ESCRTs are everywhere
The ESCRT proteins are an ancient system that buds membranes and severs membrane necks from their inner face. Three "classical" functions of the ESCRTs have dominated research into these proteins since their discovery in 2001: the biogenesis of multivesicular bodies in endolysosomal sorting; the budding of HIV-1 and other viruses from the plasma membrane of infected cells; and the membrane abscission step in cytokinesis. The past few years have seen an explosion of novel functions: the biogenesis of microvesicles and exosomes; plasma membrane wound repair; neuron pruning; extraction of defective nuclear pore comp...
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Hurley, J. H. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Review Source Type: research

Response to Heard et al
(Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Moulin, M., Voss, A. K., Thomas, T., Wong, W. W.-L., Cook, W. D., Koentgen, F., Vince, J., Silke, J., Vaux, D. L. Tags: Autophagy & Cell Death, Signal Transduction Correspondence Source Type: research

cIAP2 supports viability of mice lacking cIAP1 and XIAP
(Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Heard, K. N., Bertrand, M. J., Barker, P. A. Tags: Autophagy & Cell Death, Signal Transduction Correspondence Source Type: research

The different autophagic roads by which phagosomes travel to lysosomes
This study suggests that the autophagic machinery can regulate phagocytosis via two pathways, modification of phagosomes during LC3-associated phagocytosis (LAP) and macroautophagy of phagosomes. (Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Munz, C. Tags: Immunology, Membrane & Intracellular Transport News [amp ] Views Source Type: research

The tumor suppressor FBW7 controls ciliary length
The primary cilium provides a hub for reception of extracellular chemical and mechanical cues that influence differentiation, proliferation, and polarity, and contributes to cell cycle control. Ciliary length impacts the cilium's ability to coordinate these processes, and length control defects are linked to a number of clinically important developmental disorders. An exciting new study identifies a new mechanism of ciliary regulation based on interactions of CDK5 and the FBW7 tumor suppressor in regulating the degradation of the centrosomal protein NDE1 (Maskey et al, 2015). (Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Nikonova, A. S., Golemis, E. A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

{alpha}-Synuclein oligomers pump it up!
Oligomeric forms of the Parkinson's disease-causing protein α-synuclein are suspected to mediate neurodegeneration, but the mechanisms are not understood. The present study of Shrivastava et al (2015) provides a fresh insight into this old mystery. α-Synuclein oligomers are shown by a combination of top state-of-the-art biochemical and super-resolution microscopy methods to sequester the neuronal sodium–potassium pump. Such perturbation of ion currents would ultimately lead to Ca2+ excitotoxicity. (Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Kahle, P. J., Sugeno, N., Skodras, A. Tags: Neuroscience News [amp ] Views Source Type: research

Shp2 signaling suppresses senescence in PyMT-induced mammary gland cancer in mice
(Source: EMBO Journal)
Source: EMBO Journal - September 14, 2015 Category: Molecular Biology Authors: Lan, L., Holland, J. D., Qi, J., Grosskopf, S., Vogel, R., Gyorffy, B., Wulf-Goldenberg, A., Birchmeier, W. Tags: Corrigendum Source Type: research

RuvbL1 and RuvbL2 enhance aggresome formation and disaggregate amyloid fibrils
The aggresome is an organelle that recruits aggregated proteins for storage and degradation. We performed an siRNA screen for proteins involved in aggresome formation and identified novel mammalian AAA+ protein disaggregases RuvbL1 and RuvbL2. Depletion of RuvbL1 or RuvbL2 suppressed aggresome formation and caused buildup of multiple cytoplasmic aggregates. Similarly, downregulation of RuvbL orthologs in yeast suppressed the formation of an aggresome-like body and enhanced the aggregate toxicity. In contrast, their overproduction enhanced the resistance to proteotoxic stress independently of chaperone Hsp104. Mammalian Ruv...
Source: EMBO Journal - September 14, 2015 Category: Molecular Biology Authors: Zaarur, N., Xu, X., Lestienne, P., Meriin, A. B., McComb, M., Costello, C. E., Newnam, G. P., Ganti, R., Romanova, N. V., Shanmugasundaram, M., Silva, S. T., Bandeiras, T. M., Matias, P. M., Lobachev, K. S., Lednev, I. K., Chernoff, Y. O., Sherman, M. Y. Tags: Protein Biosynthesis & Quality Control Articles Source Type: research

