Bax assembles into large ring-like structures remodeling the mitochondrial outer membrane in apoptosis
The Bcl-2 family proteins Bax and Bak are essential for the execution of many apoptotic programs. During apoptosis, Bax translocates to the mitochondria and mediates the permeabilization of the outer membrane, thereby facilitating the release of pro-apoptotic proteins. Yet the mechanistic details of the Bax-induced membrane permeabilization have so far remained elusive. Here, we demonstrate that activated Bax molecules, besides forming large and compact clusters, also assemble, potentially with other proteins including Bak, into ring-like structures in the mitochondrial outer membrane. STED nanoscopy indicates that the are...
Source: EMBO Journal - February 14, 2016 Category: Molecular Biology Authors: Grosse, L., Wurm, C. A., Brüser, C., Neumann, D., Jans, D. C., Jakobs, S. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

Bax assembly into rings and arcs in apoptotic mitochondria is linked to membrane pores
Bax is a key regulator of apoptosis that, under cell stress, accumulates at mitochondria, where it oligomerizes to mediate the permeabilization of the mitochondrial outer membrane leading to cytochrome c release and cell death. However, the underlying mechanism behind Bax function remains poorly understood. Here, we studied the spatial organization of Bax in apoptotic cells using dual-color single-molecule localization-based super-resolution microscopy. We show that active Bax clustered into a broad distribution of distinct architectures, including full rings, as well as linear and arc-shaped oligomeric assemblies that loc...
Source: EMBO Journal - February 14, 2016 Category: Molecular Biology Authors: Salvador-Gallego, R., Mund, M., Cosentino, K., Schneider, J., Unsay, J., Schraermeyer, U., Engelhardt, J., Ries, J., Garcia-Saez, A. J. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

Touch, act and go: landing and operating on nucleosomes
Chromatin-associated enzymes are responsible for the installation, removal and reading of precise post-translation modifications on DNA and histone proteins. They are specifically recruited to the target gene by associated factors, and as a result of their activity, they contribute in modulating cell identity and differentiation. Structural and biophysical approaches are broadening our knowledge on these processes, demonstrating that DNA, histone tails and histone surfaces can each function as distinct yet functionally interconnected anchoring points promoting nucleosome binding and modification. The mechanisms underlying ...
Source: EMBO Journal - February 14, 2016 Category: Molecular Biology Authors: Speranzini, V., Pilotto, S., Sixma, T. K., Mattevi, A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Structural Biology, Transcription Review Source Type: research

In need of good neighbours: transcription factors require local DNA hypomethylation for target binding
Whether and how DNA methylation influences the binding of transcription factors (TFs) to their corresponding DNA sequence motifs in vivo remains largely unresolved. In a recent publication, Schübeler and co-workers (Domcke et al, 2015) identify a few methylation-restricted TFs in mouse embryonic stem cells, including NRF1. The authors show that NRF1 binding to its motif can be outcompeted by de novo DNA methylation, suggesting that methylation-sensitive TFs rely on neighbouring motifs in cis—bound by pioneer TFs—to ensure local hypomethylation. (Source: EMBO Journal)
Source: EMBO Journal - February 14, 2016 Category: Molecular Biology Authors: Karemaker, I. D., Vermeulen, M. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription News [amp ] Views Source Type: research

Doughnuts, daisy chains and crescent moons: the quest for the elusive apoptotic pore
How the two killer proteins Bax and Bak form the putative "apoptotic pore" that is responsible for irrevocably damaging mitochondria leading to cell death during apoptosis is considered the "holy grail" of apoptosis research. Indeed, even whether Bax and Bak form a pore remains contentious largely due to the failure to detect such structures in cells or mitochondria. Two new super-resolution microscopy studies in this issue of The EMBO Journal now provide tantalising evidence of ring-like "apoptotic pores" on mitochondria of dying cells and provide new insight into how Bax and Bak bring about ...
Source: EMBO Journal - February 14, 2016 Category: Molecular Biology Authors: Dewson, G. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Structural Biology News [amp ] Views Source Type: research

The adaptor protein p40phox as a positive regulator of the superoxide-producing phagocyte oxidase
(Source: EMBO Journal)
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Kuribayashi, F., Nunoi, H., Wakamatsu, K., Tsunawaki, S., Sato, K., Ito, T., Sumimoto, H. Tags: Corrigendum Source Type: research

Convergence of cMyc and {beta}-catenin on Tcf7l1 enables endoderm specification
The molecular machinery that directs formation of definitive endoderm from pluripotent stem cells is not well understood. Wnt/β-catenin and Nodal signalling have been implicated, but the requirements for lineage specification remain incompletely defined. Here, we demonstrate a potent effect of inhibiting glycogen synthase kinase 3 (GSK3) on definitive endoderm production. We find that downstream of GSK3 inhibition, elevated cMyc and β-catenin act in parallel to reduce transcription and DNA binding, respectively, of the transcriptional repressor Tcf7l1. Tcf7l1 represses FoxA2, a pioneer factor for endoderm specifi...
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Morrison, G., Scognamiglio, R., Trumpp, A., Smith, A. Tags: Development & Differentiation Articles Source Type: research

TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing
Intragenic 5-methylcytosine and CTCF mediate opposing effects on pre-mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5-methylcytosine evicts CTCF, leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF-binding sites were unclear. Here, we reveal the methylcytosine dioxygenases TET1 and TET2 as active regulators of CTCF-mediated alternative splicing through conversion of 5-methylcytosine to its oxidation derivatives. 5-hydroxymethylcytosine and 5-carboxylcytosine are enriched at an intragenic CTCF-binding sites in the CD45&nb...
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Marina, R. J., Sturgill, D., Bailly, M. A., Thenoz, M., Varma, G., Prigge, M. F., Nanan, K. K., Shukla, S., Haque, N., Oberdoerffer, S. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, RNA Biology, Transcription Articles Source Type: research

Targeted redox inhibition of protein phosphatase 1 by Nox4 regulates eIF2{alpha}-mediated stress signaling
Phosphorylation of translation initiation factor 2α (eIF2α) attenuates global protein synthesis but enhances translation of activating transcription factor 4 (ATF4) and is a crucial evolutionarily conserved adaptive pathway during cellular stresses. The serine–threonine protein phosphatase 1 (PP1) deactivates this pathway whereas prolonging eIF2α phosphorylation enhances cell survival. Here, we show that the reactive oxygen species-generating NADPH oxidase-4 (Nox4) is induced downstream of ATF4, binds to a PP1-targeting subunit GADD34 at the endoplasmic reticulum, and inhibits PP1 activity to increa...
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Santos, C. X., Hafstad, A. D., Beretta, M., Zhang, M., Molenaar, C., Kopec, J., Fotinou, D., Murray, T. V., Cobb, A. M., Martin, D., Zeh Silva, M., Anilkumar, N., Schröder, K., Shanahan, C. M., Brewer, A. C., Brandes, R. P., Blanc, E., Parsons, M. Tags: Autophagy & Cell Death, Signal Transduction, Structural Biology Articles Source Type: research

Microtubule-binding protein doublecortin-like kinase 1 (DCLK1) guides kinesin-3-mediated cargo transport to dendrites
In neurons, the polarized distribution of vesicles and other cellular materials is established through molecular motors that steer selective transport between axons and dendrites. It is currently unclear whether interactions between kinesin motors and microtubule-binding proteins can steer polarized transport. By screening all 45 kinesin family members, we systematically addressed which kinesin motors can translocate cargo in living cells and drive polarized transport in hippocampal neurons. While the majority of kinesin motors transport cargo selectively into axons, we identified five members of the kinesin-3 (KIF1) and k...
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Lipka, J., Kapitein, L. C., Jaworski, J., Hoogenraad, C. C. Tags: Cell Adhesion, Polarity & Cytoskeleton, Neuroscience Articles Source Type: research

TBC1D14 regulates autophagy via the TRAPP complex and ATG9 traffic
In this study, we identify the TRAPP complex, a multi-subunit tethering complex and GEF for RAB1, as an interactor of TBC1D14. TBC1D14 binds to the TRAPP complex via an N-terminal 103 amino acid region, and overexpression of this region inhibits both autophagy and secretory traffic. TRAPPC8, the mammalian orthologue of a yeast autophagy-specific TRAPP subunit, forms part of a mammalian TRAPPIII-like complex and both this complex and TBC1D14 are needed for RAB1 activation. TRAPPC8 modulates autophagy and secretory trafficking and is required for TBC1D14 to bind TRAPPIII. Importantly, TBC1D14 and TRAPPIII regulate ATG9 traff...
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Lamb, C. A., Nühlen, S., Judith, D., Frith, D., Snijders, A. P., Behrends, C., Tooze, S. A. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

Nanoscale organization and dynamics of the siglec CD22 cooperate with the cytoskeleton in restraining BCR signalling
Receptor organization and dynamics at the cell membrane are important factors of signal transduction regulation. Using super-resolution microscopy and single-particle tracking, we show how the negative coreceptor CD22 works with the cortical cytoskeleton in restraining BCR signalling. In naïve B cells, we found endogenous CD22 to be highly mobile and organized into nanodomains. The landscape of CD22 and its lateral diffusion were perturbed either in the absence of CD45 or when the CD22 lectin domain was mutated. To understand how a relatively low number of CD22 molecules can keep BCR signalling in check, we generated Bro...
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Gasparrini, F., Feest, C., Bruckbauer, A., Mattila, P. K., Müller, J., Nitschke, L., Bray, D., Batista, F. D. Tags: Immunology, Signal Transduction Articles Source Type: research

