Downregulation of basal myosin-II is required for cell shape changes and tissue invagination
Tissue invagination drives embryo remodeling and assembly of internal organs during animal development. While the role of actomyosin-mediated apical constriction in initiating inward folding is well established, computational models suggest relaxation of the basal surface as an additional requirement. However, the lack of genetic mutations interfering specifically with basal relaxation has made it difficult to test its requirement during invagination so far. Here we use optogenetics to quantitatively control myosin-II levels at the basal surface of invaginating cells during Drosophila gastrulation. We show that while basal...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Krueger, D., Tardivo, P., Nguyen, C., De Renzis, S. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation Articles Source Type: research

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation
We present a model of an E2~Ub conjugate bound to the phospho-ubiquitin-loaded C-terminus of parkin, derived from NMR chemical shift perturbation experiments. We show the UbcH7~Ub conjugate binds in the open state whereby conjugated ubiquitin binds to the RING1/IBR interface. Further, NMR and mass spectrometry experiments indicate the RING0/RING2 interface is re-modelled, remote from the E2 binding site, and this alters the reactivity of the RING2(Rcat) catalytic cysteine, needed for ubiquitin transfer. Our experiments provide evidence that parkin phosphorylation and E2~Ub recruitment act synergistically to enhance a ...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Condos, T. E., Dunkerley, K. M., Freeman, E. A., Barber, K. R., Aguirre, J. D., Chaugule, V. K., Xiao, Y., Konermann, L., Walden, H., Shaw, G. S. Tags: Post-translational Modifications, Proteolysis & Proteomics, Structural Biology Articles Source Type: research

PIF4-induced BR synthesis is critical to diurnal and thermomorphogenic growth
The Arabidopsis PIF4 and BES1/BZR1 transcription factors antagonize light signaling by facilitating co-activated expression of a large number of cell wall-loosening and auxin-related genes. While PIF4 directly activates expression of these targets, BES1 and BZR1 activity switch from a repressive to an activator function, depending on interaction with TOPLESS and other families of regulators including PIFs. However, the complexity of this regulation and its role in diurnal control of plant growth and brassinosteroid (BR) levels is little understood. We show by using a protein array that BES1, PIF4, and the BES1-PIF4 complex...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Martinez, C., Espinosa-Ruiz, A., de Lucas, M., Bernardo-Garcia, S., Franco-Zorrilla, J. M., Prat, S. Tags: Plant Biology, Signal Transduction, Transcription Articles Source Type: research

Tumor suppressor PNRC1 blocks rRNA maturation by recruiting the decapping complex to the nucleolus
Focal deletions occur frequently in the cancer genome. However, the putative tumor-suppressive genes residing within these regions have been difficult to pinpoint. To robustly identify these genes, we implemented a computational approach based on non-negative matrix factorization, NMF, and interrogated the TCGA dataset. This analysis revealed a metagene signature including a small subset of genes showing pervasive hemizygous deletions, reduced expression in cancer patient samples, and nucleolar function. Amid the genes belonging to this signature, we have identified PNRC1, a nuclear receptor coactivator. We found that PNRC...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Gaviraghi, M., Vivori, C., Pareja Sanchez, Y., Invernizzi, F., Cattaneo, A., Santoliquido, B. M., Frenquelli, M., Segalla, S., Bachi, A., Doglioni, C., Pelechano, V., Cittaro, D., Tonon, G. Tags: Cancer, RNA Biology Articles Source Type: research

Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response
Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG-I was responsible for such tumor-inhibitory effect. Interestingly, repression of HNRNPC resulted in accumulation of endogenous double-stranded RNA (dsRNA), the binding ligand of RIG-I. These ...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Wu, Y., Zhao, W., Liu, Y., Tan, X., Li, X., Zou, Q., Xiao, Z., Xu, H., Wang, Y., Yang, X. Tags: Cancer, Immunology Articles Source Type: research

Infiltrative and drug-resistant slow-cycling cells support metabolic heterogeneity in glioblastoma
Metabolic reprogramming has been described in rapidly growing tumors, which are thought to mostly contain fast-cycling cells (FCCs) that have impaired mitochondrial function and rely on aerobic glycolysis. Here, we characterize the metabolic landscape of glioblastoma (GBM) and explore metabolic specificities as targetable vulnerabilities. Our studies highlight the metabolic heterogeneity in GBM, in which FCCs harness aerobic glycolysis, and slow-cycling cells (SCCs) preferentially utilize mitochondrial oxidative phosphorylation for their functions. SCCs display enhanced invasion and chemoresistance, suggesting their import...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Hoang-Minh, L. B., Siebzehnrubl, F. A., Yang, C., Suzuki-Hatano, S., Dajac, K., Loche, T., Andrews, N., Schmoll Massari, M., Patel, J., Amin, K., Vuong, A., Jimenez-Pascual, A., Kubilis, P., Garrett, T. J., Moneypenny, C., Pacak, C. A., Huang, J., Sayour, Tags: Cancer, Metabolism, Stem Cells Articles Source Type: research

