PSEUDO RESPONSE REGULATORs stabilize CONSTANS protein to promote flowering in response to day length
Seasonal reproduction in many organisms requires detection of day length. This is achieved by integrating information on the light environment with an internal photoperiodic time-keeping mechanism. Arabidopsis thaliana promotes flowering in response to long days (LDs), and CONSTANS (CO) transcription factor represents a photoperiodic timer whose stability is higher when plants are exposed to light under LDs. Here, we show that PSEUDO RESPONSE REGULATOR (PRR) proteins directly mediate this stabilization. PRRs interact with and stabilize CO at specific times during the day, thereby mediating its accumulation under LDs. PRR-m...
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Hayama, R., Sarid-Krebs, L., Richter, R., Fernandez, V., Jang, S., Coupland, G. Tags: Plant Biology, Post-translational Modifications, Proteolysis & Proteomics, Transcription Articles Source Type: research

GTPase ROP2 binds and promotes activation of target of rapamycin, TOR, in response to auxin
Target of rapamycin (TOR) promotes reinitiation at upstream ORFs (uORFs) in genes that play important roles in stem cell regulation and organogenesis in plants. Here, we report that the small GTPase ROP2, if activated by the phytohormone auxin, promotes activation of TOR, and thus translation reinitiation of uORF-containing mRNAs. Plants with high levels of active ROP2, including those expressing constitutively active ROP2 (CA-ROP2), contain high levels of active TOR. ROP2 physically interacts with and, when GTP-bound, activates TOR in vitro. TOR activation in response to auxin is abolished in ROP-deficient rop2 rop6 ...
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Schepetilnikov, M., Makarian, J., Srour, O., Geldreich, A., Yang, Z., Chicher, J., Hammann, P., Ryabova, L. A. Tags: Plant Biology, Protein Biosynthesis & Quality Control, Signal Transduction Articles Source Type: research

Id2 controls specification of Lgr5+ intestinal stem cell progenitors during gut development
The adult intestinal stem cells (ISCs), their hierarchies, mechanisms of maintenance and differentiation have been extensively studied. However, when and how ISCs are established during embryogenesis remains unknown. We show here that the transcription regulator Id2 controls the specification of embryonic Lgr5+ progenitors in the developing murine small intestine. Cell fate mapping analysis revealed that Lgr5+ progenitors emerge at E13.5 in wild-type embryos and differ from the rest on the intestinal epithelium by a characteristic ISC signature. In the absence of Id2, the intestinal epithelium differentiates into Lgr5+ cel...
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Nigmatullina, L., Norkin, M., Dzama, M. M., Messner, B., Sayols, S., Soshnikova, N. Tags: Development & Differentiation, Stem Cells Articles Source Type: research

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis
During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a clo...
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Malyutin, A. G., Musalgaonkar, S., Patchett, S., Frank, J., Johnson, A. W. Tags: Protein Biosynthesis & Quality Control, RNA Biology, Structural Biology Articles Source Type: research

Osteopontin attenuates aging-associated phenotypes of hematopoietic stem cells
Upon aging, hematopoietic stem cells (HSCs) undergo changes in function and structure, including skewing to myeloid lineages, lower reconstitution potential and loss of protein polarity. While stem cell intrinsic mechanisms are known to contribute to HSC aging, little is known on whether age-related changes in the bone marrow niche regulate HSC aging. Upon aging, the expression of osteopontin (OPN) in the murine bone marrow stroma is reduced. Exposure of young HSCs to an OPN knockout niche results in a decrease in engraftment, an increase in long-term HSC frequency and loss of stem cell polarity. Exposure of aged HSCs to t...
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Guidi, N., Sacma, M., Ständker, L., Soller, K., Marka, G., Eiwen, K., Weiss, J. M., Kirchhoff, F., Weil, T., Cancelas, J. A., Florian, M. C., Geiger, H. Tags: Ageing, Cell Adhesion, Polarity & Cytoskeleton, Stem Cells Articles Source Type: research

Everything has its time: Id2 clocks embryonic specification of Lgr5+ gut stem cells
While adult intestinal stem cells and their niche are well characterised, their developmental specification is still poorly understood. In this issue of The EMBO Journal, Nigmatullina et al (2017) show that maturation of Lgr5+ progenitors in the small intestinal epithelium during murine embryonic development is controlled by the transcription factor Id2. (Source: EMBO Journal)
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Kretzschmar, K., Clevers, H. Tags: Development & Differentiation, Stem Cells News [amp ] Views Source Type: research

