ALBERT

Beschreibung: Publication date: Available online 7 August 2015 Source: FEBS Open Bio Author(s): Kimberley J. Anderson, Aaron P. Russell, Victoria C. Foletta The function of the stress-responsive N-myc downstream-regulated gene 2 (NDRG2) in the control of myoblast growth, and the amino acids contributing to its function, are not well characterised. Here, we investigated the effect of increased NDRG2 levels on the proliferation, differentiation and apoptosis in skeletal muscle cells under basal and stress conditions. NDRG2 overexpression increased C2C12 myoblast proliferation and the expression of positive cell cycle regulators, cdk2, cyclin B and cyclin D, and phosphorylation of Rb, while the serine/threonine-deficient NDRG2, 3A-NDRG2, had less effect. The onset of differentiation was enhanced by NDRG2 as determined through the myogenic regulatory factor expression profiles and myocyte fusion index. However, the overall level of differentiation in myotubes was not different. While NDRG2 up-regulated caspase 3/7 activities during differentiation, no increase in apoptosis was measured by TUNEL assay or through cleavage of caspase 3 and PARP proteins. During H 2 O 2 treatment to induce oxidative stress, NDRG2 helped protect against the loss of proliferation and ER stress as measured by GRP78 expression with 3A-NDRG2 displaying less protection. NDRG2 also attenuated apoptosis by reducing cleavage of PARP and caspase 3 and expression of pro-apoptotic Bax while enhancing the pro-survival Bcl-2 and Bcl-xL levels. In contrast, Mcl-1 was not altered, and NDRG2 did not protect against palmitate-induced lipotoxicity. Our findings show that NDRG2 overexpression increases myoblast proliferation and caspase 3/7 activities without increasing overall differentiation. Furthermore, NDRG2 attenuates H 2 O 2 -induced oxidative stress and specific serine and threonine amino acid residues appear to contribute to its function in muscle cells.

Beschreibung: Publication date: Available online 12 August 2015 Source: FEBS Open Bio Author(s): Yang Song, Yonghong Zhang, Haoxiang Jiang, Yanting Zhu, Lu Liu, Wei Feng, Lan Yang, Yibin Wang, Manxiang Li Activation of the Notch3 cascade is involved in the development of pulmonary arterial hypertension by stimulating the proliferation of vascular smooth muscle cells. However, the detailed molecular mechanisms underlying this effect are still unclear. The present study aims to address this issue. We demonstrated that over-expression of intracellular domain of the Notch3 receptor (NICD3) by adenovirus transfection dramatically induced proliferation of primary cultured pulmonary artery smooth muscle cells. This was accompanied with up-regulation of Hes1 protein and down-regulation of p27Kip1protein. More importantly, we observed that prior silencing of Hes1 with siRNA blocked NICD3 over-expression-induced p27Kip1 reduction and cell proliferation. The present study suggests that Hes1 lies downstream of NICD3 and particularly mediates Notch3 signaling-induced proliferation of pulmonary arterial smooth muscle cells by down-regulation of p27Kip1 expression.

Beschreibung: Publication date: Available online 11 August 2015 Source: FEBS Open Bio Author(s): Xueying Zhang, Yuanzhe Jin, Xiaohong Zhang, Mingming Lei, Yingzi Lin, Ian L. Megson, Jun Wei, Bo Yu A number of studies have reported an association between increased levels of antibodies against oxidized low-density lipoprotein (oxLDL) and cardiovascular disease, but the anti-oxLDL antibody has not been confirmed to serve as an effective biomarker for prediction of acute myocardial infarction (AMI). Apolipoprotein B 100 (ApoB 100 )-derived peptide fragments generated by proteolytic degradation and aldehyde modification are the major antigens in oxLDL, and so the present work was undertaken to detect circulating IgG for Apo-B 100 -derived peptide antigens. An in-house enzyme-linked immunosorbent assay (ELISA) was developed with eight ApoB 100 -derived peptide antigens (Ag1-Ag8) to detect circulating anti-ApoB 100 IgG levels in 267 patients with AMI and 201 control subjects. Binary logistic regression analysis revealed that circulating IgG for Ag1 was significantly higher in the patient group than the control group ( P 〈0.001) after adjustment for age, gender, smoking, hypertension, diabetes and circulating levels of cholesterol, HDL, LDL, ApoA and ApoB 100 . None of the other seven antigens detected an increase in IgG levels in AMI patients compared with control subjects. Spearman correlation analysis showed no correlation between IgG antibody for Ag1 and clinical characteristics. In conclusion, the linear peptide antigens derived from ApoB 100 may be suitable for the development of an ELISA antibody test for prediction of AMI, although further confirmation is still needed in large-scale clinical studies.

Beschreibung: Publication date: Available online 11 August 2015 Source: FEBS Open Bio Author(s): Yu-E. Hao, Dong-Fang He, Rong-Hua Yin, Hui Chen, Jian Wang, Shao-Xia Wang, Yi-Qun Zhan, Chang-Hui Ge, Chang-Yan Li, Miao Yu, Xiao-Ming Yang G protein-coupled receptor kinase interactor 2 (GIT2) is a signaling scaffold protein involved in regulation of cytoskeletal dynamics and the internalization of G protein-coupled receptors (GPCRs). The short-splice form of GIT2 is expressed in peripheral T cells and thymocytes. However, the functions of GIT2 in T cells have not yet been determined. We show that treatment with Con A in a model of polyclonal T-lymphocyte activation resulted in marked inhibitions in the intrahepatic infiltration of inflammatory cells, cytokine response and acute liver failure in Git2 -/- mice. CD4 + T cells from Git2 -/- mice showed significant impairment in proliferation, cytokine production and signal transduction upon TCR-stimulated activation. Our results suggested that GIT2 plays an important role in T-cell function in vivo and in vitro .

Beschreibung: Publication date: Available online 3 August 2015 Source: FEBS Open Bio Author(s): Johan Vande Voorde, Peter Vervaeke, Sandra Liekens, Jan Balzarini Mycoplasmas may colonize tumour tissue in patients. The cytostatic activity of gemcitabine was dramatically decreased in Mycoplasma hyorhinis -infected tumour cell cultures compared with non-infected tumour cell cultures. This mycoplasma-driven drug deamination could be prevented by exogenous administration of the cytidine deaminase (CDA) inhibitor tetrahydrouridine, but also by the natural nucleosides or by a purine nucleoside phosphorylase inhibitor. The M. hyorhinis -encoded CDA Hyor gene was cloned, expressed as a recombinant protein and purified. CDA Hyor was found to be more catalytically active than its human equivalent and efficiently deaminates (inactivates) cytosine-based anticancer drugs. CDA Hyor expression at the tumour site may result in selective drug inactivation and suboptimal therapeutic efficiency.

Beschreibung: Publication date: Available online 3 August 2015 Source: SoftwareX Author(s): Gianmarco Alberti Correspondence Analysis (CA) is a statistical exploratory technique frequently used in many research fields to graphically visualize the structure of contingency tables. Many programs, both commercial and free, perform CA but none of them as yet provides a visual aid to the interpretation of the results. The ‘CAinterprTools’ package, designed to be used in the free R statistical environment, aims at filling that gap. A novel-to-medium R user has been considered as target. 15 commands enable to easily obtain charts that help (and are relevant to) the interpretation of the CA’s results, freeing the user from the need to inspect and scrutinize tabular CA outputs, and to look up values and statistics on which further calculations are necessary. The package also implements tests to assess the significance of the input table’s total inertia and individual dimensions.

