Developmental and functional heterogeneity of white adipocytes within a single fat depot
Recent studies suggest that, even within a single adipose depot, there may be distinct subpopulations of adipocytes. To investigate this cellular heterogeneity, we have developed multiple conditionally immortalized clonal preadipocyte lines from white adipose tissue of mice. Analysis of these clones reveals at least three white adipocyte subpopulations. These subpopulations have differences in metabolism and differentially respond to inflammatory cytokines, insulin, and growth hormones. These also have distinct gene expression profiles and can be tracked by differential expression of three marker genes: Wilms’ tumor ...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Lee, K. Y., Luong, Q., Sharma, R., Dreyfuss, J. M., Ussar, S., Kahn, C. R. Tags: Development & Differentiation, Metabolism Articles Source Type: research

hnRNP L-dependent protection of normal mRNAs from NMD subverts quality control in B cell lymphoma
The human nonsense-mediated mRNA decay pathway (NMD) performs quality control and regulatory functions within complex post-transcriptional regulatory networks. In addition to degradation-promoting factors, efficient and accurate detection of NMD substrates involves proteins that safeguard normal mRNAs. Here, we identify hnRNP L as a factor that protects mRNAs with NMD-inducing features including long 3'UTRs. Using biochemical and transcriptome-wide approaches, we provide evidence that the susceptibility of a given transcript to NMD can be modulated by its 3'UTR length and ability to recruit hnRNP L. Integrating these findi...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Kishor, A., Ge, Z., Hogg, J. R. Tags: Cancer, RNA Biology Articles Source Type: research

A mitochondrial FUNDC1/HSC70 interaction organizes the proteostatic stress response at the risk of cell morbidity
Both protein quality and mitochondrial quality are vital for the cellular activity, and impaired proteostasis and mitochondrial dysfunction are common etiologies of aging and age-related disorders. Here, we report that the mitochondrial outer membrane protein FUNDC1 interacts with the chaperone HSC70 to promote the mitochondrial translocation of unfolded cytosolic proteins for degradation by LONP1 or for formation of non-aggresomal mitochondrion-associated protein aggregates (MAPAs) upon proteasome inhibition in cultured human cells. Integrative approaches including csCLEM, Apex, and biochemical analysis reveal that MAPAs ...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Li, Y., Xue, Y., Xu, X., Wang, G., Liu, Y., Wu, H., Li, W., Wang, Y., Chen, Z., Zhang, W., Zhu, Y., Ji, W., Xu, T., Liu, L., Chen, Q. Tags: Autophagy & Cell Death, Post-translational Modifications, Proteolysis & Proteomics, Protein Biosynthesis & Quality Control Articles Source Type: research

A novel form of JARID2 is required for differentiation in lineage-committed cells
Polycomb repressive complex-2 (PRC2) is a group of proteins that play an important role during development and in cell differentiation. PRC2 is a histone-modifying complex that catalyses methylation of lysine 27 of histone H3 (H3K27me3) at differentiation genes leading to their transcriptional repression. JARID2 is a co-factor of PRC2 and is important for targeting PRC2 to chromatin. Here, we show that, unlike in embryonic stem cells, in lineage-committed human cells, including human epidermal keratinocytes, JARID2 predominantly exists as a novel low molecular weight form, which lacks the N-terminal PRC2-interacting domain...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Al-Raawi, D., Jones, R., Wijesinghe, S., Halsall, J., Petric, M., Roberts, S., Hotchin, N. A., Kanhere, A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells Articles Source Type: research

TFEB controls vascular development by regulating the proliferation of endothelial cells
Transcription factor TFEB is thought to control cellular functions—including in the vascular bed—primarily via regulation of lysosomal biogenesis and autophagic flux. Here, we report that TFEB also orchestrates a non-canonical program that controls the cell cycle/VEGFR2 pathway in the developing vasculature. In endothelial cells, TFEB depletion halts proliferation at the G1-S transition by inhibiting the CDK4/Rb pathway. TFEB-deficient cells attempt to compensate for this limitation by increasing VEGFR2 levels at the plasma membrane via microRNA-mediated mechanisms and controlled membrane trafficking. TFEB stim...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Doronzo, G., Astanina, E., Cora, D., Chiabotto, G., Comunanza, V., Noghero, A., Neri, F., Puliafito, A., Primo, L., Spampanato, C., Settembre, C., Ballabio, A., Camussi, G., Oliviero, S., Bussolino, F. Tags: Cell Cycle, Transcription, Vascular Biology & Angiogenesis Articles Source Type: research

Rab29 activation of the Parkinson's disease-associated LRRK2 kinase
(Source: EMBO Journal)
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Purlyte, E., Dhekne, H. S., Sarhan, A. R., Gomez, R., Lis, P., Wightman, M., Martinez, T. N., Tonelli, F., Pfeffer, S. R., Alessi, D. R. Tags: Corrigendum Source Type: research

