A G1-like state allows HIV-1 to bypass SAMHD1 restriction in macrophages
An unresolved question is how HIV-1 achieves efficient replication in terminally differentiated macrophages despite the restriction factor SAMHD1. We reveal inducible changes in expression of cell cycle-associated proteins including MCM2 and cyclins A, E, D1/D3 in macrophages, without evidence for DNA synthesis or mitosis. These changes are induced by activation of the Raf/MEK/ERK kinase cascade, culminating in upregulation of CDK1 with subsequent SAMHD1 T592 phosphorylation and deactivation of its antiviral activity. HIV infection is limited to these G1-like phase macrophages at the single-cell level. Depletion of SAMHD1 ...
Source: EMBO Journal - February 28, 2017 Category: Molecular Biology Authors: Mlcochova, P., Sutherland, K. A., Watters, S. A., Bertoli, C., de Bruin, R. A., Rehwinkel, J., Neil, S. J., Lenzi, G. M., Kim, B., Khwaja, A., Gage, M. C., Georgiou, C., Chittka, A., Yona, S., Noursadeghi, M., Towers, G. J., Gupta, R. K. Tags: Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Young microglia restore amyloid plaque clearance of aged microglia
Alzheimer's disease (AD) is characterized by deposition of amyloid plaques, neurofibrillary tangles, and neuroinflammation. In order to study microglial contribution to amyloid plaque phagocytosis, we developed a novel ex vivo model by co-culturing organotypic brain slices from up to 20-month-old, amyloid-bearing AD mouse model (APPPS1) and young, neonatal wild-type (WT) mice. Surprisingly, co-culturing resulted in proliferation, recruitment, and clustering of old microglial cells around amyloid plaques and clearance of the plaque halo. Depletion of either old or young microglial cells prevented amyloid plaque clearan...
Source: EMBO Journal - February 28, 2017 Category: Molecular Biology Authors: Daria, A., Colombo, A., Llovera, G., Hampel, H., Willem, M., Liesz, A., Haass, C., Tahirovic, S. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Cell signaling as a cognitive process
Cellular identity as defined through morphology and function emerges from intracellular signaling networks that communicate between cells. Based on recursive interactions within and among these intracellular networks, dynamical solutions in terms of biochemical behavior are generated that can differ from those in isolated cells. In this way, cellular heterogeneity in tissues can be established, implying that cell identity is not intrinsically predetermined by the genetic code but is rather dynamically maintained in a cognitive manner. We address how to experimentally measure the flow of information in intracellular biochem...
Source: EMBO Journal - February 28, 2017 Category: Molecular Biology Authors: Koseska, A., Bastiaens, P. I. Tags: Signal Transduction, Systems & Computational Biology Review Source Type: research

Reestablishing microglia function: good news for Alzheimer's therapy?
Alzheimer's disease (AD) is the most common form of age-related neurodegenerative disease resulting in dementia. The current notion is that AD is based on a pathological plaque-forming accumulation of amyloid-β (Aβ) peptides that originate from a disturbed balance between production and removal of Aβ peptides. Loss of Aβ uptake capacity by brain microglia is linked to Aβ plaque formation and AD onset. In this issue of The EMBO Journal, Daria and colleagues show that this microglia dysfunction is reversible and that existing Aβ plaques can be cleared, suggesting that restoring microglia functio...
Source: EMBO Journal - February 28, 2017 Category: Molecular Biology Authors: Biber, K. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

Fluorescence-based ATG8 sensors monitor localization and function of LC3/GABARAP proteins
Autophagy is a cellular surveillance pathway that balances metabolic and energy resources and transports specific cargos, including damaged mitochondria, other broken organelles, or pathogens for degradation to the lysosome. Central components of autophagosomal biogenesis are six members of the LC3 and GABARAP family of ubiquitin-like proteins (mATG8s). We used phage display to isolate peptides that possess bona fide LIR (LC3-interacting region) properties and are selective for individual mATG8 isoforms. Sensitivity of the developed sensors was optimized by multiplication, charge distribution, and fusion with a membrane re...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Stolz, A., Putyrski, M., Kutle, I., Huber, J., Wang, C., Major, V., Sidhu, S. S., Youle, R. J., Rogov, V. V., Dötsch, V., Ernst, A., Dikic, I. Tags: Autophagy & Cell Death Resource Source Type: research

Mycobacterium tuberculosis protease MarP activates a peptidoglycan hydrolase during acid stress
Mycobacterium tuberculosis (Mtb) can persist in the human host in a latent state for decades, in part because it has the ability to withstand numerous stresses imposed by host immunity. Prior studies have established the essentiality of the periplasmic protease MarP for Mtb to survive in acidified phagosomes and establish and maintain infection in mice. However, the proteolytic substrates of MarP that mediate these phenotypes were unknown. Here, we used biochemical methods coupled with supravital chemical probes that facilitate imaging of nascent peptidoglycan to demonstrate that during acid stress MarP cleaves the peptido...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Botella, H., Vaubourgeix, J., Lee, M. H., Song, N., Xu, W., Makinoshima, H., Glickman, M. S., Ehrt, S. Tags: Microbiology, Virology & Host Pathogen Interaction, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