Beschreibung: Publication date: July 2015 Source: Global Ecology and Conservation, Volume 4 Author(s): David M.P. Jacoby, John M. Casselman, Vicki Crook, Mari-Beth DeLucia, Hyojin Ahn, Kenzo Kaifu, Tagried Kurwie, Pierre Sasal, Anders M.C. Silfvergrip, Kevin G. Smith, Kazuo Uchida, Alan M. Walker, Matthew J. Gollock With broad distributions, diadromous fishes can be exposed to multiple threats at different stages of development. For the primarily catadromous eels of the family Anguillidae, there is growing international concern for the population abundance and escapement trends of some of these species and yet incomplete knowledge of their remarkable life-histories hampers management and conservation. Anguillids experience a suite of pressures that include habitat loss/modification, migration barriers, pollution, parasitism, exploitation, and fluctuating oceanic conditions that likely have synergistic and regionally variable impacts, even within species. In beginning to redress this rather fragmented picture, we evaluated the extinction risk of these species using the IUCN Red List of Threatened Species Categories and Criteria to infer population-wide trends from catch and monitoring data. Here we consolidate and build upon these species assessments by presenting an overview of the current state of global eel data and conservation, categorising the knowledge gaps and geographic regions where resources are needed and discussing future recommendations to improve our understanding of anguillids. We find stark disparity between the quality and length of data available to assess population trends and conservation priorities in temperate and tropical anguillids. Of the 13 species assessed, four were listed as ‘Threatened’ (Vulnerable, Endangered or Critically Endangered); four were Near Threatened, three were Data Deficient and two were deemed Least Concern. Comparing with other diadromous species, we examine the multiple threats that impact eels during their different life-history stages, highlighting the challenges of applying the Red List Categories and Criteria to geographically-expansive, catadromous and panmictic groups of species.

Beschreibung: Publication date: Available online 19 August 2015 Source: FEBS Open Bio Author(s): Ajay Srivastava Malignant pleural mesothelioma (MPM) is an aggressive form of thoracic cancer with poor prognosis. While some studies have identified the molecular alterations associated with MPM, little is known about their role in MPM. For example, fragile X mental retardation ( FMR ) gene is up-regulated in MPM but its role in MPM is unknown. Here, utilizing Drosophila genetics, I investigate the possible role FMR may be playing in MPM. I provide evidence which suggests that FMR may contribute to tumorigenesis by up-regulating a matrix metalloprotease (MMP) and by degrading the basement membrane (BM), both important for tumor metastasis. I also demonstrate a novel link between FMR and the JNK pathway and suggest that the effects of FMR in MPM could in part be mediated by up-regulation of the JNK pathway.

Beschreibung: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Bettina Schreiner, Elisa Romanelli, Pawel Liberski, Barbara Ingold-Heppner, Bettina Sobottka-Brillout, Tom Hartwig, Vijay Chandrasekar, Helge Johannssen, Hanns Ulrich Zeilhofer, Adriano Aguzzi, Frank Heppner, Martin Kerschensteiner, Burkhard Becher Although the importance of reactive astrocytes during CNS pathology is well established, the function of astroglia in adult CNS homeostasis is less well understood. With the use of conditional, astrocyte-restricted protein synthesis termination, we found that selective paralysis of GFAP + astrocytes in vivo led to rapid neuronal cell loss and severe motor deficits. This occurred while structural astroglial support still persisted and in the absence of any major microvascular damage. Whereas loss of astrocyte function did lead to microglial activation, this had no impact on the neuronal loss and clinical decline. Neuronal injury was caused by oxidative stress resulting from the reduced redox scavenging capability of dysfunctional astrocytes and could be prevented by the in vivo treatment with scavengers of reactive oxygen and nitrogen species (ROS/RNS). Our results suggest that the subpopulation of GFAP + astrocytes maintain neuronal health by controlling redox homeostasis in the adult CNS. Graphical abstract Teaser Schreiner et al. examine the functional contribution of astrocytes to tissue homeostasis in the adult CNS and identify the redox-scavenging capacity of GFAP + astrocytes as a key factor for neuronal health in vivo. The importance of the metabolic integrity of the glia-neuron interface highlights potential therapies for the treatment of neurodegenerative diseases.

Beschreibung: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Priya Srikanth, Karam Han, Dana G. Callahan, Eugenia Makovkina, Christina R. Muratore, Matthew A. Lalli, Honglin Zhou, Justin D. Boyd, Kenneth S. Kosik, Dennis J. Selkoe, Tracy L. Young-Pearse Genetic and clinical association studies have identified disrupted in schizophrenia 1 ( DISC1 ) as a candidate risk gene for major mental illness. DISC1 is interrupted by a balanced chr(1;11) translocation in a Scottish family in which the translocation predisposes to psychiatric disorders. We investigate the consequences of DISC1 interruption in human neural cells using TALENs or CRISPR-Cas9 to target the DISC1 locus. We show that disruption of DISC1 near the site of the translocation results in decreased DISC1 protein levels because of nonsense-mediated decay of long splice variants. This results in an increased level of canonical Wnt signaling in neural progenitor cells and altered expression of fate markers such as Foxg1 and Tbr2. These gene expression changes are rescued by antagonizing Wnt signaling in a critical developmental window, supporting the hypothesis that DISC1-dependent suppression of basal Wnt signaling influences the distribution of cell types generated during cortical development. Graphical abstract Teaser Srikanth et al. report the generation of isogenic hiPSC lines with engineered mutations in two locations within the DISC1 gene. This disease-relevant disruption shows a loss of long isoforms, which, in turn, affects neural progenitor cell proliferation, baseline WNT signaling, and the expression of NPC fate markers such as FoxG1 and Tbr2.

Beschreibung: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Ivana Vonkova, Antoine-Emmanuel Saliba, Samy Deghou, Kanchan Anand, Stefano Ceschia, Tobias Doerks, Augustinus Galih, Karl G. Kugler, Kenji Maeda, Vladimir Rybin, Vera van Noort, Jan Ellenberg, Peer Bork, Anne-Claude Gavin Many cellular processes involve the recruitment of proteins to specific membranes, which are decorated with distinctive lipids that act as docking sites. The phosphoinositides form signaling hubs, and we examine mechanisms underlying recruitment. We applied a physiological, quantitative, liposome microarray-based assay to measure the membrane-binding properties of 91 pleckstrin homology (PH) domains, the most common phosphoinositide-binding target. 10,514 experiments quantified the role of phosphoinositides in membrane recruitment. For most domains examined, the observed binding specificity implied cooperativity with additional signaling lipids. Analyses of PH domains with similar lipid-binding profiles identified a conserved motif, mutations in which—including some found in human cancers—induced discrete changes in binding affinities in vitro and protein mislocalization in vivo. The data set reveals cooperativity as a key mechanism for membrane recruitment and, by enabling the interpretation of disease-associated mutations, suggests avenues for the design of small molecules targeting PH domains. Graphical abstract Teaser Vonkova et al. systematically quantify the lipid-binding properties of 91 pleckstrin homology (PH) domains using a physiological, quantitative, liposome microarray-based assay. The data set reveals that cooperativity between lipids is a key mechanism for membrane recruitment of PH domains.

Beschreibung: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Ju-Hyun Lee, Mary Kate McBrayer, Devin M. Wolfe, Luke J. Haslett, Asok Kumar, Yutaka Sato, Pearl P.Y. Lie, Panaiyur Mohan, Erin E. Coffey, Uday Kompella, Claire H. Mitchell, Emyr Lloyd-Evans, Ralph A. Nixon Presenilin 1 (PS1) deletion or Alzheimer’s disease (AD)-linked mutations disrupt lysosomal acidification and proteolysis, which inhibits autophagy. Here, we establish that this phenotype stems from impaired glycosylation and instability of vATPase V0a1 subunit, causing deficient lysosomal vATPase assembly and function. We further demonstrate that elevated lysosomal pH in Presenilin 1 knockout (PS1KO) cells induces abnormal Ca 2+ efflux from lysosomes mediated by TRPML1 and elevates cytosolic Ca 2+ . In WT cells, blocking vATPase activity or knockdown of either PS1 or the V0a1 subunit of vATPase reproduces all of these abnormalities. Normalizing lysosomal pH in PS1KO cells using acidic nanoparticles restores normal lysosomal proteolysis, autophagy, and Ca 2+ homeostasis, but correcting lysosomal Ca 2+ deficits alone neither re-acidifies lysosomes nor reverses proteolytic and autophagic deficits. Our results indicate that vATPase deficiency in PS1 loss-of-function states causes lysosomal/autophagy deficits and contributes to abnormal cellular Ca 2+ homeostasis, thus linking two AD-related pathogenic processes through a common molecular mechanism. Graphical abstract Teaser Lee et al. present evidence establishing that Presenilin 1 loss of function elevates lysosomal pH via loss of V0a1 vATPase subunits. Besides disrupting autophagy, elevated lysosomal pH hyperactivates the TRPML1 calcium channel, causing increased lysosomal calcium efflux and cytosolic calcium elevation, thus linking two AD-related presenilin phenotypes to vATPase deficiency.

