An ancient antisense-driven RNA switch drives plant sex determination
New work by Hisanaga et al (2019) uncovers the central module that regulates sexual dimorphism in haploid early land plants, opening doors toward understanding evolution of sex chromosomes in ancestors of diploid plants. (Source: EMBO Journal)
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Berger, F. Tags: Plant Biology, RNA Biology, Transcription News [amp ] Views Source Type: research

Boosting adult neurogenesis to enhance sensory performance
Although most mammalian neurons are born prenatally, there are at least a couple of specialised niches in the adult rodent brain that continually generate new neurons throughout life. The potential functions conferred by this process of adult neurogenesis, however, remain obscure, despite a sizeable literature exploring the links between alterations in neurogenic capacity and changes in behavioural ability. A new study by Bragado Alonso et al (2019) offers a novel viewpoint on this question by describing a particularly clean way to manipulate adult neurogenesis. Specifically altering cell cycle dynamics in adult neura...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Lipovsek, M., Grubb, M. S. Tags: Neuroscience News [amp ] Views Source Type: research

ABRO1 promotes NLRP3 inflammasome activation through regulation of NLRP3 deubiquitination
Deubiquitination of NLRP3 has been suggested to contribute to inflammasome activation, but the roles and molecular mechanisms are still unclear. We here demonstrate that ABRO1, a subunit of the BRISC deubiquitinase complex, is necessary for optimal NLRP3-ASC complex formation, ASC oligomerization, caspase-1 activation, and IL-1β and IL-18 production upon treatment with NLRP3 ligands after the priming step, indicating that efficient NLRP3 activation requires ABRO1. Moreover, we report that ABRO1 deficiency results in a remarkable attenuation in the syndrome severity of NLRP3-associated inflammatory diseases, including ...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Ren, G., Zhang, X., Xiao, Y., Zhang, W., Wang, Y., Ma, W., Wang, X., Song, P., Lai, L., Chen, H., Zhan, Y., Zhang, J., Yu, M., Ge, C., Li, C., Yin, R., Yang, X. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

A cis-acting bidirectional transcription switch controls sexual dimorphism in the liverwort
Plant life cycles alternate between haploid gametophytes and diploid sporophytes. While regulatory factors determining male and female sexual morphologies have been identified for sporophytic reproductive organs, such as stamens and pistils of angiosperms, those regulating sex-specific traits in the haploid gametophytes that produce male and female gametes and hence are central to plant sexual reproduction are poorly understood. Here, we identified a MYB-type transcription factor, MpFGMYB, as a key regulator of female sexual differentiation in the haploid-dominant dioicous liverwort, Marchantia polymorpha. MpFGMYB is speci...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Hisanaga, T., Okahashi, K., Yamaoka, S., Kajiwara, T., Nishihama, R., Shimamura, M., Yamato, K. T., Bowman, J. L., Kohchi, T., Nakajima, K. Tags: Plant Biology, RNA Biology, Transcription Articles Source Type: research

Unanchored tri-NEDD8 inhibits PARP-1 to protect from oxidative stress-induced cell death
NEDD8 is a ubiquitin-like protein that activates cullin-RING E3 ubiquitin ligases (CRLs). Here, we identify a novel role for NEDD8 in regulating the activity of poly(ADP-ribose) polymerase 1 (PARP-1) in response to oxidative stress. We show that treatment of cells with H2O2 results in the accumulation of NEDD8 chains, likely by directly inhibiting the deneddylase NEDP1. One chain type, an unanchored NEDD8 trimer, specifically bound to the second zinc finger domain of PARP-1 and attenuated its activation. In cells in which Nedp1 is deleted, large amounts of tri-NEDD8 constitutively form, resulting in inhibition of PARP-1 an...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Keuss, M. J., Hjerpe, R., Hsia, O., Gourlay, R., Burchmore, R., Trost, M., Kurz, T. Tags: Autophagy & Cell Death, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Nuclear import of the DSCAM-cytoplasmic domain drives signaling capable of inhibiting synapse formation
DSCAM and DSCAML1 are immunoglobulin and cell adhesion-type receptors serving important neurodevelopmental functions including control of axon growth, branching, neurite self-avoidance, and neuronal cell death. The signal transduction mechanisms or effectors of DSCAM receptors, however, remain poorly characterized. We used a human ORFeome library to perform a high-throughput screen in mammalian cells and identified novel cytoplasmic signaling effector candidates including the Down syndrome kinase Dyrk1a, STAT3, USP21, and SH2D2A. Unexpectedly, we also found that the intracellular domains (ICDs) of DSCAM and DSCAML1 specifi...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Sachse, S. M., Lievens, S., Ribeiro, L. F., Dascenco, D., Masschaele, D., Horre, K., Misbaer, A., Vanderroost, N., De Smet, A. S., Salta, E., Erfurth, M.-L., Kise, Y., Nebel, S., Van Delm, W., Plaisance, S., Tavernier, J., De Strooper, B., De Wit, J., Sch Tags: Neuroscience, Signal Transduction Articles Source Type: research