CFTR is not a gluten lover either
Coeliac disease (CD) is an inflammatory autoimmune disease caused by ingestion of gluten proteins, mainly gliadin. Undigested gliadin proline-rich peptides trigger the innate and adaptive immune response, resulting in intestinal cell stress and damage. A new study by Villella et al (2019) addressing the unclear primary cause of intestinal cell stress reports that gliadin peptides inhibit the function of the chloride and bicarbonate channel CFTR, causing intestinal cell stress, which is sufficient to trigger CD symptoms. Notably, CFTR potentiators used to treat cystic fibrosis effectively rescue CFTR function and marke...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Vachel, L., Muallem, S. Tags: Immunology, Membrane & Intracellular Transport, Molecular Biology of Disease News [amp ] Views Source Type: research

Fat-fated microglial dysfunction
Patients with lysosomal storage disorders (LSDs) exhibit activated microglia in the brain, but the mechanisms underlying microglial activation and contribution to disease pathology are unclear. In this issue, Gabandé-Rodríguez et al present intriguing data to suggest a protective function for microglia that is corrupted by sphingolipid lysosomal overload in Niemann-Pick disease type A. (Source: EMBO Journal)
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Silvin, A., Ginhoux, F. Tags: Membrane & Intracellular Transport, Neuroscience News [amp ] Views Source Type: research

A magic bullet for targeting cancers with supernumerary centrosomes
This study demonstrates the potential of developing tumor-specific treatment by specifically targeting centrosome amplification. (Source: EMBO Journal)
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Liu, Y., Pelletier, L. Tags: Cancer, Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle News [amp ] Views Source Type: research

Rethinking research reproducibility
"To boldly go where no man has gone before"! Exploring and innovating—isn't this why we are in science after all? But as exciting this may be, others must be able to confirm our results through competent replication. As Karl Popper famously put it: "Single occurrences that cannot be reproduced are of no significance to science" (Popper, 1935). However, despite its status as a founding principle of modern science, replication is often viewed as pedestrian and unoriginal. Academia rewards the explorer, not the replicator. Not surprisingly, the current biomedical literature is dominated by exploratio...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Dirnagl, U. Tags: Methods & Resources Commentary Source Type: research

A pathogenic role for cystic fibrosis transmembrane conductance regulator in celiac disease
Intestinal handling of dietary proteins usually prevents local inflammatory and immune responses and promotes oral tolerance. However, in ~ 1% of the world population, gluten proteins from wheat and related cereals trigger an HLA DQ2/8-restricted TH1 immune and antibody response leading to celiac disease. Prior epithelial stress and innate immune activation are essential for breaking oral tolerance to the gluten component gliadin. How gliadin subverts host intestinal mucosal defenses remains elusive. Here, we show that the α-gliadin-derived LGQQQPFPPQQPY peptide (P31–43) inhibits the function of cystic&nbs...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Villella, V. R., Venerando, A., Cozza, G., Esposito, S., Ferrari, E., Monzani, R., Spinella, M. C., Oikonomou, V., Renga, G., Tosco, A., Rossin, F., Guido, S., Silano, M., Garaci, E., Chao, Y.-K., Grimm, C., Luciani, A., Romani, L., Piacentini, M., Raia, Tags: Immunology, Membrane & Intracellular Transport, Molecular Biology of Disease Articles Source Type: research

Precocious expression of Blimp1 in B cells causes autoimmune disease with increased self-reactive plasma cells
The transcription factor Blimp1 is not only an essential regulator of plasma cells, but also a risk factor for the development of autoimmune disease in humans. Here, we demonstrate in the mouse that the Prdm1 (Blimp1) gene was partially activated at the chromatin and transcription level in early B cell development, although mature Prdm1 mRNA did not accumulate due to posttranscriptional regulation. By analyzing a mouse model that facilitated ectopic Blimp1 protein expression throughout B lymphopoiesis, we could demonstrate that Blimp1 impaired B cell development by interfering with the B cell gene expression program, while...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Bönelt, P., Wöhner, M., Minnich, M., Tagoh, H., Fischer, M., Jaritz, M., Kavirayani, A., Garimella, M., Karlsson, M. C., Busslinger, M. Tags: Immunology Articles Source Type: research

Parkin inhibits BAK and BAX apoptotic function by distinct mechanisms during mitophagy
We report that following mitochondrial damage-induced mitophagy, Parkin directly ubiquitinates the apoptotic effector protein BAK at a conserved lysine in its hydrophobic groove, a region that is crucial for BAK activation by BH3-only proteins and its homo-dimerisation during apoptosis. Ubiquitination inhibited BAK activity by impairing its activation and the formation of lethal BAK oligomers. Parkin also suppresses BAX-mediated apoptosis, but in the absence of BAX ubiquitination suggesting an indirect mechanism. In addition, we find that BAK-dependent mitochondrial outer membrane permeabilisation during apoptosis promotes...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Bernardini, J. P., Brouwer, J. M., Tan, I. K., Sandow, J. J., Huang, S., Stafford, C. A., Bankovacki, A., Riffkin, C. D., Wardak, A. Z., Czabotar, P. E., Lazarou, M., Dewson, G. Tags: Autophagy & Cell Death, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