Beschreibung: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Soraia Barão, Annette Gärtner, Eduardo Leyva-Díaz, Galina Demyanenko, Sebastian Munck, Tine Vanhoutvin, Lujia Zhou, Melitta Schachner, Guillermina López-Bendito, Patricia F. Maness, Bart De Strooper ΒACE1 is the major drug target for Alzheimer’s disease, but we know surprisingly little about its normal function in the CNS. Here, we show that this protease is critically involved in semaphorin 3A (Sema3A)-mediated axonal guidance processes in thalamic and hippocampal neurons. An active membrane-bound proteolytic CHL1 fragment is generated by BACE1 upon Sema3A binding. This fragment relays the Sema3A signal via ezrin-radixin-moesin (ERM) proteins to the neuronal cytoskeleton. APH1B-γ-secretase-mediated degradation of this fragment stops the Sema3A-induced collapse and sensitizes the growth cone for the next axonal guidance cue. Thus, we reveal a cycle of proteolytic activity underlying growth cone collapse and restoration used by axons to find their correct trajectory in the brain. Our data also suggest that BACE1 and γ-secretase inhibition have physiologically opposite effects in this process, supporting the idea that combination therapy might attenuate some of the side effects associated with these drugs. Graphical abstract Teaser Barão et al. show that the Alzheimer’s-disease-related proteases, BACE1 and APH1B-γ-secretase, control axonal guidance by regulating growth cone dynamics. BACE1 cleaves CHL1, inducing growth cone collapse. Subsequently, γ-secretase activity stops the collapse and axonal growth resumes. Therefore, testing of inhibitors of these proteases in humans should proceed with caution.

Beschreibung: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Alexander Harms, Frédéric Valentin Stanger, Patrick Daniel Scheu, Imke Greet de Jong, Arnaud Goepfert, Timo Glatter, Kenn Gerdes, Tilman Schirmer, Christoph Dehio Toxin-antitoxin (TA) modules are ubiquitous molecular switches controlling bacterial growth via the release of toxins that inhibit cell proliferation. Most of these toxins interfere with protein translation, but a growing variety of other mechanisms hints at a diversity that is not yet fully appreciated. Here, we characterize a group of FIC domain proteins as toxins of the conserved and abundant FicTA family of TA modules, and we reveal that they act by suspending control of cellular DNA topology. We show that FicTs are enzymes that adenylylate DNA gyrase and topoisomerase IV, the essential bacterial type IIA topoisomerases, at their ATP-binding site. This modification inactivates both targets by blocking their ATPase activity, and, consequently, causes reversible growth arrest due to the knotting, catenation, and relaxation of cellular DNA. Our results give insight into the regulation of DNA topology and highlight the remarkable plasticity of FIC domain proteins. Graphical abstract Teaser Harms et al. reveal that the FicTA toxin-antitoxin module acts via adenylylation of DNA gyrase and topoisomerase IV. This modification inactivates both targets by blocking the ATPase activity that is central to their enzymatic functions, and it reversibly inhibits bacterial growth via the knotting, catenation, and relaxation of cellular DNA.

Beschreibung: Publication date: Available online 20 August 2015 Source: Cell Reports Author(s): Takaharu Kanno, Davide G. Berta, Camilla Sjögren The structural maintenance of chromosome (SMC) protein complexes cohesin and condensin and the Smc5/6 complex (Smc5/6) are crucial for chromosome dynamics and stability. All contain essential ATPase domains, and cohesin and condensin interact with chromosomes through topological entrapment of DNA. However, how Smc5/6 binds DNA and chromosomes has remained largely unknown. Here, we show that purified Smc5/6 binds DNA through a mechanism that requires ATP hydrolysis by the complex and circular DNA to be established. This also promotes topoisomerase 2-dependent catenation of plasmids, suggesting that Smc5/6 interconnects two DNA molecules using ATP-regulated topological entrapment of DNA, similar to cohesin. We also show that a complex containing an Smc6 mutant that is defective in ATP binding fails to interact with DNA and chromosomes and leads to cell death with concomitant accumulation of DNA damage when overexpressed. Taken together, these results indicate that Smc5/6 executes its cellular functions through ATP-regulated intermolecular DNA linking. Graphical abstract Teaser Kanno et al. have found that Smc5/6 interacts with DNA by two different mechanisms. One is based on electrostatic interactions that require ATP binding to Smc6. The other leads to topological entrapment and demands ATP hydrolysis by the complex. The results show that Smc5/6 is an ATP-dependent intermolecular DNA linker.