The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis
The Dnmt2 enzyme utilizes the catalytic mechanism of eukaryotic DNA methyltransferases to methylate several tRNAs at cytosine 38. Dnmt2 mutant mice, flies, and plants were reported to be viable and fertile, and the biological function of Dnmt2 has remained elusive. Here, we show that endochondral ossification is delayed in newborn Dnmt2-deficient mice, which is accompanied by a reduction of the haematopoietic stem and progenitor cell population and a cell-autonomous defect in their differentiation. RNA bisulfite sequencing revealed that Dnmt2 methylates C38 of tRNA AspGTC, GlyGCC, and ValAAC, thus preventing tRNA fragmenta...
Source: EMBO Journal - September 14, 2015 Category: Molecular Biology Authors: Tuorto, F., Herbst, F., Alerasool, N., Bender, S., Popp, O., Federico, G., Reitter, S., Liebers, R., Stoecklin, G., Grone, H.-J., Dittmar, G., Glimm, H., Lyko, F. Tags: Development & Differentiation, Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Proteotoxic stress and ageing triggers the loss of redox homeostasis across cellular compartments
The cellular proteostasis network integrates the protein folding and clearance machineries in multiple sub-cellular compartments of the eukaryotic cell. The endoplasmic reticulum (ER) is the site of synthesis and folding of membrane and secretory proteins. A distinctive feature of the ER is its tightly controlled redox homeostasis necessary for the formation of inter- and intra-molecular disulphide bonds. Employing genetically encoded in vivo sensors reporting on the redox state in an organelle-specific manner, we show in the nematode Caenorhabditis elegans that the redox state of the ER is subject to profound changes...
Source: EMBO Journal - September 14, 2015 Category: Molecular Biology Authors: Kirstein, J., Morito, D., Kakihana, T., Sugihara, M., Minnen, A., Hipp, M. S., Nussbaum-Krammer, C., Kasturi, P., Hartl, F. U., Nagata, K., Morimoto, R. I. Tags: Ageing, Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control Articles Source Type: research

E-cadherin can limit the transforming properties of activating {beta}-catenin mutations
Wnt pathway deregulation is a common characteristic of many cancers. Only colorectal cancer predominantly harbours mutations in APC, whereas other cancer types (hepatocellular carcinoma, solid pseudopapillary tumours of the pancreas) have activating mutations in β-catenin (CTNNB1). We have compared the dynamics and the potency of β-catenin mutations in vivo. Within the murine small intestine (SI), an activating mutation of β-catenin took much longer to achieve Wnt deregulation and acquire a crypt-progenitor cell (CPC) phenotype than Apc or Gsk3 loss. Within the colon, a single activating mutation of &be...
Source: EMBO Journal - September 14, 2015 Category: Molecular Biology Authors: Huels, D. J., Ridgway, R. A., Radulescu, S., Leushacke, M., Campbell, A. D., Biswas, S., Leedham, S., Serra, S., Chetty, R., Moreaux, G., Parry, L., Matthews, J., Song, F., Hedley, A., Kalna, G., Ceteci, F., Reed, K. R., Meniel, V. S., Maguire, A., Doyle, Tags: Cancer, Cell Adhesion, Polarity & Cytoskeleton Articles Source Type: research

Collaborative protein filaments
It is now well established that prokaryotic cells assemble diverse proteins into dynamic cytoskeletal filaments that perform essential cellular functions. Although most of the filaments assemble on their own to form higher order structures, growing evidence suggests that there are a number of prokaryotic proteins that polymerise only in the presence of a matrix such as DNA, lipid membrane or even another filament. Matrix-assisted filament systems are frequently nucleotide dependent and cytomotive but rarely considered as part of the bacterial cytoskeleton. Here, we categorise this family of filament-forming systems as coll...
Source: EMBO Journal - September 14, 2015 Category: Molecular Biology Authors: Ghosal, D., Lowe, J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Microbiology, Virology & Host Pathogen Interaction Review Source Type: research

Better to burn out than it is to rust: coordinating cellular redox states during aging and stress
Both the protein homeostasis (proteostasis) and the oxidation/reduction (redox) environment of the cell play critical roles in disease- and age-associated decline, yet the relationship between the two remains mysterious. In this issue of The EMBO Journal, Kirstein et al (2015) show that both the cytosol and the ER shift their redox states in response to proteotoxic stress and that stress in one compartment can alter redox state in the other. Moreover, proteotoxic stress can induce changes in redox state across tissues, suggesting that an organism-wide surveillance mechanism modulates cellular redox environment. (Source: EMBO Journal)
Source: EMBO Journal - September 14, 2015 Category: Molecular Biology Authors: Rongo, C. Tags: Ageing, Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control News [amp ] Views Source Type: research

Cancer: leaping the E-cadherin hurdle
Aberrant activation of the Wnt signaling pathway is a common cause of colon cancer and other tumor types, accomplishing many of the hallmarks of cancer including sustained proliferative signaling, replicative immortality, reprogrammed metabolism, angiogenesis, and invasion. Yet, the dominant mutation that leads to chronic Wnt signaling in colon cancer is quite different from the spectrum of mutations that activate Wnt signaling in other tumor types. In this issue of The EMBO Journal, Huels et al (2015) focus on the influential role E-cadherin plays in shaping these differences. (Source: EMBO Journal)
Source: EMBO Journal - September 14, 2015 Category: Molecular Biology Authors: Chen, G. T., Waterman, M. L. Tags: Cancer, Cell Adhesion, Polarity & Cytoskeleton News [amp ] Views Source Type: research

