Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we compare the composition of the Sin3a-Hdac complex between pluripotent embryonic stem (ES) and differentiated cells by establishing a method that couples two independent endogenous immunoprecipitations with quantitative mass spectrometry. We define the precise composition of the Sin3a complex in multiple cell types and identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Streubel, G., Fitzpatrick, D. J., Oliviero, G., Scelfo, A., Moran, B., Das, S., Munawar, N., Watson, A., Wynne, K., Negri, G. L., Dillon, E. T., Jammula, S., Hokamp, K., O'Connor, D. P., Pasini, D., Cagney, G., Bracken, A. P. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells, Transcription Articles Source Type: research

Structural and functional dissection of the interplay between lipid and Notch binding by human Notch ligands
We present novel structures of human ligands Jagged2 and Delta-like4 and human Notch2, together with functional assays, which suggest that ligand-mediated coupling of membrane recognition and Notch binding is likely to be critical in establishing the optimal context for Notch signalling. Comparisons between the Jagged and Delta family show a huge diversity in the structures of the loops at the apex of the C2 domain implicated in membrane recognition and Jagged1 missense mutations, which affect these loops and are associated with extrahepatic biliary atresia, lead to a loss of membrane recognition, but do not alter Notch bi...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Suckling, R. J., Korona, B., Whiteman, P., Chillakuri, C., Holt, L., Handford, P. A., Lea, S. M. Tags: Signal Transduction, Structural Biology Articles Source Type: research

Endothelial cell metabolism in health and disease: impact of hypoxia
In contrast to the general belief, endothelial cell (EC) metabolism has recently been identified as a driver rather than a bystander effect of angiogenesis in health and disease. Indeed, different EC subtypes present with distinct metabolic properties, which determine their function in angiogenesis upon growth factor stimulation. One of the main stimulators of angiogenesis is hypoxia, frequently observed in disease settings such as cancer and atherosclerosis. It has long been established that hypoxic signalling and metabolism changes are highly interlinked. In this review, we will provide an overview of the literature and ...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Wong, B. W., Marsch, E., Treps, L., Baes, M., Carmeliet, P. Tags: Metabolism, Molecular Biology of Disease, Vascular Biology & Angiogenesis Review Source Type: research

A new twist to Sin3 complexes in pluripotent cells
Sin3a is a central component of a class of histone deacetylase-containing transcriptional co-regulatory complexes. In this issue of The EMBO Journal, Streubel et al (2017) purify Sin3a and identify a variant Sin3a complex containing Fam60a in undifferentiated embryonic stem cells (ESCs). Fam60a is a critical component of the ESC Sin3a complex since Fam60a knockdown leads to an extended G1 cell cycle phase and reduced ESC self-renewal. These exciting results open up new questions about how biochemical differences between variant Sin3a complexes may facilitate alterations in cell-specific function. (Source: EMBO Journal)
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Pantier, R., Mullin, N. P., Chambers, I. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells, Transcription News [amp ] Views Source Type: research

The lipid-binding side of Notch ligands
Notch signaling is adjusted to different physiological contexts by expression patterns of Notch ligands and receptors, as well as by posttranslational modifications that modulate the ligand/receptor affinity. In this issue of The EMBO Journal, Suckling et al (2017) show that an interaction of Notch ligands with membrane lipids promotes Notch binding and activation, thus proposing a new mode of Notch activity regulation. (Source: EMBO Journal)
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Shilo, B.-Z., Sprinzak, D. Tags: Signal Transduction, Structural Biology News [amp ] Views Source Type: research

Mitochondrial genome inheritance and replacement in the human germline
Mitochondria, the ubiquitous power packs in nearly every eukaryotic cell, contain their own DNA, known as mtDNA, which is inherited exclusively from the mother. The number of mitochondrial genomes varies depending on the cell's energy needs. The mature oocyte contains the highest number of mitochondria of any cell type, although there is little if any mtDNA replication after fertilization until the embryo implants. This has potential repercussions for mitochondrial replacement therapy (MRT; see description of currently employed methods below) used to prevent the transmission of mtDNA-based disorders. If only a few mitochon...
Source: EMBO Journal - August 1, 2017 Category: Molecular Biology Authors: Wolf, D. P., Hayama, T., Mitalipov, S. Tags: Genetics, Gene Therapy & Genetic Disease, Metabolism, Molecular Biology of Disease Commentary Source Type: research

ATM/Wip1 activities at chromatin control Plk1 re-activation to determine G2 checkpoint duration
After DNA damage, the cell cycle is arrested to avoid propagation of mutations. Arrest in G2 phase is initiated by ATM-/ATR-dependent signaling that inhibits mitosis-promoting kinases such as Plk1. At the same time, Plk1 can counteract ATR-dependent signaling and is required for eventual resumption of the cell cycle. However, what determines when Plk1 activity can resume remains unclear. Here, we use FRET-based reporters to show that a global spread of ATM activity on chromatin and phosphorylation of ATM targets including KAP1 control Plk1 re-activation. These phosphorylations are rapidly counteracted by the chromatin-boun...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Jaiswal, H., Benada, J., Müllers, E., Akopyan, K., Burdova, K., Koolmeister, T., Helleday, T., Medema, R. H., Macurek, L., Lindqvist, A. Tags: Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