STAT4 activation by leukemia inhibitory factor confers a therapeutic effect on intestinal inflammation
T helper 17 (Th17)-cell differentiation triggered by interleukin-6 (IL-6) via STAT3 activation promotes inflammation in inflammatory bowel disease (IBD) patients. However, leukemia inhibitory factor (LIF), an IL-6 family cytokine, restricts inflammation by blocking Th17-cell differentiation via an unknown mechanism. Here, we report that microbiota dysregulation promotes LIF secretion by intestinal epithelial cells (IECs) in a mouse colitis model. LIF greatly activates STAT4 phosphorylation on multiple SPXX elements within the C-terminal transcription regulation domain. STAT4 and STAT3 act reciprocally on both canonical cis...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Zhang, Y. S., Xin, D. E., Wang, Z., Song, X., Sun, Y., Zou, Q. C., Yue, J., Zhang, C., Zhang, J. M., Liu, Z., Zhang, X., Zhao, T. C., Su, B., Chin, Y. E. Tags: Immunology, Signal Transduction Articles Source Type: research

Multi-omics identify xanthine as a pro-survival metabolite for nematodes with mitochondrial dysfunction
Aberrant mitochondrial function contributes to the pathogenesis of various metabolic and chronic disorders. Inhibition of insulin/IGF-1 signaling (IIS) represents a promising avenue for the treatment of mitochondrial diseases, although many of the molecular mechanisms underlying this beneficial effect remain elusive. Using an unbiased multi-omics approach, we report here that IIS inhibition reduces protein synthesis and favors catabolism in mitochondrial deficient Caenorhabditis elegans. We unveil that the lifespan extension does not occur through the restoration of mitochondrial respiration, but as a consequence of an ATP...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Gioran, A., Piazzesi, A., Bertan, F., Schroer, J., Wischhof, L., Nicotera, P., Bano, D. Tags: Membrane & Intracellular Transport, Metabolism, Signal Transduction Articles Source Type: research

A multifaceted small RNA modulates gene expression upon glucose limitation in Staphylococcus aureus
Pathogenic bacteria must rapidly adapt to ever-changing environmental signals resulting in metabolism remodeling. The carbon catabolite repression, mediated by the catabolite control protein A (CcpA), is used to express genes involved in utilization and metabolism of the preferred carbon source. Here, we have identified RsaI as a CcpA-repressed small non-coding RNA that is inhibited by high glucose concentrations. When glucose is consumed, RsaI represses translation initiation of mRNAs encoding a permease of glucose uptake and the FN3K enzyme that protects proteins against damage caused by high glucose concentrations. RsaI...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Bronesky, D., Desgranges, E., Corvaglia, A., Francois, P., Caballero, C. J., Prado, L., Toledo-Arana, A., Lasa, I., Moreau, K., Vandenesch, F., Marzi, S., Romby, P., Caldelari, I. Tags: Metabolism, Microbiology, Virology & Host Pathogen Interaction, RNA Biology Articles Source Type: research

An increase in neural stem cells and olfactory bulb adult neurogenesis improves discrimination of highly similar odorants
Adult neurogenesis is involved in cognitive performance but studies that manipulated this process to improve brain function are scarce. Here, we characterized a genetic mouse model in which neural stem cells (NSC) of the subventricular zone (SVZ) were temporarily expanded by conditional expression of the cell cycle regulators Cdk4/cyclinD1, thus increasing neurogenesis. We found that supernumerary neurons matured and integrated in the olfactory bulb similarly to physiologically generated newborn neurons displaying a correct expression of molecular markers, morphology and electrophysiological activity. Olfactory performance...
Source: EMBO Journal - March 15, 2019 Category: Molecular Biology Authors: Bragado Alonso, S., Reinert, J. K., Marichal, N., Massalini, S., Berninger, B., Kuner, T., Calegari, F. Tags: Neuroscience Articles Source Type: research