Triggered Ca2+ influx is required for extended synaptotagmin 1-induced ER-plasma membrane tethering
The extended synaptotagmins (E-Syts) are ER proteins that act as Ca2+-regulated tethers between the ER and the plasma membrane (PM) and have a putative role in lipid transport between the two membranes. Ca2+ regulation of their tethering function, as well as the interplay of their different domains in such function, remains poorly understood. By exposing semi-intact cells to buffers of variable Ca2+ concentrations, we found that binding of E-Syt1 to the PI(4,5)P2-rich PM critically requires its C2C and C2E domains and that the EC50 of such binding is in the low micromolar Ca2+ range. Accordingly, E-Syt1 accumulation at ER-...
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: Idevall-Hagren, O., Lu, A., Xie, B., De Camilli, P. Tags: Membrane & Intracellular Transport Articles Source Type: research

mTOR activates the VPS34-UVRAG complex to regulate autolysosomal tubulation and cell survival
Lysosomes are essential organelles that function to degrade and recycle unwanted, damaged and toxic biological components. Lysosomes also act as signalling platforms in activating the nutrient-sensing kinase mTOR. mTOR regulates cellular growth, but it also helps to maintain lysosome identity by initiating lysosomal tubulation through a process termed autophagosome-lysosome reformation (ALR). Here we identify a lysosomal pool of phosphatidylinositol 3-phosphate that, when depleted by specific inhibition of the class III phosphoinositide 3-kinase VPS34, results in prolonged lysosomal tubulation. This tubulation requires mTO...
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: Munson, M. J., Allen, G. F., Toth, R., Campbell, D. G., Lucocq, J. M., Ganley, I. G. Tags: Membrane & Intracellular Transport, Signal Transduction Articles Source Type: research

Huntingtin proteolysis releases non-polyQ fragments that cause toxicity through dynamin 1 dysregulation
Cleavage of mutant huntingtin (HTT) is an essential process in Huntington's disease (HD), an inherited neurodegenerative disorder. Cleavage generates N-ter fragments that contain the polyQ stretch and whose nuclear toxicity is well established. However, the functional defects induced by cleavage of full-length HTT remain elusive. Moreover, the contribution of non-polyQ C-terminal fragments is unknown. Using time- and site-specific control of full-length HTT proteolysis, we show that specific cleavages are required to disrupt intramolecular interactions within HTT and to cause toxicity in cells and flies. Surprisingly, in a...
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: El-Daher, M.-T., Hangen, E., Bruyere, J., Poizat, G., Al-Ramahi, I., Pardo, R., Bourg, N., Souquere, S., Mayet, C., Pierron, G., Leveque-Fort, S., Botas, J., Humbert, S., Saudou, F. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

A large-scale functional screen identifies Nova1 and Ncoa3 as regulators of neuronal miRNA function
MicroRNAs (miRNAs) are important regulators of neuronal development, network connectivity, and synaptic plasticity. While many neuronal miRNAs were previously shown to modulate neuronal morphogenesis, little is known regarding the regulation of miRNA function. In a large-scale functional screen, we identified two novel regulators of neuronal miRNA function, Nova1 and Ncoa3. Both proteins are expressed in the nucleus and the cytoplasm of developing hippocampal neurons. We found that Nova1 and Ncoa3 stimulate miRNA function by different mechanisms that converge on Argonaute (Ago) proteins, core components of the miRNA-induce...
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: Storchel, P. H., Thummler, J., Siegel, G., Aksoy-Aksel, A., Zampa, F., Sumer, S., Schratt, G. Tags: Neuroscience, RNA Biology Articles Source Type: research

The wound inflammatory response exacerbates growth of pre-neoplastic cells and progression to cancer
There is a long-standing association between wound healing and cancer, with cancer often described as a "wound that does not heal". However, little is known about how wounding, such as following surgery, biopsy collection or ulceration, might impact on cancer progression. Here, we use a translucent zebrafish larval model of RasG12V-driven neoplasia to image the interactions between inflammatory cells drawn to a wound, and to adjacent pre-neoplastic cells. We show that neutrophils are rapidly diverted from a wound to pre-neoplastic cells and these interactions lead to increased proliferation of the pre-neoplastic ...
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: Antonio, N., Bonnelykke-Behrndtz, M. L., Ward, L. C., Collin, J., Christensen, I. J., Steiniche, T., Schmidt, H., Feng, Y., Martin, P. Tags: Immunology, Molecular Biology of Disease Articles Source Type: research