Astrocytes as secretory cells of the central nervous system: idiosyncrasies of vesicular secretion
Astrocytes are housekeepers of the central nervous system (CNS) and are important for CNS development, homeostasis and defence. They communicate with neurones and other glial cells through the release of signalling molecules. Astrocytes secrete a wide array of classic neurotransmitters, neuromodulators and hormones, as well as metabolic, trophic and plastic factors, all of which contribute to the gliocrine system. The release of neuroactive substances from astrocytes occurs through several distinct pathways that include diffusion through plasmalemmal channels, translocation by multiple transporters and regulated exocytosis...
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Verkhratsky, A., Matteoli, M., Parpura, V., Mothet, J.-P., Zorec, R. Tags: Membrane & Intracellular Transport, Neuroscience Review Source Type: research

Agile CD22 nanoclusters run rings around fenced BCR
B lymphocytes are key players in host defence, but also autoimmune diseases. Their survival depends upon tonic signals transduced by surface immunoglobulin (BCR) and the process leading to antibody secretion is initiated by interaction of BCR with a cognate antigen. CD22 limits signalling of the BCR to strike a balance between tonic signalling, reactivity to pathogens and prevention of autoimmunity. In this issue, Gasparrini et al (2016) combined super-resolution imaging approaches with single-particle tracking and simulations to show how CD22 controls the signalling state of the BCR. They demonstrated that small CD22...
Source: EMBO Journal - January 31, 2016 Category: Molecular Biology Authors: Depoil, D., Dustin, M. L. Tags: Immunology, Signal Transduction News [amp ] Views Source Type: research

BH3-in-groove dimerization initiates and helix 9 dimerization expands Bax pore assembly in membranes
Pro-apoptotic Bax induces mitochondrial outer membrane permeabilization (MOMP) by forming oligomers through a largely undefined process. Using site-specific disulfide crosslinking, compartment-specific chemical labeling, and mutational analysis, we found that activated integral membrane Bax proteins form a BH3-in-groove dimer interface on the MOM surface similar to that observed in crystals. However, after the α5 helix was released into the MOM, the remaining interface with α2, α3, and α4 helices was rearranged. Another dimer interface was formed inside the MOM by two intersected or parallel α...
Source: EMBO Journal - January 17, 2016 Category: Molecular Biology Authors: Zhang, Z., Subramaniam, S., Kale, J., Liao, C., Huang, B., Brahmbhatt, H., Condon, S. G., Lapolla, S. M., Hays, F. A., Ding, J., He, F., Zhang, X. C., Li, J., Senes, A., Andrews, D. W., Lin, J. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Structural Biology Articles Source Type: research

Subtelomeric p53 binding prevents accumulation of DNA damage at human telomeres
Telomeres and tumor suppressor protein TP53 (p53) function in genome protection, but a direct role of p53 at telomeres has not yet been described. Here, we have identified non-canonical p53-binding sites within the human subtelomeres that suppress the accumulation of DNA damage at telomeric repeat DNA. These non-canonical subtelomeric p53-binding sites conferred transcription enhancer-like functions that include an increase in local histone H3K9 and H3K27 acetylation and stimulation of subtelomeric transcripts, including telomere repeat-containing RNA (TERRA). p53 suppressed formation of telomere-associated H2AX and preven...
Source: EMBO Journal - January 17, 2016 Category: Molecular Biology Authors: Tutton, S., Azzam, G. A., Stong, N., Vladimirova, O., Wiedmer, A., Monteith, J. A., Beishline, K., Wang, Z., Deng, Z., Riethman, H., McMahon, S. B., Murphy, M., Lieberman, P. M. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation
During DNA replication, thousands of replication origins are activated across the genome. Chromatin architecture contributes to origin specification and usage, yet it remains unclear which chromatin features impact on DNA replication. Here, we perform a RNAi screen for chromatin regulators implicated in replication control by measuring RPA accumulation upon replication stress. We identify six factors required for normal rates of DNA replication and characterize a function of the bromodomain and PHD finger-containing protein 3 (BRPF3) in replication initiation. BRPF3 forms a complex with HBO1 that specifically acetylates hi...
Source: EMBO Journal - January 17, 2016 Category: Molecular Biology Authors: Feng, Y., Vlassis, A., Roques, C., Lalonde, M.-E., Gonzalez-Aguilera, C., Lambert, J.-P., Lee, S.-B., Zhao, X., Alabert, C., Johansen, J. V., Paquet, E., Yang, X.-J., Gingras, A.-C., Cote, J., Groth, A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory
In nature, plants often encounter chronic or recurring stressful conditions. Recent results indicate that plants can remember a past exposure to stress to be better prepared for a future stress incident. However, the molecular basis of this is poorly understood. Here, we report the involvement of chromatin modifications in the maintenance of acquired thermotolerance (heat stress [HS] memory). HS memory is associated with the accumulation of histone H3 lysine 4 di- and trimethylation at memory-related loci. This accumulation outlasts their transcriptional activity and marks them as recently transcriptionally active. High ac...
Source: EMBO Journal - January 17, 2016 Category: Molecular Biology Authors: Lämke, J., Brzezinka, K., Altmann, S., Bäurle, I. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Physiology, Plant Biology Articles Source Type: research