MRTF potentiates TEAD-YAP transcriptional activity causing metastasis
Yes-associated protein (YAP) and myocardin-related transcription factor (MRTF) play similar roles and exhibit significant crosstalk in directing transcriptional responses to chemical and physical extracellular cues. The mechanism underlying this crosstalk, however, remains unclear. Here, we show MRTF family proteins bind YAP via a conserved PPXY motif that interacts with the YAP WW domain. This interaction allows MRTF to recruit NcoA3 to the TEAD-YAP transcriptional complex and potentiate its transcriptional activity. We show this interaction of MRTF and YAP is critical for LPA-induced cancer cell invasion in vitro an...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Kim, T., Hwang, D., Lee, D., Kim, J.-H., Kim, S.-Y., Lim, D.-S. Tags: Cancer, Signal Transduction, Transcription Articles Source Type: research

Cell cycle-regulated ubiquitination of tankyrase 1 by RNF8 and ABRO1/BRCC36 controls the timing of sister telomere resolution
Timely resolution of sister chromatid cohesion in G2/M is essential for genome integrity. Resolution at telomeres requires the poly(ADP-ribose) polymerase tankyrase 1, but the mechanism that times its action is unknown. Here, we show that tankyrase 1 activity at telomeres is controlled by a ubiquitination/deubiquitination cycle depending on opposing ubiquitin ligase and deubiquitinase activities. In late S/G2 phase, the DNA damage-responsive E3 ligase RNF8 conjugates K63-linked ubiquitin chains to tankyrase 1, while in G1 phase such ubiquitin chains are removed by BRISC, an ABRO1/BRCC36-containing deubiquitinase complex. W...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Tripathi, E., Smith, S. Tags: DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells
Translational control during cell division determines when cells start a new cell cycle, how fast they complete it, the number of successive divisions, and how cells coordinate proliferation with available nutrients. The translational efficiencies of mRNAs in cells progressing synchronously through the mitotic cell cycle, while preserving the coupling of cell division with cell growth, remain uninvestigated. We now report comprehensive ribosome profiling of a yeast cell size series from the time of cell birth, to identify mRNAs under periodic translational control. The data reveal coordinate translational activation of mRN...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Blank, H. M., Perez, R., He, C., Maitra, N., Metz, R., Hill, J., Lin, Y., Johnson, C. D., Bankaitis, V. A., Kennedy, B. K., Aramayo, R., Polymenis, M. Tags: Cell Cycle, Metabolism, Protein Biosynthesis & Quality Control Articles Source Type: research

The complete structure of the chloroplast 70S ribosome in complex with translation factor pY
Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, requir...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Bieri, P., Leibundgut, M., Saurer, M., Boehringer, D., Ban, N. Tags: Plant Biology, Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

Calcium-permeable AMPA receptors and silent synapses in cocaine-conditioned place preference
Exposure to cocaine generates silent synapses in the nucleus accumbens (NAc), whose eventual unsilencing/maturation by recruitment of calcium-permeable AMPA-type glutamate receptors (CP-AMPARs) after drug withdrawal results in profound remodeling of NAc neuro-circuits. Silent synapse-based NAc remodeling was shown to be critical for several drug-induced behaviors, but its role in acquisition and retention of the association between drug rewarding effects and drug-associated contexts has remained unclear. Here, we find that the postsynaptic proteins PSD-93, PSD-95, and SAP102 differentially regulate excitatory synapse prope...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Shukla, A., Beroun, A., Panopoulou, M., Neumann, P. A., Grant, S. G., Olive, M. F., Dong, Y., Schlüter, O. M. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

COPI-TRAPPII activates Rab18 and regulates its lipid droplet association
The transport protein particle (TRAPP) was initially identified as a vesicle tethering factor in yeast and as a guanine nucleotide exchange factor (GEF) for Ypt1/Rab1. In mammals, structures and functions of various TRAPP complexes are beginning to be understood. We found that mammalian TRAPPII was a GEF for both Rab18 and Rab1. Inactivation of TRAPPII-specific subunits by various methods including siRNA depletion and CRISPR–Cas9-mediated deletion reduced lipolysis and resulted in aberrantly large lipid droplets. Recruitment of Rab18 onto lipid droplet (LD) surface was defective in TRAPPII-deleted cells, but the loca...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Li, C., Luo, X., Zhao, S., Siu, G. K., Liang, Y., Chan, H. C., Satoh, A., Yu, S. S. Tags: Membrane & Intracellular Transport Articles Source Type: research