Scissors for autolysosome tubules
Autophagic lysosome reformation (ALR) is a cellular process in which lysosomes are reformed through scission of proto-lysosomes from tubular structures extruded from autolysosomes. Despite recent progress, the molecular mechanism of ALR is far from clear. A paper in this issue of The EMBO Journal has identified lysosome-localized PI(3)P, which is generated by the VPS34–UVRAG complex in an mTOR-dependent manner, as an important regulator of autolysosome tubule scission (Munson et al, 2015). (Source: EMBO Journal)
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: Chen, Y., Yu, L. Tags: Membrane & Intracellular Transport, Signal Transduction News [amp ] Views Source Type: research

Huntington's disease--the sting in the tail
Huntington's disease (HD) is a progressive neurodegenerative condition caused by the abnormal expansion of a polyglutamine tract in the N-terminus of the huntingtin protein. Over the last 20 years, HD pathogenesis has been explained by the generation of N-terminal fragments containing the polyglutamine stretch. A new study from Frederic Saudou's group now investigates the function of the C-terminal fragments generated upon cleavage and shows that these products may also contribute to cellular toxicity in HD (El-Daher et al, 2015). (Source: EMBO Journal)
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: Jimenez-Sanchez, M., Rubinsztein, D. C. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

New friends for Ago2 in neuronal plasticity
MicroRNAs have emerged as central regulators of cellular homeostasis and increasing evidence suggests that they play a key role in neuronal plasticity. Major efforts are made to define microRNA networks and their targets in the brain. The mechanisms by which microRNA activity is regulated are, however, relatively unexplored. In this issue of The EMBO Journal, Störchel et al (2015) screened for proteins that affect microRNA function in neurons. They identify Nova1 and Ncoa3 as novel regulators of miRNA activity and demonstrate that both proteins are essential for neuronal plasticity in a microRNA-dependent manner....
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: Sananbenesi, F., Fischer, A. Tags: Neuroscience, RNA Biology News [amp ] Views Source Type: research

Neutrophils fan cancer's flames
This study reinforces the notion that inflammation flames carcinogenesis, which might have important implications for the improvement of antitumour therapies. (Source: EMBO Journal)
Source: EMBO Journal - September 2, 2015 Category: Molecular Biology Authors: Wculek, S. K., Malanchi, I. Tags: Immunology, Molecular Biology of Disease News [amp ] Views Source Type: research

Chimeric adaptor proteins translocate diverse type VI secretion system effectors in Vibrio cholerae
Vibrio cholerae is a diverse species of Gram-negative bacteria, commonly found in the aquatic environment and the causative agent of the potentially deadly disease cholera. These bacteria employ a type VI secretion system (T6SS) when they encounter prokaryotic and eukaryotic competitors. This contractile puncturing device translocates a set of effector proteins into neighboring cells. Translocated effectors are toxic unless the targeted cell produces immunity proteins that bind and deactivate incoming effectors. Comparison of multiple V. cholerae strains indicates that effectors are encoded in T6SS effector modules on...
Source: EMBO Journal - August 12, 2015 Category: Molecular Biology Authors: Unterweger, D., Kostiuk, B., Otjengerdes, R., Wilton, A., Diaz-Satizabal, L., Pukatzki, S. Tags: Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Assembly of Slx4 signaling complexes behind DNA replication forks
Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constit...
Source: EMBO Journal - August 12, 2015 Category: Molecular Biology Authors: Balint, A., Kim, T., Gallo, D., Cussiol, J. R., Bastos de Oliveira, F. M., Yimit, A., Ou, J., Nakato, R., Gurevich, A., Shirahige, K., Smolka, M. B., Zhang, Z., Brown, G. W. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

JNK-dependent gene regulatory circuitry governs mesenchymal fate
The epithelial to mesenchymal transition (EMT) is a biological process in which cells lose cell–cell contacts and become motile. EMT is used during development, for example, in triggering neural crest migration, and in cancer metastasis. Despite progress, the dynamics of JNK signaling, its role in genomewide transcriptional reprogramming, and involved downstream effectors during EMT remain largely unknown. Here, we show that JNK is not required for initiation, but progression of phenotypic changes associated with EMT. Such dependency resulted from JNK-driven transcriptional reprogramming of critical EMT genes and inv...
Source: EMBO Journal - August 12, 2015 Category: Molecular Biology Authors: Sahu, S. K., Garding, A., Tiwari, N., Thakurela, S., Toedling, J., Gebhard, S., Ortega, F., Schmarowski, N., Berninger, B., Nitsch, R., Schmidt, M., Tiwari, V. K. Tags: Cancer, Cell Adhesion, Polarity & Cytoskeleton, Transcription Articles Source Type: research