Activation loop phosphorylation regulates B-Raf in vivo and transformation by B-Raf mutants
Despite being mutated in cancer and RASopathies, the role of the activation segment (AS) has not been addressed for B-Raf signaling in vivo. Here, we generated a conditional knock-in mouse allowing the expression of the B-RafAVKA mutant in which the AS phosphoacceptor sites T599 and S602 are replaced by alanine residues. Surprisingly, despite producing a kinase-impaired protein, the BrafAVKA allele does not phenocopy the lethality of Braf-knockout or paradoxically acting knock-in alleles. However, BrafAVKA mice display abnormalities in the hematopoietic system, a distinct facial morphology, reduced ERK pathway activit...
Source: EMBO Journal - January 17, 2016 Category: Molecular Biology Authors: Köhler, M., Röring, M., Schorch, B., Heilmann, K., Stickel, N., Fiala, G. J., Schmitt, L. C., Braun, S., Ehrenfeld, S., Uhl, F. M., Kaltenbacher, T., Weinberg, F., Herzog, S., Zeiser, R., Schamel, W. W., Jumaa, H., Brummer, T. Tags: Cancer, Signal Transduction Articles Source Type: research

TDP-43 loss of function increases TFEB activity and blocks autophagosome-lysosome fusion
In this study, we found that loss of TDP-43 strongly induced a nuclear translocation of TFEB, the master regulator of lysosomal biogenesis and autophagy, through targeting the mTORC1 key component raptor. This regulation in turn enhanced global gene expressions in the autophagy–lysosome pathway (ALP) and increased autophagosomal and lysosomal biogenesis. However, loss of TDP-43 also impaired the fusion of autophagosomes with lysosomes through dynactin 1 downregulation, leading to accumulation of immature autophagic vesicles and overwhelmed ALP function. Importantly, inhibition of mTORC1 signaling by rapamycin treatme...
Source: EMBO Journal - January 17, 2016 Category: Molecular Biology Authors: Xia, Q., Wang, H., Hao, Z., Fu, C., Hu, Q., Gao, F., Ren, H., Chen, D., Han, J., Ying, Z., Wang, G. Tags: Autophagy & Cell Death, Neuroscience, RNA Biology Articles Source Type: research

Knock-in(g) RAF for a loop
Phosphorylation of the activation loop in RAF kinases has been suggested to be critical for changes in activity. The extent to which the activation segment is phosphorylated, the specific structural consequences, and the in vivo relevance have however remained elusive. In this issue of the The EMBO Journal, Köhler et al (2015) addressed these questions by generating a knock-in mouse expressing a B-Raf mutant with a non-phosphorylatable activation loop. The mutant causes a range of developmental phenotypes; intriguingly, it also impairs the tumorigenic potential of a subset of BRAF mutants, suggesting potential ...
Source: EMBO Journal - January 17, 2016 Category: Molecular Biology Authors: Varga, A., Baccarini, M. Tags: Cancer, Signal Transduction News [amp ] Views Source Type: research

Absence of TDP-43 is difficult to digest
It is well established that TDP-43 accumulates in degenerating neurons in patients with ALS/FTLD, which might affect normal TDP-43 function. In this issue of The EMBO Journal Xia et al (2016) show a novel connection between TDP-43 loss of function and autophagy failure. Using knockdown models of TDP-43, they observed enhanced autophagosome and lysosome biogenesis through mTORC1 activity inhibition and TFEB activation. Impaired autophagosome–lysosome fusion was also observed, however in an mTORC1-independent manner. The data identify dysfunctions at multiple stages of the autophagic pathway following TDP-43 deple...
Source: EMBO Journal - January 17, 2016 Category: Molecular Biology Authors: Skoko, N., Baralle, M., Baralle, F. E. Tags: Autophagy & Cell Death, Neuroscience, RNA Biology News [amp ] Views Source Type: research

A novel family of fluorescent hypoxia sensors reveal strong heterogeneity in tumor hypoxia at the cellular level
Hypoxia is an intensively investigated condition with profound effects on cell metabolism, migration, and angiogenesis during development and disease. Physiologically, hypoxia is linked to tissue homeostasis and maintenance of pluripotency. Hypoxia also contributes to pathologies including cardiovascular diseases and cancer. Despite its importance, microscopic visualization of hypoxia is largely restricted to the detection of reductively activated probes by immunostaining. Here, we describe a novel family of genetically encoded fluorescent sensors that detect the activation of HIF transcription factors reported by the...
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Erapaneedi, R., Belousov, V. V., Schäfers, M., Kiefer, F. Tags: Vascular Biology & Angiogenesis Resource Source Type: research