Stress-induced host membrane remodeling protects from infection by non-motile bacterial pathogens
While mucosal inflammation is a major source of stress during enteropathogen infection, it remains to be fully elucidated how the host benefits from this environment to clear the pathogen. Here, we show that host stress induced by different stimuli mimicking inflammatory conditions strongly reduces the binding of Shigella flexneri to epithelial cells. Mechanistically, stress activates acid sphingomyelinase leading to host membrane remodeling. Consequently, knockdown or pharmacological inhibition of the acid sphingomyelinase blunts the stress-dependent inhibition of Shigella binding to host cells. Interestingly, stress caus...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Tawk, C., Nigro, G., Rodrigues Lopes, I., Aguilar, C., Lisowski, C., Mano, M., Sansonetti, P., Vogel, J., Eulalio, A. Tags: Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Putting a strain on diversity
Human life expectancy is increasing on a global scale, but healthspan—the period of life free from age-associated ill health—is not improving at a comparable rate. This disconnect means that a greater proportion of the general population will spend a longer period of their life suffering from one or more debilitating age-associated diseases, such as cardiovascular disease, Alzheimer's disease, osteoporosis, sarcopenia and various cancers. Understanding the processes underlying ageing and age-related diseases is therefore a major and pressing research challenge in biomedical research. (Source: EMBO Journal)
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Selman, C., Swindell, W. R. Tags: Ageing, Genetics, Gene Therapy & Genetic Disease Commentary Source Type: research

Are you TORCing tau me? Amyloid-{beta} blocks the conversation between lysosomes and mitochondria
How amyloid-β (Aβ) and tau exacerbate Alzheimer's disease (AD) at a subcellular level is only incompletely understood. Norambuena et al (2018) report crosstalk between mitochondria and lysosomes and identify a role for lysosomal mTORC1 in the nutrient-induced activation of mitochondria. This lysosomal signalling pathway is strongly inhibited by oligomeric Aβ through the tau-dependent activation of plasma membrane-localized mTORC1. Together, these results identify a further role for tau in mediating Aβ toxicity. (Source: EMBO Journal)
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Polanco, J. C., Götz, J. Tags: Autophagy & Cell Death, Metabolism, Neuroscience News [amp ] Views Source Type: research

Hepatic ERAD takes control of the organism
Upregulation of Endoplasmic Reticulum-Associated Degradation (ERAD) in the liver upon feeding and organismal growth aggravates proteasomal turnover of the transcription factor CREBH and decreases the expression of its target gene, the hepatokine FGF21. Wei et al and Bhattacharya et al describe the systemic coordination of energy metabolism and organismal physiology mediated by hepatic-specific ERAD function. (Source: EMBO Journal)
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Dreher, L.-S., Hoppe, T. Tags: Membrane & Intracellular Transport, Metabolism, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Yap regulates glucose utilization and sustains nucleotide synthesis to enable organ growth
The Hippo pathway and its nuclear effector Yap regulate organ size and cancer formation. While many modulators of Hippo activity have been identified, little is known about the Yap target genes that mediate these growth effects. Here, we show that yap–/– mutant zebrafish exhibit defects in hepatic progenitor potential and liver growth due to impaired glucose transport and nucleotide biosynthesis. Transcriptomic and metabolomic analyses reveal that Yap regulates expression of glucose transporter glut1, causing decreased glucose uptake and use for nucleotide biosynthesis in yap–/– mutants, and impaire...
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Cox, A. G., Tsomides, A., Yimlamai, D., Hwang, K. L., Miesfeld, J., Galli, G. G., Fowl, B. H., Fort, M., Ma, K. Y., Sullivan, M. R., Hosios, A. M., Snay, E., Yuan, M., Brown, K. K., Lien, E. C., Chhangawala, S., Steinhauser, M. L., Asara, J. M., Houvras, Tags: Development & Differentiation, Metabolism Articles Source Type: research

A novel lysosome-to-mitochondria signaling pathway disrupted by amyloid-{beta} oligomers
The mechanisms of mitochondrial dysfunction in Alzheimer's disease are incompletely understood. Using two-photon fluorescence lifetime microscopy of the coenzymes, NADH and NADPH, and tracking brain oxygen metabolism with multi-parametric photoacoustic microscopy, we show that activation of lysosomal mechanistic target of rapamycin complex 1 (mTORC1) by insulin or amino acids stimulates mitochondrial activity and regulates mitochondrial DNA synthesis in neurons. Amyloid-β oligomers, which are precursors of amyloid plaques in Alzheimer's disease brain and stimulate mTORC1 protein kinase activity at the plasma membrane ...
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Norambuena, A., Wallrabe, H., Cao, R., Wang, D. B., Silva, A., Svindrych, Z., Periasamy, A., Hu, S., Tanzi, R. E., Kim, D. Y., Bloom, G. S. Tags: Autophagy & Cell Death, Metabolism, Neuroscience Articles Source Type: research

Structure of the nucleation-promoting factor SPIN90 bound to the actin filament nucleator Arp2/3 complex
Unlike the WASP family of Arp2/3 complex activators, WISH/DIP/SPIN90 (WDS) family proteins activate actin filament nucleation by the Arp2/3 complex without the need for a preformed actin filament. This allows WDS proteins to initiate branched actin network assembly by providing seed filaments that activate WASP-bound Arp2/3 complex. Despite their important role in actin network initiation, it is unclear how WDS proteins drive the activating steps that require both WASP and pre-existing actin filaments during WASP-mediated nucleation. Here, we show that SPIN90 folds into an armadillo repeat domain that binds a surface of Ar...
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Luan, Q., Liu, S.-L., Helgeson, L. A., Nolen, B. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Structural Biology Articles Source Type: research