Membrane protrusion powers clathrin-independent endocytosis of interleukin-2 receptor
Endocytosis controls many functions including nutrient uptake, cell division, migration and signal transduction. A clathrin- and caveolin-independent endocytosis pathway is used by important physiological cargos, including interleukin-2 receptors (IL-2R). However, this process lacks morphological and dynamic data. Our electron microscopy (EM) and tomography studies reveal that IL-2R-pits and vesicles are initiated at the base of protrusions. We identify the WAVE complex as a specific endocytic actor. The WAVE complex interacts with IL-2R, via a WAVE-interacting receptor sequence (WIRS) present in the receptor polypeptide, ...
Source: EMBO Journal - August 12, 2015 Category: Molecular Biology Authors: Basquin, C., Trichet, M., Vihinen, H., Malarde, V., Lagache, T., Ripoll, L., Jokitalo, E., Olivo-Marin, J.-C., Gautreau, A., Sauvonnet, N. Tags: Membrane & Intracellular Transport Articles Source Type: research

Crosstalk between Akt/GSK3{beta} signaling and dynamin-1 regulates clathrin-mediated endocytosis
Clathrin-mediated endocytosis (CME) regulates signaling from the plasma membrane. Analysis of clathrin-coated pit (CCP) dynamics led us to propose the existence of a rate-limiting, regulatory step(s) that monitor the fidelity of early stages in CCP maturation. Here we show that nascent endocytic vesicles formed in mutant cells displaying rapid, dysregulated CME are defective in early endosomal trafficking, maturation and acidification, confirming the importance of this "checkpoint." Dysregulated CME also alters EGF receptor signaling and leads to constitutive activation of the protein kinase Akt. Dynamin-1, which...
Source: EMBO Journal - August 12, 2015 Category: Molecular Biology Authors: Reis, C. R., Chen, P.-H., Srinivasan, S., Aguet, F., Mettlen, M., Schmid, S. L. Tags: Membrane & Intracellular Transport Articles Source Type: research

Lipid droplets and their component triglycerides and steryl esters regulate autophagosome biogenesis
Autophagy is a major catabolic process responsible for the delivery of proteins and organelles to the lysosome/vacuole for degradation. Malfunction of this pathway has been implicated in numerous pathological conditions. Different organelles have been found to contribute to the formation of autophagosomes, but the exact mechanism mediating this process remains obscure. Here, we show that lipid droplets (LDs) are important for the regulation of starvation-induced autophagy. Deletion of Dga1 and Lro1 enzymes responsible for triacylglycerol (TAG) synthesis, or of Are1 and Are2 enzymes responsible for the synthesis of steryl e...
Source: EMBO Journal - August 12, 2015 Category: Molecular Biology Authors: Shpilka, T., Welter, E., Borovsky, N., Amar, N., Mari, M., Reggiori, F., Elazar, Z. Tags: Autophagy & Cell Death, Metabolism Articles Source Type: research

Optochemistry to control the microtubule cytoskeleton
Microtubule drugs have a wide range of applications in cell biology research as well as cancer therapy; however their application was so far limited to the treatment of entire cell populations and tissues. In a recent paper in Cell, Borowiak et al (2015) now describe a novel type of switchable microtubule drugs. The activity of their drugs, denoted as "photostatins", can be switched on and off by violet and green light, respectively, which allows for the first time a precise spatial and temporal control of the microtubule cytoskeleton in single cells and tissues. (Source: EMBO Journal)
Source: EMBO Journal - August 12, 2015 Category: Molecular Biology Authors: Janke, C., Steinmetz, M. O. Tags: Cell Adhesion, Polarity & Cytoskeleton News [amp ] Views Source Type: research

Autophagosomes and lipid droplets: no longer just chewing the fat
Autophagosomes are organelles capable of sequestering and degrading diverse cytoplasmic cargo for nutritional and quality control purposes. Targeted are also lipid droplets (LDs), the cytoplasmic stores of neutral lipids. In this issue of The EMBO Journal, Shpilka et al (2015) show that the relationship between LDs and autophagosomes is far more intricate and that LDs regulate autophagosome biogenesis. (Source: EMBO Journal)
Source: EMBO Journal - August 12, 2015 Category: Molecular Biology Authors: Deretic, V. Tags: Autophagy & Cell Death, Metabolism News [amp ] Views Source Type: research

And-1 coordinates with Claspin for efficient Chk1 activation in response to replication stress
The replisome is important for DNA replication checkpoint activation, but how specific components of the replisome coordinate with ATR to activate Chk1 in human cells remains largely unknown. Here, we demonstrate that And-1, a replisome component, acts together with ATR to activate Chk1. And-1 is phosphorylated at T826 by ATR following replication stress, and this phosphorylation is required for And-1 to accumulate at the damage sites, where And-1 promotes the interaction between Claspin and Chk1, thereby stimulating efficient Chk1 activation by ATR. Significantly, And-1 binds directly to ssDNA and facilitates the associat...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Hao, J., de Renty, C., Li, Y., Xiao, H., Kemp, M. G., Han, Z., DePamphilis, M. L., Zhu, W. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