Autotaxin-lysophosphatidic acid-LPA3 signaling at the embryo-epithelial boundary controls decidualization pathways
During pregnancy, up-regulation of heparin-binding (HB-) EGF and cyclooxygenase-2 (COX-2) in the uterine epithelium contributes to decidualization, a series of uterine morphological changes required for placental formation and fetal development. Here, we report a key role for the lipid mediator lysophosphatidic acid (LPA) in decidualization, acting through its G-protein-coupled receptor LPA3 in the uterine epithelium. Knockout of Lpar3 or inhibition of the LPA-producing enzyme autotaxin (ATX) in pregnant mice leads to HB-EGF and COX-2 down-regulation near embryos and attenuates decidual reactions. Conversely, selective pha...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Aikawa, S., Kano, K., Inoue, A., Wang, J., Saigusa, D., Nagamatsu, T., Hirota, Y., Fujii, T., Tsuchiya, S., Taketomi, Y., Sugimoto, Y., Murakami, M., Arita, M., Kurano, M., Ikeda, H., Yatomi, Y., Chun, J., Aoki, J. Tags: Development & Differentiation, Signal Transduction Articles Source Type: research

OPA1 deficiency promotes secretion of FGF21 from muscle that prevents obesity and insulin resistance
Mitochondrial dynamics is a conserved process by which mitochondria undergo repeated cycles of fusion and fission, leading to exchange of mitochondrial genetic content, ions, metabolites, and proteins. Here, we examine the role of the mitochondrial fusion protein optic atrophy 1 (OPA1) in differentiated skeletal muscle by reducing OPA1 gene expression in an inducible manner. OPA1 deficiency in young mice results in non-lethal progressive mitochondrial dysfunction and loss of muscle mass. Mutant mice are resistant to age- and diet-induced weight gain and insulin resistance, by mechanisms that involve activation of ER stress...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Pereira, R. O., Tadinada, S. M., Zasadny, F. M., Oliveira, K. J., Pires, K. M. P., Olvera, A., Jeffers, J., Souvenir, R., Mcglauflin, R., Seei, A., Funari, T., Sesaki, H., Potthoff, M. J., Adams, C. M., Anderson, E. J., Abel, E. D. Tags: Ageing, Metabolism, Molecular Biology of Disease Articles Source Type: research

A TRPV1-to-secretagogin regulatory axis controls pancreatic {beta}-cell survival by modulating protein turnover
Ca2+-sensor proteins are generally implicated in insulin release through SNARE interactions. Here, secretagogin, whose expression in human pancreatic islets correlates with their insulin content and the incidence of type 2 diabetes, is shown to orchestrate an unexpectedly distinct mechanism. Single-cell RNA-seq reveals retained expression of the TRP family members in β-cells from diabetic donors. Amongst these, pharmacological probing identifies Ca2+-permeable transient receptor potential vanilloid type 1 channels (TRPV1) as potent inducers of secretagogin expression through recruitment of Sp1 transcription factors. A...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Malenczyk, K., Girach, F., Szodorai, E., Storm, P., Segerstolpe, A., Tortoriello, G., Schnell, R., Mulder, J., Romanov, R. A., Borok, E., Piscitelli, F., Di Marzo, V., Szabo, G., Sandberg, R., Kubicek, S., Lubec, G., Hökfelt, T., Wagner, L., Groop Tags: Molecular Biology of Disease, Signal Transduction Articles Source Type: research

Phosphorylation of Argonaute proteins affects mRNA binding and is essential for microRNA-guided gene silencing in vivo
Argonaute proteins associate with microRNAs and are key components of gene silencing pathways. With such a pivotal role, these proteins represent ideal targets for regulatory post-translational modifications. Using quantitative mass spectrometry, we find that a C-terminal serine/threonine cluster is phosphorylated at five different residues in human and Caenorhabditis elegans. In human, hyper-phosphorylation does not affect microRNA binding, localization, or cleavage activity of Ago2. However, mRNA binding is strongly affected. Strikingly, on Ago2 mutants that cannot bind microRNAs or mRNAs, the cluster remains unphosphory...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Quevillon Huberdeau, M., Zeitler, D. M., Hauptmann, J., Bruckmann, A., Fressigne, L., Danner, J., Piquet, S., Strieder, N., Engelmann, J. C., Jannot, G., Deutzmann, R., Simard, M. J., Meister, G. Tags: Post-translational Modifications, Proteolysis & Proteomics, RNA Biology Articles Source Type: research

Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF
In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C-terminal domain (CTD) of SaHPF pro...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Khusainov, I., Vicens, Q., Ayupov, R., Usachev, K., Myasnikov, A., Simonetti, A., Validov, S., Kieffer, B., Yusupova, G., Yusupov, M., Hashem, Y. Tags: Microbiology, Virology & Host Pathogen Interaction, Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization
Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In Escherichia coli, dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of E. coli 100S (Ec100S), structural insight into 100S formation by LHPF has so far be...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Beckert, B., Abdelshahid, M., Schäfer, H., Steinchen, W., Arenz, S., Berninghausen, O., Beckmann, R., Bange, G., Turgay, K., Wilson, D. N. Tags: Microbiology, Virology & Host Pathogen Interaction, Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks
During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL. Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single-stranded DNA (ssDNA)-binding replication protei...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Abdullah, U. B., McGouran, J. F., Brolih, S., Ptchelkine, D., El-Sagheer, A. H., Brown, T., McHugh, P. J. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Recruitment and positioning determine the specific role of the XPF-ERCC1 endonuclease in interstrand crosslink repair
XPF-ERCC1 is a structure-specific endonuclease pivotal for several DNA repair pathways and, when mutated, can cause multiple diseases. Although the disease-specific mutations are thought to affect different DNA repair pathways, the molecular basis for this is unknown. Here we examine the function of XPF-ERCC1 in DNA interstrand crosslink (ICL) repair. We used Xenopus egg extracts to measure both ICL and nucleotide excision repair, and we identified mutations that are specifically defective in ICL repair. One of these separation-of-function mutations resides in the helicase-like domain of XPF and disrupts binding to SLX4 an...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Klein Douwel, D., Hoogenboom, W. S., Boonen, R. A., Knipscheer, P. Tags: DNA Replication, Repair & Recombination, Molecular Biology of Disease Articles Source Type: research

ER-plasma membrane contact sites contribute to autophagosome biogenesis by regulation of local PI3P synthesis
The double-membrane-bound autophagosome is formed by the closure of a structure called the phagophore, origin of which is still unclear. The endoplasmic reticulum (ER) is clearly implicated in autophagosome biogenesis due to the presence of the omegasome subdomain positive for DFCP1, a phosphatidyl-inositol-3-phosphate (PI3P) binding protein. Contribution of other membrane sources, like the plasma membrane (PM), is still difficult to integrate in a global picture. Here we show that ER–plasma membrane contact sites are mobilized for autophagosome biogenesis, by direct implication of the tethering extended synaptotagmi...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Nascimbeni, A. C., Giordano, F., Dupont, N., Grasso, D., Vaccaro, M. I., Codogno, P., Morel, E. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

Adipose tissue: between the extremes
Adipose tissue represents a critical component in healthy energy homeostasis. It fulfills important roles in whole-body lipid handling, serves as the body's major energy storage compartment and insulation barrier, and secretes numerous endocrine mediators such as adipokines or lipokines. As a consequence, dysfunction of these processes in adipose tissue compartments is tightly linked to severe metabolic disorders, including obesity, metabolic syndrome, lipodystrophy, and cachexia. While numerous studies have addressed causes and consequences of obesity-related adipose tissue hypertrophy and hyperplasia for health, critical...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Vegiopoulos, A., Rohm, M., Herzig, S. Tags: Cancer, Metabolism, Molecular Biology of Disease Review Source Type: research

Survivor: Ribosome Edition
Bacteria owe much of their evolutionary success to the development of mechanisms that enable survival under harsh conditions; despite their importance, however, we have only recently begun to understand these survival strategies. Several of these mechanisms have been shown to target ribosomes, robustly blocking their ability to translate mRNAs into proteins and preserving their integrity in response to extreme environmental conditions. Now, two articles in The EMBO Journal reveal the structural basis of one such strategy, providing new insights and new questions regarding the mechanism and regulation of "ribosome hibe...
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Gonzalez, R. L. Tags: Microbiology, Virology & Host Pathogen Interaction, Protein Biosynthesis & Quality Control, Structural Biology News [amp ] Views Source Type: research

ERCC1-XPF endonuclease--positioned to cut
To counteract damage to our genomes, numerous endo- and exonucleases incise the DNA backbone to remove damaged and aberrant DNA structures. It is imperative that such incisions be very tightly controlled, as unwanted DNA breaks are a key source of genome instability. Two new papers in The EMBO Journal shed light on how the activity of one such nuclease—ERCC1-XPF, an enzyme involved in various DNA repair pathways—is regulated to perform incision in the vicinity of DNA interstrand crosslinks. (Source: EMBO Journal)
Source: EMBO Journal - July 14, 2017 Category: Molecular Biology Authors: Schärer, O. D. Tags: DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

PAR-1 promotes microtubule breakdown during dendrite pruning in Drosophila
Pruning of unspecific neurites is an important mechanism during neuronal morphogenesis. Drosophila sensory neurons prune their dendrites during metamorphosis. Pruning dendrites are severed in their proximal regions. Prior to severing, dendritic microtubules undergo local disassembly, and dendrites thin extensively through local endocytosis. Microtubule disassembly requires a katanin homologue, but the signals initiating microtubule breakdown are not known. Here, we show that the kinase PAR-1 is required for pruning and dendritic microtubule breakdown. Our data show that neurons lacking PAR-1 fail to break down dendritic mi...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Herzmann, S., Krumkamp, R., Rode, S., Kintrup, C., Rumpf, S. Tags: Cell Adhesion, Polarity & Cytoskeleton, Neuroscience Articles Source Type: research