An inter-dimer allosteric switch controls NMDA receptor activity
NMDA receptors (NMDARs) are glutamate-gated ion channels that are key mediators of excitatory neurotransmission and synaptic plasticity throughout the central nervous system. They form massive heterotetrameric complexes endowed with unique allosteric capacity provided by eight extracellular clamshell-like domains arranged as two superimposed layers. Despite an increasing number of full-length NMDAR structures, how these domains cooperate in an intact receptor to control its activity remains poorly understood. Here, combining single-molecule and macroscopic electrophysiological recordings, cysteine biochemistry, and in sili...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Esmenjaud, J.-B., Stroebel, D., Chan, K., Grand, T., David, M., Wollmuth, L. P., Taly, A., Paoletti, P. Tags: Neuroscience, Structural Biology Articles Source Type: research

Inhibition of CPAP-tubulin interaction prevents proliferation of centrosome-amplified cancer cells
Centrosome amplification is a hallmark of human cancers that can trigger cancer cell invasion. To survive, cancer cells cluster amplified extra centrosomes and achieve pseudobipolar division. Here, we set out to prevent clustering of extra centrosomes. Tubulin, by interacting with the centrosomal protein CPAP, negatively regulates CPAP-dependent peri-centriolar material recruitment, and concurrently microtubule nucleation. Screening for compounds that perturb CPAP–tubulin interaction led to the identification of CCB02, which selectively binds at the CPAP binding site of tubulin. Genetic and chemical perturbation of C...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Mariappan, A., Soni, K., Schorpp, K., Zhao, F., Minakar, A., Zheng, X., Mandad, S., Macheleidt, I., Ramani, A., Kubelka, T., Dawidowski, M., Golfmann, K., Wason, A., Yang, C., Simons, J., Schmalz, H.-G., Hyman, A. A., Aneja, R., Ullrich, R., Urlaub, H., O Tags: Cancer, Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle Articles Source Type: research

A selective ER-phagy exerts procollagen quality control via a Calnexin-FAM134B complex
Autophagy is a cytosolic quality control process that recognizes substrates through receptor-mediated mechanisms. Procollagens, the most abundant gene products in Metazoa, are synthesized in the endoplasmic reticulum (ER), and a fraction that fails to attain the native structure is cleared by autophagy. However, how autophagy selectively recognizes misfolded procollagens in the ER lumen is still unknown. We performed siRNA interference, CRISPR-Cas9 or knockout-mediated gene deletion of candidate autophagy and ER proteins in collagen producing cells. We found that the ER-resident lectin chaperone Calnexin (CANX) and the ER-...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Forrester, A., De Leonibus, C., Grumati, P., Fasana, E., Piemontese, M., Staiano, L., Fregno, I., Raimondi, A., Marazza, A., Bruno, G., Iavazzo, M., Intartaglia, D., Seczynska, M., van Anken, E., Conte, I., De Matteis, M. A., Dikic, I., Molinari, M., Sett Tags: Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

Prominin-1 controls stem cell activation by orchestrating ciliary dynamics
Proper temporal and spatial activation of stem cells relies on highly coordinated cell signaling. The primary cilium is the sensory organelle that is responsible for transmitting extracellular signals into a cell. Primary cilium size, architecture, and assembly–disassembly dynamics are under rigid cell cycle-dependent control. Using mouse incisor tooth epithelia as a model, we show that ciliary dynamics in stem cells require the proper functions of a cholesterol-binding membrane glycoprotein, Prominin-1 (Prom1/CD133), which controls sequential recruitment of ciliary membrane components, histone deacetylase, and trans...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Singer, D., Thamm, K., Zhuang, H., Karbanova, J., Gao, Y., Walker, J. V., Jin, H., Wu, X., Coveney, C. R., Marangoni, P., Lu, D., Grayson, P. R. C., Gulsen, T., Liu, K. J., Ardu, S., Wann, A. K., Luo, S., Zambon, A. C., Jetten, A. M., Tredwin, C., Klein, Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Stem Cells Articles Source Type: research

Lipid-induced lysosomal damage after demyelination corrupts microglia protective function in lysosomal storage disorders
Neuropathic lysosomal storage disorders (LSDs) present with activated pro-inflammatory microglia. However, anti-inflammatory treatment failed to improve disease pathology. We characterise the mechanisms underlying microglia activation in Niemann–Pick disease type A (NPA). We establish that an NPA patient and the acid sphingomyelinase knockout (ASMko) mouse model show amoeboid microglia in neurodegeneration-prone areas. In vivo microglia ablation worsens disease progression in ASMko mice. We demonstrate the coexistence of different microglia phenotypes in ASMko brains that produce cytokines or counteract neuronal deat...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Gabande-Rodriguez, E., Perez-Canamas, A., Soto-Huelin, B., Mitroi, D. N., Sanchez-Redondo, S., Martinez-Saez, E., Venero, C., Peinado, H., Ledesma, M. D. Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