TRIM5{alpha} requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription
TRIM5α is an antiviral, cytoplasmic, E3 ubiquitin (Ub) ligase that assembles on incoming retroviral capsids and induces their premature dissociation. It inhibits reverse transcription of the viral genome and can also synthesize unanchored polyubiquitin (polyUb) chains to stimulate innate immune responses. Here, we show that TRIM5α employs the E2 Ub-conjugating enzyme Ube2W to anchor the Lys63-linked polyUb chains in a process of TRIM5α auto-ubiquitination. Chain anchoring is initiated, in cells and in vitro, through Ube2W-catalyzed monoubiquitination of TRIM5α. This modification serves as a substrat...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Fletcher, A. J., Christensen, D. E., Nelson, C., Tan, C. P., Schaller, T., Lehner, P. J., Sundquist, W. I., Towers, G. J. Tags: Microbiology, Virology & Host Pathogen Interaction, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Regulation of synaptic activity by snapin-mediated endolysosomal transport and sorting
Recycling synaptic vesicles (SVs) transit through early endosomal sorting stations, which raises a fundamental question: are SVs sorted toward endolysosomal pathways? Here, we used snapin mutants as tools to assess how endolysosomal sorting and trafficking impact presynaptic activity in wild-type and snapin–/– neurons. Snapin acts as a dynein adaptor that mediates the retrograde transport of late endosomes (LEs) and interacts with dysbindin, a subunit of the endosomal sorting complex BLOC-1. Expressing dynein-binding defective snapin mutants induced SV accumulation at presynaptic terminals, mimicking the snapin...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Di Giovanni, J., Sheng, Z.-H. Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

Molecular profiling of CD8 T cells in autochthonous melanoma identifies Maf as driver of exhaustion
T cells infiltrating neoplasms express surface molecules typical of chronically virus-stimulated T cells, often termed "exhausted" T cells. We compared the transcriptome of "exhausted" CD8 T cells infiltrating autochthonous melanomas to those of naïve and acutely stimulated CD8 T cells. Despite strong similarities between transcriptional signatures of tumor- and virus-induced exhausted CD8 T cells, notable differences appeared. Among transcriptional regulators, Nr4a2 and Maf were highly overexpressed in tumor-exhausted T cells and significantly upregulated in CD8 T cells from human melanoma me...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Giordano, M., Henin, C., Maurizio, J., Imbratta, C., Bourdely, P., Buferne, M., Baitsch, L., Vanhille, L., Sieweke, M. H., Speiser, D. E., Auphan-Anezin, N., Schmitt-Verhulst, A.-M., Verdeil, G. Tags: Immunology, Molecular Biology of Disease Articles Source Type: research

Robust intestinal homeostasis relies on cellular plasticity in enteroblasts mediated by miR-8-Escargot switch
The intestinal epithelium is remarkably robust despite perturbations and demand uncertainty. Here, we investigate the basis of such robustness using novel tracing methods that allow simultaneously capturing the dynamics of stem and committed progenitor cells (called enteroblasts) and intestinal cell turnover with spatiotemporal resolution. We found that intestinal stem cells (ISCs) divide "ahead" of demand during Drosophila midgut homeostasis. Their newborn enteroblasts, on the other hand, take on a highly polarized shape, acquire invasive properties and motility. They extend long membrane protrusions that make c...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Antonello, Z. A., Reiff, T., Ballesta-Illan, E., Dominguez, M. Tags: Development & Differentiation, Stem Cells Articles Source Type: research

Single cell tuning of Myc expression by antigen receptor signal strength and interleukin-2 in T lymphocytes
Myc controls the metabolic reprogramming that supports effector T cell differentiation. The expression of Myc is regulated by the T cell antigen receptor (TCR) and pro-inflammatory cytokines such as interleukin-2 (IL-2). We now show that the TCR is a digital switch for Myc mRNA and protein expression that allows the strength of the antigen stimulus to determine the frequency of T cells that express Myc. IL-2 signalling strength also directs Myc expression but in an analogue process that fine-tunes Myc quantity in individual cells via post-transcriptional control of Myc protein. Fine-tuning Myc matters and is possible ...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Preston, G. C., Sinclair, L. V., Kaskar, A., Hukelmann, J. L., Navarro, M. N., Ferrero, I., MacDonald, H. R., Cowling, V. H., Cantrell, D. A. Tags: Immunology, Signal Transduction Articles Source Type: research

Transcriptional repression by MYB3R proteins regulates plant organ growth
In multicellular organisms, temporal and spatial regulation of cell proliferation is central for generating organs with defined sizes and morphologies. For establishing and maintaining the post-mitotic quiescent state during cell differentiation, it is important to repress genes with mitotic functions. We found that three of the Arabidopsis MYB3R transcription factors synergistically maintain G2/M-specific genes repressed in post-mitotic cells and restrict the time window of mitotic gene expression in proliferating cells. The combined mutants of the three repressor-type MYB3R genes displayed long roots, enlarged leaves, em...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Kobayashi, K., Suzuki, T., Iwata, E., Nakamichi, N., Suzuki, T., Chen, P., Ohtani, M., Ishida, T., Hosoya, H., Muller, S., Leviczky, T., Pettko-Szandtner, A., Darula, Z., Iwamoto, A., Nomoto, M., Tada, Y., Higashiyama, T., Demura, T., Doonan, J. H., Hause Tags: Cell Cycle, Plant Biology, Transcription Articles Source Type: research

