The virtuous self-tolerance of virtual memory T cells
"Virtual" memory CD8+ T cells are a subset of immune cells produced by homeostatic mechanisms involving response to self-antigens, raising the possibility that these cells could mediate autoimmunity. New work by Drobek et al demonstrates that virtual memory T cells are indeed favored by stronger T-cell receptor signals but exhibit minimal autoreactivity while maintaining self-tolerance. (Source: EMBO Journal)
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Truckenbrod, E. N., Jameson, S. C. Tags: Immunology News [amp ] Views Source Type: research

Periodic fasting starves cisplatin-resistant cancers to death
Treatment of cancers with the cytotoxic agent cisplatin frequently evokes resistance, accompanied by rewiring of metabolic pathways, limiting its clinical use. Recent research by Obrist et al (2018) shows that cisplatin-resistant growth of lung adenocarcinoma is particularly vulnerable to periodic fasting cycles and starvation-induced cell death, due to its dependency on glutamine, required for nucleoside biosynthesis, suggesting an opportunity for nutritional anti-cancer interventions. (Source: EMBO Journal)
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Guidi, N., Longo, V. D. Tags: Cancer, Autophagy & Cell Death, Metabolism News [amp ] Views Source Type: research

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease
The failure of DNA ligases to complete their catalytic reactions generates cytotoxic adenylated DNA strand breaks. The APTX RNA-DNA deadenylase protects genome integrity and corrects abortive DNA ligation arising during ribonucleotide excision repair and base excision DNA repair, and APTX human mutations cause the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1). How APTX senses cognate DNA nicks and is inactivated in AOA1 remains incompletely defined. Here, we report X-ray structures of APTX engaging nicked RNA-DNA substrates that provide direct evidence for a wedge-pivot-cut strategy for 5'-AMP resolutio...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Tumbale, P., Schellenberg, M. J., Mueller, G. A., Fairweather, E., Watson, M., Little, J. N., Krahn, J., Waddell, I., London, R. E., Williams, R. S. Tags: DNA Replication, Repair & Recombination, Molecular Biology of Disease, Structural Biology Articles Source Type: research

Lmo2 expression defines tumor cell identity during T-cell leukemogenesis
The impact of LMO2 expression on cell lineage decisions during T-cell leukemogenesis remains largely elusive. Using genetic lineage tracing, we have explored the potential of LMO2 in dictating a T-cell malignant phenotype. We first initiated LMO2 expression in hematopoietic stem/progenitor cells and maintained its expression in all hematopoietic cells. These mice develop exclusively aggressive human-like T-ALL. In order to uncover a potential exclusive reprogramming effect of LMO2 in murine hematopoietic stem/progenitor cells, we next showed that transient LMO2 expression is sufficient for oncogenic function and induction ...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Garcia-Ramirez, I., Bhatia, S., Rodriguez-Hernandez, G., Gonzalez-Herrero, I., Walter, C., Gonzalez de Tena-Davila, S., Parvin, S., Haas, O., Woessmann, W., Stanulla, M., Schrappe, M., Dugas, M., Natkunam, Y., Orfao, A., Dominguez, V., Pintado, B., Blanco Tags: Cancer, Development & Differentiation, Immunology Articles Source Type: research

Secretory kinase Fam20C tunes endoplasmic reticulum redox state via phosphorylation of Ero1{alpha}
Family with sequence similarity 20C (Fam20C), the physiological Golgi casein kinase, phosphorylates numerous secreted proteins that are involved in a wide variety of biological processes. However, the role of Fam20C in regulating proteins in the endoplasmic reticulum (ER) lumen is largely unknown. Here, we report that Fam20C interacts with various luminal proteins and that its depletion results in a more reduced ER lumen. We further show that ER oxidoreductin 1α (Ero1α), the pivotal sulfhydryl oxidase that catalyzes disulfide formation in the ER, is phosphorylated by Fam20C in the Golgi apparatus and retrograde...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Zhang, J., Zhu, Q., Wang, X., Yu, J., Chen, X., Wang, J., Wang, X., Xiao, J., Wang, C.-c., Wang, L. Tags: Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Metabolic vulnerability of cisplatin-resistant cancers
Cisplatin is the most widely used chemotherapeutic agent, and resistance of neoplastic cells against this cytoxicant poses a major problem in clinical oncology. Here, we explored potential metabolic vulnerabilities of cisplatin-resistant non-small human cell lung cancer and ovarian cancer cell lines. Cisplatin-resistant clones were more sensitive to killing by nutrient deprivation in vitro and in vivo than their parental cisplatin-sensitive controls. The susceptibility of cisplatin-resistant cells to starvation could be explained by a particularly strong dependence on glutamine. Glutamine depletion was sufficient...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Obrist, F., Michels, J., Durand, S., Chery, A., Pol, J., Levesque, S., Joseph, A., Astesana, V., Pietrocola, F., Wu, G. S., Castedo, M., Kroemer, G. Tags: Cancer, Autophagy & Cell Death, Metabolism Articles Source Type: research