Beschreibung: Publication date: 18 August 2015 Source: Cell Reports, Volume 12, Issue 7 Author(s): Marvin L. Meistrich, Gunapala Shetty In this issue of Cell Reports , DeFalco et al. (2015) characterize a novel macrophage population associated with the peritubular lamina of mouse testes. These macrophages may create a niche not for the self-renewal of stem cells but rather the induction of their differentiation.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Kavita R. Sharma, Brittany L. Enzmann, Yvonne Schmidt, Dani Moore, Graeme R. Jones, Jane Parker, Shelley L. Berger, Danny Reinberg, Laurence J. Zwiebel, Bernhard Breit, Jürgen Liebig, Anandasankar Ray The sophisticated organization of eusocial insect societies is largely based on the regulation of complex behaviors by hydrocarbon pheromones present on the cuticle. We used electrophysiology to investigate the detection of cuticular hydrocarbons (CHCs) by female-specific olfactory sensilla basiconica on the antenna of Camponotus floridanus ants through the utilization of one of the largest family of odorant receptors characterized so far in insects. These sensilla, each of which contains multiple olfactory receptor neurons, are differentially sensitive to CHCs and allow them to be classified into three broad groups that collectively detect every hydrocarbon tested, including queen and worker-enriched CHCs. This broad-spectrum sensitivity is conserved in a related species, Camponotus laevigatus , allowing these ants to detect CHCs from both nestmates and non-nestmates. Behavioral assays demonstrate that these ants are excellent at discriminating CHCs detected by the antenna, including enantiomers of a candidate queen pheromone that regulates the reproductive division of labor. Graphical abstract Teaser Sharma et al. show that ants can detect a number of hydrocarbons present on the cuticle, therefore recognizing different castes such as workers and queens from their own colony as well as different colonies. They also show that ants are able to smell and discriminate minor differences among hydrocarbons.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Sanjeev Kumar, Jing Liu, Paul Pang, A. Michaela Krautzberger, Antoine Reginensi, Haruhiko Akiyama, Andreas Schedl, Benjamin D. Humphreys, Andrew P. McMahon After acute kidney injury (AKI), surviving cells within the nephron proliferate and repair. We identify Sox9 as an acute epithelial stress response in renal regeneration. Translational profiling after AKI revealed a rapid upregulation of Sox9 within proximal tubule (PT) cells, the nephron cell type most vulnerable to AKI. Descendants of Sox9 + cells generate the bulk of the nephron during development and regenerate functional PT epithelium after AKI-induced reactivation of Sox9 after renal injury. After restoration of renal function post-AKI, persistent Sox9 expression highlights regions of unresolved damage within injured nephrons. Inactivation of Sox9 in PT cells pre-injury indicates that Sox9 is required for the normal course of post-AKI recovery. These findings link Sox9 to cell intrinsic mechanisms regulating development and repair of the mammalian nephron. Graphical abstract Teaser Surviving tubular epithelial cells repair the nephron after acute kidney injury (AKI). Kumar et al. identify Sox9 activation as a rapid response to AKI within repairing cells of the damaged proximal tubule segment. Sox9 activation is required for a normal repair process.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Rheinallt M. Jones, Chirayu Desai, Trevor M. Darby, Liping Luo, Alexandra A. Wolfarth, Christopher D. Scharer, Courtney S. Ardita, April R. Reedy, Erin S. Keebaugh, Andrew S. Neish An optimal gut microbiota influences many beneficial processes in the metazoan host. However, the molecular mechanisms that mediate and function in symbiont-induced host responses have not yet been fully characterized. Here, we report that cellular ROS enzymatically generated in response to contact with lactobacilli in both mice and Drosophila has salutary effects against exogenous insults to the intestinal epithelium via the activation of Nrf2 responsive cytoprotective genes. These data show that the xenobiotic-inducible Nrf2 pathway participates as a signaling conduit between the prokaryotic symbiont and the eukaryotic host. Indeed, our data imply that the capacity of lactobacilli to induce redox signaling in epithelial cells is a highly conserved hormetic adaptation to impel cellular conditioning to exogenous biotic stimuli. These data also highlight the role the microbiota plays in eukaryotic cytoprotective pathways and may have significant implications in the characterization of a eubiotic microbiota. Graphical abstract Teaser Jones et al. report that the commensal gut bacterial taxa lactobacilli are able to mediate beneficial cytoprotective effects in the gut of both flies and mice. These highly conserved events are mediated by ROS-dependent activation of the Nrf2 xenobiotic pathway and conserved effector genes.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Neel Mehta, Arthur H. Cheng, Cheng-Kang Chiang, Lucia Mendoza-Viveros, Harrod H. Ling, Abhilasha Patel, Bo Xu, Daniel Figeys, Hai-Ying M. Cheng The pacemaker properties of the suprachiasmatic nucleus (SCN) circadian clock are shaped by mechanisms that influence the expression and behavior of clock proteins. Here, we reveal that G-protein-coupled receptor kinase 2 (GRK2) modulates the period, amplitude, and entrainment characteristics of the SCN. Grk2 -deficient mice show phase-dependent alterations in light-induced entrainment, slower recovery from jetlag, and longer behavioral rhythms. Grk2 ablation perturbs intrinsic rhythmic properties of the SCN, increasing amplitude and decreasing period. At the cellular level, GRK2 suppresses the transcription of the mPeriod1 gene and the trafficking of PERIOD1 and PERIOD2 proteins to the nucleus. Moreover, GRK2 can physically interact with PERIOD1/2 and promote PERIOD2 phosphorylation at Ser545, effects that may underlie its ability to regulate PERIOD1/2 trafficking. Together, our findings identify GRK2 as an important modulator of circadian clock speed, amplitude, and entrainment by controlling PERIOD at the transcriptional and post-translational levels. Graphical abstract Teaser Mehta et al. demonstrate the importance of GRK2 in regulating both the pace of the circadian clock and its response to environmental time cues (i.e., light). GRK2 functionally interacts with the molecular clock at the transcriptional and post-translational levels, dampening mPeriod1 gene transcription and suppressing nuclear trafficking of PERIOD1/2 proteins.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Juan F. Linares, Angeles Duran, Miguel Reina-Campos, Pedro Aza-Blanc, Alex Campos, Jorge Moscat, Maria T. Diaz-Meco The mTORC1 complex is central to the cellular response to changes in nutrient availability. The signaling adaptor p62 contributes to mTORC1 activation in response to amino acids and interacts with TRAF6, which is required for the translocation of mTORC1 to the lysosome and the subsequent K63 polyubiquitination and activation of mTOR. However, the signal initiating these p62-driven processes was previously unknown. Here, we show that p62 is phosphorylated via a cascade that includes MEK3/6 and p38δ and is driven by the PB1-containing kinase MEKK3. This phosphorylation results in the recruitment of TRAF6 to p62, the ubiquitination and activation of mTOR, and the regulation of autophagy and cell proliferation. Genetic inactivation of MEKK3 or p38δ mimics that of p62 in that it leads to inhibited growth of PTEN-deficient prostate organoids. Analysis of human prostate cancer samples showed upregulation of these three components of the pathway, which correlated with enhanced mTORC1 activation. Graphical abstract Teaser Linares et al. identify a kinase cascade that regulates the phosphorylation of the signal adaptor p62 in response to amino acids to control mTORC1 activation. This nutrient-sensing mechanism is relevant for autophagy regulation and tumor growth.

Beschreibung: Publication date: 4 August 2015 Source: Cell Reports, Volume 12, Issue 5 Author(s): Obinna Chijioke, Anne Müller, Regina Feederle, Mario Henrique M. Barros, Carsten Krieg, Vanessa Emmel, Emanuela Marcenaro, Carol S. Leung, Olga Antsiferova, Vanessa Landtwing, Walter Bossart, Alessandro Moretta, Rocio Hassan, Onur Boyman, Gerald Niedobitek, Henri-Jacques Delecluse, Riccarda Capaul, Christian Münz

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Matthew T. Maurano, Hao Wang, Sam John, Anthony Shafer, Theresa Canfield, Kristen Lee, John A. Stamatoyannopoulos Although DNA methylation is commonly invoked as a mechanism for transcriptional repression, the extent to which it actively silences transcription factor (TF) occupancy sites in vivo is unknown. To study the role of DNA methylation in the active modulation of TF binding, we quantified the effect of DNA methylation depletion on the genomic occupancy patterns of CTCF, an abundant TF with known methylation sensitivity that is capable of autonomous binding to its target sites in chromatin. Here, we show that the vast majority (>98.5%) of the tens of thousands of unoccupied, methylated CTCF recognition sequences remain unbound upon abrogation of DNA methylation. The small fraction of sites that show methylation-dependent binding in vivo are in turn characterized by highly variable CTCF occupancy across cell types. Our results suggest that DNA methylation is not a primary groundskeeper of genomic TF landscapes, but rather a specialized mechanism for stabilizing intrinsically labile sites. Graphical abstract Teaser Alterations of DNA methylation in malignancy and development are frequently interpreted as affecting transcriptional activity. Maurano et al. find that, upon genomic abrogation of DNA methylation, binding of the canonically methylation-sensitive transcriptional regulator CTCF is largely unaffected. Their results suggest that a limited set of methylation-sensitive CTCF sites are variable across cell types and that key sequence and chromatin features predict methylation sensitivity of CTCF binding.

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Swea-Ling Khaw, Chua Min-Wen, Cheng-Gee Koh, Bing Lim, Ng Shyh-Chang Oocyte factors not only drive somatic cell nuclear transfer reprogramming but also augment the efficiency and quality of induced pluripotent stem cell (iPSC) reprogramming. Here, we show that the oocyte-enriched factors Tcl1 and Tcl1b1 significantly enhance reprogramming efficiency. Clonal analysis of pluripotency biomarkers further show that the Tcl1 oocyte factors improve the quality of reprogramming. Mechanistically, we find that the enhancement effect of Tcl1b1 depends on Akt, one of its putative targets. In contrast, Tcl1 suppresses the mitochondrial polynucleotide phosphorylase (PnPase) to promote reprogramming. Knockdown of PnPase rescues the inhibitory effect from Tcl1 knockdown during reprogramming, whereas PnPase overexpression abrogates the enhancement from Tcl1 overexpression. We further demonstrate that Tcl1 suppresses PnPase’s mitochondrial localization to inhibit mitochondrial biogenesis and oxidation phosphorylation, thus remodeling the metabolome. Hence, we identified the Tcl1-PnPase pathway as a critical mitochondrial switch during reprogramming. Graphical abstract Teaser Khaw et al. identify the oocyte Tcl1-PnPase pathway as a critical mitochondrial switch during reprogramming into iPSCs. They find that Tcl1 suppresses the mitochondrial localization of PNPase, thus inhibiting mitochondrial biogenesis and oxidation phosphorylation.