Myc or no Myc, that is the question
The transcription factor c-MYC functions as the master transcription factor for establishing highly active metabolic states in proliferating cells. c-Myc is essential for rapid proliferation of normal cells and has causal relationship with many cancers, including leukemia and lymphoma. While the expression of c-MYC can be aberrantly driven by genetic abnormalities, such as chromosomal translocations directly involving the MYC locus or mutations of its upstream regulators, how c-MYC expression is induced and amplified in normal lymphocytes in response to antigen stimulation remains elusive. In this issue of The EMBO Journal...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Chou, C., Egawa, T. Tags: Immunology, Signal Transduction Have you seen? Source Type: research

Does Arabidopsis thaliana DREAM of cell cycle control?
Strict temporal control of cell cycle gene expression is essential for all eukaryotes including animals and plants. DREAM complexes have been identified in worm, fly, and mammals, linking several distinct transcription factors to coordinate gene expression throughout the cell cycle. In this issue of The EMBO Journal, Kobayashi et al (2015) identify distinct activator and repressor complexes for genes expressed during the G2 and M phases in Arabidopsis that can be temporarily separated during proliferating and post-mitotic stages of development. The complexes incorporate specific activator and repressor MYB and E2F tra...
Source: EMBO Journal - August 3, 2015 Category: Molecular Biology Authors: Fischer, M., DeCaprio, J. A. Tags: Cell Cycle, Plant Biology, Transcription Have you seen? Source Type: research

Regulation of the Rev1-pol {zeta} complex during bypass of a DNA interstrand cross-link
DNA interstrand cross-links (ICLs) are repaired in S phase by a complex, multistep mechanism involving translesion DNA polymerases. After replication forks collide with an ICL, the leading strand approaches to within one nucleotide of the ICL ("approach"), a nucleotide is inserted across from the unhooked lesion ("insertion"), and the leading strand is extended beyond the lesion ("extension"). How DNA polymerases bypass the ICL is incompletely understood. Here, we use repair of a site-specific ICL in Xenopus egg extracts to study the mechanism of lesion bypass. Deep sequencing of ICL repair pr...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Budzowska, M., Graham, T. G., Sobeck, A., Waga, S., Walter, J. C. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase
The human DNA polymerase gamma (Pol ) is responsible for DNA replication in mitochondria. Pol is particularly susceptible to inhibition by dideoxynucleoside-based inhibitors designed to fight viral infection. Here, we report crystal structures of the replicating Pol –DNA complex bound to either substrate or zalcitabine, an inhibitor used for HIV reverse transcriptase. The structures reveal that zalcitabine binds to the Pol active site almost identically to the substrate dCTP, providing a structural basis for Pol -mediated drug toxicity. When compared to the apo form, Pol undergoes intra- and inter-subunit conformatio...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Szymanski, M. R., Kuznetsov, V. B., Shumate, C., Meng, Q., Lee, Y.-S., Patel, G., Patel, S., Yin, Y. W. Tags: DNA Replication, Repair & Recombination, Structural Biology Articles Source Type: research

RPA prevents G-rich structure formation at lagging-strand telomeres to allow maintenance of chromosome ends
Replication protein A (RPA) is a highly conserved heterotrimeric single-stranded DNA-binding protein involved in DNA replication, recombination, and repair. In fission yeast, the Rpa1-D223Y mutation provokes telomere shortening. Here, we show that this mutation impairs lagging-strand telomere replication and leads to the accumulation of secondary structures and recruitment of the homologous recombination factor Rad52. The presence of these secondary DNA structures correlates with reduced association of shelterin subunits Pot1 and Ccq1 at telomeres. Strikingly, heterologous expression of the budding yeast Pif1 known to effi...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Audry, J., Maestroni, L., Delagoutte, E., Gauthier, T., Nakamura, T. M., Gachet, Y., Saintome, C., Geli, V., Coulon, S. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Reconstitution of the human U snRNP assembly machinery reveals stepwise Sm protein organization
The assembly of spliceosomal U snRNPs depends on the coordinated action of PRMT5 and SMN complexes in vivo. These trans-acting factors enable the faithful delivery of seven Sm proteins onto snRNA and the formation of the common core of snRNPs. To gain mechanistic insight into their mode of action, we reconstituted the assembly machinery from recombinant sources. We uncover a stepwise and ordered formation of distinct Sm protein complexes on the PRMT5 complex, which is facilitated by the assembly chaperone pICln. Upon completion, the formed pICln-Sm units are displaced by new pICln-Sm protein substrates and transferred...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Neuenkirchen, N., Englbrecht, C., Ohmer, J., Ziegenhals, T., Chari, A., Fischer, U. Tags: RNA Biology Articles Source Type: research