Final touches and quality control on the assembly of the eukaryotic ribosome
One of the most fundamental processes of life is protein synthesis by the ribosome. Although much is known about the function and structure of this macromolecular complex, our understanding on its assembly is still vague. In this issue of The EMBO Journal, Malyutin et al (2017) provide a detailed picture of one of the latest assembly stages of the yeast 60S ribosomal subunit. The cryo-EM map of the 60S-Nmd3-Lsg1-Tif6 complex sheds new light on the function of Nmd3, Lsg1 and Tif6—and their release mechanisms—right before the 60S subunit joins the pool of actively translating ribosomes. (Source: EMBO Journal)
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Razi, A., Ortega, J. Tags: Protein Biosynthesis & Quality Control, RNA Biology, Structural Biology News [amp ] Views Source Type: research

Written in bone: young bone makes young blood
Ageing of bone marrow haematopoietic stem cells has been mostly associated with cell-intrinsic mechanisms. New findings published in The EMBO Journal now show that reduced levels of the secreted matrix protein osteopontin in old bone marrow stroma cause ageing-associated features in HSCs. In line, old HSCs are functionally rejuvenated by interaction with protease-cleaved osteopontin fragment, and perform like young blood stem cells in vivo. (Source: EMBO Journal)
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Gustafsson, K., Scadden, D. T. Tags: Ageing, Cell Adhesion, Polarity & Cytoskeleton, Stem Cells News [amp ] Views Source Type: research

Conformational change of syntaxin linker region induced by Munc13s initiates SNARE complex formation in synaptic exocytosis
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein syntaxin-1 adopts a closed conformation when bound to Munc18-1, preventing binding to synaptobrevin-2 and SNAP-25 to form the ternary SNARE complex. Although it is known that the MUN domain of Munc13-1 catalyzes the transition from the Munc18-1/syntaxin-1 complex to the SNARE complex, the molecular mechanism is unclear. Here, we identified two conserved residues (R151, I155) in the syntaxin-1 linker region as key sites for the MUN domain interaction. This interaction is essential for SNARE complex formation in vitro and synaptic ...
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Wang, S., Choi, U. B., Gong, J., Yang, X., Li, Y., Wang, A. L., Yang, X., Brunger, A. T., Ma, C. Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

Mitochondria control store-operated Ca2+ entry through Na+ and redox signals
Mitochondria exert important control over plasma membrane (PM) Orai1 channels mediating store-operated Ca2+ entry (SOCE). Although the sensing of endoplasmic reticulum (ER) Ca2+ stores by STIM proteins and coupling to Orai1 channels is well understood, how mitochondria communicate with Orai1 channels to regulate SOCE activation remains elusive. Here, we reveal that SOCE is accompanied by a rise in cytosolic Na+ that is critical in activating the mitochondrial Na+/Ca2+ exchanger (NCLX) causing enhanced mitochondrial Na+ uptake and Ca2+ efflux. Omission of extracellular Na+ prevents the cytosolic Na+ rise, inhibits NCLX acti...
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Ben-Kasus Nissim, T., Zhang, X., Elazar, A., Roy, S., Stolwijk, J. A., Zhou, Y., Motiani, R. K., Gueguinou, M., Hempel, N., Hershfinkel, M., Gill, D. L., Trebak, M., Sekler, I. Tags: Membrane & Intracellular Transport, Metabolism Articles Source Type: research

Hsp70 displaces small heat shock proteins from aggregates to initiate protein refolding
Small heat shock proteins (sHsps) are an evolutionary conserved class of ATP-independent chaperones that protect cells against proteotoxic stress. sHsps form assemblies with aggregation-prone misfolded proteins, which facilitates subsequent substrate solubilization and refolding by ATP-dependent Hsp70 and Hsp100 chaperones. Substrate solubilization requires disruption of sHsp association with trapped misfolded proteins. Here, we unravel a specific interplay between Hsp70 and sHsps at the initial step of the solubilization process. We show that Hsp70 displaces surface-bound sHsps from sHsp–substrate assemblies. This H...
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Zwirowski, S., Kłosowska, A., Obuchowski, I., Nillegoda, N. B., Pirog, A., Zietkiewicz, S., Bukau, B., Mogk, A., Liberek, K. Tags: Protein Biosynthesis & Quality Control Articles Source Type: research

Protein synthesis inhibition and GADD34 control IFN-{beta} heterogeneous expression in response to dsRNA
In innate immune responses, induction of type-I interferons (IFNs) prevents virus spreading while viral replication is delayed by protein synthesis inhibition. We asked how cells perform these apparently contradictory activities. Using single fibroblast monitoring by flow cytometry and mathematical modeling, we demonstrate that type-I IFN production is linked to cell's ability to enter dsRNA-activated PKR-dependent translational arrest and then overcome this inhibition by decreasing eIF2α phosphorylation through phosphatase 1c cofactor GADD34 (Ppp1r15a) expression. GADD34 expression, shown here to be dependent on the...
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Dalet, A., Argüello, R. J., Combes, A., Spinelli, L., Jaeger, S., Fallet, M., Vu Manh, T.-P., Mendes, A., Perego, J., Reverendo, M., Camosseto, V., Dalod, M., Weil, T., Santos, M. A., Gatti, E., Pierre, P. Tags: Immunology Articles Source Type: research