Akt-mediated phosphorylation of MICU1 regulates mitochondrial Ca2+ levels and tumor growth
Although mitochondria play a multifunctional role in cancer progression and Ca2+ signaling is remodeled in a wide variety of tumors, the underlying mechanisms that link mitochondrial Ca2+ homeostasis with malignant tumor formation and growth remain elusive. Here, we show that phosphorylation at the N-terminal region of the mitochondrial calcium uniporter (MCU) regulatory subunit MICU1 leads to a notable increase in the basal mitochondrial Ca2+ levels. A pool of active Akt in the mitochondria is responsible for MICU1 phosphorylation, and mitochondrion-targeted Akt strongly regulates the mitochondrial Ca2+ content. The Akt-m...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Marchi, S., Corricelli, M., Branchini, A., Vitto, V. A. M., Missiroli, S., Morciano, G., Perrone, M., Ferrarese, M., Giorgi, C., Pinotti, M., Galluzzi, L., Kroemer, G., Pinton, P. Tags: Cancer, Membrane & Intracellular Transport Articles Source Type: research

Miro proteins prime mitochondria for Parkin translocation and mitophagy
The Parkinson's disease-associated protein kinase PINK1 and ubiquitin ligase Parkin coordinate the ubiquitination of mitochondrial proteins, which marks mitochondria for degradation. Miro1, an atypical GTPase involved in mitochondrial trafficking, is one of the substrates tagged by Parkin after mitochondrial damage. Here, we demonstrate that a small pool of Parkin interacts with Miro1 before mitochondrial damage occurs. This interaction does not require PINK1, does not involve ubiquitination of Miro1 and also does not disturb Miro1 function. However, following mitochondrial damage and PINK1 accumulation, this initial pool ...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Safiulina, D., Kuum, M., Choubey, V., Gogichaishvili, N., Liiv, J., Hickey, M. A., Cagalinec, M., Mandel, M., Zeb, A., Liiv, M., Kaasik, A. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

Identification of ILK as a critical regulator of VEGFR3 signalling and lymphatic vascular growth
Vascular endothelial growth factor receptor-3 (VEGFR3) signalling promotes lymphangiogenesis. While there are many reported mechanisms of VEGFR3 activation, there is little understanding of how VEGFR3 signalling is attenuated to prevent lymphatic vascular overgrowth and ensure proper lymph vessel development. Here, we show that endothelial cell-specific depletion of integrin-linked kinase (ILK) in mouse embryos hyper-activates VEGFR3 signalling and leads to overgrowth of the jugular lymph sacs/primordial thoracic ducts, oedema and embryonic lethality. Lymphatic endothelial cell (LEC)-specific deletion of Ilk in adult mice ...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Urner, S., Planas-Paz, L., Hilger, L. S., Henning, C., Branopolski, A., Kelly-Goss, M., Stanczuk, L., Pitter, B., Montanez, E., Peirce, S. M., Mäkinen, T., Lammert, E. Tags: Development & Differentiation, Signal Transduction, Vascular Biology & Angiogenesis Articles Source Type: research

TCF/LEF dependent and independent transcriptional regulation of Wnt/{beta}-catenin target genes
During canonical Wnt signalling, the activity of nuclear β-catenin is largely mediated by the TCF/LEF family of transcription factors. To challenge this view, we used the CRISPR/Cas9 genome editing approach to generate HEK 293T cell clones lacking all four TCF/LEF genes. By performing unbiased whole transcriptome sequencing analysis, we found that a subset of β-catenin transcriptional targets did not require TCF/LEF factors for their regulation. Consistent with this finding, we observed in a genome-wide analysis that β-catenin occupied specific genomic regions in the absence of TCF/LEF. Finally, we revealed ...
Source: EMBO Journal - January 15, 2019 Category: Molecular Biology Authors: Doumpas, N., Lampart, F., Robinson, M. D., Lentini, A., Nestor, C. E., Cantu, C., Basler, K. Tags: Signal Transduction, Transcription Articles Source Type: research

SUMOning the base excision repair machinery for differentiation
Besides critical and well-studied roles in maintaining genome stability, DNA repair pathways including base excision repair (BER) are also employed by mammalian cells for targeted events such as the generation of diverse antibody repertoires and the differentiation of pluripotent cells. In this issue of The EMBO Journal, Steinacher et al (2019) provide novel mechanistic insights into the complex role of SUMOylation of key BER proteins during active DNA demethylation—a role they demonstrate to be important for cellular differentiation and that has broader implications for BER as a whole. (Source: EMBO Journal)
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Wiest, N. E., Tomkinson, A. E. Tags: Development & Differentiation, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Let it RE:IN: integrating experimental observations to predict pluripotency network behaviour
Our ability to reprogram cells and induce transitions between states has fast become a commonplace tool, but our understanding of the underlying processes and capacity to predict these is still relatively rudimentary. A new article by Dunn et al (2019) combines a computational reasoning approach with experimental observation to construct a network-level understanding of the transcription factors instructing acquisition of naïve pluripotency during reprogramming. (Source: EMBO Journal)
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Rackham, O. J., Polo, J. M. Tags: Stem Cells, Systems & Computational Biology, Transcription News [amp ] Views Source Type: research