Gatekeeper role of brain antigen-presenting CD11c+ cells in neuroinflammation
Multiple sclerosis is the most frequent chronic inflammatory disease of the CNS. The entry and survival of pathogenic T cells in the CNS are crucial for the initiation and persistence of autoimmune neuroinflammation. In this respect, contradictory evidence exists on the role of the most potent type of antigen-presenting cells, dendritic cells. Applying intravital two-photon microscopy, we demonstrate the gatekeeper function of CNS professional antigen-presenting CD11c+ cells, which preferentially interact with Th17 cells. IL-17 expression correlates with expression of GM-CSF by T cells and with accumulation of CNS CD11c+ c...
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Paterka, M., Siffrin, V., Voss, J. O., Werr, J., Hoppmann, N., Gollan, R., Belikan, P., Bruttger, J., Birkenstock, J., Jung, S., Esplugues, E., Yogev, N., Flavell, R. A., Bopp, T., Zipp, F. Tags: Immunology, Neuroscience Articles Source Type: research

Fundamental physical cellular constraints drive self-organization of tissues
Morphogenesis is driven by small cell shape changes that modulate tissue organization. Apical surfaces of proliferating epithelial sheets have been particularly well studied. Currently, it is accepted that a stereotyped distribution of cellular polygons is conserved in proliferating tissues among metazoans. In this work, we challenge these previous findings showing that diverse natural packed tissues have very different polygon distributions. We use Voronoi tessellations as a mathematical framework that predicts this diversity. We demonstrate that Voronoi tessellations and the very different tissues analysed share an overr...
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Sanchez-Gutierrez, D., Tozluoglu, M., Barry, J. D., Pascual, A., Mao, Y., Escudero, L. M. Tags: Development & Differentiation Articles Source Type: research

PTPRN2 and PLC{beta}1 promote metastatic breast cancer cell migration through PI(4,5)P2-dependent actin remodeling
Altered abundance of phosphatidyl inositides (PIs) is a feature of cancer. Various PIs mark the identity of diverse membranes in normal and malignant cells. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) resides predominantly in the plasma membrane, where it regulates cellular processes by recruiting, activating, or inhibiting proteins at the plasma membrane. We find that PTPRN2 and PLCβ1 enzymatically reduce plasma membrane PI(4,5)P2 levels in metastatic breast cancer cells through two independent mechanisms. These genes are upregulated in highly metastatic breast cancer cells, and their increased expression assoc...
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Sengelaub, C. A., Navrazhina, K., Ross, J. B., Halberg, N., Tavazoie, S. F. Tags: Cancer, Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

Danger peptide receptor signaling in plants ensures basal immunity upon pathogen-induced depletion of BAK1
We report that BAK1 depletion is linked to defense activation through the endogenous PROPEP peptides (Pep epitopes) and their LRR receptor kinases PEPR1/PEPR2, despite critical defects in MAMP signaling. In bak1-knockout plants, PEPR elicitation results in extensive cell death and the prioritization of salicylate-based defenses over jasmonate-based defenses, in addition to elevated proligand and receptor accumulation. BAK1 disruption stimulates the release of PROPEP3, produced in response to Pep application and during pathogen challenge, and renders PEPRs necessary for basal resistance. These findings are biologically rele...
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Yamada, K., Yamashita-Yamada, M., Hirase, T., Fujiwara, T., Tsuda, K., Hiruma, K., Saijo, Y. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction, Plant Biology Articles Source Type: research

NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program
Cell fate specification relies on the action of critical transcription factors that become available at distinct stages of embryonic development. One such factor is NeuroD1, which is essential for eliciting the neuronal development program and possesses the ability to reprogram other cell types into neurons. Given this capacity, it is important to understand its targets and the mechanism underlying neuronal specification. Here, we show that NeuroD1 directly binds regulatory elements of neuronal genes that are developmentally silenced by epigenetic mechanisms. This targeting is sufficient to initiate events that confer tran...
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Pataskar, A., Jung, J., Smialowski, P., Noack, F., Calegari, F., Straub, T., Tiwari, V. K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Neuroscience, Transcription Articles Source Type: research

Spatiotemporal regulation of posttranslational modifications in the DNA damage response
A timely and accurate cellular response to DNA damage requires tight regulation of the action of DNA damage response (DDR) proteins at lesions. A multitude of posttranslational modifications (PTMs) of chromatin and chromatin-associated proteins coordinates the recruitment of critical proteins that dictate the appropriate DNA repair pathway and enable the actual repair of lesions. Phosphorylation, ubiquitylation, SUMOylation, neddylation, poly(ADP-ribosyl)ation, acetylation, and methylation are among the DNA damage-induced PTMs that have taken center stage as important DDR regulators. Redundant and multivalent interactions ...
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Dantuma, N. P., van Attikum, H. Tags: DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Review Source Type: research

PEPRs spice up plant immunity
Some pattern recognition receptors (PRRs) in plants, such as PEPRs, sense endogenous, damage-associated molecular patterns (DAMPs) that are released during pathogen infection. In this issue of The EMBO Journal, Yamada and colleagues show that genetic or pathogen-induced depletion of Arabidopsis BAK1, a co-receptor for multiple PRRs, primes immune activation through PEPRs. The work illustrates a link between pathogen-induced perturbation of BAK1 and DAMP signaling. (Source: EMBO Journal)
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Tang, D., Zhou, J.-M. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction, Plant Biology News [amp ] Views Source Type: research