Strong homeostatic TCR signals induce formation of self-tolerant virtual memory CD8 T cells
We describe two molecular mechanisms driving the formation of virtual memory T cells. First, virtual memory T cells originate exclusively from strongly self-reactive T cells. Second, the stoichiometry of the CD8 interaction with Lck regulates the size of the virtual memory T-cell compartment via modulating the self-reactivity of individual T cells. Although virtual memory T cells descend from the highly self-reactive clones and acquire a partial memory program, they are not more potent in inducing experimental autoimmune diabetes than naìˆve T cells. These data underline the importance of the variable level of self-reacti...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Drobek, A., Moudra, A., Mueller, D., Huranova, M., Horkova, V., Pribikova, M., Ivanek, R., Oberle, S., Zehn, D., McCoy, K. D., Draber, P., Stepanek, O. Tags: Immunology Articles Source Type: research

Transcriptional control and exploitation of an immune-responsive family of plant retrotransposons
In this study, we employed an ATCOPIA93 long-terminal repeat (LTR) promoter-GUS fusion to show that this retrotransposon behaves like an immune-responsive gene during pathogen defense in Arabidopsis. We also showed that the endogenous ATCOPIA93 copy "EVD", which is activated in the presence of bacterial stress, is negatively regulated by both DNA methylation and polycomb-mediated silencing, a mode of repression typically found at protein-coding and microRNA genes. Interestingly, an ATCOPIA93-derived soloLTR is located upstream of the disease resistance gene RPP4 and is devoid of DNA methylation and H3K27m3 marks....
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Zervudacki, J., Yu, A., Amesefe, D., Wang, J., Drouaud, J., Navarro, L., Deleris, A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Microbiology, Virology & Host Pathogen Interaction, Plant Biology Articles Source Type: research

Mechanism of membrane pore formation by human gasdermin-D
Gasdermin-D (GSDMD), a member of the gasdermin protein family, mediates pyroptosis in human and murine cells. Cleaved by inflammatory caspases, GSDMD inserts its N-terminal domain (GSDMDNterm) into cellular membranes and assembles large oligomeric complexes permeabilizing the membrane. So far, the mechanisms of GSDMDNterm insertion, oligomerization, and pore formation are poorly understood. Here, we apply high-resolution (≤ 2 nm) atomic force microscopy (AFM) to describe how GSDMDNterm inserts and assembles in membranes. We observe GSDMDNterm inserting into a variety of lipid compositions, among which phosphat...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Mulvihill, E., Sborgi, L., Mari, S. A., Pfreundschuh, M., Hiller, S., Müller, D. J. Tags: Autophagy & Cell Death, Immunology Articles Source Type: research

Dimer-specific immunoprecipitation of active caspase-2 identifies TRAF proteins as novel activators
Caspase-2 has been shown to initiate apoptotic cell death in response to specific intracellular stressors such as DNA damage. However, the molecular mechanisms immediately upstream of its activation are still poorly understood. We combined a caspase-2 bimolecular fluorescence complementation (BiFC) system with fluorophore-specific immunoprecipitation to isolate and study the active caspase-2 dimer and its interactome. Using this technique, we found that tumor necrosis factor receptor-associated factor 2 (TRAF2), as well as TRAF1 and 3, directly binds to the active caspase-2 dimer. TRAF2 in particular is necessary for caspa...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Robeson, A. C., Lindblom, K. R., Wojton, J., Kornbluth, S., Matsuura, K. Tags: Autophagy & Cell Death Articles Source Type: research

A protein that controls the onset of a Salmonella virulence program
The mechanism of action and contribution to pathogenesis of many virulence genes are understood. By contrast, little is known about anti-virulence genes, which contribute to the start, progression, and outcome of an infection. We now report how an anti-virulence factor in Salmonella enterica serovar Typhimurium dictates the onset of a genetic program that governs metabolic adaptations and pathogen survival in host tissues. Specifically, we establish that the anti-virulence protein CigR directly restrains the virulence protein MgtC, thereby hindering intramacrophage survival, inhibition of ATP synthesis, stabilization ...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Yeom, J., Pontes, M. H., Choi, J., Groisman, E. A. Tags: Microbiology, Virology & Host Pathogen Interaction, Transcription Articles Source Type: research

hDNA2 nuclease/helicase promotes centromeric DNA replication and genome stability
DNA2 is a nuclease/helicase that is involved in Okazaki fragment maturation, replication fork processing, and end resection of DNA double-strand breaks. Similar such helicase activity for resolving secondary structures and structure-specific nuclease activity are needed during DNA replication to process the chromosome-specific higher order repeat units present in the centromeres of human chromosomes. Here, we show that DNA2 binds preferentially to centromeric DNA. The nuclease and helicase activities of DNA2 are both essential for resolution of DNA structural obstacles to facilitate DNA replication fork movement. Loss of D...
Source: EMBO Journal - July 13, 2018 Category: Molecular Biology Authors: Li, Z., Liu, B., Jin, W., Wu, X., Zhou, M., Liu, V. Z., Goel, A., Shen, Z., Zheng, L., Shen, B. Tags: Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