Alpha-ketoglutarate: a "magic" metabolite in early germ cell development
A causal relationship between cell metabolism and the fate of pluripotent stem cells through epigenome regulation is emerging. A recent study shows that the tricarboxylic acid cycle intermediate alpha-ketoglutarate (αKG) can both sustain naïve mouse embryonic stem cell pluripotency and promote primordial germ cell differentiation. This observation together with other studies provides intriguing possibilities for stabilizing ephemeral embryonic cell states and enhancing desired fate transitions through specific metabolite manipulations. (Source: EMBO Journal)
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Lu, V., Teitell, M. A. Tags: Development & Differentiation, Metabolism, Stem Cells News [amp ] Views Source Type: research

A common molecular logic determines embryonic stem cell self-renewal and reprogramming
During differentiation and reprogramming, new cell identities are generated by reconfiguration of gene regulatory networks. Here, we combined automated formal reasoning with experimentation to expose the logic of network activation during induction of naïve pluripotency. We find that a Boolean network architecture defined for maintenance of naïve state embryonic stem cells (ESC) also explains transcription factor behaviour and potency during resetting from primed pluripotency. Computationally identified gene activation trajectories were experimentally substantiated at single-cell resolution by RT–qPCR. Contingenc...
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Dunn, S.-J., Li, M. A., Carbognin, E., Smith, A., Martello, G. Tags: Stem Cells, Systems & Computational Biology, Transcription Resource Source Type: research

EGR2 phosphatase regulates OST1 kinase activity and freezing tolerance in Arabidopsis
This study thus unravels a molecular mechanism underlying cold activation of OST1 by membrane-localized EGR2 and suggests that a myristoyl switch on EGR2 helps plants to adapt to cold stress. (Source: EMBO Journal)
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Ding, Y., Lv, J., Shi, Y., Gao, J., Hua, J., Song, C., Gong, Z., Yang, S. Tags: Plant Biology, Post-translational Modifications, Proteolysis & Proteomics, Signal Transduction Articles Source Type: research

Lipin1 deficiency causes sarcoplasmic reticulum stress and chaperone-responsive myopathy
As a consequence of impaired glucose or fatty acid metabolism, bioenergetic stress in skeletal muscles may trigger myopathy and rhabdomyolysis. Genetic mutations causing loss of function of the LPIN1 gene frequently lead to severe rhabdomyolysis bouts in children, though the metabolic alterations and possible therapeutic interventions remain elusive. Here, we show that lipin1 deficiency in mouse skeletal muscles is sufficient to trigger myopathy. Strikingly, muscle fibers display strong accumulation of both neutral and phospholipids. The metabolic lipid imbalance can be traced to an altered fatty acid synthesis and fatty a...
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Rashid, T., Nemazanyy, I., Paolini, C., Tatsuta, T., Crespin, P., de Villeneuve, D., Brodesser, S., Benit, P., Rustin, P., Baraibar, M. A., Agbulut, O., Olivier, A., Protasi, F., Langer, T., Chrast, R., de Lonlay, P., de Foucauld, H., Blaauw, B., Pende, M Tags: Metabolism, Molecular Biology of Disease, Protein Biosynthesis & Quality Control Articles Source Type: research

Pentraxin 3 regulates synaptic function by inducing AMPA receptor clustering via ECM remodeling and {beta}1-integrin
Control of synapse number and function in the developing central nervous system is critical to the formation of neural circuits. Astrocytes play a key role in this process by releasing factors that promote the formation of excitatory synapses. Astrocyte-secreted thrombospondins (TSPs) induce the formation of structural synapses, which however remain post-synaptically silent, suggesting that completion of early synaptogenesis may require a two-step mechanism. Here, we show that the humoral innate immune molecule Pentraxin 3 (PTX3) is expressed in the developing rodent brain. PTX3 plays a key role in promoting functionally-a...
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Fossati, G., Pozzi, D., Canzi, A., Mirabella, F., Valentino, S., Morini, R., Ghirardini, E., Filipello, F., Moretti, M., Gotti, C., Annis, D. S., Mosher, D. F., Garlanda, C., Bottazzi, B., Taraboletti, G., Mantovani, A., Matteoli, M., Menna, E. Tags: Neuroscience Articles Source Type: research

Metabolic regulation of pluripotency and germ cell fate through {alpha}-ketoglutarate
An intricate link is becoming apparent between metabolism and cellular identities. Here, we explore the basis for such a link in an in vitro model for early mouse embryonic development: from naïve pluripotency to the specification of primordial germ cells (PGCs). Using single-cell RNA-seq with statistical modelling and modulation of energy metabolism, we demonstrate a functional role for oxidative mitochondrial metabolism in naïve pluripotency. We link mitochondrial tricarboxylic acid cycle activity to IDH2-mediated production of alpha-ketoglutarate and through it, the activity of key epigenetic regulators. Accord...
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Tischler, J., Gruhn, W. H., Reid, J., Allgeyer, E., Buettner, F., Marr, C., Theis, F., Simons, B. D., Wernisch, L., Surani, M. A. Tags: Development & Differentiation, Metabolism, Stem Cells Articles Source Type: research