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Xinfang Huang, Jingjing Li, Stephanie Dorta-Estremera, Jeremy Di Domizio, Scott M. Anthony, Stephanie S. Watowich, Daniel Popkin, Zheng Liu, Philip Brohawn, Yihong Yao, Kimberly S. Schluns, Lewis L. Lanier, Wei Cao Here, we examine the mechanism by which plasmacytoid dendritic cells (pDCs) and type I interferons promote humoral autoimmunity. In an amyloid-induced experimental autoimmune model, neutrophil depletion enhanced anti-nuclear antibody development, which correlated with heightened IFN-γ production by natural killer (NK) cells. IFN-α/β produced by pDCs activated NK cells via IL-15 induction. Neutrophils released reactive oxygen species (ROS), which negatively modulated the levels of IL-15, thereby inhibiting IFN-γ production. Mice deficient in NADPH oxidase 2 produced increased amounts of IFN-γ and developed augmented titers of autoantibodies. Both the pDC-IFN-α/β pathway and IFN-γ were indispensable in stimulating humoral autoimmunity. Male NZB/W F1 mice expressed higher levels of superoxide than their female lupus-prone siblings, and depletion of neutrophils resulted in spontaneous NK cell and autoimmune B cell activation. Our findings suggest a regulatory role for neutrophils in vivo and highlight the importance of an NK-IFN-γ axis downstream of the pDC-IFN-α/β pathway in systemic autoimmunity. Graphical abstract Teaser Huang et al. find that IFN-α/β produced by plasmacytoid dendritic cells (pDCs) stimulates NK cells to secrete IFN-γ, which is essential for the development of autoantibodies. ROS-producing neutrophils negatively regulate this NK-IFN-γ pathway and control autoimmune progression in lupus-prone mice.

Beschreibung: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Laura W. Dillon , Pankaj Kumar , Yoshiyuki Shibata , Yuh-Hwa Wang , Smaranda Willcox , Jack D. Griffith , Yves Pommier , Shunichi Takeda , Anindya Dutta MicroDNAs are 〈400-base extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs have been found in all tissue types, including sperm. MicroDNAs arise preferentially from areas with high gene density, GC content, and exon density from promoters with activating chromatin modifications and in sperm from the 5′-UTR of full-length LINE-1 elements, but are depleted from lamin-associated heterochromatin. Analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cells defective in various DNA repair proteins reveals that homologous recombination and non-homologous end joining repair pathways are not required for microDNA production. Deletion of the MSH3 DNA mismatch repair protein results in a significant decrease in microDNA abundance, specifically from non-CpG genomic regions. Thus, microDNAs arise as part of normal cellular physiology—either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair. Graphical abstract Teaser Through isolating and sequencing small extrachromosomal circular microDNAs across multiple species and cell types, Dillon et al. identify specific genomic features associated with the generation of microDNAs and link the DNA mismatch repair pathway to this process.

Beschreibung: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Caroline Ramspacher , Emily Steed , Francesco Boselli , Rita Ferreira , Nathalie Faggianelli , Stéphane Roth , Coralie Spiegelhalter , Nadia Messaddeq , Le Trinh , Michael Liebling , Nikhil Chacko , Federico Tessadori , Jeroen Bakkers , Jocelyn Laporte , Karim Hnia , Julien Vermot Desminopathies belong to a family of muscle disorders called myofibrillar myopathies that are caused by Desmin mutations and lead to protein aggregates in muscle fibers. To date, the initial pathological steps of desminopathies and the impact of desmin aggregates in the genesis of the disease are unclear. Using live, high-resolution microscopy, we show that Desmin loss of function and Desmin aggregates promote skeletal muscle defects and alter heart biomechanics. In addition, we show that the calcium dynamics associated with heart contraction are impaired and are associated with sarcoplasmic reticulum dilatation as well as abnormal subcellular distribution of Ryanodine receptors. Our results demonstrate that desminopathies are associated with perturbed excitation-contraction coupling machinery and that aggregates are more detrimental than Desmin loss of function. Additionally, we show that pharmacological inhibition of aggregate formation and Desmin knockdown revert these phenotypes. Our data suggest alternative therapeutic approaches and further our understanding of the molecular determinants modulating Desmin aggregate formation. Graphical abstract Teaser Desminopathies are myopathies and cardiomyopathies associated with Desmin mutations leading to protein aggregates. Ramspacher et al. demonstrate that altered Desmin function or expression affect the EC coupling machinery and calcium dynamics. They show that aggregates are more toxic than the loss of function and can be rescued by knockdown and pharmacological treatment.

Beschreibung: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Peng Liu , Miranda N. Reed , Linda A. Kotilinek , Marianne K.O. Grant , Colleen L. Forster , Wei Qiang , Samantha L. Shapiro , John H. Reichl , Angie C.A. Chiang , Joanna L. Jankowsky , Carrie M. Wilmot , James P. Cleary , Kathleen R. Zahs , Karen H. Ashe The accumulation of amyloid-β (Aβ) as amyloid fibrils and toxic oligomers is an important step in the development of Alzheimer’s disease (AD). However, there are numerous potentially toxic oligomers and little is known about their neurological effects when generated in the living brain. Here we show that Aβ oligomers can be assigned to one of at least two classes (type 1 and type 2) based on their temporal, spatial, and structural relationships to amyloid fibrils. The type 2 oligomers are related to amyloid fibrils and represent the majority of oligomers generated in vivo, but they remain confined to the vicinity of amyloid plaques and do not impair cognition at levels relevant to AD. Type 1 oligomers are unrelated to amyloid fibrils and may have greater potential to cause global neural dysfunction in AD because they are dispersed. These results refine our understanding of the pathogenicity of Aβ oligomers in vivo. Graphical abstract Teaser Liu et al. classify brain-derived amyloid-β oligomers into type 1 and type 2. Type 2, but not type 1, oligomers have a spatiotemporal and structural relationship with amyloid plaques. Highly abundant type 2 oligomers do not impair cognition in situ, possibly due to spatial sequestration around plaques.

Beschreibung: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Alessandro Fantin , Anastasia Lampropoulou , Gaia Gestri , Claudio Raimondi , Valentina Senatore , Ian Zachary , Christiana Ruhrberg Sprouting blood vessels are led by filopodia-studded endothelial tip cells that respond to angiogenic signals. Mosaic lineage tracing previously revealed that NRP1 is essential for tip cell function, although its mechanistic role in tip cells remains poorly defined. Here, we show that NRP1 is dispensable for genetic tip cell identity. Instead, we find that NRP1 is essential to form the filopodial bursts that distinguish tip cells morphologically from neighboring stalk cells, because it enables the extracellular matrix (ECM)-induced activation of CDC42, a key regulator of filopodia formation. Accordingly, NRP1 knockdown and pharmacological CDC42 inhibition similarly impaired filopodia formation in vitro and in developing zebrafish in vivo. During mouse retinal angiogenesis, CDC42 inhibition impaired tip cell and vascular network formation, causing defects that resembled those due to loss of ECM-induced, but not VEGF-induced, NRP1 signaling. We conclude that NRP1 enables ECM-induced filopodia formation for tip cell function during sprouting angiogenesis. Graphical abstract Teaser During angiogenesis, new blood vessel sprouts are led by filopodia-studded tip cells to sense environmental signals and enable directional migration. NRP1 is a tip cell protein that senses angiogenic cues. Fantin et al. now show that NRP1 promotes tip cell function by enabling CDC42 activation for filopodia formation and actin remodeling.

