 ubiquitin ligase RNF26 is responsible for establishing and maintaining the architecture of the perinuclear cloud and that this spatiotemporal positioning is critical for effective regulation of the endocytic and exocytic systems. (Source: EMBO Journal)
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Dellibovi-Ragheb, T., Altan-Bonnet, N. Tags: Membrane & Intracellular Transport News [amp ] Views Source Type: research

Messages from forgotten friends: classic cell adhesion molecules inhibit regeneration too
A necessary step toward complete functional recovery after spinal cord injury is the regeneration of axons. Axon regrowth after injury is prevented by a myriad of intrinsic and extrinsic factors. In this issue of The EMBO Journal, Huang et al (2016) demonstrate that the cell adhesion molecule NB-3 (CNTN6) functions as a major brake on axon regrowth when it is activated by NB-3 from scar-forming cells at the injury site. Disruption of this NB-3 trans-cellular signaling led to impressive axon regrowth after spinal cord transection. (Source: EMBO Journal)
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Danzi, M. C., Lemmon, V. P. Tags: Neuroscience News [amp ] Views Source Type: research

Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock
In the Neurospora crassa circadian clock, a protein complex of frequency (FRQ), casein kinase 1a (CK1a), and the FRQ-interacting RNA Helicase (FRH) rhythmically represses gene expression by the white-collar complex (WCC). FRH crystal structures in several conformations and bound to ADP/RNA reveal differences between FRH and the yeast homolog Mtr4 that clarify the distinct role of FRH in the clock. The FRQ-interacting region at the FRH N-terminus has variable structure in the absence of FRQ. A known mutation that disrupts circadian rhythms (R806H) resides in a positively charged surface of the KOW domain, far removed from t...
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Conrad, K. S., Hurley, J. M., Widom, J., Ringelberg, C. S., Loros, J. J., Dunlap, J. C., Crane, B. R. Tags: Metabolism, Structural Biology Articles Source Type: research

Crystal structure of yeast V1-ATPase in the autoinhibited state
Vacuolar ATPases (V-ATPases) are essential proton pumps that acidify the lumen of subcellular organelles in all eukaryotic cells and the extracellular space in some tissues. V-ATPase activity is regulated by a unique mechanism referred to as reversible disassembly, wherein the soluble catalytic sector, V1, is released from the membrane and its MgATPase activity silenced. The crystal structure of yeast V1 presented here shows that activity silencing involves a large conformational change of subunit H, with its C-terminal domain rotating ~150° from a position near the membrane in holo V-ATPase to a position at the bottom...
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Oot, R. A., Kane, P. M., Berry, E. A., Wilkens, S. Tags: Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

Mfn2 deficiency links age-related sarcopenia and impaired autophagy to activation of an adaptive mitophagy pathway
Mitochondrial dysfunction and accumulation of damaged mitochondria are considered major contributors to aging. However, the molecular mechanisms responsible for these mitochondrial alterations remain unknown. Here, we demonstrate that mitofusin 2 (Mfn2) plays a key role in the control of muscle mitochondrial damage. We show that aging is characterized by a progressive reduction in Mfn2 in mouse skeletal muscle and that skeletal muscle Mfn2 ablation in mice generates a gene signature linked to aging. Furthermore, analysis of muscle Mfn2-deficient mice revealed that aging-induced Mfn2 decrease underlies the age-related alter...
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Sebastian, D., Sorianello, E., Segales, J., Irazoki, A., Ruiz-Bonilla, V., Sala, D., Planet, E., Berenguer-Llergo, A., Munoz, J. P., Sanchez-Feutrie, M., Plana, N., Hernandez-Alvarez, M. I., Serrano, A. L., Palacin, M., Zorzano, A. Tags: Ageing, Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

The C9orf72 protein interacts with Rab1a and the ULK1 complex to regulate initiation of autophagy
A GGGGCC hexanucleotide repeat expansion in the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD). C9orf72 encodes two C9orf72 protein isoforms of unclear function. Reduced levels of C9orf72 expression have been reported in C9ALS/FTD patients, and although C9orf72 haploinsufficiency has been proposed to contribute to C9ALS/FTD, its significance is not yet clear. Here, we report that C9orf72 interacts with Rab1a and the Unc-51-like kinase 1 (ULK1) autophagy initiation complex. As a Rab1a effector, C9orf72 controls initiation of autophagy by regulating the ...
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Webster, C. P., Smith, E. F., Bauer, C. S., Moller, A., Hautbergue, G. M., Ferraiuolo, L., Myszczynska, M. A., Higginbottom, A., Walsh, M. J., Whitworth, A. J., Kaspar, B. K., Meyer, K., Shaw, P. J., Grierson, A. J., De Vos, K. J. Tags: Neuroscience Articles Source Type: research