Nuclear lncRNA stabilization in the host response to bacterial infection
Long non-coding RNAs (lncRNAs) play important roles in many cellular pathways, but their contribution to the defense of eukaryotic cells against pathogens remains poorly understood. A new study from Imamura et al in The EMBO Journal reports that Salmonella infection in human cells impacts nuclear RNA decay, which in turn drives the accumulation of otherwise unstable nuclear lncRNAs, some of which may have protective effects against this common bacterial pathogen. These unexpected findings demand more efforts to fully decrypt the molecular functions of lncRNAs in innate and adaptive immunity. (Source: EMBO Journal)
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Munschauer, M., Vogel, J. Tags: Microbiology, Virology & Host Pathogen Interaction, RNA Biology News [amp ] Views Source Type: research

miR-200/375 control epithelial plasticity-associated alternative splicing by repressing the RNA-binding protein Quaking
Members of the miR-200 family are critical gatekeepers of the epithelial state, restraining expression of pro-mesenchymal genes that drive epithelial–mesenchymal transition (EMT) and contribute to metastatic cancer progression. Here, we show that miR-200c and another epithelial-enriched miRNA, miR-375, exert widespread control of alternative splicing in cancer cells by suppressing the RNA-binding protein Quaking (QKI). During EMT, QKI-5 directly binds to and regulates hundreds of alternative splicing targets and exerts pleiotropic effects, such as increasing cell migration and invasion and restraining tumour growth, ...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Pillman, K. A., Phillips, C. A., Roslan, S., Toubia, J., Dredge, B. K., Bert, A. G., Lumb, R., Neumann, D. P., Li, X., Conn, S. J., Liu, D., Bracken, C. P., Lawrence, D. M., Stylianou, N., Schreiber, A. W., Tilley, W. D., Hollier, B. G., Khew-Goodall, Y., Tags: Cancer, Cell Adhesion, Polarity & Cytoskeleton, RNA Biology Articles Source Type: research

Helicobacter pylori adhesin HopQ disrupts trans dimerization in human CEACAMs
The human gastric pathogen Helicobacter pylori is a major causative agent of gastritis, peptic ulcer disease, and gastric cancer. As part of its adhesive lifestyle, the bacterium targets members of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family by the conserved outer membrane adhesin HopQ. The HopQ–CEACAM1 interaction is associated with inflammatory responses and enables the intracellular delivery and phosphorylation of the CagA oncoprotein via a yet unknown mechanism. Here, we generated crystal structures of HopQ isotypes I and II bound to the N-terminal domain of human CEACAM1...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Moonens, K., Hamway, Y., Neddermann, M., Reschke, M., Tegtmeyer, N., Kruse, T., Kammerer, R., Mejias-Luque, R., Singer, B. B., Backert, S., Gerhard, M., Remaut, H. Tags: Cell Adhesion, Polarity & Cytoskeleton, Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

The Helicobacter pylori adhesin protein HopQ exploits the dimer interface of human CEACAMs to facilitate translocation of the oncoprotein CagA
Helicobacter pylori infects half of the world's population, and strains that encode the cag type IV secretion system for injection of the oncoprotein CagA into host gastric epithelial cells are associated with elevated levels of cancer. CagA translocation into host cells is dependent on interactions between the H. pylori adhesin protein HopQ and human CEACAMs. Here, we present high-resolution structures of several HopQ-CEACAM complexes and CEACAMs in their monomeric and dimeric forms establishing that HopQ uses a coupled folding and binding mechanism to engage the canonical CEACAM dimerization interface for CEACAM rec...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Bonsor, D. A., Zhao, Q., Schmidinger, B., Weiss, E., Wang, J., Deredge, D., Beadenkopf, R., Dow, B., Fischer, W., Beckett, D., Wintrode, P. L., Haas, R., Sundberg, E. J. Tags: Cell Adhesion, Polarity & Cytoskeleton, Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

Photodynamic therapy with redaporfin targets the endoplasmic reticulum and Golgi apparatus
Preclinical evidence depicts the capacity of redaporfin (Redp) to act as potent photosensitizer, causing direct antineoplastic effects as well as indirect immune-dependent destruction of malignant lesions. Here, we investigated the mechanisms through which photodynamic therapy (PDT) with redaporfin kills cancer cells. Subcellular localization and fractionation studies based on the physicochemical properties of redaporfin revealed its selective tropism for the endoplasmic reticulum (ER) and the Golgi apparatus (GA). When activated, redaporfin caused rapid reactive oxygen species-dependent perturbation of ER/GA compartments,...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Gomes-da-Silva, L. C., Zhao, L., Bezu, L., Zhou, H., Sauvat, A., Liu, P., Durand, S., Leduc, M., Souquere, S., Loos, F., Mondragon, L., Sveinbjornsson, B., Rekdal, O., Boncompain, G., Perez, F., Arnaut, L. G., Kepp, O., Kroemer, G. Tags: Cancer, Autophagy & Cell Death Articles Source Type: research

In vivo expansion of functionally integrated GABAergic interneurons by targeted increase in neural progenitors
A central hypothesis for brain evolution is that it might occur via expansion of progenitor cells and subsequent lineage-dependent formation of neural circuits. Here, we report in vivo amplification and functional integration of lineage-specific circuitry in Drosophila. Levels of the cell fate determinant Prospero were attenuated in specific brain lineages within a range that expanded not only progenitors but also neuronal progeny, without tumor formation. Resulting supernumerary neural stem cells underwent normal functional transitions, progressed through the temporal patterning cascade, and generated progeny with mo...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Shaw, R. E., Kottler, B., Ludlow, Z. N., Buhl, E., Kim, D., Morais da Silva, S., Miedzik, A., Coum, A., Hodge, J. J., Hirth, F., Sousa-Nunes, R. Tags: Development & Differentiation, Neuroscience Articles Source Type: research