Paired Siglec receptors generate opposite inflammatory responses to a human-specific pathogen
Paired immune receptors display near-identical extracellular ligand-binding regions but have intracellular sequences with opposing signaling functions. While inhibitory receptors dampen cellular activation by recognizing self-associated molecules, the functions of activating counterparts are less clear. Here, we studied the inhibitory receptor Siglec-11 that shows uniquely human expression in brain microglia and engages endogenous polysialic acid to suppress inflammation. We demonstrated that the human-specific pathogen Escherichia coli K1 uses its polysialic acid capsule as a molecular mimic to engage Siglec-11 and escape...
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Schwarz, F., Landig, C. S., Siddiqui, S., Secundino, I., Olson, J., Varki, N., Nizet, V., Varki, A. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

ZRF1 is a novel S6 kinase substrate that drives the senescence programme
The inactivation of S6 kinases mimics several aspects of caloric restriction, including small body size, increased insulin sensitivity and longevity. However, the impact of S6 kinase activity on cellular senescence remains to be established. Here, we show that the constitutive activation of mammalian target of rapamycin complex 1 (mTORC1) by tuberous sclerosis complex (TSC) mutations induces a premature senescence programme in fibroblasts that relies on S6 kinases. To determine novel molecular targets linking S6 kinase activation to the control of senescence, we set up a chemical genetic screen, leading to the identificati...
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Barilari, M., Bonfils, G., Treins, C., Koka, V., De Villeneuve, D., Fabrega, S., Pende, M. Tags: Ageing, Autophagy & Cell Death, Signal Transduction Articles Source Type: research

Molecular role of the PAX5-ETV6 oncoprotein in promoting B-cell acute lymphoblastic leukemia
PAX5 is a tumor suppressor in B-ALL, while the role of PAX5 fusion proteins in B-ALL development is largely unknown. Here, we studied the function of PAX5-ETV6 and PAX5-FOXP1 in mice expressing these proteins from the Pax5 locus. Both proteins arrested B-lymphopoiesis at the pro-B to pre-B-cell transition and, contrary to their proposed dominant-negative role, did not interfere with the expression of most regulated Pax5 target genes. Pax5-Etv6, but not Pax5-Foxp1, cooperated with loss of the Cdkna2a/b tumor suppressors in promoting B-ALL development. Regulated Pax5-Etv6 target genes identified in these B-ALLs encode protei...
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Smeenk, L., Fischer, M., Jurado, S., Jaritz, M., Azaryan, A., Werner, B., Roth, M., Zuber, J., Stanulla, M., den Boer, M. L., Mullighan, C. G., Strehl, S., Busslinger, M. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, Immunology Articles Source Type: research

Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maize
In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops. (Source: EMBO Journal)
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Gilles, L. M., Khaled, A., Laffaire, J.-B., Chaignon, S., Gendrot, G., Laplaige, J., Berges, H., Beydon, G., Bayle, V., Barret, P., Comadran, J., Martinant, J.-P., Rogowsky, P. M., Widiez, T. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology Articles Source Type: research

Dangerous fusions: a path to cancer for arrested lymphoid progenitors
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a common malignancy associated with variable chromosomal translocations, leading to fusion proteins of unknown function. To investigate how such translocations contribute to the development of BCP-ALL , Smeenk et al (2017) generated mouse models for Pax5 fusion proteins. The results show that a PAX5 fusion is required for BCP-ALL development by preventing B-cell differentiation and retaining cells in an arrested progenitor stage. The occurrence of further genetic aberrations eventually results in oncogenic transformation and proliferation of the arrested cells...
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Alsadeq, A., Jumaa, H. Tags: Cancer, Immunology, Transcription News [amp ] Views Source Type: research

No sex please, we're (in)breeding
A genetic trick allows induction of haploid maize plants by a process known as gynogenesis, which is a useful tool for breeders. In this issue of The EMBO Journal, Gilles et al (2017) show that loss of function of a patatin-like phospholipase A underlies the induction of gynogenesis, findings that were also made in two other recent studies (Kelliher et al, 2017; Liu et al, 2017). (Source: EMBO Journal)
Source: EMBO Journal - March 15, 2017 Category: Molecular Biology Authors: Jackson, D. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology News [amp ] Views Source Type: research