Phosphorylation of Pkp1 by RIPK4 regulates epidermal differentiation and skin tumorigenesis
In this study, we survey the epidermal cell differentiation in a systematic manner by combining quantitative phosphoproteomics with mammalian kinome cDNA library screen. This approach identified a key signaling event, phosphorylation of a desmosome component, PKP1 (plakophilin-1) by RIPK4 (receptor-interacting serine–threonine kinase 4) during epidermal differentiation. With genome-editing and mouse genetics approach, we show that loss of function of either Pkp1 or Ripk4 impairs skin differentiation and enhances epidermal carcinogenesis in vivo. Phosphorylation of PKP1's N-terminal domain by RIPK4 is essential f...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Lee, P., Jiang, S., Li, Y., Yue, J., Gou, X., Chen, S.-Y., Zhao, Y., Schober, M., Tan, M., Wu, X. Tags: Cancer, Development & Differentiation, Signal Transduction Articles Source Type: research

AMPK{alpha}1-LDH pathway regulates muscle stem cell self-renewal by controlling metabolic homeostasis
Control of stem cell fate to either enter terminal differentiation versus returning to quiescence (self-renewal) is crucial for tissue repair. Here, we showed that AMP-activated protein kinase (AMPK), the master metabolic regulator of the cell, controls muscle stem cell (MuSC) self-renewal. AMPKα1–/– MuSCs displayed a high self-renewal rate, which impairs muscle regeneration. AMPKα1–/– MuSCs showed a Warburg-like switch of their metabolism to higher glycolysis. We identified lactate dehydrogenase (LDH) as a new functional target of AMPKα1. LDH, which is a non-limiting enzyme of gly...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Theret, M., Gsaier, L., Schaffer, B., Juban, G., Ben Larbi, S., Weiss-Gayet, M., Bultot, L., Collodet, C., Foretz, M., Desplanches, D., Sanz, P., Zang, Z., Yang, L., Vial, G., Viollet, B., Sakamoto, K., Brunet, A., Chazaud, B., Mounier, R. Tags: Metabolism, Stem Cells Articles Source Type: research

Intrinsic regulation of enteroendocrine fate by Numb
How terminal cell fates are specified in dynamically renewing adult tissues is not well understood. Here we explore terminal cell fate establishment during homeostasis using the enteroendocrine cells (EEs) of the adult Drosophila midgut as a paradigm. Our data argue against the existence of local feedback signals, and we identify Numb as an intrinsic regulator of EE fate. Our data further indicate that Numb, with alpha-adaptin, acts upstream or in parallel of known regulators of EE fate to limit Notch signaling, thereby facilitating EE fate acquisition. We find that Numb is regulated in part through its asymmetric and symm...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Salle, J., Gervais, L., Boumard, B., Stefanutti, M., Siudeja, K., Bardin, A. J. Tags: Development & Differentiation, Signal Transduction Articles Source Type: research

DNA-binding determinants and cellular thresholds for human telomerase repeat addition processivity
The reverse transcriptase telomerase adds telomeric repeats to chromosome ends. Purified human telomerase catalyzes processive repeat synthesis, which could restore the full ~100 nucleotides of (T2AG3)n lost from replicated chromosome ends as a single elongation event. Processivity inhibition is proposed to be a basis of human disease, but the impacts of different levels of processivity on telomere maintenance have not been examined. Here, we delineate side chains in the telomerase active-site cavity important for repeat addition processivity, determine how they contribute to duplex and single-stranded DNA handling, and te...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Wu, R. A., Tam, J., Collins, K. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

In vitro expansion of mouse primordial germ cell-like cells recapitulates an epigenetic blank slate
The expansion of primordial germ cells (PGCs), the precursors for the oocytes and spermatozoa, is a key challenge in reproductive biology/medicine. Using a chemical screening exploiting PGC-like cells (PGCLCs) induced from mouse embryonic stem cells (ESCs), we here identify key signaling pathways critical for PGCLC proliferation. We show that the combinatorial application of Forskolin and Rolipram, which stimulate cAMP signaling via different mechanisms, expands PGCLCs up to ~50-fold in culture. The expanded PGCLCs maintain robust capacity for spermatogenesis, rescuing the fertility of infertile mice. Strikingly, during ex...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Ohta, H., Kurimoto, K., Okamoto, I., Nakamura, T., Yabuta, Y., Miyauchi, H., Yamamoto, T., Okuno, Y., Hagiwara, M., Shirane, K., Sasaki, H., Saitou, M. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Stem Cells Articles Source Type: research