Ubiquitin--a beacon for all during quality control on the ribosome
Ribosome stalling triggers no-go decay (NGD) and ribosome-associated quality control (RQC) pathways to rapidly degrade the aberrant mRNA and the incomplete nascent peptide, respectively. Two recent studies in yeast and mammalian systems reveal the importance of stalling-induced ribosomal protein ubiquitination by Hel2/ZNF598 for both NGD and RQC. The studies also structurally explain how collided ribosomes generate a unique interface not present in monosomes, which can be recognized by Hel2/ZNF598 ubiquitin ligases. (Source: EMBO Journal)
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Yan, L. L., Zaher, H. S. Tags: Post-translational Modifications, Proteolysis & Proteomics, Protein Biosynthesis & Quality Control, Structural Biology News [amp ] Views Source Type: research

Length doesn't matter--telomere damage triggers cellular senescence in the ageing heart
Telomere shortening induces cellular senescence in proliferative cells. Yet, it is presently unclear how it is triggered in post-mitotic cells such as cardiac myocytes. A new study by Anderson et al (2019) reports that during ageing of the heart, cellular senescence develops independently of telomere length, but is evoked by DNA damage, which preferentially accumulates at the telomere. Removal of senescent cells using senolytic drugs ameliorated cardiac hypertrophy and fibrosis and may inform novel approaches to improve the conditions for the ageing heart. (Source: EMBO Journal)
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Brand, T. Tags: Ageing, DNA Replication, Repair & Recombination, Metabolism News [amp ] Views Source Type: research

Vav mediates Ras stimulation by direct activation of the GDP/GTP exchange factor Ras GRP1
(Source: EMBO Journal)
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Caloca, M. J., Zugaza, J. L., Matallanas, D., Crespo, P., Bustelo, X. R. Tags: Corrigendum Source Type: research

Abnormal TDP-43 function impairs activity-dependent BDNF secretion, synaptic plasticity, and cognitive behavior through altered Sortilin splicing
Aberrant function of the RNA-binding protein TDP-43 has been causally linked to multiple neurodegenerative diseases. Due to its large number of targets, the mechanisms through which TDP-43 malfunction cause disease are unclear. Here, we report that knockdown, aggregation, or disease-associated mutation of TDP-43 all impair intracellular sorting and activity-dependent secretion of the neurotrophin brain-derived neurotrophic factor (BDNF) through altered splicing of the trafficking receptor Sortilin. Adult mice lacking TDP-43 specifically in hippocampal CA1 show memory impairment and synaptic plasticity defects that can be r...
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Tann, J. Y., Wong, L.-W., Sajikumar, S., Ibanez, C. F. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

The herpesviral antagonist m152 reveals differential activation of STING-dependent IRF and NF-{kappa}B signaling and STING's dual role during MCMV infection
Cytomegaloviruses (CMVs) are master manipulators of the host immune response. Here, we reveal that the murine CMV (MCMV) protein m152 specifically targets the type I interferon (IFN) response by binding to stimulator of interferon genes (STING), thereby delaying its trafficking to the Golgi compartment from where STING initiates type I IFN signaling. Infection with an MCMV lacking m152 induced elevated type I IFN responses and this leads to reduced viral transcript levels both in vitro and in vivo. This effect is ameliorated in the absence of STING. Interestingly, while m152 inhibits STING-mediated IRF signaling,...
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Stempel, M., Chan, B., Juranic Lisnic, V., Krmpotic, A., Hartung, J., Paludan, S. R., Füllbrunn, N., Lemmermann, N. A., Brinkmann, M. M. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Length-independent telomere damage drives post-mitotic cardiomyocyte senescence
Ageing is the biggest risk factor for cardiovascular disease. Cellular senescence, a process driven in part by telomere shortening, has been implicated in age-related tissue dysfunction. Here, we address the question of how senescence is induced in rarely dividing/post-mitotic cardiomyocytes and investigate whether clearance of senescent cells attenuates age-related cardiac dysfunction. During ageing, human and murine cardiomyocytes acquire a senescent-like phenotype characterised by persistent DNA damage at telomere regions that can be driven by mitochondrial dysfunction and crucially can occur independently of cell divis...
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Anderson, R., Lagnado, A., Maggiorani, D., Walaszczyk, A., Dookun, E., Chapman, J., Birch, J., Salmonowicz, H., Ogrodnik, M., Jurk, D., Proctor, C., Correia-Melo, C., Victorelli, S., Fielder, E., Berlinguer-Palmini, R., Owens, A., Greaves, L. C., Kolsky, Tags: Ageing, DNA Replication, Repair & Recombination, Metabolism Articles Source Type: research