Loss of VGLL4 suppresses tumor PD-L1 expression and immune evasion
Targeting immune checkpoints, such as PD-L1 and its receptor PD-1, has opened a new avenue for treating cancers. Understanding the regulatory mechanism of PD-L1 and PD-1 will improve the clinical response rate and efficacy of PD-1/PD-L1 blockade in cancer patients and the development of combinatorial strategies. VGLL4 inhibits YAP-induced cell proliferation and tumorigenesis through competition with YAP for binding to TEADs. However, whether VGLL4 has a role in anti-tumor immunity is largely unknown. Here, we found that disruption of Vgll4 results in potent T cell-mediated tumor regression in murine syngeneic models. VGLL4...
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Wu, A., Wu, Q., Deng, Y., Liu, Y., Lu, J., Liu, L., Li, X., Liao, C., Zhao, B., Song, H. Tags: Cancer, Immunology Articles Source Type: research

SUMOylation coordinates BERosome assembly in active DNA demethylation during cell differentiation
During active DNA demethylation, 5-methylcytosine (5mC) is oxidized by TET proteins to 5-formyl-/5-carboxylcytosine (5fC/5caC) for replacement by unmethylated C by TDG-initiated DNA base excision repair (BER). Base excision generates fragile abasic sites (AP-sites) in DNA and has to be coordinated with subsequent repair steps to limit accumulation of genome destabilizing secondary DNA lesions. Here, we show that 5fC/5caC is generated at a high rate in genomes of differentiating mouse embryonic stem cells and that SUMOylation and the BER protein XRCC1 play critical roles in orchestrating TDG-initiated BER of these lesions. ...
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Steinacher, R., Barekati, Z., Botev, P., Kusnierczyk, A., Slupphaug, G., Schär, P. Tags: Development & Differentiation, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Loss of T-bet confers survival advantage to influenza-bacterial superinfection
The transcription factor, T-bet, regulates type 1 inflammatory responses against a range of infections. Here, we demonstrate a previously unaddressed role of T-bet, to influenza virus and bacterial superinfection. Interestingly, we found that T-bet deficiency did not adversely affect the efficacy of viral clearance or recovery compared to wild-type hosts. Instead, increased infiltration of neutrophils and production of Th17 cytokines (IL-17 and IL-22), in lungs of influenza virus-infected T-bet–/– mice, were correlated with survival advantage against subsequent infection by Streptococcus pneumoniae. Neutralizat...
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Er, J. Z., Koean, R. A. G., Ding, J. L. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

The kinetochore module Okp1CENP-Q/Ame1CENP-U is a reader for N-terminal modifications on the centromeric histone Cse4CENP-A
Kinetochores are supramolecular assemblies that link centromeres to microtubules for sister chromatid segregation in mitosis. For this, the inner kinetochore CCAN/Ctf19 complex binds to centromeric chromatin containing the histone variant CENP-A, but whether the interaction of kinetochore components to centromeric nucleosomes is regulated by posttranslational modifications is unknown. Here, we investigated how methylation of arginine 37 (R37Me) and acetylation of lysine 49 (K49Ac) on the CENP-A homolog Cse4 from Saccharomyces cerevisiae regulate molecular interactions at the inner kinetochore. Importantly, we found that th...
Source: EMBO Journal - January 3, 2019 Category: Molecular Biology Authors: Anedchenko, E. A., Samel-Pommerencke, A., Tran Nguyen, T. M., Shahnejat-Bushehri, S., Pöpsel, J., Lauster, D., Herrmann, A., Rappsilber, J., Cuomo, A., Bonaldi, T., Ehrenhofer-Murray, A. E. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Open Access--or Open Science?
Open Access mandates in Europe raise the question if the priority is to reduce publishing costs, or the overdue conversion to Open Science communication. At risk are not only high-quality journals, but also community institutions and international research collaboration. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Pulverer, B. Tags: Editorial Source Type: research

Optimized Chronos sets the clock for optogenetic hearing restoration
The coming of age of optogenetics has motivated the development of clinical applications. Improved hearing restoration by optical cochlear implants is one such promising development. However, slow closing of light-gated ion channels has remained an obstacle for achieving the high temporal fidelity required for optogenetic coding. In a study published in this issue, Keppeler et al demonstrate that optimized trafficking of the fast channelrhodopsin Chronos enables auditory nerve fibers to fire in response to light at near physiological rates. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Ronzitti, E., Zampini, V., Emiliani, V. Tags: Neuroscience News [amp ] Views Source Type: research

More than just an I{kappa}B kinase: the IKK complex coordinates mRNA stability and transcription
The IB kinase (IKK) complex is best known as the core regulator of NF-B signalling. Recent work from Mikuda et al reveals a new and unexpected function for IKK in the regulation of mRNA stability. Through interacting with and phosphorylating EDC4, a key component of the mRNA decapping complex, IKK regulates P-body formation and the stability of numerous mRNAs, including many encoding inflammatory cytokines. Activation of IKK can therefore be more generally thought of as programming the cellular response to stress and infection through both mRNA stability and transcription. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Perkins, N. D. Tags: Immunology, RNA Biology, Signal Transduction News [amp ] Views Source Type: research