Ubiquitylation-dependent oligomerization regulates activity of Nedd4 ligases
Ubiquitylation controls protein function and degradation. Therefore, ubiquitin ligases need to be tightly controlled. We discovered an evolutionarily conserved allosteric restraint mechanism for Nedd4 ligases and demonstrated its function with diverse substrates: the yeast soluble proteins Rpn10 and Rvs167, and the human receptor tyrosine kinase FGFR1 and cardiac IKS potassium channel. We found that a potential trimerization interface is structurally blocked by the HECT domain α1-helix, which further undergoes ubiquitylation on a conserved lysine residue. Genetic, bioinformatics, biochemical and biophysical data show...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Attali, I., Tobelaim, W. S., Persaud, A., Motamedchaboki, K., Simpson-Lavy, K. J., Mashahreh, B., Levin-Kravets, O., Keren-Kaplan, T., Pilzer, I., Kupiec, M., Wiener, R., Wolf, D. A., Rotin, D., Prag, G. Tags: Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

ANGPTL2 expression in the intestinal stem cell niche controls epithelial regeneration and homeostasis
The intestinal epithelium continually self-renews and can rapidly regenerate after damage. Dysregulation of intestinal epithelial homeostasis leads to severe inflammatory bowel disease. Additionally, aberrant signaling by the secreted protein angiopoietin-like protein 2 (ANGPTL2) causes chronic inflammation in a variety of diseases. However, little is known about the physiologic role of ANGPTL2 in normal tissue homeostasis and during wound repair following injury. Here, we assessed ANGPTL2 function in intestinal physiology and disease in vivo. Although intestinal development proceeded normally in Angptl2-deficient mic...
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Horiguchi, H., Endo, M., Kawane, K., Kadomatsu, T., Terada, K., Morinaga, J., Araki, K., Miyata, K., Oike, Y. Tags: Signal Transduction, Stem Cells Articles Source Type: research

Nutrient sensing and TOR signaling in yeast and mammals
Coordinating cell growth with nutrient availability is critical for cell survival. The evolutionarily conserved TOR (target of rapamycin) controls cell growth in response to nutrients, in particular amino acids. As a central controller of cell growth, mTOR (mammalian TOR) is implicated in several disorders, including cancer, obesity, and diabetes. Here, we review how nutrient availability is sensed and transduced to TOR in budding yeast and mammals. A better understanding of how nutrient availability is transduced to TOR may allow novel strategies in the treatment for mTOR-related diseases. (Source: EMBO Journal)
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Gonzalez, A., Hall, M. N. Tags: Metabolism, Signal Transduction Review Source Type: research

TRAPPing Rab18 in lipid droplets
A number of membrane trafficking components are associated with lipid droplets (LDs) and/or are involved in their biogenesis. In this issue of The EMBO Journal, Li et al (2017) show that the mammalian TRAPPII (TRAnsport Protein Particle) complex acts as an LD-associated GEF for Rab18, thereby regulating LD homeostasis. (Source: EMBO Journal)
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Zappa, F., Venditti, R., De Matteis, M. A. Tags: Membrane & Intracellular Transport News [amp ] Views Source Type: research

Self-regulating ubiquitin ligases
Occasional auto-modification of ubiquitin ligases typically leads to their proteasomal destruction, but new findings published in The EMBO Journal now show that in the case of Rsp5/Nedd4, auto-ubiquitylation instead triggers oligomerization and concomitant reduction of ligase activity. This novel mechanism therefore creates silenced ligases that remain poised for reactivation. (Source: EMBO Journal)
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: Hill, S., Kleiger, G. Tags: Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Balancing signals in the intestinal niche
During intestinal regeneration, opposing gradients of Wnt and BMP signaling ensure successful differentiation along the crypt/villus axis. In this issue of The EMBO Journal, Horiguchi et al (2017) show how intestinal subepithelial myofibroblasts can influence cell fate decisions in the regenerating intestine via autocrine secretion of angiopoietin-like protein 2 (ANGPTL2). (Source: EMBO Journal)
Source: EMBO Journal - February 14, 2017 Category: Molecular Biology Authors: van Neerven, S. M., Vermeulen, L. Tags: Signal Transduction, Stem Cells News [amp ] Views Source Type: research

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E
RNA sequencing studies have identified hundreds of non-coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high-throughput analysis of RNA–RNA interactions in bacteria. Here we demonstrate that in vivo sRNA–mRNA duplexes can be recovered using UV-crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base-paired sRNA–mRNA duplexes in association with RNase E, al...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Waters, S. A., McAteer, S. P., Kudla, G., Pang, I., Deshpande, N. P., Amos, T. G., Leong, K. W., Wilkins, M. R., Strugnell, R., Gally, D. L., Tollervey, D., Tree, J. J. Tags: Methods & Resources, Microbiology, Virology & Host Pathogen Interaction, RNA Biology Source Type: research