Hepatic Sel1L-Hrd1 ER-associated degradation (ERAD) manages FGF21 levels and systemic metabolism via CREBH
This study not only establishes the importance of Sel1L-Hrd1 ERAD in the liver in the regulation of systemic energy metabolism, but also reveals a novel hepatic "ERAD-Crebh-Fgf21" axis directly linking ER protein turnover to gene transcription and systemic metabolic regulation. (Source: EMBO Journal)
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Bhattacharya, A., Sun, S., Wang, H., Liu, M., Long, Q., Yin, L., Kersten, S., Zhang, K., Qi, L. Tags: Membrane & Intracellular Transport, Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Local activation of mammalian separase in interphase promotes double-strand break repair and prevents oncogenic transformation
Separase halves eukaryotic chromosomes in M-phase by cleaving cohesin complexes holding sister chromatids together. Whether this essential protease functions also in interphase and/or impacts carcinogenesis remains largely unknown. Here, we show that mammalian separase is recruited to DNA double-strand breaks (DSBs) where it is activated to locally cleave cohesin and facilitate homology-directed repair (HDR). Inactivating phosphorylation of its NES, arginine methylation of its RG-repeats, and sumoylation redirect separase from the cytosol to DSBs. In vitro assays suggest that DNA damage response-relevant ATM, PRMT1, and Mm...
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Hellmuth, S., Gutierrez-Caballero, C., Llano, E., Pendas, A. M., Stemmann, O. Tags: Cell Cycle, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Protein kinase D1 deletion in adipocytes enhances energy dissipation and protects against adiposity
Nutrient overload in combination with decreased energy dissipation promotes obesity and diabetes. Obesity results in a hormonal imbalance, which among others activates G protein-coupled receptors utilizing diacylglycerol (DAG) as secondary messenger. Protein kinase D1 (PKD1) is a DAG effector, which integrates multiple nutritional and hormonal inputs, but its physiological role in adipocytes is unknown. Here, we show that PKD1 promotes lipogenesis and suppresses mitochondrial fragmentation, biogenesis, respiration, and energy dissipation in an AMP-activated protein kinase (AMPK)-dependent manner. Moreover, mice lacking PKD...
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Löffler, M. C., Mayer, A. E., Trujillo Viera, J., Loza Valdes, A., El-Merahbi, R., Ade, C. P., Karwen, T., Schmitz, W., Slotta, A., Erk, M., Janaki-Raman, S., Matesanz, N., Torres, J. L., Marcos, M., Sabio, G., Eilers, M., Schulze, A., Sumara, G. Tags: Development & Differentiation, Metabolism Articles Source Type: research

HRD1-ERAD controls production of the hepatokine FGF21 through CREBH polyubiquitination
The endoplasmic reticulum-associated protein degradation (ERAD) is responsible for recognizing and retro-translocating protein substrates, misfolded or not, from the ER for cytosolic proteasomal degradation. HMG-CoA Reductase (HMGCR) Degradation protein—HRD1—was initially identified as an E3 ligase critical for ERAD. However, its physiological functions remain largely undefined. Herein, we discovered that hepatic HRD1 expression is induced in the postprandial condition upon mouse refeeding. Mice with liver-specific HRD1 deletion failed to repress FGF21 production in serum and liver even in the refeeding conditi...
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Wei, J., Chen, L., Li, F., Yuan, Y., Wang, Y., Xia, W., Zhang, Y., Xu, Y., Yang, Z., Gao, B., Jin, C., Melo-Cardenas, J., Green, R. M., Pan, H., Wang, J., He, F., Zhang, K., Fang, D. Tags: Membrane & Intracellular Transport, Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Distinct roles of VE-cadherin for development and maintenance of specific lymph vessel beds
Endothelial cells line blood and lymphatic vessels and form intercellular junctions, which preserve vessel structure and integrity. The vascular endothelial cadherin, VE-cadherin, mediates endothelial adhesion and is indispensible for blood vessel development and permeability regulation. However, its requirement for lymphatic vessels has not been addressed. During development, VE-cadherin deletion in lymphatic endothelial cells resulted in abortive lymphangiogenesis, edema, and prenatal death. Unexpectedly, inducible postnatal or adult deletion elicited vessel bed-specific responses. Mature dermal lymph vessels resisted VE...
Source: EMBO Journal - November 15, 2018 Category: Molecular Biology Authors: Hägerling, R., Hoppe, E., Dierkes, C., Stehling, M., Makinen, T., Butz, S., Vestweber, D., Kiefer, F. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Vascular Biology & Angiogenesis Articles Source Type: research

The hypothalamic-LC-PFC axis: a new "ace" in the brain for fast-behavioral stress response
>The prefrontal cortex (PFC) is a key site for orchestrating responses to acute stress. In this issue of The EMBO Journal, Alpár et al (2018) unveil a novel pathway converting hypothalamic activation into fast enhancement of cortical excitability following acute stress. The route is initiated by corticotropin-releasing hormone (CRH) hypothalamic neurons, triggering the release of ciliary neurotrophic factor (CNTF) in the brain aqueductal system, which in turns selectively heightens the activity of noradrenergic neurons projecting to the PFC. (Source: EMBO Journal)
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Pozzi, D., Matteoli, M. Tags: Neuroscience News [amp ] Views Source Type: research