Beschreibung: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Chien-Der Lee , Benjamin P. Tu PUF proteins are post-transcriptional regulators that bind to the 3′ UTRs of mRNA transcripts. Herein, we show how a yeast PUF protein, Puf3p, responds to glucose availability to switch the fate of its bound transcripts that encode proteins required for mitochondrial biogenesis. Upon glucose depletion, Puf3p becomes heavily phosphorylated within its N-terminal region of low complexity, associates with polysomes, and promotes translation of its target mRNAs. Such nutrient-responsive phosphorylation toggles the activity of Puf3p to promote either degradation or translation of these mRNAs according to the needs of the cell. Moreover, activation of translation of pre-existing mRNAs might enable rapid adjustment to environmental changes without the need for de novo transcription. Strikingly, a Puf3p phosphomutant no longer promotes translation but becomes trapped in intracellular foci in an mRNA-dependent manner. Our findings suggest that the inability to properly resolve Puf3p-containing RNA-protein granules via a phosphorylation-based mechanism might be toxic to a cell. Graphical abstract Teaser Lee and Tu report that the PUF protein Puf3 becomes phosphorylated in its low-complexity region upon glucose depletion to promote the translation of its bound mRNAs that are important for mitochondrial biogenesis. A Puf3 phosphomutant becomes trapped in punctate foci, providing insights into the dynamic nature of RNA granules.

Beschreibung: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Takashi Izawa , Nidhi Rohatgi , Tomohiro Fukunaga , Qun-Tian Wang , Matthew J. Silva , Michael J. Gardner , Michael L. McDaniel , Nada A. Abumrad , Clay F. Semenkovich , Steven L. Teitelbaum , Wei Zou ASXL2 is an ETP family protein that interacts with PPARγ. We find that ASXL2−/− mice are insulin resistant, lipodystrophic, and fail to respond to a high-fat diet. Consistent with genetic variation at the ASXL2 locus and human bone mineral density, ASXL2−/− mice are also severely osteopetrotic because of failed osteoclast differentiation attended by normal bone formation. ASXL2 regulates the osteoclast via two distinct signaling pathways. It induces osteoclast formation in a PPARγ/c-Fos-dependent manner and is required for RANK ligand- and thiazolidinedione-induced bone resorption independent of PGC-1β. ASXL2 also promotes osteoclast mitochondrial biogenesis in a process mediated by PGC-1β but independent of c-Fos. Thus, ASXL2 is a master regulator of skeletal, lipid, and glucose homeostasis. Graphical abstract Teaser ASXL2 regulates glucose homeostasis, adipogenesis, and osteoclast differentiation by activating PPARγ. Izawa et al. find that ASXL2-deficient mice are insulin resistant, lipodystrophic, and osteopetrotic. ASXL2 promotes osteoclast formation in a Fos-dependent manner independent of PGC-1β. ASXL2 enhances osteoclast mitochondrial biogenesis in a process mediated by PGC-1β but independent of c-Fos.

Beschreibung: Publication date: Available online 4 June 2015 Source: Cell Reports Author(s): Jan-Philipp Mallm , Karsten Rippe Non-coding RNAs can modulate histone modifications that, at the same time, affect transcript expression levels. Here, we dissect such a network in mouse embryonic stem cells (ESCs). It regulates the activity of the reverse transcriptase telomerase, which synthesizes telomeric repeats at the chromosome ends. We find that histone H3 serine 10 phosphorylation set by Aurora kinase B (AURKB) in ESCs during the S phase of the cell cycle at centromeric and (sub)telomeric loci promotes the expression of non-coding minor satellite RNA ( cen RNA). Inhibition of AURKB induces silencing of cen RNA transcription and establishment of a repressive chromatin state with histone H3 lysine 9 trimethylation and heterochromatin protein 1 accumulation. This process results in a continuous shortening of telomeres. We further show that AURKB interacts with both telomerase and cen RNA and activates telomerase in trans . Thus, in mouse ESCs, telomere maintenance is regulated via expression of cen RNA in a cell-cycle-dependent manner. Graphical abstract Teaser Mallm and Rippe find that AURKB kinase and centromeric RNA regulate telomerase activity. AURKB phosphorylates serine 10 of histone H3 at chromosome p-arms during S phase in embryonic stem cells to induce centromere repeat transcription. Together, AURKB and centromere transcripts activate telomerase and ensure telomere maintenance.

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Jenea M. Bin, Dong Han, Karen Lai Wing Sun, Louis-Philippe Croteau, Emilie Dumontier, Jean-Francois Cloutier, Artur Kania, Timothy E. Kennedy Netrin-1 regulates cell migration and adhesion during the development of the nervous system, vasculature, lung, pancreas, muscle, and mammary gland. It is also proposed to function as a dependence ligand that inhibits apoptosis; however, studies disagree regarding whether netrin-1 loss-of-function mice exhibit increased cell death. Furthermore, previously studied netrin-1 loss-of-function gene-trap mice express a netrin-1-β-galactosidase protein chimera with potential for toxic gain-of-function effects, as well as a small amount of wild-type netrin-1 protein. To unambiguously assess loss of function, we generated netrin-1 floxed and netrin-1 null mouse lines. Netrin-1 −/− mice die earlier and exhibit more severe axon guidance defects than netrin-1 gene-trap mice, revealing that complete loss of function is more severe than previously reported. Netrin-1 −/− embryos also exhibit increased expression of the netrin receptors DCC and neogenin that are proposed dependence receptors; however, increased apoptosis was not detected, inconsistent with netrin-1 being an essential dependence receptor ligand in the embryonic spinal cord. Graphical abstract Teaser Bin et al. have generated a netrin-1 null mouse that displays phenotypes more severe than those of the reported netrin-1 gene-trap mouse, including embryonic lethality and exacerbated axon guidance defects. No increased apoptosis was detected, indicating that netrin-1 is not an essential dependence ligand, despite increased DCC and neogenin in netrin-1 nulls.

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Michael S. Werner, Alexander J. Ruthenburg A number of long noncoding RNAs (lncRNAs) have been reported to regulate transcription via recruitment of chromatin modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA sequencing. We provide genome-wide identification of human chromatin-associated lncRNAs and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs) that share molecular properties with known lncRNAs. Although distinct from eRNAs derived from active prototypical enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population correlated with active genes and may prove useful in de novo enhancer annotation. Graphical abstract Teaser Werner and Ruthenburg report a compendium of tightly chromatin-associated human lncRNAs, which is substantially larger than previously appreciated and also encompasses thousands of chromatin-enriched RNAs (cheRNAs) largely attached to chromatin via RNAPII. CheRNAs may provide a way to annotate enhancers de novo.

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Tony DeFalco, Sarah J. Potter, Alyna V. Williams, Brittain Waller, Matthew J. Kan, Blanche Capel The testis produces sperm throughout the male reproductive lifespan by balancing self-renewal and differentiation of spermatogonial stem cells (SSCs). Part of the SSC niche is thought to lie outside the seminiferous tubules of the testis; however, specific interstitial components of the niche that regulate spermatogonial divisions and differentiation remain undefined. We identified distinct populations of testicular macrophages, one of which lies on the surface of seminiferous tubules, in close apposition to areas of tubules enriched for undifferentiated spermatogonia. These macrophages express spermatogonial proliferation- and differentiation-inducing factors, such as colony-stimulating factor 1 (CSF1) and enzymes involved in retinoic acid (RA) biosynthesis. We show that transient depletion of macrophages leads to a disruption in spermatogonial differentiation. These findings reveal an unexpected role for macrophages in the spermatogonial niche in the testis and raise the possibility that macrophages play previously unappreciated roles in stem/progenitor cell regulation in other tissues. Graphical abstract Teaser Macrophages are abundant in the adult mammalian testis, but not much is known about how they directly affect spermatogenesis. DeFalco et al. describe a role for testicular macrophages, showing that they are enriched near spermatogonial precursors and are required for spermatogonial differentiation, potentially acting through CSF1 and retinoic acid pathways.