Spatial control of lipid droplet proteins by the ERAD ubiquitin ligase Doa10
The endoplasmic reticulum (ER) plays a central role in the biogenesis of most membrane proteins. Among these are proteins localized to the surface of lipid droplets (LDs), fat storage organelles delimited by a phospholipid monolayer. The LD monolayer is often continuous with the membrane of the ER allowing certain membrane proteins to diffuse between the two organelles. In these connected organelles, how some proteins concentrate specifically at the surface of LDs is not known. Here, we show that the ERAD ubiquitin ligase Doa10 controls the levels of some LD proteins. Their degradation is dependent on the localization to t...
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Ruggiano, A., Mora, G., Buxo, L., Carvalho, P. Tags: Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control Articles Source Type: research

Substrate recruitment of {gamma}-secretase and mechanism of clinical presenilin mutations revealed by photoaffinity mapping
Intramembrane proteases execute fundamental biological processes ranging from crucial signaling events to general membrane proteostasis. Despite the availability of structural information on these proteases, it remains unclear how these enzymes bind and recruit substrates, particularly for the Alzheimer's disease-associated -secretase. Systematically scanning amyloid precursor protein substrates containing a genetically inserted photocrosslinkable amino acid for binding to -secretase allowed us to identify residues contacting the protease. These were primarily found in the transmembrane cleavage domain of the substrate and...
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Fukumori, A., Steiner, H. Tags: Membrane & Intracellular Transport, Molecular Biology of Disease, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

TssA forms a gp6-like ring attached to the type VI secretion sheath
The type VI secretion system (T6SS) is a supra-molecular bacterial complex that resembles phage tails. It is a killing machine which fires toxins into target cells upon contraction of its TssBC sheath. Here, we show that TssA1 is a T6SS component forming dodecameric ring structures whose dimensions match those of the TssBC sheath and which can accommodate the inner Hcp tube. The TssA1 ring complex binds the T6SS sheath and impacts its behaviour in vivo. In the phage, the first disc of the gp18 sheath sits on a baseplate wherein gp6 is a dodecameric ring. We found remarkable sequence and structural similarities between...
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Planamente, S., Salih, O., Manoli, E., Albesa-Jove, D., Freemont, P. S., Filloux, A. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

Droplet organelles?
Cells contain numerous, molecularly distinct cellular compartments that are not enclosed by lipid bilayers. These compartments are implicated in a wide range of cellular activities, and they have been variously described as bodies, granules, or organelles. Recent evidence suggests that a liquid–liquid phase separation (LLPS) process may drive their formation, possibly justifying the unifying term "droplet organelle". A veritable deluge of recent publications points to the importance of low-complexity proteins and RNA in determining the physical properties of phase-separated structures. Many of the proteins ...
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Courchaine, E. M., Lu, A., Neugebauer, K. M. Tags: Membrane & Intracellular Transport, Neuroscience, RNA Biology Review Source Type: research

Muscles cannot break a NuRDy heart
The recent article from Gómez-del Arco et al (2016) in Cell Metabolism reveals the essential role of chromodomain-helicase-DNA-binding protein 4 (CHD4) in the control of alternative gene expression in cell types that share seemingly redundant, yet distinct, biological properties, such as the contractile activities of striated cardiac or skeletal muscles. An altered expression of genes for alternative sarcomeric and metabolic programs occurred upon genetic inactivation of Chd4 in skeletal or cardiac cells, leading to formation of "hybrid" striated muscles and pathological outcomes. (Source: EMBO Journal)
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Malecova, B., Dall'Agnese, A., Puri, P. L. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation News [amp ] Views Source Type: research