Topoisomerase I-mediated cleavage at unrepaired ribonucleotides generates DNA double-strand breaks
Ribonuclease activity of topoisomerase I (Top1) causes DNA nicks bearing 2',3'-cyclic phosphates at ribonucleotide sites. Here, we provide genetic and biochemical evidence that DNA double-strand breaks (DSBs) can be directly generated by Top1 at sites of genomic ribonucleotides. We show that RNase H2-deficient yeast cells displayed elevated frequency of Rad52 foci, inactivation of RNase H2 and RAD52 led to synthetic lethality, and combined loss of RNase H2 and RAD51 induced slow growth and replication stress. Importantly, these phenotypes were rescued upon additional deletion of TOP1, implicating homologous recombination f...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Huang, S.-y. N., Williams, J. S., Arana, M. E., Kunkel, T. A., Pommier, Y. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

miRNA profiling of human naive CD4 T cells links miR-34c-5p to cell activation and HIV replication
Cell activation is a vital step for T-cell memory/effector differentiation as well as for productive HIV infection. To identify novel regulators of this process, we used next-generation sequencing to profile changes in microRNA expression occurring in purified human naive CD4 T cells in response to TCR stimulation and/or HIV infection. Our results demonstrate, for the first time, the transcriptional up-regulation of miR-34c-5p in response to TCR stimulation in naive CD4 T cells. The induction of this miR was further consistently found to be reduced by both HIV-1 and HIV-2 infections. Overexpression of miR-34c-5p led to cha...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Amaral, A. J., Andrade, J., Foxall, R. B., Matoso, P., Matos, A. M., Soares, R. S., Rocha, C., Ramos, C. G., Tendeiro, R., Serra-Caetano, A., Guerra-Assuncao, J. A., Santa-Marta, M., Goncalves, J., Gama-Carvalho, M., Sousa, A. E. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Hippo kinases maintain polarity during directional cell migration in Caenorhabditis elegans
Precise positioning of cells is crucial for metazoan development. Despite immense progress in the elucidation of the attractive cues of cell migration, the repulsive mechanisms that prevent the formation of secondary leading edges remain less investigated. Here, we demonstrate that Caenorhabditis elegans Hippo kinases promote cell migration along the anterior–posterior body axis via the inhibition of dorsal–ventral (DV) migration. Ectopic DV polarization was also demonstrated in gain-of-function mutant animals for C. elegans RhoG MIG-2. We identified serine 139 of MIG-2 as a novel conserved Hippo kinase ph...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Feng, G., Zhu, Z., Li, W.-J., Lin, Q., Chai, Y., Dong, M.-Q., Ou, G. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation Articles Source Type: research

An RNA-binding atypical tropomyosin recruits kinesin-1 dynamically to oskar mRNPs
Localization and local translation of oskar mRNA at the posterior pole of the Drosophila oocyte directs abdominal patterning and germline formation in the embryo. The process requires recruitment and precise regulation of motor proteins to form transport-competent mRNPs. We show that the posterior-targeting kinesin-1 is loaded upon nuclear export of oskar mRNPs, prior to their dynein-dependent transport from the nurse cells into the oocyte. We demonstrate that kinesin-1 recruitment requires the DmTropomyosin1-I/C isoform, an atypical RNA-binding tropomyosin that binds directly to dimerizing oskar 3'UTRs. Finally, we show t...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Gaspar, I., Sysoev, V., Komissarov, A., Ephrussi, A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation, Membrane & Intracellular Transport Articles Source Type: research

Replication fork passage drives asymmetric dynamics of a critical nucleoid-associated protein in Caulobacter
In bacteria, chromosome dynamics and gene expression are modulated by nucleoid-associated proteins (NAPs), but little is known about how NAP activity is coupled to cell cycle progression. Using genomic techniques, quantitative cell imaging, and mathematical modeling, our study in Caulobacter crescentus identifies a novel NAP (GapR) whose activity over the cell cycle is shaped by DNA replication. GapR activity is critical for cellular function, as loss of GapR causes severe, pleiotropic defects in growth, cell division, DNA replication, and chromosome segregation. GapR also affects global gene expression with a chromosomal ...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Arias-Cartin, R., Dobihal, G. S., Campos, M., Surovtsev, I. V., Parry, B., Jacobs-Wagner, C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode
Mitochondrial cytochrome c oxidase (CcO) transfers electrons from cytochrome c (Cyt.c) to O2 to generate H2O, a process coupled to proton pumping. To elucidate the mechanism of electron transfer, we determined the structure of the mammalian Cyt.c–CcO complex at 2.0-Å resolution and identified an electron transfer pathway from Cyt.c to CcO. The specific interaction between Cyt.c and CcO is stabilized by a few electrostatic interactions between side chains within a small contact surface area. Between the two proteins are three water layers with a long inter-molecular span, one of which lies between the other two ...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Shimada, S., Shinzawa-Itoh, K., Baba, J., Aoe, S., Shimada, A., Yamashita, E., Kang, J., Tateno, M., Yoshikawa, S., Tsukihara, T. Tags: Membrane & Intracellular Transport, Metabolism, Structural Biology Articles Source Type: research