Localized incorporation of outer membrane components in the pathogen Brucella abortus
The zoonotic pathogen Brucella abortus is part of the Rhizobiales, which are alpha-proteobacteria displaying unipolar growth. Here, we show that this bacterium exhibits heterogeneity in its outer membrane composition, with clusters of rough lipopolysaccharide co-localizing with the essential outer membrane porin Omp2b, which is proposed to allow facilitated diffusion of solutes through the porin. We also show that the major outer membrane protein Omp25 and peptidoglycan are incorporated at the new pole and the division site, the expected growth sites. Interestingly, lipopolysaccharide is also inserted at the same growth si...
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Vassen, V., Valotteau, C., Feuillie, C., Formosa-Dague, C., Dufrene, Y. F., De Bolle, X. Tags: Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways
Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo-EM analysis...
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Ikeuchi, K., Tesina, P., Matsuo, Y., Sugiyama, T., Cheng, J., Saeki, Y., Tanaka, K., Becker, T., Beckmann, R., Inada, T. Tags: Post-translational Modifications, Proteolysis & Proteomics, Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

Endophilin-A regulates presynaptic Ca2+ influx and synaptic vesicle recycling in auditory hair cells
Ribbon synapses of cochlear inner hair cells (IHCs) operate with high rates of neurotransmission; yet, the molecular regulation of synaptic vesicle (SV) recycling at these synapses remains poorly understood. Here, we studied the role of endophilins-A1-3, endocytic adaptors with curvature-sensing and curvature-generating properties, in mouse IHCs. Single-cell RT–PCR indicated the expression of endophilins-A1-3 in IHCs, and immunoblotting confirmed the presence of endophilin-A1 and endophilin-A2 in the cochlea. Patch-clamp recordings from endophilin-A-deficient IHCs revealed a reduction of Ca2+ influx and exocytosis, w...
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Kroll, J., Jaime Tobon, L. M., Vogl, C., Neef, J., Kondratiuk, I., König, M., Strenzke, N., Wichmann, C., Milosevic, I., Moser, T. Tags: Neuroscience Articles Source Type: research

Structures of the heart specific SERCA2a Ca2+-ATPase
The sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 2a (SERCA2a) performs active reuptake of cytoplasmic Ca2+ and is a major regulator of cardiac muscle contractility. Dysfunction or dysregulation of SERCA2a is associated with heart failure, while restoring its function is considered as a therapeutic strategy to restore cardiac performance. However, its structure has not yet been determined. Based on native, active protein purified from pig ventricular muscle, we present the first crystal structures of SERCA2a, determined in the CPA-stabilized E2–AlF4– form (3.3 Å) and the Ca2+-occluded [Ca2]E1-AMPPCP...
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Sitsel, A., De Raeymaecker, J., Drachmann, N. D., Derua, R., Smaardijk, S., Andersen, J. L., Vandecaetsbeek, I., Chen, J., De Maeyer, M., Waelkens, E., Olesen, C., Vangheluwe, P., Nissen, P. Tags: Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