Right time, right place--DNA damage and DNA replication checkpoints collectively safeguard S phase
The DNA replication checkpoint (DRC) and the DNA damage checkpoint (DDC) are two closely linked signaling cascades that adjust S phase to the presence of DNA lesions and other replication impediments. Two recent studies published in The EMBO Journal shed new light on their relationship in budding yeast, collectively showing that the two pathways—while sharing several factors—differ in the location and kinetics of their activation, suggesting that they constitute different branches of an integrated cellular response to impaired DNA replication. (Source: EMBO Journal)
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Galanti, L., Pfander, B. Tags: DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

Hypothalamic CNTF volume transmission shapes cortical noradrenergic excitability upon acute stress
Stress-induced cortical alertness is maintained by a heightened excitability of noradrenergic neurons innervating, notably, the prefrontal cortex. However, neither the signaling axis linking hypothalamic activation to delayed and lasting noradrenergic excitability nor the molecular cascade gating noradrenaline synthesis is defined. Here, we show that hypothalamic corticotropin-releasing hormone-releasing neurons innervate ependymal cells of the 3rd ventricle to induce ciliary neurotrophic factor (CNTF) release for transport through the brain's aqueductal system. CNTF binding to its cognate receptors on norepinephrinergic n...
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Alpar, A., Zahola, P., Hanics, J., Hevesi, Z., Korchynska, S., Benevento, M., Pifl, C., Zachar, G., Perugini, J., Severi, I., Leitgeb, P., Bakker, J., Miklosi, A. G., Tretiakov, E., Keimpema, E., Arque, G., Tasan, R. O., Sperk, G., Malenczyk, K., Mate, Z. Tags: Neuroscience Articles Source Type: research

Conformational dynamics of the ABC transporter McjD seen by single-molecule FRET
ABC transporters utilize ATP for export processes to provide cellular resistance against toxins, antibiotics, and harmful metabolites in eukaryotes and prokaryotes. Based on static structure snapshots, it is believed that they use an alternating access mechanism, which couples conformational changes to ATP binding (outward-open conformation) and hydrolysis (inward-open) for unidirectional transport driven by ATP. Here, we analyzed the conformational states and dynamics of the antibacterial peptide exporter McjD from Escherichia coli using single-molecule Förster resonance energy transfer (smFRET). For the first time, we ...
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Husada, F., Bountra, K., Tassis, K., de Boer, M., Romano, M., Rebuffat, S., Beis, K., Cordes, T. Tags: Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

ESCRT-mediated lysosome repair precedes lysophagy and promotes cell survival
Although lysosomes perform a number of essential cellular functions, damaged lysosomes represent a potential hazard to the cell. Such lysosomes are therefore engulfed by autophagic membranes in the process known as lysophagy, which is initiated by recognition of luminal glycoprotein domains by cytosolic lectins such as Galectin-3. Here, we show that, under various conditions that cause injury to the lysosome membrane, components of the endosomal sorting complex required for transport (ESCRT)-I, ESCRT-II, and ESCRT-III are recruited. This recruitment occurs before that of Galectin-3 and the lysophagy machinery. Subunits of ...
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Radulovic, M., Schink, K. O., Wenzel, E. M., Nähse, V., Bongiovanni, A., Lafont, F., Stenmark, H. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Mrc1 and Rad9 cooperate to regulate initiation and elongation of DNA replication in response to DNA damage
The S-phase checkpoint maintains the integrity of the genome in response to DNA replication stress. In budding yeast, this pathway is initiated by Mec1 and is amplified through the activation of Rad53 by two checkpoint mediators: Mrc1 promotes Rad53 activation at stalled forks, and Rad9 is a general mediator of the DNA damage response. Here, we have investigated the interplay between Mrc1 and Rad9 in response to DNA damage and found that they control DNA replication through two distinct but complementary mechanisms. Mrc1 rapidly activates Rad53 at stalled forks and represses late-firing origins but is unable to maintain th...
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Bacal, J., Moriel-Carretero, M., Pardo, B., Barthe, A., Sharma, S., Chabes, A., Lengronne, A., Pasero, P. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Nonsense-mediated mRNA decay involves two distinct Upf1-bound complexes
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway involved in many cellular pathways and crucial for telomere maintenance and embryo development. Core NMD factors Upf1, Upf2 and Upf3 are conserved from yeast to mammals, but a universal NMD model is lacking. We used affinity purification coupled with mass spectrometry and an improved data analysis protocol to characterize the composition and dynamics of yeast NMD complexes in yeast (112 experiments). Unexpectedly, we identified two distinct complexes associated with Upf1: Upf1-23 (Upf1, Upf2, Upf3) and Upf1-decapping. Upf1-decapping conta...
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Dehecq, M., Decourty, L., Namane, A., Proux, C., Kanaan, J., Le Hir, H., Jacquier, A., Saveanu, C. Tags: Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Syntaxin 17 regulates the localization and function of PGAM5 in mitochondrial division and mitophagy
PGAM5, a mitochondrial protein phosphatase that is genetically and biochemically linked to PINK1, facilitates mitochondrial division by dephosphorylating the mitochondrial fission factor Drp1. At the onset of mitophagy, PGAM5 is cleaved by PARL, a rhomboid protease that degrades PINK1 in healthy cells, and the cleaved form facilitates the engulfment of damaged mitochondria by autophagosomes by dephosphorylating the mitophagy receptor FUNDC1. Here, we show that the function and localization of PGAM5 are regulated by syntaxin 17 (Stx17), a mitochondria-associated membrane/mitochondria protein implicated in mitochondrial dyna...
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Sugo, M., Kimura, H., Arasaki, K., Amemiya, T., Hirota, N., Dohmae, N., Imai, Y., Inoshita, T., Shiba-Fukushima, K., Hattori, N., Cheng, J., Fujimoto, T., Wakana, Y., Inoue, H., Tagaya, M. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