Probing {gamma}-secretase-substrate interactions at the single amino acid residue level
Intramembrane proteolysis by -secretases plays major roles in disease pathology and cellular signalling, yet the dynamics of these enzyme complexes and how they recognize substrates remains poorly understood. New work in The EMBO Journal utilizes photo-affinity cross-linking to map APP interactions to different -secretase subunits, suggesting a succession of recruitment and engagement steps that lead up to substrate cleavage. (Source: EMBO Journal)
Source: EMBO Journal - July 31, 2016 Category: Molecular Biology Authors: Chavez-Gutierrez, L., De Strooper, B. Tags: Membrane & Intracellular Transport, Molecular Biology of Disease, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries
Chromosomes in all organisms are highly organized and divided into multiple chromosomal interaction domains, or topological domains. Regions of active, high transcription help establish and maintain domain boundaries, but precisely how this occurs remains unclear. Here, using fluorescence microscopy and chromosome conformation capture in conjunction with deep sequencing (Hi-C), we show that in Caulobacter crescentus, both transcription rate and transcript length, independent of concurrent translation, drive the formation of domain boundaries. We find that long, highly expressed genes do not form topological boundaries simp...
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Le, T. B., Laub, M. T. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Nucleosome eviction in mitosis assists condensin loading and chromosome condensation
Condensins associate with DNA and shape mitotic chromosomes. Condensins are enriched nearby highly expressed genes during mitosis, but how this binding is achieved and what features associated with transcription attract condensins remain unclear. Here, we report that condensin accumulates at or in the immediate vicinity of nucleosome-depleted regions during fission yeast mitosis. Two transcriptional coactivators, the Gcn5 histone acetyltransferase and the RSC chromatin-remodelling complex, bind to promoters adjoining condensin-binding sites and locally evict nucleosomes to facilitate condensin binding and allow efficient m...
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Toselli-Mollereau, E., Robellet, X., Fauque, L., Lemaire, S., Schiklenk, C., Klein, C., Hocquet, C., Legros, P., N'Guyen, L., Mouillard, L., Chautard, E., Auboeuf, D., Haering, C. H., Bernard, P. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics Articles Source Type: research

Continual removal of H3K9 promoter methylation by Jmjd2 demethylases is vital for ESC self-renewal and early development
We report that while individual Jmjd2 family members are dispensable for ESC maintenance and embryogenesis, combined deficiency for specifically Jmjd2a and Jmjd2c leads to early embryonic lethality and impaired ESC self-renewal, with spontaneous differentiation towards primitive endoderm under permissive culture conditions. We further show that Jmjd2a and Jmjd2c both localize to H3K4me3-positive promoters, where they have widespread and redundant roles in preventing accumulation of H3K9me3 and H3K36me3. Jmjd2 catalytic activity is required for ESC maintenance, and increased H3K9me3 levels in knockout ESCs compromise the ex...
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Pedersen, M. T., Kooistra, S. M., Radzisheuskaya, A., Laugesen, A., Johansen, J. V., Hayward, D. G., Nilsson, J., Agger, K., Helin, K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells, Transcription Articles Source Type: research

DnaJ/Hsc70 chaperone complexes control the extracellular release of neurodegenerative-associated proteins
It is now known that proteins associated with neurodegenerative disease can spread throughout the brain in a prionlike manner. However, the mechanisms regulating the trans-synaptic spread propagation, including the neuronal release of these proteins, remain unknown. The interaction of neurodegenerative disease-associated proteins with the molecular chaperone Hsc70 is well known, and we hypothesized that much like disaggregation, refolding, degradation, and even normal function, Hsc70 may dictate the extracellular fate of these proteins. Here, we show that several proteins, including TDP-43, α-synuclein, and the micro...
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Fontaine, S. N., Zheng, D., Sabbagh, J. J., Martin, M. D., Chaput, D., Darling, A., Trotter, J. H., Stothert, A. R., Nordhues, B. A., Lussier, A., Baker, J., Shelton, L., Kahn, M., Blair, L. J., Stevens, S. M., Dickey, C. A. Tags: Neuroscience Articles Source Type: research