EZH2 cooperates with gain-of-function p53 mutants to promote cancer growth and metastasis
In light of the increasing number of identified cancer-driven gain-of-function (GOF) mutants of p53, it is important to define a common mechanism to systematically target several mutants, rather than developing strategies tailored to inhibit each mutant individually. Here, using RNA immunoprecipitation-sequencing (RIP-seq), we identified the Polycomb-group histone methyltransferase EZH2 as a p53 mRNA-binding protein. EZH2 bound to an internal ribosome entry site (IRES) in the 5'UTR of p53 mRNA and enhanced p53 protein translation in a methyltransferase-independent manner. EZH2 augmented p53 GOF mutant-mediated cancer growt...
Source: EMBO Journal - March 1, 2019 Category: Molecular Biology Authors: Zhao, Y., Ding, L., Wang, D., Ye, Z., He, Y., Ma, L., Zhu, R., Pan, Y., Wu, Q., Pang, K., Hou, X., Weroha, S. J., Han, C., Coleman, R., Coleman, I., Karnes, R. J., Zhang, J., Nelson, P. S., Wang, L., Huang, H. Tags: Cancer, Molecular Biology of Disease, Protein Biosynthesis & Quality Control Articles Source Type: research

An airway organoid is forever
In the last decade, the generation and maintenance of organotypic structures has been propelled to the center stage of biomedical research. In the lung, a variety of protocols has been devised to generate organoids mimicking lung structures, but most methods with human cells have complicated lengthy protocols or a progressive decline in differentiation potential and physiological function with increasing passaging. A new study from Sachs et al (2019) seeks to solve these issues, providing a versatile methodology to efficiently isolate, indefinitely culture, and manipulate human airway organoids, potentially allowing t...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Paschini, M., Kim, C. F. Tags: Development & Differentiation, Methods & Resources, Molecular Biology of Disease News [amp ] Views Source Type: research

Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signaling
(Source: EMBO Journal)
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Qiu, R., DeRocco, V. C., Harris, C., Sharma, A., Hingorani, M. M., Erie, D. A., Weninger, K. R. Tags: Corrigendum Source Type: research

Cas9 slide-and-seek for phage defense and genome engineering
How does the Cas9 nuclease locate a specific 20-nucleotide target sequence in a crowded intracellular environment packed with mega bases of distracting non-target DNA? Previously, it was shown that Cas9 finds DNA targets via three-dimensional diffusion. In this issue of The EMBO Journal, Globyte et al (2019) reveal another dimension of the search process, which involves short-range one-dimensional sliding. These results have implications for understanding the natural function of Cas9 and its applications in genome engineering experiments. (Source: EMBO Journal)
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Santiago-Frangos, A., Wiegand, T., Wiedenheft, B. Tags: DNA Replication, Repair & Recombination, Methods & Resources News [amp ] Views Source Type: research

The nature of the biological material and the irreproducibility problem in biomedical research
Biomedical research has a reproducibility problem since various crucial landmark papers could not be independently reproduced. While there are many causes related to statistical analysis, methodology or insufficient reporting of experimental details, this commentary argues that the complexity of biological material itself is, until now, a largely ignored source of irreproducibility. By discussing examples from evolutionary biology, intrinsically disordered proteins and current biomedical research, it contends that some results are irreproducible because we do not have the knowledge, the tools or the analytical ability to u...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Papamokos, G. V. Tags: Commentary Source Type: research

A dual role for cell plate-associated PI4K{beta} in endocytosis and phragmoplast dynamics during plant somatic cytokinesis
Plant cytokinesis involves membrane trafficking and cytoskeletal rearrangements. Here, we report that the phosphoinositide kinases PI4Kβ1 and PI4Kβ2 integrate these processes in Arabidopsis thaliana (Arabidopsis) roots. Cytokinetic defects of an Arabidopsis pi4kβ1 pi4kβ2 double mutant are accompanied by defects in membrane trafficking. Specifically, we show that trafficking of the proteins KNOLLE and PIN2 at the cell plate, clathrin recruitment, and endocytosis is impaired in pi4kβ1 pi4kβ2 double mutants, accompanied by unfused vesicles at the nascent cell plate and around cell wall stubs. Int...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Lin, F., Krishnamoorthy, P., Schubert, V., Hause, G., Heilmann, M., Heilmann, I. Tags: Membrane & Intracellular Transport, Plant Biology Articles Source Type: research

Long-term expanding human airway organoids for disease modeling
Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here, we describe a method to establish long-term-expanding human airway organoids from broncho-alveolar resections or lavage material. The pseudostratified airway organoids consist of basal cells, functional multi-ciliated cells, mucus-producing secretory cells, and CC10-secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR function in an organoid swelling assay. Organoids established from lung cancer resections and metastasis biopsies r...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Sachs, N., Papaspyropoulos, A., Zomer-van Ommen, D. D., Heo, I., Böttinger, L., Klay, D., Weeber, F., Huelsz-Prince, G., Iakobachvili, N., Amatngalim, G. D., de Ligt, J., van Hoeck, A., Proost, N., Viveen, M. C., Lyubimova, A., Teeven, L., Derakhs Tags: Cancer, Methods & Resources, Molecular Biology of Disease Source Type: research