Tuberous sclerosis complex is required for tumor maintenance in MYC-driven Burkitt's lymphoma
The tuberous sclerosis complex (TSC) 1/2 is a negative regulator of the nutrient-sensing kinase mechanistic target of rapamycin complex (mTORC1), and its function is generally associated with tumor suppression. Nevertheless, biallelic loss of function of TSC1 or TSC2 is rarely found in malignant tumors. Here, we show that TSC1/2 is highly expressed in Burkitt's lymphoma cell lines and patient samples of human Burkitt's lymphoma, a prototypical MYC-driven cancer. Mechanistically, we show that MYC induces TSC1 expression by transcriptional activation of the TSC1 promoter and repression of miR-15a. TSC1 knockdown results in e...
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Hartleben, G., Müller, C., Krämer, A., Schimmel, H., Zidek, L. M., Dornblut, C., Winkler, R., Eichwald, S., Kortman, G., Kosan, C., Kluiver, J., Petersen, I., van den Berg, A., Wang, Z.-Q., Calkhoven, C. F. Tags: Cancer, Signal Transduction Articles Source Type: research

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation
Self-renewal of embryonic stem cells (ESCs) cultured in LIF/fetal calf serum (FCS) is incomplete with some cells initiating differentiation. While this is reflected in heterogeneous expression of naive pluripotency transcription factors (TFs), the link between TF heterogeneity and differentiation is not fully understood. Here, we purify ESCs with distinct TF expression levels from LIF/FCS cultures to uncover early events during commitment from naïve pluripotency. ESCs carrying fluorescent Nanog and Esrrb reporters show Esrrb downregulation only in Nanoglow cells. Independent Esrrb reporter lines demonstrate that Esrrbneg...
Source: EMBO Journal - November 2, 2018 Category: Molecular Biology Authors: Festuccia, N., Halbritter, F., Corsinotti, A., Gagliardi, A., Colby, D., Tomlinson, S. R., Chambers, I. Tags: Development & Differentiation, Stem Cells, Transcription Articles Source Type: research

ATF4-amino acid circuits: a recipe for resistance in melanoma
Lactate dehydrogenase A (LDHA) has appropriately received attention as a therapeutic target for the treatment of a broad spectrum of tumor types, yet little is known regarding intrinsic resistance to LDHA inhibitors. Pathria et al (2018) now establish that ATF4-dependent control of enzymes that direct amino acid metabolism confers resistance to LDHA inhibitors in melanoma and identify chokepoints that can be exploited to overcome metabolic compensation, setting the stage for trials with such combinations. (Source: EMBO Journal)
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Fernandez, M. R., Cleveland, J. L. Tags: Cancer, Metabolism News [amp ] Views Source Type: research

Epigenetically jump starting de novo shoot regeneration
The ability to regenerate lost organs or tissues is a central requirement for animals and plants in order to cope with injury. Regeneration of a whole body is rare in animals but is more commonly found in plants where in vitro regeneration has become a widely used tool in plant research. In a new study, Kim et al find that epigenetic changes via the histone acetyltransferase HAG1 establish the competency for shoot regeneration from callus by promoting the expression of root stem cell factors. (Source: EMBO Journal)
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Zhang, N., Laux, T. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Plant Biology News [amp ] Views Source Type: research

Postsynaptic localization and regulation of AMPA receptors and Cav1.2 by {beta}2 adrenergic receptor/PKA and Ca2+/CaMKII signaling
The synapse transmits, processes, and stores data within its tiny space. Effective and specific signaling requires precise alignment of the relevant components. This review examines current insights into mechanisms of AMPAR and NMDAR localization by PSD-95 and their spatial distribution at postsynaptic sites to illuminate the structural and functional framework of postsynaptic signaling. It subsequently delineates how β2 adrenergic receptor (β2 AR) signaling via adenylyl cyclase and the cAMP-dependent protein kinase PKA is organized within nanodomains. Here, we discuss targeting of β2 AR, adenylyl cyclase, a...
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Patriarchi, T., Buonarati, O. R., Hell, J. W. Tags: Neuroscience, Signal Transduction Review Source Type: research

Targeting the Warburg effect via LDHA inhibition engages ATF4 signaling for cancer cell survival
Nutrient restriction reprograms cellular signaling and metabolic network to shape cancer phenotype. Lactate dehydrogenase A (LDHA) has a key role in aerobic glycolysis (the Warburg effect) through regeneration of the electron acceptor NAD+ and is widely regarded as a desirable target for cancer therapeutics. However, the mechanisms of cellular response and adaptation to LDHA inhibition remain largely unknown. Here, we show that LDHA activity supports serine and aspartate biosynthesis. Surprisingly, however, LDHA inhibition fails to impact human melanoma cell proliferation, survival, or tumor growth. Reduced intracellular s...
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Pathria, G., Scott, D. A., Feng, Y., Sang Lee, J., Fujita, Y., Zhang, G., Sahu, A. D., Ruppin, E., Herlyn, M., Osterman, A. L., Ronai, Z. A. Tags: Cancer, Metabolism, Transcription Articles Source Type: research