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Evgeny Ivashkin, Marina Yu. Khabarova, Victoria Melnikova, Leonid P. Nezlin, Olga Kharchenko, Elena E. Voronezhskaya, Igor Adameyko Many organisms survive in constantly changing environments, including cycling seasons. Developing embryos show remarkable instant adaptations to the variable environmental challenges they encounter during their adult life, despite having no direct contact with the changing environment until after birth or hatching. The mechanisms by which such non-genetic information is transferred to the developing embryos are largely unknown. Here, we address this question by using a freshwater pond snail ( Lymnaea stagnalis ) as a model system. This snail normally lives in a seasonal climate, and the seasons define its locomotion, feeding, and reproductive behavior. We discovered that the serotonergic system plays a crucial role in transmitting a non-genetic instructive signal from mother to progeny. This maternal serotonin-based signal functions in embryos during a short time window at exclusively early pre-neural developmental stages and modulates the dynamics of embryonic and juvenile growth, feeding behavior, and locomotion. Graphical abstract Teaser Ivashkin et al. reveal that maternally derived serotonin tunes the developmental dynamics and behavior of snail offspring under changing environmental conditions. The balance of intra- and extracellular serotonin exclusively during the non-neural stage of development, as well as serotonylation of proteins, is crucial for the transmission of a serotonin-based non-genetic signal.

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Cheng Li, Yahui Lan, Lianna Schwartz-Orbach, Evgenia Korol, Mamta Tahiliani, Todd Evans, Mary G. Goll The Tet family of methylcytosine dioxygenases (Tet1, Tet2, and Tet3) convert 5-methylcytosine to 5-hydroxymethylcytosine. To date, functional overlap among Tet family members has not been examined systematically in the context of embryonic development. To clarify the potential for overlap among Tet enzymes during development, we mutated the zebrafish orthologs of Tet1 , Tet2 , and Tet3 and examined single-, double-, and triple-mutant genotypes. Here, we identify Tet2 and Tet3 as the major 5-methylcytosine dioxygenases in the zebrafish embryo and uncover a combined requirement for Tet2 and Tet3 in hematopoietic stem cell (HSC) emergence. We demonstrate that Notch signaling in the hemogenic endothelium is regulated by Tet2/3 prior to HSC emergence and show that restoring expression of the downstream gata2b/scl/runx1 transcriptional network can rescue HSCs in tet2/3 double mutant larvae. Our results reveal essential, overlapping functions for tet genes during embryonic development and uncover a requirement for 5hmC in regulating HSC production. Graphical abstract Teaser The Tet proteins comprise a family of dioxygenases that convert 5-methylcytosine to 5-hydroxymethylcytosine. Li et al. identify Tet2 and Tet3 as the major 5-methylcytosine dioxygenases in the zebrafish embryo and uncover an overlapping requirement for Tet2 and Tet3 in hematopoietic stem cell emergence.

Beschreibung: Publication date: Available online 6 August 2015 Source: Cell Reports Author(s): Ann V. Griffith, Thomas Venables, Jianjun Shi, Andrew Farr, Holly van Remmen, Luke Szweda, Mohammad Fallahi, Peter Rabinovitch, Howard T. Petrie T lymphocytes are essential mediators of immunity that are produced by the thymus in proportion to its size. The thymus atrophies rapidly with age, resulting in progressive diminution of new T cell production. This decreased output is compensated by duplication of existing T cells, but it results in gradual dominance by memory T cells and decreased ability to respond to new pathogens or vaccines. Here, we show that accelerated and irreversible thymic atrophy results from stromal deficiency in the reducing enzyme catalase, leading to increased damage by hydrogen peroxide generated by aerobic metabolism. Genetic complementation of catalase in stromal cells diminished atrophy, as did chemical antioxidants, thus providing a mechanistic link between antioxidants, metabolism, and normal immune function. We propose that irreversible thymic atrophy represents a conventional aging process that is accelerated by stromal catalase deficiency in the context of an intensely anabolic (lymphoid) environment. Graphical abstract Teaser Thymic function is essential for maintenance of immunity but decreases with age. Griffith et al. show that stromal deficiency in catalase leads to mitochondrial dysfunction and DNA damage in stromal cells and that atrophy is ameliorated by genetic complementation of catalase or biochemical antioxidants.

Beschreibung: Publication date: Available online 8 August 2015 Source: FEBS Open Bio Author(s): Jonghwan Lee, Do Won Hwang, Seung U Kim, Dong Soo Lee, Yong Seung Lee, Hyejung Heo, Bahy A. Ali, Abdulaziz A. Al-Khedhairy, Soonhag Kim Evaluation of the function of microRNAs (miRNAs or miRs) through miRNA expression profiles during neuronal differentiation plays a critical role not only in identifying unique miRNAs relevant to cellular development but also in understanding regulatory functions of the cell-specific miRNAs in living organisms. Here, we examined the microarray-based miRNA expression profiles of G2 cells (recently developed human neural stem cells) and monitored the expression pattern of known neuron-specific miR-9 and miR-124a during neuronal differentiation of G2 cells in vitro and in vivo . Of 500 miRNAs analyzed by microarray of G2 cells, the expression of 90 miRNAs was significantly increased during doxycycline-dependent neuronal differentiation of G2 cells and about 60 miRNAs showed a gradual enhancement of gene expression as neuronal differentiation progressed. Real-time PCR showed that expression of endogenous mature miR-9 was continuously and gradually increased in a pattern dependent on the period of neuronal differentiation of G2 cells while the increased expression of neuron-specific mature miR-124a was barely observed during neurogenesis. Our recently developed miRNA reporter imaging vectors (CMV/Gluc/3×PT_miR-9 and CMV/Gluc/3×PT_miR-124a) containing Gaussia luciferase, CMV promoter and three copies of complementary nucleotides of each corresponding miRNA showed that luciferase activity from CMV/Gluc/3×PT_miR-9 was gradually decreased both in vitro and in vivo in G2 cells induced to differentiate into neurons. However, in vitro and in vivo bioluminescence signals for CMV/Gluc/3×PT_miR-124a were not significantly different between undifferentiated and differentiated G2 cells. Our results demonstrate that biogenesis of neuron-specific miR-124a is not necessary for doxycycline-dependent neurogenesis of G2 cells.