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters
An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/TATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analy...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: de Jonge, W. J., O'Duibhir, E., Lijnzaad, P., van Leenen, D., Groot Koerkamp, M. J., Kemmeren, P., Holstege, F. C. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

The pseudophosphatase STYX targets the F-box of FBXW7 and inhibits SCFFBXW7 function
The F-box protein FBXW7 is the substrate-recruiting subunit of an SCF ubiquitin ligase and a major tumor-suppressor protein that is altered in several human malignancies. Loss of function of FBXW7 results in the stabilization of numerous proteins that orchestrate cell proliferation and survival. Little is known about proteins that directly regulate the function of this protein. In the current work, we have mapped the interactome of the enigmatic pseudophosphatase STYX. We reasoned that a catalytically inactive phosphatase might have adopted novel mechanisms of action. The STYX interactome contained several F-box proteins, ...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Reiterer, V., Figueras-Puig, C., Le Guerroue, F., Confalonieri, S., Vecchi, M., Jalapothu, D., Kanse, S. M., Deshaies, R. J., Di Fiore, P. P., Behrends, C., Farhan, H. Tags: Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Hypoxia-inducible factors: coupling glucose metabolism and redox regulation with induction of the breast cancer stem cell phenotype
Reduced oxygen availability (hypoxia) leads to increased production of reactive oxygen species (ROS) by the electron transport chain. Here, I review recent work delineating mechanisms by which hypoxia-inducible factor 1 (HIF-1) mediates adaptive metabolic responses to hypoxia, including increased flux through the glycolytic pathway and decreased flux through the tricarboxylic acid cycle, in order to decrease mitochondrial ROS production. HIF-1 also mediates increased flux through the serine synthesis pathway and mitochondrial one-carbon (folate cycle) metabolism to increase mitochondrial antioxidant production (NADPH and g...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Semenza, G. L. Tags: Cancer, Metabolism Review Source Type: research

Brief encounters of cytochrome c
Transient protein interactions are paramount to life where fast and efficient transfer of information and cargo are often integral to pathways and networks. However, complexes formed by transient protein interactions are often times resistant to direct structural characterization due to their inherent, dynamic nature, so our knowledge to date typically derives from biochemical, biophysical and computational methods. In this issue, Shimada and co-authors present the crystal structure of the mammalian cytochrome c oxidase in complex with its electron donor cytochrome c, identifying a new class of protein–protein intera...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Lyons, J. A., Nissen, P. Tags: Membrane & Intracellular Transport, Metabolism, Structural Biology News [amp ] Views Source Type: research

TFIID or not TFIID, a continuing transcriptional SAGA
Eukaryotic protein-coding genes are typically classified into two groups: those with expression regulated by specific signals versus the relatively constant "housekeeping" genes. Although these differences are associated with alternative modes of RNA polymerase II (RNAP II) pre-initiation complex (PIC) assembly, a role for gene-specific activators in controlling "regulatability" has been difficult to rule out. To address this question, de Jonge et al (2017) studied a group of genes controlled by a common activator but dependent on either TFIID or SAGA and found that the magnitude of regulation stro...
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Kubik, S., Bruzzone, M. J., Shore, D. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription News [amp ] Views Source Type: research

Global snapshots of bacterial RNA networks
While bacteria were long thought to rely primarily on transcriptional control, it is now well established that they also use numerous small RNAs to regulate mRNA translation and stability. There has recently been a surge in studies, including one by Waters et al (2017) in this issue of The EMBO Journal, that have used clever variations of the RNA-seq technique to comprehensively map small RNA–target networks. (Source: EMBO Journal)
Source: EMBO Journal - January 31, 2017 Category: Molecular Biology Authors: Hör, J., Vogel, J. Tags: Methods & Resources, Microbiology, Virology & Host Pathogen Interaction, RNA Biology News [amp ] Views Source Type: research

mGluR long-term depression regulates GluA2 association with COPII vesicles and exit from the endoplasmic reticulum
mGluR long-term depression (mGluR-LTD) is a form of synaptic plasticity induced at excitatory synapses by metabotropic glutamate receptors (mGluRs). mGluR-LTD reduces synaptic strength and is relevant to learning and memory, autism, and sensitization to cocaine; however, the mechanism is not known. Here we show that activation of Group I mGluRs in medium spiny neurons induces trafficking of GluA2 from the endoplasmic reticulum (ER) to the synapse by enhancing GluA2 binding to essential COPII vesicle proteins, Sec23 and Sec13. GluA2 exit from the ER further depends on IP3 and Ryanodine receptor-controlled Ca2+ release as we...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Pick, J. E., Khatri, L., Sathler, M. F., Ziff, E. B. Tags: Neuroscience Articles Source Type: research