Ubiquitin-like domains can target to the proteasome but proteolysis requires a disordered region
Ubiquitin and some of its homologues target proteins to the proteasome for degradation. Other ubiquitin-like domains are involved in cellular processes unrelated to the proteasome, and proteins containing these domains remain stable in the cell. We find that the 10 yeast ubiquitin-like domains tested bind to the proteasome, and that all 11 identified domains can target proteins for degradation. Their apparent proteasome affinities are not directly related to their stabilities or functions. That is, ubiquitin-like domains in proteins not part of the ubiquitin proteasome system may bind the proteasome more tightly than domai...
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Yu, H., Kago, G., Yellman, C. M., Matouschek, A. Tags: Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants
Fused in sarcoma (FUS) is a ubiquitously expressed RNA-binding protein proposed to function in various RNA metabolic pathways, including transcription regulation, pre-mRNA splicing, RNA transport and microRNA processing. Mutations in the FUS gene were identified in patients with amyotrophic lateral sclerosis (ALS), but the pathomechanisms by which these mutations cause ALS are not known. Here, we show that FUS interacts with the minor spliceosome constituent U11 snRNP, binds preferentially to minor introns and directly regulates their removal. Furthermore, a FUS knockout in neuroblastoma cells strongly disturbs the splicin...
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Reber, S., Stettler, J., Filosa, G., Colombo, M., Jutzi, D., Lenzken, S. C., Schweingruber, C., Bruggmann, R., Bachi, A., Barabino, S. M., Mühlemann, O., Ruepp, M.-D. Tags: Neuroscience, RNA Biology Articles Source Type: research

SIRT7 promotes genome integrity and modulates non-homologous end joining DNA repair
Sirtuins, a family of protein deacetylases, promote cellular homeostasis by mediating communication between cells and environment. The enzymatic activity of the mammalian sirtuin SIRT7 targets acetylated lysine in the N-terminal tail of histone H3 (H3K18Ac), thus modulating chromatin structure and transcriptional competency. SIRT7 deletion is associated with reduced lifespan in mice through unknown mechanisms. Here, we show that SirT7-knockout mice suffer from partial embryonic lethality and a progeroid-like phenotype. Consistently, SIRT7-deficient cells display increased replication stress and impaired DNA repair. SIRT7 i...
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Vazquez, B. N., Thackray, J. K., Simonet, N. G., Kane-Goldsmith, N., Martinez-Redondo, P., Nguyen, T., Bunting, S., Vaquero, A., Tischfield, J. A., Serrano, L. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

The minor spliceosome could be the major key for FUS/TLS mutants in ALS
Despite its name, minor spliceosome alterations are often involved in human disease origin. Work by Reber et al (2016) in this issue of The EMBO Journal now demonstrates a connection between minor spliceosome components and FUS/TLS, one of the major proteins aggregating in the brain of patients affected by amyotrophic lateral sclerosis (ALS). This finding has important implications as it extends the spectrum of diseases where minor spliceosome plays a role. It may also represent a new opportunity for specific therapeutic targets. (Source: EMBO Journal)
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Buratti, E. Tags: Neuroscience, RNA Biology News [amp ] Views Source Type: research

SIRT7 clears the way for DNA repair
Histone modification by reversible lysine acetylation is a key regulatory mechanism in chromatin and nuclear signaling, whose deregulation is linked to aging, cancer, and other diseases. New work by Vazquez et al (2016) uncovers a role for the sirtuin family deacetylase SIRT7, which controls epigenetic maintenance of oncogenic gene expression programs, mitochondrial homeostasis, and ribosome biogenesis, in promoting genomic stability and DNA repair via site-specific deacetylation of a damage-associated histone mark, H3K18Ac. (Source: EMBO Journal)
Source: EMBO Journal - July 14, 2016 Category: Molecular Biology Authors: Paredes, S., Chua, K. F. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly
Nap1 is a histone chaperone involved in the nuclear import of H2A–H2B and nucleosome assembly. Here, we report the crystal structure of Nap1 bound to H2A–H2B together with in vitro and in vivo functional studies that elucidate the principles underlying Nap1-mediated H2A–H2B chaperoning and nucleosome assembly. A Nap1 dimer provides an acidic binding surface and asymmetrically engages a single H2A–H2B heterodimer. Oligomerization of the Nap1–H2A–H2B complex results in burial of surfaces required for deposition of H2A–H2B into nucleosomes. Chromatin immunoprecipitation-exon...
Source: EMBO Journal - June 30, 2016 Category: Molecular Biology Authors: Aguilar-Gurrieri, C., Larabi, A., Vinayachandran, V., Patel, N. A., Yen, K., Reja, R., Ebong, I.-O., Schoehn, G., Robinson, C. V., Pugh, B. F., Panne, D. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Structural Biology Articles Source Type: research