A new consensus for evaluating CDKL5/STK9-dependent signalling mechanisms
Mutation or inactivation of CDKL5 kinase is associated with a human neurodevelopmental condition commonly referred to as CDKL5 deficiency disorder.§ Two recent phosphoproteomics studies identify the first physiological substrates of mammalian CDKL5 and evaluate functional consequences of their phosphorylation and its loss in cells lacking functional CDKL5, highlighting potential roles for this kinase in regulating neuronal microtubule dynamics. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Eyers, P. A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Genetics, Gene Therapy & Genetic Disease, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Attenuation of PKC{delta} enhances metabolic activity and promotes expansion of blood progenitors
A finely tuned balance of self-renewal, differentiation, proliferation, and survival governs the pool size and regenerative capacity of blood-forming hematopoietic stem and progenitor cells (HSPCs). Here, we report that protein kinase C delta (PKC) is a critical regulator of adult HSPC number and function that couples the proliferative and metabolic activities of HSPCs. PKC-deficient mice showed a pronounced increase in HSPC numbers, increased competence in reconstituting lethally irradiated recipients, enhanced long-term competitive advantage in serial transplantation studies, and an augmented HSPC recovery during stress....
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Rao, T. N., Gupta, M. K., Softic, S., Wang, L. D., Jang, Y. C., Thomou, T., Bezy, O., Kulkarni, R. N., Kahn, C. R., Wagers, A. J. Tags: Immunology, Metabolism, Stem Cells Articles Source Type: research

Chemical genetic identification of CDKL5 substrates reveals its role in neuronal microtubule dynamics
Loss-of-function mutations in CDKL5 kinase cause severe neurodevelopmental delay and early-onset seizures. Identification of CDKL5 substrates is key to understanding its function. Using chemical genetics, we found that CDKL5 phosphorylates three microtubule-associated proteins: MAP1S, EB2 and ARHGEF2, and determined the phosphorylation sites. Substrate phosphorylations are greatly reduced in CDKL5 knockout mice, verifying these as physiological substrates. In CDKL5 knockout mouse neurons, dendritic microtubules have longer EB3-labelled plus-end growth duration and these altered dynamics are rescued by reduction of MAP1S le...
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Baltussen, L. L., Negraes, P. D., Silvestre, M., Claxton, S., Moeskops, M., Christodoulou, E., Flynn, H. R., Snijders, A. P., Muotri, A. R., Ultanir, S. K. Tags: Cell Adhesion, Polarity & Cytoskeleton, Genetics, Gene Therapy & Genetic Disease, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Ultrafast optogenetic stimulation of the auditory pathway by targeting-optimized Chronos
In conclusion, efficient virus-mediated expression of targeting-optimized Chronos-ES/TS achieves ultrafast optogenetic control of neurons. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Keppeler, D., Merino, R. M., Lopez de la Morena, D., Bali, B., Huet, A. T., Gehrt, A., Wrobel, C., Subramanian, S., Dombrowski, T., Wolf, F., Rankovic, V., Neef, A., Moser, T. Tags: Methods & Resources, Neuroscience Source Type: research

Phosphoproteomic screening identifies physiological substrates of the CDKL5 kinase
Mutations in the gene encoding the protein kinase CDKL5 cause a debilitating neurodevelopmental disease termed CDKL5 disorder. The impact of these mutations on CDKL5 function is poorly understood because the substrates and cellular processes controlled by CDKL5 are unclear. Here, we describe a quantitative phosphoproteomic screening which identified MAP1S, CEP131 and DLG5—regulators of microtubule and centrosome function—as cellular substrates of CDKL5. Antibodies against MAP1S phospho-Ser900 and CEP131 phospho-Ser35 confirmed CDKL5-dependent phosphorylation of these targets in human cells. The phospho-acceptor...
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Munoz, I. M., Morgan, M. E., Peltier, J., Weiland, F., Gregorczyk, M., Brown, F. C., Macartney, T., Toth, R., Trost, M., Rouse, J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Genetics, Gene Therapy & Genetic Disease, Post-translational Modifications, Proteolysis & Proteomics Resource Source Type: research

CNOT6L couples the selective degradation of maternal transcripts to meiotic cell cycle progression in mouse oocyte
This study provides the first direct genetic evidence that CCR4–NOT-dependent and particularly CNOT6L-dependent decay of selective maternal mRNAs is a prerequisite for meiotic maturation of oocytes. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Sha, Q.-Q., Yu, J.-L., Guo, J.-X., Dai, X.-X., Jiang, J.-C., Zhang, Y.-L., Yu, C., Ji, S.-Y., Jiang, Y., Zhang, S.-Y., Shen, L., Ou, X.-H., Fan, H.-Y. Tags: Cell Cycle, Development & Differentiation, RNA Biology Articles Source Type: research

The I{kappa}B kinase complex is a regulator of mRNA stability
The IB kinase (IKK) is considered to control gene expression primarily through activation of the transcription factor NF-B. However, we show here that IKK additionally regulates gene expression on post-transcriptional level. IKK interacted with several mRNA-binding proteins, including a Processing (P) body scaffold protein, termed enhancer of decapping 4 (EDC4). IKK bound to and phosphorylated EDC4 in a stimulus-sensitive manner, leading to co-recruitment of P body components, mRNA decapping proteins 1a and 2 (DCP1a and DCP2) and to an increase in P body numbers. Using RNA sequencing, we identified scores of transcripts wh...
Source: EMBO Journal - December 14, 2018 Category: Molecular Biology Authors: Mikuda, N., Kolesnichenko, M., Beaudette, P., Popp, O., Uyar, B., Sun, W., Tufan, A. B., Perder, B., Akalin, A., Chen, W., Mertins, P., Dittmar, G., Hinz, M., Scheidereit, C. Tags: Immunology, RNA Biology, Signal Transduction Articles Source Type: research