Putting chromatin in its place: the pioneer factor NeuroD1 modulates chromatin state to drive cell fate decisions
Cell fate decisions require the deployment of distinct transcriptional programmes—how this is controlled and orchestrated is a key question from basic developmental biology to regenerative medicine. In this issue of The EMBO Journal, Pataskar and Jung et al (Pataskar et al, 2015) demonstrate how the transcription factor NeuroD1 acts genome-wide to elicit a specific neurogenic programme, including differentiation and migration. Much of that activity is due to NeuroD1 acting as a pioneer factor. NeuroD1 is able to bind its targets within repressive chromatin and can induce a more open chromatin state amenable...
Source: EMBO Journal - January 3, 2016 Category: Molecular Biology Authors: Glahs, A., Zinzen, R. P. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Neuroscience, Transcription News [amp ] Views Source Type: research

Protein localisation by electron microscopy reveals the architecture of the yeast spliceosomal B complex
The spliceosome assembles on a pre-mRNA intron by binding of five snRNPs and numerous proteins, leading to the formation of the pre-catalytic B complex. While the general morphology of the B complex is known, the spatial arrangement of proteins and snRNP subunits within it remain to be elucidated. To shed light on the architecture of the yeast B complex, we immuno-labelled selected proteins and located them by negative-stain electron microscopy. The B complex exhibited a triangular shape with main body, head and neck domains. We located the U5 snRNP components Brr2 at the top and Prp8 and Snu114 in the centre of the main b...
Source: EMBO Journal - December 14, 2015 Category: Molecular Biology Authors: Rigo, N., Sun, C., Fabrizio, P., Kastner, B., Lührmann, R. Tags: RNA Biology, Structural Biology Articles Source Type: research

Molecular architecture of the ribosome-bound Hepatitis C Virus internal ribosomal entry site RNA
Internal ribosomal entry sites (IRESs) are structured cis-acting RNAs that drive an alternative, cap-independent translation initiation pathway. They are used by many viruses to hijack the translational machinery of the host cell. IRESs facilitate translation initiation by recruiting and actively manipulating the eukaryotic ribosome using only a subset of canonical initiation factor and IRES transacting factors. Here we present cryo-EM reconstructions of the ribosome 80S- and 40S-bound Hepatitis C Virus (HCV) IRES. The presence of four subpopulations for the 80S•HCV IRES complex reveals dynamic conformational modes of...
Source: EMBO Journal - December 14, 2015 Category: Molecular Biology Authors: Yamamoto, H., Collier, M., Loerke, J., Ismer, J., Schmidt, A., Hilal, T., Sprink, T., Yamamoto, K., Mielke, T., Bürger, J., Shaikh, T. R., Dabrowski, M., Hildebrand, P. W., Scheerer, P., Spahn, C. M. Tags: Protein Biosynthesis & Quality Control, Structural Biology Articles Source Type: research

Removing endogenous tau does not prevent tau propagation yet reduces its neurotoxicity
In Alzheimer's disease and tauopathies, tau protein aggregates into neurofibrillary tangles that progressively spread to synaptically connected brain regions. A prion-like mechanism has been suggested: misfolded tau propagating through the brain seeds neurotoxic aggregation of soluble tau in recipient neurons. We use transgenic mice and viral tau expression to test the hypotheses that trans-synaptic tau propagation, aggregation, and toxicity rely on the presence of endogenous soluble tau. Surprisingly, mice expressing human P301Ltau in the entorhinal cortex showed equivalent tau propagation and accumulation in recipient ne...
Source: EMBO Journal - December 14, 2015 Category: Molecular Biology Authors: Wegmann, S., Maury, E. A., Kirk, M. J., Saqran, L., Roe, A., DeVos, S. L., Nicholls, S., Fan, Z., Takeda, S., Cagsal-Getkin, O., William, C. M., Spires-Jones, T. L., Pitstick, R., Carlson, G. A., Pooler, A. M., Hyman, B. T. Tags: Neuroscience Articles Source Type: research

tRNA processing defects induce replication stress and Chk2-dependent disruption of piRNA transcription
RNase P is a conserved endonuclease that processes the 5' trailer of tRNA precursors. We have isolated mutations in Rpp30, a subunit of RNase P, and find that these induce complete sterility in Drosophila females. Here, we show that sterility is not due to a shortage of mature tRNAs, but that atrophied ovaries result from the activation of several DNA damage checkpoint proteins, including p53, Claspin, and Chk2. Indeed, we find that tRNA processing defects lead to increased replication stress and de-repression of transposable elements in mutant ovaries. We also report that transcription of major piRNA sources collapse in m...
Source: EMBO Journal - December 14, 2015 Category: Molecular Biology Authors: Molla-Herman, A., Valles, A. M., Ganem-Elbaz, C., Antoniewski, C., Huynh, J.-R. Tags: Development & Differentiation, DNA Replication, Repair & Recombination, RNA Biology Articles Source Type: research