Unloading of homologous recombination factors is required for restoring double-stranded DNA at damage repair loci
Cells use homology-dependent DNA repair to mend chromosome breaks and restore broken replication forks, thereby ensuring genome stability and cell survival. DNA break repair via homology-based mechanisms involves nuclease-dependent DNA end resection, which generates long tracts of single-stranded DNA required for checkpoint activation and loading of homologous recombination proteins Rad52/51/55/57. While recruitment of the homologous recombination machinery is well characterized, it is not known how its presence at repair loci is coordinated with downstream re-synthesis of resected DNA. We show that Rad51 inhibits recruitm...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Vasianovich, Y., Altmannova, V., Kotenko, O., Newton, M. D., Krejci, L., Makovets, S. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Negative regulation of type I IFN signaling by phosphorylation of STAT2 on T387
The transcription factor ISGF3, comprised of IRF9 and tyrosine-phosphorylated STATs 1 and 2, transmits the signal from the type I interferon receptor to the genome. We have discovered a novel phosphorylation of STAT2 on T387 that negatively regulates this response. In most untreated cell types, the majority of STAT2 is phosphorylated on T387 constitutively. In response to interferon-β, the T387A mutant of STAT2 is much more effective than wild-type STAT2 in mediating the expression of many interferon-stimulated genes, in protecting cells against virus infection, and in inhibiting cell growth. Interferon-β-tr...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Wang, Y., Nan, J., Willard, B., Wang, X., Yang, J., Stark, G. R. Tags: Signal Transduction Articles Source Type: research

Endothelial basement membrane laminin 511 is essential for shear stress response
Shear detection and mechanotransduction by arterial endothelium requires junctional complexes containing PECAM-1 and VE-cadherin, as well as firm anchorage to the underlying basement membrane. While considerable information is available for junctional complexes in these processes, gained largely from in vitro studies, little is known about the contribution of the endothelial basement membrane. Using resistance artery explants, we show that the integral endothelial basement membrane component, laminin 511 (laminin α5), is central to shear detection and mechanotransduction and its elimination at this site results ...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Di Russo, J., Luik, A.-L., Yousif, L., Budny, S., Oberleithner, H., Hofschröer, V., Klingauf, J., van Bavel, E., Bakker, E. N., Hellstrand, P., Bhattachariya, A., Albinsson, S., Pincet, F., Hallmann, R., Sorokin, L. M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Vascular Biology & Angiogenesis Articles Source Type: research

Hair follicle stem cell cultures reveal self-organizing plasticity of stem cells and their progeny
Understanding how complex tissues are formed, maintained, and regenerated through local growth, differentiation, and remodeling requires knowledge on how single-cell behaviors are coordinated on the population level. The self-renewing hair follicle, maintained by a distinct stem cell population, represents an excellent paradigm to address this question. A major obstacle in mechanistic understanding of hair follicle stem cell (HFSC) regulation has been the lack of a culture system that recapitulates HFSC behavior while allowing their precise monitoring and manipulation. Here, we establish an in vitro culture system bas...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Chacon-Martinez, C. A., Klose, M., Niemann, C., Glauche, I., Wickström, S. A. Tags: Development & Differentiation, Stem Cells, Systems & Computational Biology Articles Source Type: research

VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy
Rupture of endosomes and lysosomes is a major cellular stress condition leading to cell death and degeneration. Here, we identified an essential role for the ubiquitin-directed AAA-ATPase, p97, in the clearance of damaged lysosomes by autophagy. Upon damage, p97 translocates to lysosomes and there cooperates with a distinct set of cofactors including UBXD1, PLAA, and the deubiquitinating enzyme YOD1, which we term ELDR components for Endo-Lysosomal Damage Response. Together, they act downstream of K63-linked ubiquitination and p62 recruitment, and selectively remove K48-linked ubiquitin conjugates from a subpopulation of d...
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Papadopoulos, C., Kirchner, P., Bug, M., Grum, D., Koerver, L., Schulze, N., Poehler, R., Dressler, A., Fengler, S., Arhzaouy, K., Lux, V., Ehrmann, M., Weihl, C. C., Meyer, H. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Maintaining hair follicle stem cell identity in a dish
Identifying and mimicking the signals that regulate stem cell self-renewal, differentiation and maintenance in a petri dish is crucial to faithfully recapitulate stem cell behaviour in vitro. In this issue, Chacón-Martínez et al (2017) describe novel culture conditions that allow the long-term expansion and maintenance of functional murine hair follicle stem cells. This exciting discovery provides a faithful platform to study hair follicle stem cells in vitro and potentially perform drug screening for skin and hair follicle disorders. (Source: EMBO Journal)
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Sanchez-Danes, A., Blanpain, C. Tags: Development & Differentiation, Stem Cells, Systems & Computational Biology News [amp ] Views Source Type: research