CDK phosphorylation of Xenopus laevis M18BP1 promotes its metaphase centromere localization
Chromosome segregation requires the centromere, the site on chromosomes where kinetochores assemble in mitosis to attach chromosomes to the mitotic spindle. Centromere identity is defined epigenetically by the presence of nucleosomes containing the histone H3 variant CENP-A. New CENP-A nucleosome assembly occurs at the centromere every cell cycle during G1, but how CENP-A nucleosome assembly is spatially and temporally restricted remains poorly understood. Centromere recruitment of factors required for CENP-A assembly is mediated in part by the three-protein Mis18 complex (Mis18α, Mis18β, M18BP1). Here, we show ...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: French, B. T., Straight, A. F. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics Articles Source Type: research

Atoh1+ secretory progenitors possess renewal capacity independent of Lgr5+ cells during colonic regeneration
During homeostasis, the colonic epithelium is replenished every 3–5 days by rapidly cycling Lgr5+ stem cells. However, various insults can lead to depletion of Lgr5+ stem cells, and colonic epithelium can be regenerated from Lgr5-negative cells. While studies in the small intestine have addressed the lineage identity of the Lgr5-negative regenerative cell population, in the colon this question has remained unanswered. Here, we set out to identify which cell(s) contribute to colonic regeneration by performing genetic fate-mapping studies of progenitor populations in mice. First, using keratin-19 (Krt19) to mark a...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Castillo-Azofeifa, D., Fazio, E. N., Nattiv, R., Good, H. J., Wald, T., Pest, M. A., de Sauvage, F. J., Klein, O. D., Asfaha, S. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells Articles Source Type: research

Bacterial killing by complement requires membrane attack complex formation via surface-bound C5 convertases
The immune system kills bacteria by the formation of lytic membrane attack complexes (MACs), triggered when complement enzymes cleave C5. At present, it is not understood how the MAC perturbs the composite cell envelope of Gram-negative bacteria. Here, we show that the role of C5 convertase enzymes in MAC assembly extends beyond the cleavage of C5 into the MAC precursor C5b. Although purified MAC complexes generated from preassembled C5b6 perforate artificial lipid membranes and mammalian cells, these components lack bactericidal activity. In order to permeabilize both the bacterial outer and inner membrane and thus kill a...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Heesterbeek, D. A., Bardoel, B. W., Parsons, E. S., Bennett, I., Ruyken, M., Doorduijn, D. J., Gorham, R. D., Berends, E. T., Pyne, A. L., Hoogenboom, B. W., Rooijakkers, S. H. Tags: Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

The pseudokinase TRIB1 toggles an intramolecular switch to regulate COP1 nuclear export
COP1 is a highly conserved ubiquitin ligase that regulates diverse cellular processes in plants and metazoans. Tribbles pseudokinases, which only exist in metazoans, act as scaffolds that interact with COP1 and its substrates to facilitate ubiquitination. Here, we report that, in addition to this scaffolding role, TRIB1 promotes nuclear localization of COP1 by disrupting an intramolecular interaction between the WD40 domain and a previously uncharacterized regulatory site within COP1. This site, which we have termed the pseudosubstrate latch (PSL), resembles the consensus COP1-binding motif present in known COP1 substrates...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Kung, J. E., Jura, N. Tags: Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion
The Streptococcus pyogenes CRISPR/Cas9 (SpCas9) nuclease has been widely applied in genetic engineering. Despite its importance in genome editing, aspects of the precise molecular mechanism of Cas9 activity remain ambiguous. In particular, because of the lack of a method with high spatio-temporal resolution, transient interactions between Cas9 and DNA could not be reliably investigated. It therefore remains controversial how Cas9 searches for protospacer adjacent motif (PAM) sequences. We have developed single-molecule Förster resonance energy transfer (smFRET) assays to monitor transient interactions of Cas9 and DNA in ...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Globyte, V., Lee, S. H., Bae, T., Kim, J.-S., Joo, C. Tags: DNA Replication, Repair & Recombination, Methods & Resources Articles Source Type: research