Subunit composition of VRAC channels determines substrate specificity and cellular resistance to Pt-based anti-cancer drugs
Although platinum-based drugs are widely used chemotherapeutics for cancer treatment, the determinants of tumor cell responsiveness remain poorly understood. We show that the loss of subunits LRRC8A and LRRC8D of the heteromeric LRRC8 volume-regulated anion channels (VRACs) increased resistance to clinically relevant cisplatin/carboplatin concentrations. Under isotonic conditions, about 50% of cisplatin uptake depended on LRRC8A and LRRC8D, but neither on LRRC8C nor on LRRC8E. Cell swelling strongly enhanced LRRC8-dependent cisplatin uptake, bolstering the notion that cisplatin enters cells through VRAC. LRRC8A disruption ...
Source: EMBO Journal - December 14, 2015 Category: Molecular Biology Authors: Planells-Cases, R., Lutter, D., Guyader, C., Gerhards, N. M., Ullrich, F., Elger, D. A., Kucukosmanoglu, A., Xu, G., Voss, F. K., Reincke, S. M., Stauber, T., Blomen, V. A., Vis, D. J., Wessels, L. F., Brummelkamp, T. R., Borst, P., Rottenberg, S., Jentsc Tags: Cancer, Autophagy & Cell Death, Membrane & Intracellular Transport Articles Source Type: research

No full admission for tau to the exclusive prion club yet
Aggregation of the microtubule-associated protein tau is a key feature of Alzheimer's disease and other so-called tauopathies, yet what causes this protein to aggregate and what renders it toxic is only slowly being revealed. Because tau spreads in a stereotypical pattern through the diseased brain, it has been proposed that it possesses prion-like properties, with aggregation-prone tau facilitating the conversion of "naïve" tau into "toxic" forms. The current study by Wegmann et al (2015) addresses whether tau fulfils classical "prion criteria" by assessing its spreading and toxicity i...
Source: EMBO Journal - December 14, 2015 Category: Molecular Biology Authors: Polanco, J. C., Götz, J. Tags: Neuroscience News [amp ] Views Source Type: research

Misprocessed tRNA response targets piRNA clusters
Germline PIWI-interacting RNA (piRNA) clusters have a characteristic transcriptional status; although they do not have their own promoters, both genomic strands are transcribed, while splicing and 3' processing signals are neglected. How this transcription is maintained remains unknown. Molla-Herman et al (2015) discovered that mutations in a tRNA processing factor cause the loss of transcription at some piRNA clusters, leading to sterility in Drosophila melanogaster. This defect in piRNA cluster transcription is restored by mutations in genes required for the DNA damage checkpoint or replication. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2015 Category: Molecular Biology Authors: Yamanaka, S., Siomi, H. Tags: Development & Differentiation, DNA Replication, Repair & Recombination, RNA Biology News [amp ] Views Source Type: research

VRACs swallow platinum drugs
Platinum-based drugs such as cisplatin and carboplatin are on the WHO model list of essential medicines, as highly effective chemotherapeutic drugs for the treatment of various solid tumors. These drugs react with purine residues in DNA, thereby causing DNA damage, inhibition of cell division, and eventually cell death. However, the mechanisms whereby platinum-based drugs enter cancer cells remained poorly understood. In this issue, Planells-Cases et al (2015) provide evidence that cells take up cisplatin and carboplatin via volume-regulated anion channels (VRACs), more specifically VRACs composed of LRRC8A and LRRC8D...
Source: EMBO Journal - December 14, 2015 Category: Molecular Biology Authors: Voets, T., Nilius, B., Vennekens, R. Tags: Cancer, Autophagy & Cell Death, Membrane & Intracellular Transport News [amp ] Views Source Type: research

Oct4-induced oligodendrocyte progenitor cells enhance functional recovery in spinal cord injury model
This study provides a simple strategy to generate functional self-renewing iOPCs and yields insights for the in-depth study of demyelination and regenerative medicine. (Source: EMBO Journal)
Source: EMBO Journal - December 2, 2015 Category: Molecular Biology Authors: Kim, J. B., Lee, H., Arauzo-Bravo, M. J., Hwang, K., Nam, D., Park, M. R., Zaehres, H., Park, K. I., Lee, S.-J. Tags: Neuroscience, Stem Cells Articles Source Type: research

EglN2 associates with the NRF1-PGC1{alpha} complex and controls mitochondrial function in breast cancer
The EglN2/PHD1 prolyl hydroxylase is an important oxygen sensor contributing to breast tumorigenesis. Emerging studies suggest that there is functional cross talk between oxygen sensing and mitochondrial function, both of which play an essential role for sustained tumor growth. However, the potential link between EglN2 and mitochondrial function remains largely undefined. Here, we show that EglN2 depletion decreases mitochondrial respiration in breast cancer under normoxia and hypoxia, which correlates with decreased mitochondrial DNA in a HIF1/2α-independent manner. Integrative analyses of gene expression profile an...
Source: EMBO Journal - December 2, 2015 Category: Molecular Biology Authors: Zhang, J., Wang, C., Chen, X., Takada, M., Fan, C., Zheng, X., Wen, H., Liu, Y., Wang, C., Pestell, R. G., Aird, K. M., Kaelin, W. G., Liu, X. S., Zhang, Q. Tags: Cancer, Metabolism, Transcription Articles Source Type: research