A Pseudomonas aeruginosa TIR effector mediates immune evasion by targeting UBAP1 and TLR adaptors
Bacterial pathogens often subvert the innate immune system to establish a successful infection. The direct inhibition of downstream components of innate immune pathways is particularly well documented but how bacteria interfere with receptor proximal events is far less well understood. Here, we describe a Toll/interleukin 1 receptor (TIR) domain-containing protein (PumA) of the multi-drug resistant Pseudomonas aeruginosa PA7 strain. We found that PumA is essential for virulence and inhibits NF-B, a property transferable to non-PumA strain PA14, suggesting no additional factors are needed for PumA function. The TIR domain i...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Imbert, P. R., Louche, A., Luizet, J.-B., Grandjean, T., Bigot, S., Wood, T. E., Gagne, S., Blanco, A., Wunderley, L., Terradot, L., Woodman, P., Garvis, S., Filloux, A., Guery, B., Salcedo, S. P. Tags: Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

The MYC mRNA 3'-UTR couples RNA polymerase II function to glutamine and ribonucleotide levels
Deregulated expression of MYC enhances glutamine utilization and renders cell survival dependent on glutamine, inducing "glutamine addiction". Surprisingly, colon cancer cells that express high levels of MYC due to WNT pathway mutations are not glutamine-addicted but undergo a reversible cell cycle arrest upon glutamine deprivation. We show here that glutamine deprivation suppresses translation of endogenous MYC via the 3'-UTR of the MYC mRNA, enabling escape from apoptosis. This regulation is mediated by glutamine-dependent changes in adenosine-nucleotide levels. Glutamine deprivation causes a global reduction i...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Dejure, F. R., Royla, N., Herold, S., Kalb, J., Walz, S., Ade, C. P., Mastrobuoni, G., Vanselow, J. T., Schlosser, A., Wolf, E., Kempa, S., Eilers, M. Tags: Cancer, Metabolism, Transcription Articles Source Type: research

The FTD-like syndrome causing TREM2 T66M mutation impairs microglia function, brain perfusion, and glucose metabolism
Genetic variants in the triggering receptor expressed on myeloid cells 2 (TREM2) increase the risk for several neurodegenerative diseases including Alzheimer's disease and frontotemporal dementia (FTD). Homozygous TREM2 missense mutations, such as p.T66M, lead to the FTD-like syndrome, but how they cause pathology is unknown. Using CRISPR/Cas9 genome editing, we generated a knock-in mouse model for the disease-associated Trem2 p.T66M mutation. Consistent with a loss-of-function mutation, we observe an intracellular accumulation of immature mutant Trem2 and reduced generation of soluble Trem2 similar to patients with the ho...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Kleinberger, G., Brendel, M., Mracsko, E., Wefers, B., Groeneweg, L., Xiang, X., Focke, C., Deussing, M., Suarez-Calvet, M., Mazaheri, F., Parhizkar, S., Pettkus, N., Wurst, W., Feederle, R., Bartenstein, P., Mueggler, T., Arzberger, T., Knuesel, I., Romi Tags: Metabolism, Molecular Biology of Disease, Neuroscience Articles Source Type: research

Molecular definitions of autophagy and related processes
Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the fie...
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Galluzzi, L., Baehrecke, E. H., Ballabio, A., Boya, P., Bravo-San Pedro, J. M., Cecconi, F., Choi, A. M., Chu, C. T., Codogno, P., Colombo, M. I., Cuervo, A. M., Debnath, J., Deretic, V., Dikic, I., Eskelinen, E.-L., Fimia, G. M., Fulda, S., Gewirtz, D. A Tags: Autophagy & Cell Death Review Source Type: research

Suppressing mTORC1 on the lysosome
The mechanistic target of rapamycin, mTOR, is a protein kinase that integrates environmental and nutritional inputs into regulation of cell growth and metabolism. Key outputs of mTOR signalling occur from the lysosome membrane in the form of the multi-subunit mTOR complex 1 (mTORC1), which phosphorylates multiple targets. While class I phosphoinositide kinase (PI3K-I) is a well-known activator of mTORC1, a recent paper (Marat et al, 2017) shows that a class II PI3K with a different substrate specificity, PI3K-C2β, serves to inhibit mTORC1 on lysosomes under conditions of growth factor deprivation. (Source: EMBO Journal)
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Raiborg, C., Schink, K. O., Stenmark, H. Tags: Membrane & Intracellular Transport, Metabolism News [amp ] Views Source Type: research

c-MYC mRNA tail tale about glutamine control of transcription
Dejure et al (2017) demonstrates an intriguing link between glutamine, c-MYC protein levels, and c-MYC-dependent transcription. Glutamine-dependent c-MYC protein level, which is sensed through the c-MYC mRNA 3'-UTR, determines global transcriptional response to glutamine deprivation in HCT116 colon cancer cells. These findings add another layer of complexity to c-MYC's role as a nexus in metabolic regulation. (Source: EMBO Journal)
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Dang, C. V. Tags: Cancer, Metabolism, Transcription News [amp ] Views Source Type: research