Beclin1-driven autophagy modulates the inflammatory response of microglia via NLRP3
Alzheimer's disease is characterized not only by extracellular amyloid plaques and neurofibrillary tangles, but also by microglia-mediated neuroinflammation. Recently, autophagy has been linked to the regulation of the inflammatory response. Thus, we investigated how an impairment of autophagy mediated by BECN1/Beclin1 reduction, as described in Alzheimer's disease patients, would influence cytokine production of microglia. Acutely stimulated microglia from Becn1+/– mice exhibited increased expression of IL-1beta and IL-18 compared to wild-type microglia. Becn1+/–APPPS1 mice also contained enhanced IL-1beta lev...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Houtman, J., Freitag, K., Gimber, N., Schmoranzer, J., Heppner, F. L., Jendrach, M. Tags: Immunology, Neuroscience Articles Source Type: research

Selective inhibition of the Fc{varepsilon}RI-induced de novo synthesis of mediators by an inhibitory receptor
(Source: EMBO Journal)
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Abramson, J., Licht, A., Pecht, I. Tags: Corrigendum Source Type: research

Nonsense shielding: protecting RNA from decay leads to cancer
Despite intense scrutiny, the signals that determine whether a given RNA is degraded by the highly conserved and selective nonsense-mediated RNA decay (NMD) pathway remain murky. In this issue of The EMBO Journal, Kishor et al shed light on this issue by demonstrating that the RNA-binding protein, hnRNP L, protects a subset of RNAs from degradation by NMD. This mechanism is responsible for stabilizing the mRNA encoding the pro-survival "oncogenic" protein, BCL-2, in B-cell lymphoma. (Source: EMBO Journal)
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Wilkinson, M. F., Cook-Andersen, H. Tags: Cancer, RNA Biology News [amp ] Views Source Type: research

Revealing the Superpowers of PrimPol: rescuing replicating microsatellites
R-loops are potentially mutagenic three-stranded structures where RNA has hybridized to one strand of DNA and displaced the other, exposing ssDNA. Long repeated R-loop-forming sequences are known to cause genomic instability and are associated with disease. Šviković et al (2019) show that even short tandem (microsatellite) repeats, abundant in the vertebrate genome, do form R-loops and present a barrier to replication. However, the replication fork can move past these short R-loop-forming repeats through the re-priming action of primase–polymerase (PrimPol), thus avoiding the loss of epigenetic informati...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Reid, J. E., Fischer, T. Tags: DNA Replication, Repair & Recombination News [amp ] Views Source Type: research

Getting into shape: tissue tension drives oriented cell divisions during organogenesis
The shapes and architecture of the organs in the animal body develop through complex coordination of cell shape change, cell migration, and cell proliferation. Finegan et al (2019) use the simple model of the Drosophila ovary and elongation of each egg chamber to explore this process. They find that a gradient of myosin-driven tension exists along the axis of organ elongation and that this orients the division of the constituent cells. This and other recent work highlight how tissue-level tension plays a key role in regulating tissue architecture. (Source: EMBO Journal)
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Manning, L. A., Peifer, M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation News [amp ] Views Source Type: research

Tissue tension and not interphase cell shape determines cell division orientation in the Drosophila follicular epithelium
We examined the orientation of cell divisions with respect to the planar tissue axis and found a bias toward the primary direction of tissue expansion. However, interphase cell shapes demonstrate the opposite bias. Hertwig's rule, which holds that cell elongation determines division orientation, is therefore broken in this tissue. This observation cannot be explained by the anisotropic activity of the conserved Pins/Mud spindle-orienting machinery, which controls division orientation in the apical–basal axis and planar division orientation in other epithelial tissues. Rather, cortical tension at the apical surface tr...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Finegan, T. M., Na, D., Cammarota, C., Skeeters, A. V., Nadasi, T. J., Dawney, N. S., Fletcher, A. G., Oakes, P. W., Bergstralh, D. T. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation Articles Source Type: research