Live imaging of wound angiogenesis reveals macrophage orchestrated vessel sprouting and regression
Wound angiogenesis is an integral part of tissue repair and is impaired in many pathologies of healing. Here, we investigate the cellular interactions between innate immune cells and endothelial cells at wounds that drive neoangiogenic sprouting in real time and in vivo. Our studies in mouse and zebrafish wounds indicate that macrophages are drawn to wound blood vessels soon after injury and are intimately associated throughout the repair process and that macrophage ablation results in impaired neoangiogenesis. Macrophages also positively influence wound angiogenesis by driving resolution of anti-angiogenic wound...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Gurevich, D. B., Severn, C. E., Twomey, C., Greenhough, A., Cash, J., Toye, A. M., Mellor, H., Martin, P. Tags: Development & Differentiation, Vascular Biology & Angiogenesis Articles Source Type: research

Centrosomal ALIX regulates mitotic spindle orientation by modulating astral microtubule dynamics
The orientation of the mitotic spindle (MS) is tightly regulated, but the molecular mechanisms are incompletely understood. Here we report a novel role for the multifunctional adaptor protein ALG-2-interacting protein X (ALIX) in regulating MS orientation in addition to its well-established role in cytokinesis. We show that ALIX is recruited to the pericentriolar material (PCM) of the centrosomes and promotes correct orientation of the MS in asymmetrically dividing Drosophila stem cells and epithelial cells, and symmetrically dividing Drosophila and human epithelial cells. ALIX-deprived cells display defective formation of...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Malerod, L., Le Borgne, R., Lie-Jensen, A., Eikenes, A. H., Brech, A., Liestol, K., Stenmark, H., Haglund, K. Tags: Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle Articles Source Type: research

Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs
Cytoplasmic mRNA degradation controls gene expression to help eliminate pathogens during infection. However, it has remained unclear whether such regulation also extends to nuclear RNA decay. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stab...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Imamura, K., Takaya, A., Ishida, Y.-i., Fukuoka, Y., Taya, T., Nakaki, R., Kakeda, M., Imamachi, N., Sato, A., Yamada, T., Onoguchi-Mizutani, R., Akizuki, G., Tanu, T., Tao, K., Miyao, S., Suzuki, Y., Nagahama, M., Yamamoto, T., Jensen, T. H., Akimitsu, N Tags: Microbiology, Virology & Host Pathogen Interaction, RNA Biology Articles Source Type: research

The trimeric coiled-coil HSBP1 protein promotes WASH complex assembly at centrosomes
The Arp2/3 complex generates branched actin networks that exert pushing forces onto different cellular membranes. WASH complexes activate Arp2/3 complexes at the surface of endosomes and thereby fission transport intermediates containing endocytosed receptors, such as α5β1 integrins. How WASH complexes are assembled in the cell is unknown. Here, we identify the small coiled-coil protein HSBP1 as a factor that specifically promotes the assembly of a ternary complex composed of CCDC53, WASH, and FAM21 by dissociating the CCDC53 homotrimeric precursor. HSBP1 operates at the centrosome, which concentrates the buildi...
Source: EMBO Journal - July 2, 2018 Category: Molecular Biology Authors: Visweshwaran, S. P., Thomason, P. A., Guerois, R., Vacher, S., Denisov, E. V., Tashireva, L. A., Lomakina, M. E., Lazennec-Schurdevin, C., Lakisic, G., Lilla, S., Molinie, N., Henriot, V., Mechulam, Y., Alexandrova, A. Y., Cherdyntseva, N. V., Bieche, I., Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

How DNA vicinity controls SUMO E3 ligase activity
Little is known about the regulation of SUMO E3 ligases and how they are activated upon stress. New findings from the Reverter and Torres-Rosell laboratories in The EMBO Journal demonstrate that vicinity of preferentially ssDNA activates the SUMO E3 ligase Nse2 when in complex with SMC5-6. (Source: EMBO Journal)
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Pichler, A. Tags: DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics, Structural Biology News [amp ] Views Source Type: research

Algorithmically outsourcing the detection of statistical errors and other problems
Software to check texts for spelling errors is commonplace, but catching errors of a more technical nature, such as incorrect P-value calculations, is still a manual endeavor. Nonetheless, text-mining technology to catch a growing number of error types within scientific manuscripts has been developed by studies interested in broad, literature-wide surveys. The same algorithms that are now used to retrospectively identify potential errors in published papers can also be used pre-emptively to identify errors before publication. So far, these algorithms have focused on finding errors of commission, such as incorrect calculati...
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Wren, J. D. Tags: Methods & Resources, Systems & Computational Biology Commentary Source Type: research

FAM35A associates with REV7 and modulates DNA damage responses of normal and BRCA1-defective cells
To exploit vulnerabilities of tumors, it is urgent to identify associated defects in genome maintenance. One unsolved problem is the mechanism of regulation of DNA double-strand break repair by REV7 in complex with 53BP1 and RIF1, and its influence on repair pathway choice between homologous recombination and non-homologous end-joining. We searched for REV7-associated factors in human cells and found FAM35A, a previously unstudied protein with an unstructured N-terminal region and a C-terminal region harboring three OB-fold domains similar to single-stranded DNA-binding protein RPA, as novel interactor of REV7/RIF1/53BP1. ...
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Tomida, J., Takata, K.-i., Bhetawal, S., Person, M. D., Chao, H.-P., Tang, D. G., Wood, R. D. Tags: Cancer, DNA Replication, Repair & Recombination Articles Source Type: research