OH MYeloid! Immune cells wreaking havoc on brain homeostasis
Genetic mutations responsible for neurodegenerative Nasu-Hakola disease have been localized to the gene TREM2 and its adaptor DAP12, but it remained unclear what causes the brain to deteriorate. In this issue of The EMBO Journal, Kleinberger et al (2017) provide intriguing evidence suggesting a TREM2 mutation alone can lead to striking microglial dysfunction and precipitate changes in cerebral blood flow and metabolism in mice. (Source: EMBO Journal)
Source: EMBO Journal - July 3, 2017 Category: Molecular Biology Authors: Bonanno, L., Wyss-Coray, T. Tags: Metabolism, Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

An activated Q-SNARE/SM protein complex as a possible intermediate in SNARE assembly
Assembly of the SNARE proteins syntaxin1, SNAP25, and synaptobrevin into a SNARE complex is essential for exocytosis in neurons. For efficient assembly, SNAREs interact with additional proteins but neither the nature of the intermediates nor the sequence of protein assembly is known. Here, we have characterized a ternary complex between syntaxin1, SNAP25, and the SM protein Munc18-1 as a possible acceptor complex for the R-SNARE synaptobrevin. The ternary complex binds synaptobrevin with fast kinetics, resulting in the rapid formation of a fully zippered SNARE complex to which Munc18-1 remains tethered by the N-terminal do...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Jakhanwal, S., Lee, C.-T., Urlaub, H., Jahn, R. Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

A microRNA-129-5p/Rbfox crosstalk coordinates homeostatic downscaling of excitatory synapses
Synaptic downscaling is a homeostatic mechanism that allows neurons to reduce firing rates during chronically elevated network activity. Although synaptic downscaling is important in neural circuit development and epilepsy, the underlying mechanisms are poorly described. We performed small RNA profiling in picrotoxin (PTX)-treated hippocampal neurons, a model of synaptic downscaling. Thereby, we identified eight microRNAs (miRNAs) that were increased in response to PTX, including miR-129-5p, whose inhibition blocked synaptic downscaling in vitro and reduced epileptic seizure severity in vivo. Using transcriptome,...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Rajman, M., Metge, F., Fiore, R., Khudayberdiev, S., Aksoy-Aksel, A., Bicker, S., Ruedell Reschke, C., Raoof, R., Brennan, G. P., Delanty, N., Farrell, M. A., O'Brien, D. F., Bauer, S., Norwood, B., Veno, M. T., Krüger, M., Braun, T., Kjems, J., R Tags: Neuroscience, RNA Biology Articles Source Type: research

A postprandial FGF19-SHP-LSD1 regulatory axis mediates epigenetic repression of hepatic autophagy
This study demonstrates that the FGF19-SHP-LSD1 axis maintains homeostasis by suppressing unnecessary autophagic breakdown of cellular components, including lipids, under nutrient-rich postprandial conditions. (Source: EMBO Journal)
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Byun, S., Kim, Y.-C., Zhang, Y., Kong, B., Guo, G., Sadoshima, J., Ma, J., Kemper, B., Kemper, J. K. Tags: Autophagy & Cell Death, Chromatin, Epigenetics, Genomics & Functional Genomics, Metabolism Articles Source Type: research

Sphingolipid metabolic flow controls phosphoinositide turnover at the trans-Golgi network
Sphingolipids are membrane lipids globally required for eukaryotic life. The sphingolipid content varies among endomembranes with pre- and post-Golgi compartments being poor and rich in sphingolipids, respectively. Due to this different sphingolipid content, pre- and post-Golgi membranes serve different cellular functions. The basis for maintaining distinct subcellular sphingolipid levels in the presence of membrane trafficking and metabolic fluxes is only partially understood. Here, we describe a homeostatic regulatory circuit that controls sphingolipid levels at the trans-Golgi network (TGN). Specifically, we show that s...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Capasso, S., Sticco, L., Rizzo, R., Pirozzi, M., Russo, D., Dathan, N. A., Campelo, F., van Galen, J., Hölttä-Vuori, M., Turacchio, G., Hausser, A., Malhotra, V., Riezman, I., Riezman, H., Ikonen, E., Luberto, C., Parashuraman, S., Luini, Tags: Membrane & Intracellular Transport, Metabolism Articles Source Type: research

Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains
The autophagosome, a double-membrane structure mediating degradation of cytoplasmic materials by macroautophagy, is formed in close proximity to the endoplasmic reticulum (ER). However, how the ER membrane is involved in autophagy initiation and to which membrane structures the autophagy-initiation complex is localized have not been fully characterized. Here, we were able to biochemically analyze autophagic intermediate membranes and show that the autophagy-initiation complex containing ULK and FIP200 first associates with the ER membrane. To further characterize the ER subdomain, we screened phospholipid biosynthetic enzy...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Nishimura, T., Tamura, N., Kono, N., Shimanaka, Y., Arai, H., Yamamoto, H., Mizushima, N. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