Not4-dependent translational repression is important for cellular protein homeostasis in yeast
Translation of aberrant or problematic mRNAs can cause ribosome stalling which leads to the production of truncated or defective proteins. Therefore, cells evolved cotranslational quality control mechanisms that eliminate these transcripts and target arrested nascent polypeptides for proteasomal degradation. Here we show that Not4, which is part of the multifunctional Ccr4–Not complex in yeast, associates with polysomes and contributes to the negative regulation of protein synthesis. Not4 is involved in translational repression of transcripts that cause transient ribosome stalling. The absence of Not4 affected global...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Preissler, S., Reuther, J., Koch, M., Scior, A., Bruderek, M., Frickey, T., Deuerling, E. Tags: Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Chromatin signatures at Notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation
The conserved Notch pathway functions in diverse developmental and disease-related processes, requiring mechanisms to ensure appropriate target selection and gene activation in each context. To investigate the influence of chromatin organisation and dynamics on the response to Notch signalling, we partitioned Drosophila chromatin using histone modifications and established the preferred chromatin conditions for binding of Su(H), the Notch pathway transcription factor. By manipulating activity of a co-operating factor, Lozenge/Runx, we showed that it can help facilitate these conditions. While many histone modifications wer...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Skalska, L., Stojnic, R., Li, J., Fischer, B., Cerda-Moya, G., Sakai, H., Tajbakhsh, S., Russell, S., Adryan, B., Bray, S. J. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Post-translational Modifications, Proteolysis & Proteomics, Systems & Computational Biology Articles Source Type: research

Loss of MT1-MMP causes cell senescence and nuclear defects which can be reversed by retinoic acid
MT1-MMP (MMP14) is a collagenolytic enzyme located at the cell surface and implicated in extracellular matrix (ECM) remodeling. Mmp14–/– mice present dwarfism, bone abnormalities, and premature death. We demonstrate herein that the loss of MT1-MMP also causes cardiac defects and severe metabolic changes, and alters the cytoskeleton and the nuclear lamina structure. Moreover, the absence of MT1-MMP induces a senescent phenotype characterized by up-regulation of p16INK4a and p21CIP1/WAF1, increased activity of senescence-associated β-galactosidase, generation of a senescence-associated secretory phenotype, a...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Gutierrez-Fernandez, A., Soria-Valles, C., Osorio, F. G., Gutierrez-Abril, J., Garabaya, C., Aguirre, A., Fueyo, A., Fernandez-Garcia, M. S., Puente, X. S., Lopez-Otin, C. Tags: Ageing, Molecular Biology of Disease, Physiology Articles Source Type: research

Discrete domains of gene expression in germinal layers distinguish the development of gyrencephaly
We present a large-scale transcriptomic analysis of individual germinal layers in the developing cortex of the gyrencephalic ferret, comparing between regions prospective of fold and fissure. We find unique transcriptional signatures in each germinal compartment, where thousands of genes are differentially expressed between regions, including ~80% of genes mutated in human cortical malformations. These regional differences emerge from the existence of discrete domains of gene expression, which occur at multiple locations across the developing cortex of ferret and human, but not the lissencephalic mouse. Complex expression ...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: de Juan Romero, C., Bruder, C., Tomasello, U., Sanz-Anquela, J. M., Borrell, V. Tags: Development & Differentiation, Neuroscience Resource Source Type: research

ER-endosome contact sites: molecular compositions and functions
Recent studies have revealed the existence of numerous contact sites between the endoplasmic reticulum (ER) and endosomes in mammalian cells. Such contacts increase during endosome maturation and play key roles in cholesterol transfer, endosome positioning, receptor dephosphorylation, and endosome fission. At least 7 distinct contact sites between the ER and endosomes have been identified to date, which have diverse molecular compositions. Common to these contact sites is that they impose a close apposition between the ER and endosome membranes, which excludes membrane fusion while allowing the flow of molecular signals be...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Raiborg, C., Wenzel, E. M., Stenmark, H. Tags: Membrane & Intracellular Transport, Metabolism, Molecular Biology of Disease Review Source Type: research

Clever space saving--how the cerebral cortex folds
The human cerebral cortex controls complex cognitive behaviors. During mammalian evolution, the number of neurons increased in many lineages, requiring a larger cortical surface area to fit into a skull that did not scale proportionally. This space problem was solved by cortical folding, resulting in gyrencephalic (folded) brains. While several hypotheses have been proposed to explain cortical gyrification, we lack mechanistic insights to understand the process itself and in particular its underlying genomic changes, that lead to the appearance of cortical folds. In this issue of The EMBO Journal, de Juan Romero et al...
Source: EMBO Journal - July 13, 2015 Category: Molecular Biology Authors: Albert, M., Huttner, W. B. Tags: Neuroscience Have you seen? Source Type: research