Removing the waste bags: how p97 drives autophagy of lysosomes
Removal of ruptured lysosomes by autophagy is one of the mechanisms by which cells alleviate detrimental consequences of lysosome leakage and may prevent the initiation of signaling cascades that lead to cell death. In this issue of The EMBO Journal, Papadopoulos et al (2017) report an essential role of p97 and its cofactors in autophagic clearance of damaged lysosomes and provide evidences for the relevance of p97 in neurodegenerative conditions. (Source: EMBO Journal)
Source: EMBO Journal - January 16, 2017 Category: Molecular Biology Authors: Seczynska, M., Dikic, I. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Aryl hydrocarbon receptor is required for optimal B-cell proliferation
The aryl hydrocarbon receptor (AhR), a transcription factor known for mediating xenobiotic toxicity, is expressed in B cells, which are known targets for environmental pollutants. However, it is unclear what the physiological functions of AhR in B cells are. We show here that expression of Ahr in B cells is up-regulated upon B-cell receptor (BCR) engagement and IL-4 treatment. Addition of a natural ligand of AhR, FICZ, induces AhR translocation to the nucleus and transcription of the AhR target gene Cyp1a1, showing that the AhR pathway is functional in B cells. AhR-deficient (Ahr–/–) B cells proliferate less th...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Villa, M., Gialitakis, M., Tolaini, M., Ahlfors, H., Henderson, C. J., Wolf, C. R., Brink, R., Stockinger, B. Tags: Immunology Articles Source Type: research

IL-1 signaling is critical for expansion but not generation of autoreactive GM-CSF+ Th17 cells
Interleukin-1 (IL-1) is implicated in numerous pathologies, including multiple sclerosis and its animal model experimental autoimmune encephalomyelitis (EAE). However, the exact mechanism by which IL-1 is involved in the generation of pathogenic T cells and in disease development remains largely unknown. We found that following EAE induction, pertussis toxin administration leads to IL-1 receptor type 1 (IL-1R1)-dependent IL-1β expression by myeloid cells in the draining lymph nodes. This myeloid-derived IL-1β did not vitally contribute to the generation and plasticity of Th17 cells, but rather promoted the expans...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Mufazalov, I. A., Schelmbauer, C., Regen, T., Kuschmann, J., Wanke, F., Gabriel, L. A., Hauptmann, J., Müller, W., Pinteaux, E., Kurschus, F. C., Waisman, A. Tags: Immunology Articles Source Type: research

Stabilization of the metaphase spindle by Cdc14 is required for recombinational DNA repair
Cells are constantly threatened by multiple sources of genotoxic stress that cause DNA damage. To maintain genome integrity, cells have developed a coordinated signalling network called DNA damage response (DDR). While multiple kinases have been thoroughly studied during DDR activation, the role of protein dephosphorylation in the damage response remains elusive. Here, we show that the phosphatase Cdc14 is essential to fulfil recombinational DNA repair in budding yeast. After DNA double-strand break (DSB) generation, Cdc14 is transiently released from the nucleolus and activated. In this state, Cdc14 targets the spindle po...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Villoria, M. T., Ramos, F., Duenas, E., Faull, P., Cutillas, P. R., Clemente-Blanco, A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

Gata6 promotes hair follicle progenitor cell renewal by genome maintenance during proliferation
Cell proliferation is essential to rapid tissue growth and repair, but can result in replication-associated genome damage. Here, we implicate the transcription factor Gata6 in adult mouse hair follicle regeneration where it controls the renewal of rapidly proliferating epithelial (matrix) progenitors and hence the extent of production of terminally differentiated lineages. We find that Gata6 protects against DNA damage associated with proliferation, thus preventing cell cycle arrest and apoptosis. Furthermore, we show that in vivo Gata6 stimulates EDA-receptor signaling adaptor Edaradd level and NF-B pathway activatio...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Wang, A. B., Zhang, Y. V., Tumbar, T. Tags: Development & Differentiation, DNA Replication, Repair & Recombination, Stem Cells Articles Source Type: research