Deletion of PIKfyve alters alveolar macrophage populations and exacerbates allergic inflammation in mice
Alveolar macrophages (AMs) are specialized tissue-resident macrophages that orchestrate the immune responses to inhaled pathogens and maintain organ homeostasis of the lung. Dysregulation of AMs is associated with allergic inflammation and asthma. Here, we examined the role of a phosphoinositide kinase PIKfyve in AM development and function. Mice with conditionally deleted PIKfyve in macrophages have altered AM populations. PIKfyve deficiency results in a loss of AKT activation in response to GM-CSF, a cytokine critical for AM development. Upon exposure to house dust mite extract, mutant mice display severe lung inflammati...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Kawasaki, T., Ito, K., Miyata, H., Akira, S., Kawai, T. Tags: Immunology Articles Source Type: research

Programmed mitophagy is essential for the glycolytic switch during cell differentiation
Retinal ganglion cells (RGCs) are the sole projecting neurons of the retina and their axons form the optic nerve. Here, we show that embryogenesis-associated mouse RGC differentiation depends on mitophagy, the programmed autophagic clearance of mitochondria. The elimination of mitochondria during RGC differentiation was coupled to a metabolic shift with increased lactate production and elevated expression of glycolytic enzymes at the mRNA level. Pharmacological and genetic inhibition of either mitophagy or glycolysis consistently inhibited RGC differentiation. Local hypoxia triggered expression of the mitophagy regulator B...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Esteban-Martinez, L., Sierra-Filardi, E., McGreal, R. S., Salazar-Roa, M., Marino, G., Seco, E., Durand, S., Enot, D., Grana, O., Malumbres, M., Cvekl, A., Cuervo, A. M., Kroemer, G., Boya, P. Tags: Autophagy & Cell Death, Metabolism, Neuroscience Articles Source Type: research

An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function
Stress granules (SG) are membrane-less compartments involved in regulating mRNAs during stress. Aberrant forms of SGs have been implicated in age-related diseases, such as amyotrophic lateral sclerosis (ALS), but the molecular events triggering their formation are still unknown. Here, we find that misfolded proteins, such as ALS-linked variants of SOD1, specifically accumulate and aggregate within SGs in human cells. This decreases the dynamics of SGs, changes SG composition, and triggers an aberrant liquid-to-solid transition of in vitro reconstituted compartments. We show that chaperone recruitment prevents the form...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Mateju, D., Franzmann, T. M., Patel, A., Kopach, A., Boczek, E. E., Maharana, S., Lee, H. O., Carra, S., Hyman, A. A., Alberti, S. Tags: Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Zika virus induces massive cytoplasmic vacuolization and paraptosis-like death in infected cells
We report that ZIKV induces massive vacuolization followed by "implosive" cell death in human epithelial cells, primary skin fibroblasts and astrocytes, a phenomenon which is exacerbated when IFITM3 levels are low. It is reminiscent of paraptosis, a caspase-independent, non-apoptotic form of cell death associated with the formation of large cytoplasmic vacuoles. We further show that ZIKV-induced vacuoles are derived from the endoplasmic reticulum (ER) and dependent on the PI3K/Akt signaling axis. Inhibiting the Sec61 ER translocon in ZIKV-infected cells blocked vacuole formation and viral production. Our results ...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Monel, B., Compton, A. A., Bruel, T., Amraoui, S., Burlaud-Gaillard, J., Roy, N., Guivel-Benhassine, F., Porrot, F., Genin, P., Meertens, L., Sinigaglia, L., Jouvenet, N., Weil, R., Casartelli, N., Demangel, C., Simon-Loriere, E., Moris, A., Roingeard, P. Tags: Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

NIX-ing mitochondria: from development to pathology
Hypoxia occurs physiologically in the developing body, and changing oxygen tensions are known to direct tissue differentiation; however, in the context of pathology, the same hypoxia-activated mechanisms may negatively affect tissue function. In this issue of The EMBO Journal, Esteban-Martínez et al (2017) report that programmed mitophagy, dependent on hypoxia-induced NIP-3-like protein X (BNIP3L, best known as NIX), is an essential step in differentiation of both retinal neurons and inflammatory macrophages. (Source: EMBO Journal)
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Deczkowska, A., Schwartz, M. Tags: Autophagy & Cell Death, Development & Differentiation, Metabolism News [amp ] Views Source Type: research

Getting stress out of stressed-out stress granules
Amyotrophic lateral sclerosis (ALS) pathology is linked to the aberrant aggregation of specific proteins, including TDP-43, FUS, and SOD1, but it is not clear why these aggregation events cause ALS. In this issue of The EMBO Journal, Mateju et al (2017) report a direct link between misfolded proteins accumulating in stress granules and the phase transition of these stress granules from liquid to solid. This discovery provides a model connecting protein aggregation to stress granule dysfunction. (Source: EMBO Journal)
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Siwach, P., Kaganovich, D. Tags: Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research

Is magnetogenetics the new optogenetics?
Optogenetics has revolutionised neuroscience as it enables investigators to establish causal relationships between neuronal activity and a behavioural outcome in a temporally precise manner. It is a powerful technology, but limited by the necessity to deliver light to the cells of interest, which often requires invasive surgery and a tethered light source. Magnetogenetics aims to overcome these issues by manipulating neurons with magnetic stimuli. As magnetic fields can pass freely through organic tissue, it requires no surgery or tethering the animals to an energy source. In this commentary, we assess the utility of ...
Source: EMBO Journal - June 14, 2017 Category: Molecular Biology Authors: Nimpf, S., Keays, D. A. Tags: Neuroscience Commentary Source Type: research