GTSF-1 is required for formation of a functional RNA-dependent RNA Polymerase complex in Caenorhabditis elegans
We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying rrf-3 mutants. We show, both in vivo and in vitro, that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activiti...
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Almeida, M. V., Dietz, S., Redl, S., Karaulanov, E., Hildebrandt, A., Renz, C., Ulrich, H. D., König, J., Butter, F., Ketting, R. F. Tags: Development & Differentiation, RNA Biology Articles Source Type: research

The assembly of lipid droplets and their roles in challenged cells
Cytoplasmic lipid droplets are important organelles in nearly every eukaryotic and some prokaryotic cells. Storing and providing energy is their main function, but they do not work in isolation. They respond to stimuli initiated either on the cell surface or in the cytoplasm as conditions change. Cellular stresses such as starvation and invasion are internal insults that evoke changes in droplet metabolism and dynamics. This review will first outline lipid droplet assembly and then discuss how droplets respond to stress and in particular nutrient starvation. Finally, the role of droplets in viral and microbial invasion wil...
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Henne, W. M., Reese, M. L., Goodman, J. M. Tags: Metabolism, Microbiology, Virology & Host Pathogen Interaction Review Source Type: research

{alpha}-Synuclein stimulation of monoamine oxidase-B and legumain protease mediates the pathology of Parkinson's disease
Dopaminergic neurodegeneration in Parkinson's disease (PD) is associated with abnormal dopamine metabolism by MAO-B (monoamine oxidase-B) and intracellular α-Synuclein (α-Syn) aggregates, called the Lewy body. However, the molecular relationship between α-Syn and MAO-B remains unclear. Here, we show that α-Syn directly binds to MAO-B and stimulates its enzymatic activity, which triggers AEP (asparagine endopeptidase; legumain) activation and subsequent α-Syn cleavage at N103, leading to dopaminergic neurodegeneration. Interestingly, the dopamine metabolite, DOPAL, strongly activates AEP, and t...
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Kang, S. S., Ahn, E. H., Zhang, Z., Liu, X., Manfredsson, F. P., Sandoval, I. M., Dhakal, S., Iuvone, P. M., Cao, X., Ye, K. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

LRRK2 is a negative regulator of Mycobacterium tuberculosis phagosome maturation in macrophages
Mutations in the leucine-rich repeat kinase 2 (LRRK2) are associated with Parkinson's disease, chronic inflammation and mycobacterial infections. Although there is evidence supporting the idea that LRRK2 has an immune function, the cellular function of this kinase is still largely unknown. By using genetic, pharmacological and proteomics approaches, we show that LRRK2 kinase activity negatively regulates phagosome maturation via the recruitment of the Class III phosphatidylinositol-3 kinase complex and Rubicon to the phagosome in macrophages. Moreover, inhibition of LRRK2 kinase activity in mouse and human macrophages enha...
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Härtlova, A., Herbst, S., Peltier, J., Rodgers, A., Bilkei-Gorzo, O., Fearns, A., Dill, B. D., Lee, H., Flynn, R., Cowley, S. A., Davies, P., Lewis, P. A., Ganley, I. G., Martinez, J., Alessi, D. R., Reith, A. D., Trost, M., Gutierrez, M. G. Tags: Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

DNA activates the Nse2/Mms21 SUMO E3 ligase in the Smc5/6 complex
Modification of chromosomal proteins by conjugation to SUMO is a key step to cope with DNA damage and to maintain the integrity of the genome. The recruitment of SUMO E3 ligases to chromatin may represent one layer of control on protein sumoylation. However, we currently do not understand how cells upregulate the activity of E3 ligases on chromatin. Here we show that the Nse2 SUMO E3 in the Smc5/6 complex, a critical player during recombinational DNA repair, is directly stimulated by binding to DNA. Activation of sumoylation requires the electrostatic interaction between DNA and a positively charged patch in the ARM domain...
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Varejao, N., Ibars, E., Lascorz, J., Colomina, N., Torres-Rosell, J., Reverter, D. Tags: DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics, Structural Biology Articles Source Type: research

Interplay of cell-cell contacts and RhoA/MRTF-A signaling regulates cardiomyocyte identity
Cell–cell and cell–matrix interactions guide organ development and homeostasis by controlling lineage specification and maintenance, but the underlying molecular principles are largely unknown. Here, we show that in human developing cardiomyocytes cell–cell contacts at the intercalated disk connect to remodeling of the actin cytoskeleton by regulating the RhoA-ROCK signaling to maintain an active MRTF/SRF transcriptional program essential for cardiomyocyte identity. Genetic perturbation of this mechanosensory pathway activates an ectopic fat gene program during cardiomyocyte differentiation, which ultimat...
Source: EMBO Journal - June 15, 2018 Category: Molecular Biology Authors: Dorn, T., Kornherr, J., Parrotta, E. I., Zawada, D., Ayetey, H., Santamaria, G., Iop, L., Mastantuono, E., Sinnecker, D., Goedel, A., Dirschinger, R. J., My, I., Laue, S., Bozoglu, T., Baarlink, C., Ziegler, T., Graf, E., Hinkel, R., Cuda, G., Käa Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Stem Cells Articles Source Type: research