Pool size estimations for dense-core vesicles in mammalian CNS neurons
Neuropeptides are essential signaling molecules transported and secreted by dense-core vesicles (DCVs), but the number of DCVs available for secretion, their subcellular distribution, and release probability are unknown. Here, we quantified DCV pool sizes in three types of mammalian CNS neurons in vitro and in vivo. Super-resolution and electron microscopy reveal a total pool of 1,400–18,000 DCVs, correlating with neurite length. Excitatory hippocampal and inhibitory striatal neurons in vitro have a similar DCV density, and thalamo-cortical axons in vivo have a slightly higher density. Synapses co...
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Persoon, C. M., Moro, A., Nassal, J. P., Farina, M., Broeke, J. H., Arora, S., Dominguez, N., van Weering, J. R., Toonen, R. F., Verhage, M. Tags: Neuroscience Articles Source Type: research

Ubiquitin-specific protease USP34 controls osteogenic differentiation and bone formation by regulating BMP2 signaling
The osteogenic differentiation of mesenchymal stem cells (MSCs) is governed by multiple mechanisms. Growing evidence indicates that ubiquitin-dependent protein degradation is critical for the differentiation of MSCs and bone formation; however, the function of ubiquitin-specific proteases, the largest subfamily of deubiquitylases, remains unclear. Here, we identify USP34 as a previously unknown regulator of osteogenesis. The expression of USP34 in human MSCs increases after osteogenic induction while depletion of USP34 inhibits osteogenic differentiation. Conditional knockout of Usp34 from MSCs or pre-osteoblasts leads to ...
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Guo, Y.-c., Wang, M.-y., Zhang, S.-w., Wu, Y.-s., Zhou, C.-c., Zheng, R.-x., Shao, B., Wang, Y., Xie, L., Liu, W.-q., Sun, N.-y., Jing, J.-j., Ye, L., Chen, Q.-m., Yuan, Q. Tags: Development & Differentiation, Post-translational Modifications, Proteolysis & Proteomics, Signal Transduction Articles Source Type: research

CDK1-mediated BCL9 phosphorylation inhibits clathrin to promote mitotic Wnt signalling
Uncontrolled cell division is a hallmark of cancer. Deregulation of Wnt components has been linked to aberrant cell division by multiple mechanisms, including Wnt-mediated stabilisation of proteins signalling, which was notably observed in mitosis. Analysis of Wnt components revealed an unexpected role of B-cell CLL/lymphoma 9 (BCL9) in maintaining mitotic Wnt signalling to promote precise cell division and growth of cancer cell. Mitotic interactome analysis revealed a mechanistic role of BCL9 in inhibiting clathrin-mediated degradation of LRP6 signalosome components by interacting with clathrin and the components in Wnt d...
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Chen, J., Rajasekaran, M., Xia, H., Kong, S. N., Deivasigamani, A., Sekar, K., Gao, H., Swa, H. L., Gunaratne, J., Ooi, L. L., Xie, T., Hong, W., Hui, K. M. Tags: Cancer, Cell Cycle, Signal Transduction Articles Source Type: research

Endolysosomal degradation of Tau and its role in glucocorticoid-driven hippocampal malfunction
Emerging studies implicate Tau as an essential mediator of neuronal atrophy and cognitive impairment in Alzheimer's disease (AD), yet the factors that precipitate Tau dysfunction in AD are poorly understood. Chronic environmental stress and elevated glucocorticoids (GC), the major stress hormones, are associated with increased risk of AD and have been shown to trigger intracellular Tau accumulation and downstream Tau-dependent neuronal dysfunction. However, the mechanisms through which stress and GC disrupt Tau clearance and degradation in neurons remain unclear. Here, we demonstrate that Tau undergoes degradation via endo...
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Vaz-Silva, J., Gomes, P., Jin, Q., Zhu, M., Zhuravleva, V., Quintremil, S., Meira, T., Silva, J., Dioli, C., Soares-Cunha, C., Daskalakis, N. P., Sousa, N., Sotiropoulos, I., Waites, C. L. Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

CPEB2-dependent translation of long 3'-UTR Ucp1 mRNA promotes thermogenesis in brown adipose tissue
Expression of mitochondrial proton transporter uncoupling protein 1 (UCP1) in brown adipose tissue (BAT) is essential for mammalian thermogenesis. While human UCP1 mRNA exists in a long form only, alternative polyadenylation creates two different isoforms in mice with 10% of UCP1 mRNA found in the long form (Ucp1L) and ~90% in the short form (Ucp1S). We generated a mouse model expressing only Ucp1S and found that it showed impaired thermogenesis due to a 60% drop in UCP1 protein levels, suggesting that Ucp1L is more efficiently translated than Ucp1S. In addition, we found that β3 adrenergic receptor signaling promoted...
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Chen, H.-F., Hsu, C.-M., Huang, Y.-S. Tags: Metabolism, Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Epigenetic reprogramming by histone acetyltransferase HAG1/AtGCN5 is required for pluripotency acquisition in Arabidopsis
Shoot regeneration can be achieved in vitro through a two-step process involving the acquisition of pluripotency on callus-induction media (CIM) and the formation of shoots on shoot-induction media. Although the induction of root-meristem genes in callus has been noted recently, the mechanisms underlying their induction and their roles in de novo shoot regeneration remain unanswered. Here, we show that the histone acetyltransferase HAG1/AtGCN5 is essential for de novo shoot regeneration. In developing callus, it catalyzes histone acetylation at several root-meristem gene loci including WOX5, WOX14, SCR, PLT1, and PLT2...
Source: EMBO Journal - October 15, 2018 Category: Molecular Biology Authors: Kim, J.-Y., Yang, W., Forner, J., Lohmann, J. U., Noh, B., Noh, Y.-S. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Plant Biology Articles Source Type: research