Histone H3.3 promotes IgV gene diversification by enhancing formation of AID-accessible single-stranded DNA
Immunoglobulin diversification is driven by activation-induced deaminase (AID), which converts cytidine to uracil within the Ig variable (IgV) regions. Central to the recruitment of AID to the IgV genes are factors that regulate the generation of single-stranded DNA (ssDNA), the enzymatic substrate of AID. Here, we report that chicken DT40 cells lacking variant histone H3.3 exhibit reduced IgV sequence diversification. We show that this results from impairment of the ability of AID to access the IgV genes due to reduced formation of ssDNA during IgV transcription. Loss of H3.3 also diminishes IgV R-loop formation. However,...
Source: EMBO Journal - June 30, 2016 Category: Molecular Biology Authors: Romanello, M., Schiavone, D., Frey, A., Sale, J. E. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Immunology Articles Source Type: research

WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress
Accurate handling of stalled replication forks is crucial for the maintenance of genome stability. RAD51 defends stalled replication forks from nucleolytic attack, which otherwise can threaten genome stability. However, the identity of other factors that can collaborate with RAD51 in this task is poorly elucidated. Here, we establish that human Werner helicase interacting protein 1 (WRNIP1) is localized to stalled replication forks and cooperates with RAD51 to safeguard fork integrity. We show that WRNIP1 is directly involved in preventing uncontrolled MRE11-mediated degradation of stalled replication forks by promoting RA...
Source: EMBO Journal - June 30, 2016 Category: Molecular Biology Authors: Leuzzi, G., Marabitti, V., Pichierri, P., Franchitto, A. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Novel function of Tau in regulating the effects of external stimuli on adult hippocampal neurogenesis
Tau is a microtubule-associated neuronal protein found mainly in axons. However, its presence in dendrites and dendritic spines is particularly relevant due to its involvement in synaptic plasticity and neurodegeneration. Here, we show that Tau plays a novel in vivo role in the morphological and synaptic maturation of newborn hippocampal granule neurons under basal conditions. Furthermore, we reveal that Tau is involved in the selective cell death of immature granule neurons caused by acute stress. Also, Tau deficiency protects newborn neurons from the stress-induced dendritic atrophy and loss of postsynaptic densitie...
Source: EMBO Journal - June 30, 2016 Category: Molecular Biology Authors: Pallas-Bazarra, N., Jurado-Arjona, J., Navarrete, M., Esteban, J. A., Hernandez, F., Avila, J., Llorens-Martin, M. Tags: Neuroscience Articles Source Type: research

SCF (Fbxl17) ubiquitylation of Sufu regulates Hedgehog signaling and medulloblastoma development
Skp1-Cul1-F-box protein (SCF) ubiquitin ligases direct cell survival decisions by controlling protein ubiquitylation and degradation. Sufu (Suppressor of fused) is a central regulator of Hh (Hedgehog) signaling and acts as a tumor suppressor by maintaining the Gli (Glioma-associated oncogene homolog) transcription factors inactive. Although Sufu has a pivotal role in Hh signaling, the players involved in controlling Sufu levels and their role in tumor growth are unknown. Here, we show that Fbxl17 (F-box and leucine-rich repeat protein 17) targets Sufu for proteolysis in the nucleus. The ubiquitylation of Sufu, mediated by ...
Source: EMBO Journal - June 30, 2016 Category: Molecular Biology Authors: Raducu, M., Fung, E., Serres, S., Infante, P., Barberis, A., Fischer, R., Bristow, C., Thezenas, M.-L., Finta, C., Christianson, J. C., Buffa, F. M., Kessler, B. M., Sibson, N. R., Di Marcotullio, L., Toftgard, R., D'Angiolella, V. Tags: Cancer, Post-translational Modifications, Proteolysis & Proteomics, Signal Transduction Articles Source Type: research

HSV-1 ICP27 targets the TBK1-activated STING signalsome to inhibit virus-induced type I IFN expression
Herpes simplex virus (HSV) 1 stimulates type I IFN expression through the cGAS–STING–TBK1 signaling axis. Macrophages have recently been proposed to be an essential source of IFN during viral infection. However, it is not known how HSV-1 inhibits IFN expression in this cell type. Here, we show that HSV-1 inhibits type I IFN induction through the cGAS–STING–TBK1 pathway in human macrophages, in a manner dependent on the conserved herpesvirus protein ICP27. This viral protein was expressed de novo in macrophages with early nuclear localization followed by later translocation to the cytoplasm where ICP...
Source: EMBO Journal - June 30, 2016 Category: Molecular Biology Authors: Christensen, M. H., Jensen, S. B., Miettinen, J. J., Luecke, S., Prabakaran, T., Reinert, L. S., Mettenleiter, T., Chen, Z. J., Knipe, D. M., Sandri-Goldin, R. M., Enquist, L. W., Hartmann, R., Mogensen, T. H., Rice, S. A., Nyman, T. A., Matikainen, S., P Tags: Immunology Articles Source Type: research