Cytosolic thioredoxin reductase 1 is required for correct disulfide formation in the ER
Folding of proteins entering the secretory pathway in mammalian cells frequently requires the insertion of disulfide bonds. Disulfide insertion can result in covalent linkages found in the native structure as well as those that are not, so-called non-native disulfides. The pathways for disulfide formation are well characterized, but our understanding of how non-native disulfides are reduced so that the correct or native disulfides can form is poor. Here, we use a novel assay to demonstrate that the reduction in non-native disulfides requires NADPH as the ultimate electron donor, and a robust cytosolic thioredoxin system, d...
Source: EMBO Journal - March 1, 2017 Category: Molecular Biology Authors: Poet, G. J., Oka, O. B., van Lith, M., Cao, Z., Robinson, P. J., Pringle, M. A., Arner, E. S., Bulleid, N. J. Tags: Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control Articles Source Type: research

Structural intermediates in the fusion-associated transition of vesiculovirus glycoprotein
Vesiculoviruses enter cells by membrane fusion, driven by a large, low-pH-induced, conformational change in the fusion glycoprotein G that involves transition from a trimeric pre-fusion toward a trimeric post-fusion state via monomeric intermediates. Here, we present the structure of the G fusion protein at intermediate pH for two vesiculoviruses, vesicular stomatitis virus (VSV) and Chandipura virus (CHAV), which is responsible for deadly encephalopathies. First, a CHAV G crystal structure shows two intermediate conformations forming a flat dimer of heterodimers. On virions, electron microscopy (EM) and tomography reveal ...
Source: EMBO Journal - March 1, 2017 Category: Molecular Biology Authors: Baquero, E., Albertini, A. A., Raux, H., Abou-Hamdan, A., Boeri-Erba, E., Ouldali, M., Buonocore, L., Rose, J. K., Lepault, J., Bressanelli, S., Gaudin, Y. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis
DNA repair by homologous recombination is under stringent cell cycle control. This includes the last step of the reaction, disentanglement of DNA joint molecules (JMs). Previous work has established that JM resolving nucleases are activated specifically at the onset of mitosis. In case of budding yeast Mus81-Mms4, this cell cycle stage-specific activation is known to depend on phosphorylation by CDK and Cdc5 kinases. Here, we show that a third cell cycle kinase, Cdc7-Dbf4 (DDK), targets Mus81-Mms4 in conjunction with Cdc5—both kinases bind to as well as phosphorylate Mus81-Mms4 in an interdependent manner. Moreover, ...
Source: EMBO Journal - March 1, 2017 Category: Molecular Biology Authors: Princz, L. N., Wild, P., Bittmann, J., Aguado, F. J., Blanco, M. G., Matos, J., Pfander, B. Tags: Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

Discrete cytosolic macromolecular BRAF complexes exhibit distinct activities and composition
As a central element within the RAS/ERK pathway, the serine/threonine kinase BRAF plays a key role in development and homeostasis and represents the most frequently mutated kinase in tumors. Consequently, it has emerged as an important therapeutic target in various malignancies. Nevertheless, the BRAF activation cycle still raises many mechanistic questions as illustrated by the paradoxical action and side effects of RAF inhibitors. By applying SEC-PCP-SILAC, we analyzed protein–protein interactions of hyperactive BRAFV600E and wild-type BRAF (BRAFWT). We identified two macromolecular, cytosolic BRAF complexes of dis...
Source: EMBO Journal - March 1, 2017 Category: Molecular Biology Authors: Diedrich, B., Rigbolt, K. T., Röring, M., Herr, R., Kaeser-Pebernard, S., Gretzmeier, C., Murphy, R. F., Brummer, T., Dengjel, J. Tags: Molecular Biology of Disease, Signal Transduction Articles Source Type: research

Conformational equilibria and intrinsic affinities define integrin activation
We show that the three conformational states of integrin α5β1 have discrete free energies and define activation by measuring intrinsic affinities for ligand of each state and the equilibria linking them. The 5,000-fold higher affinity of the extended-open state than the bent-closed and extended-closed states demonstrates profound regulation of affinity. Free energy requirements for activation are defined with protein fragments and intact α5β1. On the surface of K562 cells, α5β1 is 99.8% bent-closed. Stabilization of the bent conformation by integrin transmembrane and cytoplasmic domains mus...
Source: EMBO Journal - March 1, 2017 Category: Molecular Biology Authors: Li, J., Su, Y., Xia, W., Qin, Y., Humphries, M. J., Vestweber, D., Cabanas, C., Lu, C., Springer, T. A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Structural Biology Articles Source Type: research

DNA sequence properties that predict susceptibility to epiallelic switching
Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles,...
Source: EMBO Journal - March 1, 2017 Category: Molecular Biology Authors: Catoni, M., Griffiths, J., Becker, C., Zabet, N. R., Bayon, C., Dapp, M., Lieberman-Lazarovich, M., Weigel, D., Paszkowski, J. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology Articles Source Type: research

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 - March 1, 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 - March 1, 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 - March 1, 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 - March 1, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 15, 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 - February 1, 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 - February 1, 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 - February 1, 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 - February 1, 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 - February 1, 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 - February 1, 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 - February 1, 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 - February 1, 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