Plant virus-mediated induction of miR168 is associated with repression of ARGONAUTE1 accumulation
(Source: EMBO Journal)
Source: EMBO Journal - June 1, 2017 Category: Molecular Biology Authors: Varallyay, E., Valoczi, A., Agyi, A., Burgyan, J., Havelda, Z. Tags: RNA Biology Corrigenda Source Type: research

BAX inhibitor-1 regulates autophagy by controlling the IRE1{alpha} branch of the unfolded protein response
(Source: EMBO Journal)
Source: EMBO Journal - June 1, 2017 Category: Molecular Biology Authors: Castillo, K., Rojas-Rivera, D., Lisbona, F., Caballero, B., Nassif, M., Court, F. A., Schuck, S., Ibar, C., Walter, P., Sierralta, J., Glavic, A., Hetz, C. Tags: Corrigenda Source Type: research

USP4 inhibits SMAD4 monoubiquitination and promotes activin and BMP signaling
SMAD4 is a common intracellular effector for TGF-β family cytokines, but the mechanism by which its activity is dynamically regulated is unclear. We demonstrated that ubiquitin-specific protease (USP) 4 strongly induces activin/BMP signaling by removing the inhibitory monoubiquitination from SMAD4. This modification was triggered by the recruitment of the E3 ligase, SMURF2, to SMAD4 following ligand-induced regulatory (R)-SMAD–SMAD4 complex formation. Whereas the interaction of the negative regulator c-SKI inhibits SMAD4 monoubiquitination, the ligand stimulates the recruitment of SMURF2 to the c-SKI-SMAD2 compl...
Source: EMBO Journal - June 1, 2017 Category: Molecular Biology Authors: Zhou, F., Xie, F., Jin, K., Zhang, Z., Clerici, M., Gao, R., van Dinther, M., Sixma, T. K., Huang, H., Zhang, L., ten Dijke, P. Tags: Development & Differentiation, Signal Transduction Articles Source Type: research

A new sub-pathway of long-patch base excision repair involving 5' gap formation
Base excision repair (BER) is one of the most frequently used cellular DNA repair mechanisms and modulates many human pathophysiological conditions related to DNA damage. Through live cell and in vitro reconstitution experiments, we have discovered a major sub-pathway of conventional long-patch BER that involves formation of a 9-nucleotide gap 5' to the lesion. This new sub-pathway is mediated by RECQ1 DNA helicase and ERCC1-XPF endonuclease in cooperation with PARP1 poly(ADP-ribose) polymerase and RPA. The novel gap formation step is employed during repair of a variety of DNA lesions, including oxidative and alkylati...
Source: EMBO Journal - June 1, 2017 Category: Molecular Biology Authors: Woodrick, J., Gupta, S., Camacho, S., Parvathaneni, S., Choudhury, S., Cheema, A., Bai, Y., Khatkar, P., Erkizan, H. V., Sami, F., Su, Y., Schärer, O. D., Sharma, S., Roy, R. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Sen1 has unique structural features grafted on the architecture of the Upf1-like helicase family
The superfamily 1B (SF1B) helicase Sen1 is an essential protein that plays a key role in the termination of non-coding transcription in yeast. Here, we identified the ~90 kDa helicase core of Saccharomyces cerevisiae Sen1 as sufficient for transcription termination in vitro and determined the corresponding structure at 1.8 Å resolution. In addition to the catalytic and auxiliary subdomains characteristic of the SF1B family, Sen1 has a distinct and evolutionarily conserved structural feature that "braces" the helicase core. Comparative structural analyses indicate that the "brace" is...
Source: EMBO Journal - June 1, 2017 Category: Molecular Biology Authors: Leonaite, B., Han, Z., Basquin, J., Bonneau, F., Libri, D., Porrua, O., Conti, E. Tags: RNA Biology, Structural Biology Articles Source Type: research

Short FtsZ filaments can drive asymmetric cell envelope constriction at the onset of bacterial cytokinesis
FtsZ, the bacterial homologue of eukaryotic tubulin, plays a central role in cell division in nearly all bacteria and many archaea. It forms filaments under the cytoplasmic membrane at the division site where, together with other proteins it recruits, it drives peptidoglycan synthesis and constricts the cell. Despite extensive study, the arrangement of FtsZ filaments and their role in division continue to be debated. Here, we apply electron cryotomography to image the native structure of intact dividing cells and show that constriction in a variety of Gram-negative bacterial cells, including Proteus mirabilis and Caulobact...
Source: EMBO Journal - June 1, 2017 Category: Molecular Biology Authors: Yao, Q., Jewett, A. I., Chang, Y.-W., Oikonomou, C. M., Beeby, M., Iancu, C. V., Briegel, A., Ghosal, D., Jensen, G. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research