Clustering of Tau fibrils impairs the synaptic composition of {alpha}3-Na+/K+-ATPase and AMPA receptors
We report that fibrillar Tau forms clusters at the plasma membrane following lateral diffusion. We found that the fibrils interact with the Na+/K+-ATPase (NKA) and AMPA receptors. The consequence of the clustering is a reduction in the amount of α3-NKA and an increase in the amount of GluA2-AMPA receptor at synapses. Furthermore, fibrillar Tau destabilizes functional NKA complexes. Tau and α-synuclein aggregates often co-exist in patients’ brains. We now show evidences for cross-talk between these pathogenic aggregates with α-synuclein fibrils dramatically enhancing fibrillar Tau clustering and syna...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Shrivastava, A. N., Redeker, V., Pieri, L., Bousset, L., Renner, M., Madiona, K., Mailhes-Hamon, C., Coens, A., Buee, L., Hantraye, P., Triller, A., Melki, R. Tags: Neuroscience Articles Source Type: research

R-loop formation during S phase is restricted by PrimPol-mediated repriming
During DNA replication, conflicts with ongoing transcription are frequent and require careful management to avoid genetic instability. R-loops, three-stranded nucleic acid structures comprising a DNA:RNA hybrid and displaced single-stranded DNA, are important drivers of damage arising from such conflicts. How R-loops stall replication and the mechanisms that restrain their formation during S phase are incompletely understood. Here, we show in vivo how R-loop formation drives a short purine-rich repeat, (GAA)10, to become a replication impediment that engages the repriming activity of the primase-polymerase PrimPol. Fu...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Svikovic, S., Crisp, A., Tan-Wong, S. M., Guilliam, T. A., Doherty, A. J., Proudfoot, N. J., Guilbaud, G., Sale, J. E. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Avidity-driven polarity establishment via multivalent lipid-GTPase module interactions
While Rho GTPases are indispensible regulators of cellular polarity, the mechanisms underlying their anisotropic activation at membranes have been elusive. Using the budding yeast Cdc42 GTPase module, which includes a guanine nucleotide exchange factor (GEF) Cdc24 and the scaffold Bem1, we find that avidity generated via multivalent anionic lipid interactions is a critical mechanistic constituent of polarity establishment. We identify basic cluster (BC) motifs in Bem1 that drive the interaction of the scaffold–GEF complex with anionic lipids at the cell pole. This interaction appears to influence lipid acyl chain ord...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Meca, J., Massoni-Laporte, A., Martinez, D., Sartorel, E., Loquet, A., Habenstein, B., McCusker, D. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

RagC phosphorylation autoregulates mTOR complex 1
The mechanistic (or mammalian) target of rapamycin complex 1 (mTORC1) controls cell growth, proliferation, and metabolism in response to diverse stimuli. Two major parallel pathways are implicated in mTORC1 regulation including a growth factor-responsive pathway mediated via TSC2/Rheb and an amino acid-responsive pathway mediated via the Rag GTPases. Here, we identify and characterize three highly conserved growth factor-responsive phosphorylation sites on RagC, a component of the Rag heterodimer, implicating cross talk between amino acid and growth factor-mediated regulation of mTORC1. We find that RagC phosphorylation is...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Yang, G., Humphrey, S. J., Murashige, D. S., Francis, D., Wang, Q.-P., Cooke, K. C., Neely, G. G., James, D. E. Tags: Development & Differentiation, Signal Transduction Articles Source Type: research

Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells
Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of Listeria bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography. We show that the structure of the tube-baseplate compl...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Guerrero-Ferreira, R. C., Hupfeld, M., Nazarov, S., Taylor, N. M., Shneider, M. M., Obbineni, J. M., Loessner, M. J., Ishikawa, T., Klumpp, J., Leiman, P. G. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

Disease-associated tau impairs mitophagy by inhibiting Parkin translocation to mitochondria
Accumulation of the protein tau characterises Alzheimer's disease and other tauopathies, including familial forms of frontotemporal dementia (FTD) that carry pathogenic tau mutations. Another hallmark feature of these diseases is the accumulation of dysfunctional mitochondria. Although disease-associated tau is known to impair several aspects of mitochondrial function, it is still unclear whether it also directly impinges on mitochondrial quality control, specifically Parkin-dependent mitophagy. Using the mito-QC mitophagy reporter, we found that both human wild-type (hTau) and FTD mutant tau (hP301L) inhibited mitophagy i...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Cummins, N., Tweedie, A., Zuryn, S., Bertran-Gonzalez, J., Götz, J. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

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