Unmasking the skiptic task of TDP-43
The mechanism by which mutations in TAR DNA-binding protein 43 (TDP-43) cause neurodegeneration remains incompletely understood. In this issue of The EMBO Journal, Fratta et al (2018) describe how a point mutation in the C-terminal low complexity domain of TDP-43 leads to the skipping of otherwise constitutively conserved exons. In vivo, this mutation triggers late-onset progressive neuromuscular disturbances, as seen in amyotrophic lateral sclerosis (ALS), suggesting that TDP-43 splicing gain-of-function contributes to ALS pathogenesis. (Source: EMBO Journal)
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Rouaux, C., Gonzalez De Aguilar, J.-L., Dupuis, L. Tags: Molecular Biology of Disease, Neuroscience, RNA Biology News [amp ] Views Source Type: research

The Hfq chaperone helps the ribosome mature
Ribosome biogenesis is a complex process that is facilitated by a large number of assembly factors. In this issue, Andrade et al (2018) provide evidence that a widely conserved RNA chaperone, Hfq, acts as a ribosomal assembly factor in bacteria. Hfq is known to support regulation of stress response genes by small RNAs. Andrade et al (2018) show that the absence of Hfq results in higher levels of immature 30S ribosomes and error-prone translation, suggesting that Hfq globally affects the quality of protein synthesis when bacteria are under stress. (Source: EMBO Journal)
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Sharma, I. M., Korman, A., Woodson, S. A. Tags: Microbiology, Virology & Host Pathogen Interaction, Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research

The complex relationship between TFEB transcription factor phosphorylation and subcellular localization
The MiT-TFE family of basic helix-loop-helix leucine-zipper transcription factors includes four members: TFEB, TFE3, TFEC, and MITF. Originally described as oncogenes, these factors play a major role as regulators of lysosome biogenesis, cellular energy homeostasis, and autophagy. An important mechanism by which these transcription factors are regulated involves their shuttling between the surface of lysosomes, the cytoplasm, and the nucleus. Such dynamic changes in subcellular localization occur in response to nutrient fluctuations and various forms of cell stress and are mediated by changes in the phosphorylation of mult...
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Puertollano, R., Ferguson, S. M., Brugarolas, J., Ballabio, A. Tags: Autophagy & Cell Death, Metabolism, Signal Transduction Reviews Source Type: research

Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis
TDP-43 (encoded by the gene TARDBP) is an RNA binding protein central to the pathogenesis of amyotrophic lateral sclerosis (ALS). However, how TARDBP mutations trigger pathogenesis remains unknown. Here, we use novel mouse mutants carrying point mutations in endogenous Tardbp to dissect TDP-43 function at physiological levels both in vitro and in vivo. Interestingly, we find that mutations within the C-terminal domain of TDP-43 lead to a gain of splicing function. Using two different strains, we are able to separate TDP-43 loss- and gain-of-function effects. TDP-43 gain-of-function effects in these mice reveal a ...
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Fratta, P., Sivakumar, P., Humphrey, J., Lo, K., Ricketts, T., Oliveira, H., Brito-Armas, J. M., Kalmar, B., Ule, A., Yu, Y., Birsa, N., Bodo, C., Collins, T., Conicella, A. E., Mejia Maza, A., Marrero-Gagliardi, A., Stewart, M., Mianne, J., Corrochano, S Tags: Molecular Biology of Disease, Neuroscience, RNA Biology Articles Source Type: research

Distinct in vivo roles of secreted APP ectodomain variants APPs{alpha} and APPs{beta} in regulation of spine density, synaptic plasticity, and cognition
Increasing evidence suggests that synaptic functions of the amyloid precursor protein (APP), which is key to Alzheimer pathogenesis, may be carried out by its secreted ectodomain (APPs). The specific roles of APPsα and APPsβ fragments, generated by non-amyloidogenic or amyloidogenic APP processing, respectively, remain however unclear. Here, we expressed APPsα or APPsβ in the adult brain of conditional double knockout mice (cDKO) lacking APP and the related APLP2. APPsα efficiently rescued deficits in spine density, synaptic plasticity (LTP and PPF), and spatial reference memory of cDKO mice. In...
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Richter, M. C., Ludewig, S., Winschel, A., Abel, T., Bold, C., Salzburger, L. R., Klein, S., Han, K., Weyer, S. W., Fritz, A.-K., Laube, B., Wolfer, D. P., Buchholz, C. J., Korte, M., Müller, U. C. Tags: Neuroscience Articles Source Type: research

Continuous signaling of CD79b and CD19 is required for the fitness of Burkitt lymphoma B cells
Expression of the B-cell antigen receptor (BCR) is essential not only for the development but also for the maintenance of mature B cells. Similarly, many B-cell lymphomas, including Burkitt lymphoma (BL), require continuous BCR signaling for their tumor growth. This growth is driven by immunoreceptor tyrosine-based activation motif (ITAM) and PI3 kinase (PI3K) signaling. Here, we employ CRISPR/Cas9 to delete BCR and B-cell co-receptor genes in the human BL cell line Ramos. We find that Ramos B cells require the expression of the BCR signaling component Igβ (CD79b), and the co-receptor CD19, for their fitness and compe...
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: He, X., Kläsener, K., Iype, J. M., Becker, M., Maity, P. C., Cavallari, M., Nielsen, P. J., Yang, J., Reth, M. Tags: Immunology, Signal Transduction Articles Source Type: research