FUNDC1 regulates mitochondrial dynamics at the ER-mitochondrial contact site under hypoxic conditions
In hypoxic cells, dysfunctional mitochondria are selectively removed by a specialized autophagic process called mitophagy. The ER–mitochondrial contact site (MAM) is essential for fission of mitochondria prior to engulfment, and the outer mitochondrial membrane protein FUNDC1 interacts with LC3 to recruit autophagosomes, but the mechanisms integrating these processes are poorly understood. Here, we describe a new pathway mediating mitochondrial fission and subsequent mitophagy under hypoxic conditions. FUNDC1 accumulates at the MAM by associating with the ER membrane protein calnexin. As mitophagy proceeds, FUNDC1/ca...
Source: EMBO Journal - June 30, 2016 Category: Molecular Biology Authors: Wu, W., Lin, C., Wu, K., Jiang, L., Wang, X., Li, W., Zhuang, H., Zhang, X., Chen, H., Li, S., Yang, Y., Lu, Y., Wang, J., Zhu, R., Zhang, L., Sui, S., Tan, N., Zhao, B., Zhang, J., Li, L., Feng, D. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Metabolism Articles Source Type: research

Mitochondria just wanna have FUN(DC1)
A fascinating story is unfolding at the interface between mitochondria and the ER. Two new papers, one in this issue of The EMBO Journal (Wu et al, 2016) and one in the journal Autophagy (Chen et al, 2016), further clarify the role of mitochondrial outer membrane protein FUNDC1 in autophagy and connect it to mitochondrial fission occurring at the interface between mitochondria and the ER. (Source: EMBO Journal)
Source: EMBO Journal - June 30, 2016 Category: Molecular Biology Authors: van der Bliek, A. M. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Metabolism News [amp ] Views Source Type: research

Phosphorylation-dependent Akt-Inversin interaction at the basal body of primary cilia
A primary cilium is a microtubule-based sensory organelle that plays an important role in human development and disease. However, regulation of Akt in cilia and its role in ciliary development has not been demonstrated. Using yeast two-hybrid screening, we demonstrate that Inversin (INVS) interacts with Akt. Mutation in the INVS gene causes nephronophthisis type II (NPHP2), an autosomal recessive chronic tubulointerstitial nephropathy. Co-immunoprecipitation assays show that Akt interacts with INVS via the C-terminus. In vitro kinase assays demonstrate that Akt phosphorylates INVS at amino acids 864–866 that are requ...
Source: EMBO Journal - June 13, 2016 Category: Molecular Biology Authors: Suizu, F., Hirata, N., Kimura, K., Edamura, T., Tanaka, T., Ishigaki, S., Donia, T., Noguchi, H., Iwanaga, T., Noguchi, M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Molecular Biology of Disease, Signal Transduction Articles Source Type: research

Phosphorylation of Cav1.2 on S1928 uncouples the L-type Ca2+ channel from the {beta}2 adrenergic receptor
Agonist-triggered downregulation of β-adrenergic receptors (ARs) constitutes vital negative feedback to prevent cellular overexcitation. Here, we report a novel downregulation of β2AR signaling highly specific for Cav1.2. We find that β2-AR binding to Cav1.2 residues 1923–1942 is required for β-adrenergic regulation of Cav1.2. Despite the prominence of PKA-mediated phosphorylation of Cav1.2 S1928 within the newly identified β2AR binding site, its physiological function has so far escaped identification. We show that phosphorylation of S1928 displaces the β2AR from Cav1.2 upon β-adre...
Source: EMBO Journal - June 13, 2016 Category: Molecular Biology Authors: Patriarchi, T., Qian, H., Di Biase, V., Malik, Z. A., Chowdhury, D., Price, J. L., Hammes, E. A., Buonarati, O. R., Westenbroek, R. E., Catterall, W. A., Hofmann, F., Xiang, Y. K., Murphy, G. G., Chen, C.-Y., Navedo, M. F., Hell, J. W. Tags: Neuroscience Articles Source Type: research

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