Uncovering the "secret" lives of vacuolar fusion pores in living cells
Non-expanding fusion pores have been predicted to constitute rate-limiting metastable intermediates in a broad range of fusion processes ranging from exocytosis to cell–cell fusion. However, their existence and nature, in particular in intracellular non-exocytic compartments, remained largely intangible. In this issue, D'Agostino et al demonstrate that non-expanding pores are likely long-lived steady-state intermediates in yeast vacuoles allowing the cells to adjust their volume to rapidly changing physiology. These pores are stabilized against closure by SNAREs and the attached vacuolar vesicle tethering comple...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Söllner, T. H., Malsam, J. Tags: Membrane & Intracellular Transport News [amp ] Views Source Type: research

Buried in PEAT--discovery of a new silencing complex with opposing activities
Posttranslational histone modifications serve critical roles in gene regulation by determining the functional status of chromatin. Histone-modifying enzymes often work in large multiprotein complexes. A paper in this issue of The EMBO Journal describes a new chromatin-modifying complex called PEAT that acts via histone deacetylation. The PEAT complex is involved in heterochromatin formation and gene repression but also appears to have a locus-specific activating role, possibly through promoting histone acetylation. (Source: EMBO Journal)
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Tsuzuki, M., Wierzbicki, A. T. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology, RNA Biology News [amp ] Views Source Type: research

SNARE-mediated membrane fusion arrests at pore expansion to regulate the volume of an organelle
Constitutive membrane fusion within eukaryotic cells is thought to be controlled at its initial steps, membrane tethering and SNARE complex assembly, and to rapidly proceed from there to full fusion. Although theory predicts that fusion pore expansion faces a major energy barrier and might hence be a rate-limiting and regulated step, corresponding states with non-expanding pores are difficult to assay and have remained elusive. Here, we show that vacuoles in living yeast are connected by a metastable, non-expanding, nanoscopic fusion pore. This is their default state, from which full fusion is regulated. Molecular dynamics...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: D'Agostino, M., Risselada, H. J., Endter, L. J., Comte-Miserez, V., Mayer, A. Tags: Membrane & Intracellular Transport Articles Source Type: research

SCA8 RAN polySer protein preferentially accumulates in white matter regions and is regulated by eIF3F
We report a novel toxic SCA8 polySer protein which accumulates in white matter (WM) regions as aggregates that increase with age and disease severity. WM regions with polySer aggregates show demyelination and axonal degeneration in SCA8 human and mouse brains. Additionally, knockdown of the eukaryotic translation initiation factor eIF3F in cells reduces steady-state levels of SCA8 polySer and other RAN proteins. Taken together, these data show polySer and WM abnormalities contribute to SCA8 and identify eIF3F as a novel modulator of RAN protein accumulation. (Source: EMBO Journal)
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Ayhan, F., Perez, B. A., Shorrock, H. K., Zu, T., Banez-Coronel, M., Reid, T., Furuya, H., Clark, H. B., Troncoso, J. C., Ross, C. A., Subramony, S., Ashizawa, T., Wang, E. T., Yachnis, A. T., Ranum, L. P. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Histone H2A-H2B binding by Pol {alpha} in the eukaryotic replisome contributes to the maintenance of repressive chromatin
The eukaryotic replisome disassembles parental chromatin at DNA replication forks, but then plays a poorly understood role in the re-deposition of the displaced histone complexes onto nascent DNA. Here, we show that yeast DNA polymerase α contains a histone-binding motif that is conserved in human Pol α and is specific for histones H2A and H2B. Mutation of this motif in budding yeast cells does not affect DNA synthesis, but instead abrogates gene silencing at telomeres and mating-type loci. Similar phenotypes are produced not only by mutations that displace Pol α from the replisome, but also by mutation o...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Evrin, C., Maman, J. D., Diamante, A., Pellegrini, L., Labib, K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