Don't go in circles: confounding factors in gene expression profiling
Quantification of gene expression is a crucial research tool in the life sciences, which makes it important to identify any factors that could compromise its accuracy. One of these factors are non-polyadenylated (poly(A)–) transcripts, including circular RNAs (circRNAs) that can skew quantification of gene expression as they resemble messenger RNAs (mRNAs). Here, we highlight the impact circRNAs and other poly(A)– transcripts have on gene expression profiling and the biological conclusions drawn from such experiments. We also propose easily adoptable strategies to increase the accuracy of gene expression quanti...
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Toubia, J., Conn, V. M., Conn, S. J. Tags: Methods & Resources, RNA Biology, Transcription Commentary Source Type: research

NMDAR-dependent Argonaute 2 phosphorylation regulates miRNA activity and dendritic spine plasticity
MicroRNAs (miRNAs) repress translation of target mRNAs by associating with Argonaute (Ago) proteins to form the RNA-induced silencing complex (RISC), underpinning a powerful mechanism for fine-tuning protein expression. Specific miRNAs are required for NMDA receptor (NMDAR)-dependent synaptic plasticity by modulating the translation of proteins involved in dendritic spine morphogenesis or synaptic transmission. However, it is unknown how NMDAR stimulation stimulates RISC activity to rapidly repress translation of synaptic proteins. We show that NMDAR stimulation transiently increases Akt-dependent phosphorylation of Ago2 a...
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Rajgor, D., Sanderson, T. M., Amici, M., Collingridge, G. L., Hanley, J. G. Tags: Neuroscience, RNA Biology Articles Source Type: research

dNTP metabolism links mechanical cues and YAP/TAZ to cell growth and oncogene-induced senescence
This study indicates that YAP/TAZ couples cell proliferation with a metabolism suited for DNA replication and facilitates escape from oncogene-induced senescence. We speculate that this activity might be relevant during the initial phases of tumour progression or during experimental stem cell reprogramming induced by YAP. (Source: EMBO Journal)
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Santinon, G., Brian, I., Pocaterra, A., Romani, P., Franzolin, E., Rampazzo, C., Bicciato, S., Dupont, S. Tags: Cancer, Metabolism Articles Source Type: research

The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity
Ribosome biogenesis is a complex process involving multiple factors. Here, we show that the widely conserved RNA chaperone Hfq, which can regulate sRNA-mRNA basepairing, plays a critical role in rRNA processing and ribosome assembly in Escherichia coli. Hfq binds the 17S rRNA precursor and facilitates its correct processing and folding to mature 16S rRNA. Hfq assists ribosome assembly and associates with pre-30S particles but not with mature 30S subunits. Inactivation of Hfq strikingly decreases the pool of mature 70S ribosomes. The reduction in ribosome levels depends on residues located in the distal face of Hfq but not ...
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Andrade, J. M., dos Santos, R. F., Chelysheva, I., Ignatova, Z., Arraiano, C. M. Tags: Microbiology, Virology & Host Pathogen Interaction, Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

SUPERMAN regulates floral whorl boundaries through control of auxin biosynthesis
Proper floral patterning, including the number and position of floral organs in most plant species, is tightly controlled by the precise regulation of the persistence and size of floral meristems (FMs). In Arabidopsis, two known feedback pathways, one composed of WUSCHEL (WUS) and CLAVATA3 (CLV3) and the other composed of AGAMOUS (AG) and WUS, spatially and temporally control floral stem cells, respectively. However, mounting evidence suggests that other factors, including phytohormones, are also involved in floral meristem regulation. Here, we show that the boundary gene SUPERMAN (SUP) bridges floral organogenesis and flo...
Source: EMBO Journal - June 1, 2018 Category: Molecular Biology Authors: Xu, Y., Prunet, N., Gan, E.-S., Wang, Y., Stewart, D., Wellmer, F., Huang, J., Yamaguchi, N., Tatsumi, Y., Kojima, M., Kiba, T., Sakakibara, H., Jack, T. P., Meyerowitz, E. M., Ito, T. Tags: Plant Biology Articles Source Type: research

Anti-cancer therapy: senescence is the new black
Cellular senescence is a natural safeguard against cancer. Pharmacologically, it can be induced by drugs that inhibit the CDK4/6 kinases such as palbociclib, but the exact mechanism has never been dissected. Recent research by Miettinen et al (2018) reveals that senescence induced by this class of drugs is mediated by proteasome hyper-activation. (Source: EMBO Journal)
Source: EMBO Journal - May 15, 2018 Category: Molecular Biology Authors: Leite de Oliveira, R., Bernards, R. Tags: Cancer, Molecular Biology of Disease, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Phosphoproteome dynamics during mitotic exit in budding yeast
The cell division cycle culminates in mitosis when two daughter cells are born. As cyclin-dependent kinase (Cdk) activity reaches its peak, the anaphase-promoting complex/cyclosome (APC/C) is activated to trigger sister chromatid separation and mitotic spindle elongation, followed by spindle disassembly and cytokinesis. Degradation of mitotic cyclins and activation of Cdk-counteracting phosphatases are thought to cause protein dephosphorylation to control these sequential events. Here, we use budding yeast to analyze phosphorylation dynamics of 3,456 phosphosites on 1,101 proteins with high temporal resolution as cells pro...
Source: EMBO Journal - May 15, 2018 Category: Molecular Biology Authors: Touati, S. A., Kataria, M., Jones, A. W., Snijders, A. P., Uhlmann, F. Tags: Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics Resource Source Type: research

Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib
In conclusion, thermal proteome profiling identifies the proteasome and ECM29 protein as mediators of palbociclib activity in breast cancer cells. (Source: EMBO Journal)
Source: EMBO Journal - May 15, 2018 Category: Molecular Biology Authors: Miettinen, T. P., Peltier, J., Härtlova, A., Gierlinski, M., Jansen, V. M., Trost, M., Björklund, M. Tags: Cancer, Molecular Biology of Disease, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

The long non-coding RNA Paupar promotes KAP1-dependent chromatin changes and regulates olfactory bulb neurogenesis
Many long non-coding RNAs (lncRNAs) are expressed during central nervous system (CNS) development, yet their in vivo roles and mechanisms of action remain poorly understood. Paupar, a CNS-expressed lncRNA, controls neuroblastoma cell growth by binding and modulating the activity of transcriptional regulatory elements in a genome-wide manner. We show here that the Paupar lncRNA directly binds KAP1, an essential epigenetic regulatory protein, and thereby regulates the expression of shared target genes important for proliferation and neuronal differentiation. Paupar promotes KAP1 chromatin occupancy and H3K9me3 depositio...
Source: EMBO Journal - May 15, 2018 Category: Molecular Biology Authors: Pavlaki, I., Alammari, F., Sun, B., Clark, N., Sirey, T., Lee, S., Woodcock, D. J., Ponting, C. P., Szele, F. G., Vance, K. W. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Neuroscience, RNA Biology Articles Source Type: research

Cell type-specific regulation of ciliary transition zone assembly in vertebrates
Ciliopathies are life-threatening human diseases caused by defective cilia. They can often be traced back to mutations of genes encoding transition zone (TZ) proteins demonstrating that the understanding of TZ organisation is of paramount importance. The TZ consists of multimeric protein modules that are subject to a stringent assembly hierarchy. Previous reports place Rpgrip1l at the top of the TZ assembly hierarchy in Caenorhabditis elegans. By performing quantitative immunofluorescence studies in RPGRIP1L–/– mouse embryos and human embryonic cells, we recognise a different situation in vertebrates in wh...
Source: EMBO Journal - May 15, 2018 Category: Molecular Biology Authors: Wiegering, A., Dildrop, R., Kalfhues, L., Spychala, A., Kuschel, S., Lier, J. M., Zobel, T., Dahmen, S., Leu, T., Struchtrup, A., Legendre, F., Vesque, C., Schneider-Maunoury, S., Saunier, S., Rüther, U., Gerhardt, C. Tags: Cell Adhesion, Polarity & Cytoskeleton Articles Source Type: research

Intragenic transcriptional interference regulates the human immune ligand MICA
Many human genes have tandem promoters driving overlapping transcription, but the value of this distributed promoter configuration is generally unclear. Here we show that MICA, a gene encoding a ligand for the activating immune receptor NKG2D, contains a conserved upstream promoter that expresses a noncoding transcript. Transcription from the upstream promoter represses the downstream standard promoter activity in cis through transcriptional interference. The effect of transcriptional interference depends on the strength of transcription from the upstream promoter and can be described quantitatively by a simple reciprocal ...
Source: EMBO Journal - May 15, 2018 Category: Molecular Biology Authors: Lin, D., Hiron, T. K., O'Callaghan, C. A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Signal Transduction, Transcription Articles Source Type: research

Real-time observation of flexible domain movements in CRISPR-Cas9
The CRISPR-associated protein Cas9 is widely used for genome editing because it cleaves target DNA through the assistance of a single-guide RNA (sgRNA). Structural studies have revealed the multi-domain architecture of Cas9 and suggested sequential domain movements of Cas9 upon binding to the sgRNA and the target DNA. These studies also hinted at the flexibility between domains; however, it remains unclear whether these flexible movements occur in solution. Here, we directly observed dynamic fluctuations of multiple Cas9 domains, using single-molecule FRET. We found that the flexible domain movements allow Cas9 to adopt tr...
Source: EMBO Journal - May 15, 2018 Category: Molecular Biology Authors: Osuka, S., Isomura, K., Kajimoto, S., Komori, T., Nishimasu, H., Shima, T., Nureki, O., Uemura, S. Tags: Methods & Resources, RNA Biology, Structural Biology Articles Source Type: research

Mitochondrial DNA and TLR9 drive muscle inflammation upon Opa1 deficiency
Opa1 participates in inner mitochondrial membrane fusion and cristae morphogenesis. Here, we show that muscle-specific Opa1 ablation causes reduced muscle fiber size, dysfunctional mitochondria, enhanced Fgf21, and muscle inflammation characterized by NF-B activation, and enhanced expression of pro-inflammatory genes. Chronic sodium salicylate treatment ameliorated muscle alterations and reduced the muscle expression of Fgf21. Muscle inflammation was an early event during the progression of the disease and occurred before macrophage infiltration, indicating that it is a primary response to Opa1 deficiency. Moreover, Opa1 r...
Source: EMBO Journal - May 15, 2018 Category: Molecular Biology Authors: Rodriguez-Nuevo, A., Diaz-Ramos, A., Noguera, E., Diaz-Saez, F., Duran, X., Munoz, J. P., Romero, M., Plana, N., Sebastian, D., Tezze, C., Romanello, V., Ribas, F., Seco, J., Planet, E., Doctrow, S. R., Gonzalez, J., Borras, M., Liesa, M., Palacin, M., Ve Tags: Autophagy & Cell Death, Immunology, Metabolism Articles Source Type: research