Beschreibung: Publication date: Available online 7 August 2015 Source: FEBS Open Bio Author(s): Tao Liu, Xuan-Cheng Fang, Zhen Ding, Ze-Gan Sun, Li-Ming Sun, Yi-Lian Wang Inflammatory markers have been proposed to predict clinical outcomes in many types of cancers. The purpose of this study was to explore the influence of the lymphocyte-to-monocyte ratio (LMR) on clinical prognosis of patients with osteosarcoma. This study collected 327 patients who underwent surgical treatment for osteosarcoma during the period 2006 2010. LMR was calculated from pre-operative peripheral blood cells counts. The optimal cut-off value of LMR was determined based on receiver operating characteristic curve analysis. Overall survival (OS) and event free survival (EFS) was plotted using the Kaplan–Meier method and evaluated by the log-rank test. A predictive model was established to predict clinical prognosis for OS, and the predictive accuracy of this model was determined by concordance index (c-index). Our results showed that young age, elevated alkaline phosphatase, metastasis at diagnosis, chemotherapy, lymphocyte and monocyte counts were significantly associated with LMR. Low LMR was associated with shorter OS and EFS ( P 〈 0.001), and was an independent predictor of both OS and EFS (HR=1.72, 95% CI=1.14-2.60, P = 0.010; HR=1.89, 95% CI=1.32-2.57, P = 0.009). The nomogram performed well in the prediction of overall survival in patients with osteosarcoma (c-index 0.630). In conclusion, low pre-operative LMR is associated with a poor prognosis in patients suffering from osteosarcoma. A prospective study is warranted for further validation of our results.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Sergei A. Manakov, Dubravka Pezic, Georgi K. Marinov, William A. Pastor, Ravi Sachidanandam, Alexei A. Aravin In developing male germ cells, prospermatogonia, two Piwi proteins, MILI and MIWI2, use Piwi-interacting RNA (piRNA) guides to repress transposable element (TE) expression and ensure genome stability and proper gametogenesis. In addition to their roles in post-transcriptional TE repression, both proteins are required for DNA methylation of TE sequences. Here, we analyzed the effect of Miwi2 deficiency on piRNA biogenesis and transposon repression. Miwi2 deficiency had only a minor impact on piRNA biogenesis; however, the piRNA profile of Miwi2 -knockout mice indicated overexpression of several LINE1 TE families that led to activation of the ping-pong piRNA cycle. Furthermore, we found that MILI and MIWI2 have distinct functions in TE repression in the nucleus. MILI is responsible for DNA methylation of a larger subset of TE families than MIWI2 is, suggesting that the proteins have independent roles in establishing DNA methylation patterns. Graphical abstract Teaser Two components in the piRNA pathway, MILI and MIWI2, were proposed to work in a linear hierarchy to generate piRNAs and methylate transposon sequences. Manakov et al. now profile transcription and methylation patterns in Mili and Miwi2 mutants and demonstrate that these proteins are in part functionally independent.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Sang Woo Seo, Donghyuk Kim, Richard Szubin, Bernhard O. Palsson Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional regulation of the defense system for oxidative stress in bacteria. However, their full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OxyR, SoxR, and SoxS regulons in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 68 genes in 51 transcription units (TUs) belong to these regulons. Among them, 48 genes showed more than 2-fold changes in expression level under single-TF-knockout conditions. This reconstruction expands the genome-wide roles of these factors to include direct activation of genes related to amino acid biosynthesis (methionine and aromatic amino acids), cell wall synthesis (lipid A biosynthesis and peptidoglycan growth), and divalent metal ion transport (Mn 2+ , Zn 2+ , and Mg 2+ ). Investigating the co-regulation of these genes with other stress-response TFs reveals that they are independently regulated by stress-specific TFs. Graphical abstract Teaser Seo et al. reconstruct OxyR, SoxR, and SoxS transcriptional regulatory networks under oxidative stress in E. coli and expand their roles to include direct activation of amino acid biosynthesis, cell wall synthesis, and divalent metal ion transport. These processes are independently regulated by TFs specific to oxidative stress.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Anders S. Hansen, Erin K. O’Shea Although the relationship between DNA cis -regulatory sequences and gene expression has been extensively studied at steady state, how cis -regulatory sequences affect the dynamics of gene induction is not known. The dynamics of gene induction can be described by the promoter activation timescale (AcTime) and amplitude threshold (AmpThr). Combining high-throughput microfluidics with quantitative time-lapse microscopy, we control the activation dynamics of the budding yeast transcription factor, Msn2, and reveal how cis -regulatory motifs in 20 promoter variants of the Msn2-target-gene SIP18 affect AcTime and AmpThr. By modulating Msn2 binding sites, we can decouple AmpThr from AcTime and switch the SIP18 promoter class from high AmpThr and slow AcTime to low AmpThr and either fast or slow AcTime. We present a model that quantitatively explains gene-induction dynamics on the basis of the Msn2-binding-site number, TATA box location, and promoter nucleosome organization. Overall, we elucidate the cis- regulatory logic underlying promoter decoding of TF dynamics. Graphical abstract Teaser Cells control gene expression in part by regulating the dynamics of transcription-factor activity. Hansen and O’Shea investigate the cis -regulatory logic underlying promoter decoding of transcription-factor dynamics for 20 promoter variants and reveal that two properties characterizing the gene expression response—threshold and activation timescale—can be decoupled.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): David Lau, C. Peter Bengtson, Bettina Buchthal, Hilmar Bading The health of neurons is critically dependent on the relative signaling intensities of survival-promoting synaptic and death-inducing extrasynaptic NMDA receptors. Here, we show that BDNF is a regulator of this balance and promotes neuroprotection by reducing toxic NMDA receptor signaling. BDNF acts by initiating synaptic NMDA-receptor/nuclear-calcium-driven adaptogenomics, leading to increased expression of inhibin β- A ( inhba ). Inhibin β- A (its homodimer is known as activin A) in turn reduces neurotoxic extrasynaptic NMDA-receptor-mediated calcium influx, thereby shielding neurons against mitochondrial dysfunction, a major cause of excitotoxicity. Thus, BDNF induces acquired neuroprotection by enhancing synaptic activity and lowering extrasynaptic NMDA receptor death signaling through a nuclear calcium- inhibin β- A pathway. This process, which confers protection against ischemic brain damage in a mouse stroke model, may be compromised in Huntington’s disease, Alzheimer’s disease, or aging-related neurodegenerative conditions that are associated with reduced BDNF levels and/or enhanced extrasynaptic NMDA receptor signaling. Graphical abstract Teaser Lau et al. show that BDNF-induced neuroprotection is mediated by synaptic NMDA-receptor-dependent nuclear calcium signals activating transcription of inhibin β-A (activin A). Activin A in turn reduces toxic extrasynaptic NMDA-receptor-mediated calcium influx, shields neurons from mitochondrial dysfunction, and protects against stroke-induced brain damage.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Corina E. Antal, Julia A. Callender, Alexandr P. Kornev, Susan S. Taylor, Alexandra C. Newton The signaling output of protein kinase C (PKC) is exquisitely controlled, with its disruption resulting in pathophysiologies. Identifying the structural basis for autoinhibition is central to developing effective therapies for cancer, where PKC activity needs to be enhanced, or neurodegenerative diseases, where PKC activity should be inhibited. Here, we reinterpret a previously reported crystal structure of PKCβII and use docking and functional analysis to propose an alternative structure that is consistent with previous literature on PKC regulation. Mutagenesis of predicted contact residues establishes that the Ca 2+ -sensing C2 domain interacts intramolecularly with the kinase domain and the carboxyl-terminal tail, locking PKC in an inactive conformation. Ca 2+ -dependent bridging of the C2 domain to membranes provides the first step in activating PKC via conformational selection. Although the placement of the C1 domains remains to be determined, elucidation of the structural basis for autoinhibition of PKCβII unveils a unique direction for therapeutically targeting PKC. Graphical abstract Teaser Kinase autoinhibition is essential for suppressing signaling when appropriate signals are absent. Antal et al. reinterpret a protein kinase C βII crystal structure to show that its Ca 2+ -sensing C2 domain autoinhibits by binding over the kinase domain, unveiling an interface that can potentially be therapeutically targeted to enhance or restrain activity.

Beschreibung: Publication date: Available online 13 August 2015 Source: Cell Reports Author(s): Yoosoo Yang, Jaewook Kim, Hye Yun Kim, Nayeon Ryoo, Sejin Lee, YoungSoo Kim, Hyewhon Rhim, Yeon-Kyun Shin Alzheimer’s disease (AD) is closely associated with synaptic dysfunction, and thus current treatments often aim to stimulate neurotransmission to improve cognitive impairment. Whereas the formation of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex is essential for synaptic transmission, the correlation between SNAREs and AD neuropathology is unknown. Here, we report that intracellular amyloid-β (Aβ) oligomers directly inhibit SNARE-mediated exocytosis by impairing SNARE complex formation. We observe abnormal reduction of SNARE complex levels in the brains of APP/PS1 transgenic (TG) mice compared to age-matched wild-types. We demonstrate that Aβ oligomers block SNARE complex assembly through the direct interaction with a target membrane (t)-SNARE syntaxin 1a in vitro. Furthermore, the results of the in vitro single-vesicle content-mixing assay reveal that Aβ oligomers inhibit SNARE-mediated fusion pores. Thus, our study identifies a potential molecular mechanism by which intracellular Aβ oligomers hamper SNARE-mediated exocytosis, likely leading to AD-associated synaptic dysfunctions. Graphical abstract Teaser The role of Aβ in cognitive impairment in Alzheimer’s disease still remains elusive. Yang et al. now show that Aβ oligomers bind to syntaxin 1a to impair SNARE complex formation to inhibit exocytosis. The resulting inhibition of neurotransmission could therefore lead to cognitive impairments.