Molecular dissection of plasmacytoid dendritic cell activation in vivo during a viral infection
Plasmacytoid dendritic cells (pDC) are the major source of type I interferons (IFN-I) during viral infections, in response to triggering of endosomal Toll-like receptors (TLRs) 7 or 9 by viral single-stranded RNA or unmethylated CpG DNA, respectively. Synthetic ligands have been used to disentangle the underlying signaling pathways. The adaptor protein AP3 is necessary to transport molecular complexes of TLRs, synthetic CpG DNA, and MyD88 into endosomal compartments allowing interferon regulatory factor 7 (IRF7) recruitment whose phosphorylation then initiates IFN-I production. High basal expression of IRF7 by pDC and its ...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Tomasello, E., Naciri, K., Chelbi, R., Bessou, G., Fries, A., Gressier, E., Abbas, A., Pollet, E., Pierre, P., Lawrence, T., Vu Manh, T.-P., Dalod, M. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing
In eukaryotes, heterochromatin regions are typically subjected to transcriptional silencing. DNA methylation has an important role in such silencing and has been studied extensively. However, little is known about how methylated heterochromatin regions are subjected to silencing. We conducted a genetic screen and identified an epcr (enhancer of polycomb-related) mutant that releases heterochromatin silencing in Arabidopsis thaliana. We demonstrated that EPCR1 functions redundantly with its paralog EPCR2 and interacts with PWWP domain-containing proteins (PWWPs), AT-rich interaction domain-containing proteins (ARIDs), and t...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Tan, L.-M., Zhang, C.-J., Hou, X.-M., Shao, C.-R., Lu, Y.-J., Zhou, J.-X., Li, Y.-Q., Li, L., Chen, S., He, X.-J. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, RNA Biology Articles Source Type: research

Evidence for the nuclear import of histones H3.1 and H4 as monomers
Newly synthesised histones are thought to dimerise in the cytosol and undergo nuclear import in complex with histone chaperones. Here, we provide evidence that human H3.1 and H4 are imported into the nucleus as monomers. Using a tether-and-release system to study the import dynamics of newly synthesised histones, we find that cytosolic H3.1 and H4 can be maintained as stable monomeric units. Cytosolically tethered histones are bound to importin-alpha proteins (predominantly IPO4), but not to histone-specific chaperones NASP, ASF1a, RbAp46 (RBBP7) or HAT1, which reside in the nucleus in interphase cells. Release of monomeri...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Apta-Smith, M. J., Hernandez-Fernaud, J. R., Bowman, A. J. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control Articles Source Type: research

Arabidopsis O-GlcNAc transferase SEC activates histone methyltransferase ATX1 to regulate flowering
Post-translational modification of proteins by O-linked β-N-acetylglucosamine (O-GlcNAc) is catalyzed by O-GlcNAc transferases (OGTs). O-GlcNAc modification of proteins regulates multiple important biological processes in metazoans. However, whether protein O-GlcNAcylation is involved in epigenetic processes during plant development is largely unknown. Here, we show that loss of function of SECRET AGENT (SEC), an OGT in Arabidopsis, leads to an early flowering phenotype. This results from reduced histone H3 lysine 4 trimethylation (H3K4me3) of FLOWERING LOCUS C (FLC) locus, which encodes a key negative regulator of fl...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Xing, L., Liu, Y., Xu, S., Xiao, J., Wang, B., Deng, H., Lu, Z., Xu, Y., Chong, K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Lipase maturation factor 1 affects redox homeostasis in the endoplasmic reticulum
Lipoprotein lipase (LPL) is a secreted lipase that clears triglycerides from the blood. Proper LPL folding and exit from the endoplasmic reticulum (ER) require lipase maturation factor 1 (LMF1), an ER-resident transmembrane protein, but the mechanism involved is unknown. We used proteomics to identify LMF1-binding partners necessary for LPL secretion in HEK293 cells and found these to include oxidoreductases and lectin chaperones, suggesting that LMF1 facilitates the formation of LPL's five disulfide bonds. In accordance with this role, we found that LPL aggregates in LMF1-deficient cells due to the formation of incorrect ...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Roberts, B. S., Babilonia-Rosa, M. A., Broadwell, L. J., Wu, M. J., Neher, S. B. Tags: Protein Biosynthesis & Quality Control Articles Source Type: research

RNA editing of Filamin A pre-mRNA regulates vascular contraction and diastolic blood pressure
Epitranscriptomic events such as adenosine-to-inosine (A-to-I) RNA editing by ADAR can recode mRNAs to translate novel proteins. Editing of the mRNA that encodes actin crosslinking protein Filamin A (FLNA) mediates a Q-to-R transition in the interactive C-terminal region. While FLNA editing is conserved among vertebrates, its physiological function remains unclear. Here, we show that cardiovascular tissues in humans and mice show massive editing and that FLNA RNA is the most prominent substrate. Patient-derived RNA-Seq data demonstrate a significant drop in FLNA editing associated with cardiovascular diseases. Using mice w...
Source: EMBO Journal - October 1, 2018 Category: Molecular Biology Authors: Jain, M., Mann, T. D., Stulic, M., Rao, S. P., Kirsch, A., Pullirsch, D., Strobl, X., Rath, C., Reissig, L., Moreth, K., Klein-Rodewald, T., Bekeredjian, R., Gailus-Durner, V., Fuchs, H., Hrabe de Angelis, M., Pablik, E., Cimatti, L., Martin, D., Zinnanti Tags: Development & Differentiation, RNA Biology, Vascular Biology & Angiogenesis Articles Source Type: research

Queuing up the ribosome: nutrition and the microbiome control protein synthesis
The health of an organism is intricately linked to its gut microbiome. However, the mechanisms by which the microbiome affect the host gene regulation are still not well established. A new study by Tuorto et al (2018) shows that queuine, a nitrogenous base obtained from the gut microbiota, is used to modify tRNAs and affects cellular behavior. Dietary queuine is required for proper protein synthesis, and its depletion activates cellular stress responses in vitro and in vivo. (Source: EMBO Journal)
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Kozlovski, I., Agami, R. Tags: Metabolism, Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research