More is not always better: hyperglutamylation leads to neurodegeneration
Post-translational modifications of tubulin can regulate the dynamics and mechanical properties of microtubules and their interactions with different proteins, such as molecular motors. Two studies now demonstrate that excessive accumulation of a specific modification, polyglutamylation, leads to neurodegeneration in mice and humans, likely due to defects in axonal microtubule-based transport. (Source: EMBO Journal)
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Akhmanova, A., Hoogenraad, C. C. Tags: Neuroscience, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Optogenetic control of morphogenesis goes 3D
The generation of form in living embryos, a process termed "morphogenesis" from the Greek word μooacute;, is one of the most fascinating unsolved problems in biology. In embryonic epithelia, most attention has been paid to events occurring at the apical surface of epithelia, particularly the regulation of actomyosin contractility during morphogenetic change. In a new report, De Renzis and colleagues demonstrate a key role for regulated actomyosin contractility at the basal surface of the epithelium during formation of the first epithelial fold in Drosophila (the "ventral furrow") (Krueger et al,...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Thompson, B. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation News [amp ] Views Source Type: research

Friend and foe, HNRNPC takes on immunostimulatory RNAs in breast cancer cells
The RNA-binding protein HNRNPC is highly expressed in breast cancer, but its contribution to tumorigenesis was unclear. In this issue, Wu et al (2018) demonstrate that elevated HNRNPC is essential for the proliferative ability of two breast cancer cell lines. Reducing HNRNPC results in the accumulation of short Alu-derived dsRNAs that bind RNA receptor RIG-I and stimulate the production of IFN, a cytokine with known antiproliferative activity. (Source: EMBO Journal)
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Sarbanes, S. L., Le Pen, J., Rice, C. M. Tags: Cancer, Immunology News [amp ] Views Source Type: research

Decapping enzymes STOP "cancer" ribosomes in their tracks
The production of ribosomes plays a central role in regulating cell cycle progression and cancer proliferation. A new study by Gaviraghi et al (2018) shows that mRNA decapping coactivator PNRC1 acts as a tumor suppressor by regulating ribosome biogenesis. PNRC1 relocalizes the Dcp1/Dcp2 mRNA decapping complex to the nucleolus and promotes decapping of specific snoRNAs to disrupt the processing of ribosomal RNA. By slowing rRNA processing, and thus ribosome biogenesis, PNRC1 acts as a gatekeeper that restrains oncogenic potential. (Source: EMBO Journal)
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Mugridge, J. S., Gross, J. D. Tags: Cancer, RNA Biology News [amp ] Views Source Type: research

Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration
A set of glutamylases and deglutamylases controls levels of tubulin polyglutamylation, a prominent post-translational modification of neuronal microtubules. Defective tubulin polyglutamylation was first linked to neurodegeneration in the Purkinje cell degeneration (pcd) mouse, which lacks deglutamylase CCP1, displays massive cerebellar atrophy, and accumulates abnormally glutamylated tubulin in degenerating neurons. We found biallelic rare and damaging variants in the gene encoding CCP1 in 13 individuals with infantile-onset neurodegeneration and confirmed the absence of functional CCP1 along with dysregulated tubulin poly...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Shashi, V., Magiera, M. M., Klein, D., Zaki, M., Schoch, K., Rudnik-Schöneborn, S., Norman, A., Lopes Abath Neto, O., Dusl, M., Yuan, X., Bartesaghi, L., De Marco, P., Alfares, A. A., Marom, R., Arold, S. T., Guzman-Vega, F. J., Pena, L. D., Smith Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Excessive tubulin polyglutamylation causes neurodegeneration and perturbs neuronal transport
Posttranslational modifications of tubulin are emerging regulators of microtubule functions. We have shown earlier that upregulated polyglutamylation is linked to rapid degeneration of Purkinje cells in mice with a mutation in the deglutamylating enzyme CCP1. How polyglutamylation leads to degeneration, whether it affects multiple neuron types, or which physiological processes it regulates in healthy neurons has remained unknown. Here, we demonstrate that excessive polyglutamylation induces neurodegeneration in a cell-autonomous manner and can occur in many parts of the central nervous system. Degeneration of selected neur...
Source: EMBO Journal - December 3, 2018 Category: Molecular Biology Authors: Magiera, M. M., Bodakuntla, S., Ziak, J., Lacomme, S., Marques Sousa, P., Leboucher, S., Hausrat, T. J., Bosc, C., Andrieux, A., Kneussel, M., Landry, M., Calas, A., Balastik, M., Janke, C. Tags: Cell Adhesion, Polarity & Cytoskeleton, Neuroscience, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research