Dedicated SNAREs and specialized TRIM cargo receptors mediate secretory autophagy
Autophagy is a process delivering cytoplasmic components to lysosomes for degradation. Autophagy may, however, play a role in unconventional secretion of leaderless cytosolic proteins. How secretory autophagy diverges from degradative autophagy remains unclear. Here we show that in response to lysosomal damage, the prototypical cytosolic secretory autophagy cargo IL-1β is recognized by specialized secretory autophagy cargo receptor TRIM16 and that this receptor interacts with the R-SNARE Sec22b to recruit cargo to the LC3-II+ sequestration membranes. Cargo secretion is unaffected by downregulation of syntaxin 17, a SN...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Kimura, T., Jia, J., Kumar, S., Choi, S. W., Gu, Y., Mudd, M., Dupont, N., Jiang, S., Peters, R., Farzam, F., Jain, A., Lidke, K. A., Adams, C. M., Johansen, T., Deretic, V. Tags: Autophagy & Cell Death, Immunology, Membrane & Intracellular Transport Articles Source Type: research

Polarized cortical tension drives zebrafish epiboly movements
The principles underlying the biomechanics of morphogenesis are largely unknown. Epiboly is an essential embryonic event in which three tissues coordinate to direct the expansion of the blastoderm. How and where forces are generated during epiboly, and how these are globally coupled remains elusive. Here we developed a method, hydrodynamic regression (HR), to infer 3D pressure fields, mechanical power, and cortical surface tension profiles. HR is based on velocity measurements retrieved from 2D+T microscopy and their hydrodynamic modeling. We applied HR to identify biomechanically active structures and changes in cortex lo...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Hernandez-Vega, A., Marsal, M., Pouille, P.-A., Tosi, S., Colombelli, J., Luque, T., Navajas, D., Pagonabarraga, I., Martin-Blanco, E. Tags: Development & Differentiation, Systems & Computational Biology Articles Source Type: research

Prostaglandin E2 promotes intestinal repair through an adaptive cellular response of the epithelium
Adaptive cellular responses are often required during wound repair. Following disruption of the intestinal epithelium, wound-associated epithelial (WAE) cells form the initial barrier over the wound. Our goal was to determine the critical factor that promotes WAE cell differentiation. Using an adaptation of our in vitro primary epithelial cell culture system, we found that prostaglandin E2 (PGE2) signaling through one of its receptors, Ptger4, was sufficient to drive a differentiation state morphologically and transcriptionally similar to in vivo WAE cells. WAE cell differentiation was a permanent state and domin...
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Miyoshi, H., VanDussen, K. L., Malvin, N. P., Ryu, S. H., Wang, Y., Sonnek, N. M., Lai, C.-W., Stappenbeck, T. S. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells Articles Source Type: research

The Wae to repair: prostaglandin E2 (PGE2) triggers intestinal wound repair
Accurate wound repair is a crucial step to protect organisms from environmental damage, for example infection and toxin exposure. In this issue of The EMBO Journal, Miyoshi et al (2017) have elucidated a new mechanism underpinning this process within the intestine where mesenchymal prostaglandin E2 produced following damage drives intestinal regeneration. (Source: EMBO Journal)
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Jackstadt, R., Sansom, O. J. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells News [amp ] Views Source Type: research

Stefan Jentsch (1955-2016)--Maestro of the ubiquitin family
(Source: EMBO Journal)
Source: EMBO Journal - January 3, 2017 Category: Molecular Biology Authors: Hoppe, T., Branzei, D. Tags: Obituary Source Type: research

Seipin regulates ER-lipid droplet contacts and cargo delivery
Seipin is an endoplasmic reticulum (ER) membrane protein implicated in lipid droplet (LD) biogenesis and mutated in severe congenital lipodystrophy (BSCL2). Here, we show that seipin is stably associated with nascent ER–LD contacts in human cells, typically via one mobile focal point per LD. Seipin appears critical for such contacts since ER–LD contacts were completely missing or morphologically aberrant in seipin knockout and BSCL2 patient cells. In parallel, LD mobility was increased and protein delivery from the ER to LDs to promote LD growth was decreased. Moreover, while growing LDs normally acquire lipid ...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Salo, V. T., Belevich, I., Li, S., Karhinen, L., Vihinen, H., Vigouroux, C., Magre, J., Thiele, C., Hölttä-Vuori, M., Jokitalo, E., Ikonen, E. Tags: Membrane & Intracellular Transport Articles Source Type: research

Cohesin acetylation and Wapl-Pds5 oppositely regulate translocation of cohesin along DNA
This study provides insight into the nature of individual cohesin dynamics and the mechanisms by which cohesin achieves cohesion in different chromatin contexts. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Kanke, M., Tahara, E., Huis in't Veld, P. J., Nishiyama, T. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research