Unexpected features and mechanism of heterodimer formation of a herpesvirus nuclear egress complex
Herpesvirus nucleocapsids escape from the nucleus in a process orchestrated by a highly conserved, viral nuclear egress complex. In human cytomegalovirus, the complex consists of two proteins, UL50 and UL53. We solved structures of versions of UL53 and the complex by X-ray crystallography. The UL53 structures, determined at 1.93 and 3.0 Å resolution, contained unexpected features including a Bergerat fold resembling that found in certain nucleotide-binding proteins, and a Cys3His zinc finger. Substitutions of zinc-coordinating residues decreased UL50–UL53 co-localization in transfected cells, and, when incorpor...
Source: EMBO Journal - December 2, 2015 Category: Molecular Biology Authors: Lye, M. F., Sharma, M., El Omari, K., Filman, D. J., Schuermann, J. P., Hogle, J. M., Coen, D. M. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

Structural basis of membrane budding by the nuclear egress complex of herpesviruses
During nuclear egress, herpesvirus capsids bud at the inner nuclear membrane forming perinuclear viral particles that subsequently fuse with the outer nuclear membrane, releasing capsids into the cytoplasm. This unusual budding process is mediated by the nuclear egress complex (NEC) composed of two conserved viral proteins, UL31 and UL34. Earlier, we discovered that the herpesvirus nuclear egress complex (NEC) could bud synthetic membranes in vitro without the help of other proteins by forming a coat-like hexagonal scaffold inside the budding membrane. To understand the structural basis of NEC-mediated membrane buddin...
Source: EMBO Journal - December 2, 2015 Category: Molecular Biology Authors: Bigalke, J. M., Heldwein, E. E. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

A non-canonical role of the p97 complex in RIG-I antiviral signaling
RIG-I is a well-studied sensor of viral RNA that plays a key role in innate immunity. p97 regulates a variety of cellular events such as protein quality control, membrane reassembly, DNA repair, and the cell cycle. Here, we report a new role for p97 with Npl4-Ufd1 as its cofactor in reducing antiviral innate immune responses by facilitating proteasomal degradation of RIG-I. The p97 complex is able to directly bind both non-ubiquitinated RIG-I and the E3 ligase RNF125, promoting K48-linked ubiquitination of RIG-I at residue K181. Viral infection significantly strengthens the interaction between RIG-I and the p97 complex by ...
Source: EMBO Journal - December 2, 2015 Category: Molecular Biology Authors: Hao, Q., Jiao, S., Shi, Z., Li, C., Meng, X., Zhang, Z., Wang, Y., Song, X., Wang, W., Zhang, R., Zhao, Y., Wong, C. C., Zhou, Z. Tags: Immunology, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

The Mediator subunit MED23 couples H2B mono-ubiquitination to transcriptional control and cell fate determination
The Mediator complex orchestrates multiple transcription factors with the Pol II apparatus for precise transcriptional control. However, its interplay with the surrounding chromatin remains poorly understood. Here, we analyze differential histone modifications between WT and MED23–/– (KO) cells and identify H2B mono-ubiquitination at lysine 120 (H2Bub) as a MED23-dependent histone modification. Using tandem affinity purification and mass spectrometry, we find that MED23 associates with the RNF20/40 complex, the enzyme for H2Bub, and show that this association is critical for the recruitment of RNF20/40 to chrom...
Source: EMBO Journal - December 2, 2015 Category: Molecular Biology Authors: Yao, X., Tang, Z., Fu, X., Yin, J., Liang, Y., Li, C., Li, H., Tian, Q., Roeder, R. G., Wang, G. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Post-translational Modifications, Proteolysis & Proteomics, Transcription Articles Source Type: research

Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain
Evidence on the role of long non-coding (lnc) RNAs has been accumulating over decades, but it has been only recently that advances in sequencing technologies have allowed the field to fully appreciate their abundance and diversity. Despite this, only a handful of lncRNAs have been phenotypically or mechanistically studied. Moreover, novel lncRNAs and new classes of RNAs are being discovered at growing pace, suggesting that this class of molecules may have functions as diverse as protein-coding genes. Interestingly, the brain is the organ where lncRNAs have the most peculiar features including the highest number of lncRNAs ...
Source: EMBO Journal - December 2, 2015 Category: Molecular Biology Authors: Aprea, J., Calegari, F. Tags: Neuroscience, RNA Biology Review Source Type: research

MED23: a new Mediator of H2B monoubiquitylation
The Mediator multiprotein complex physically links transcription factors to RNA polymerase II and the basal transcription machinery. While the Mediator complex has been shown to be required for transcriptional initiation and elongation, the understanding of its interplay with histone modifying enzymes and post-translational modifications remains elusive. In this issue of The EMBO Journal, Yao et al (2015) report that the MED23 subunit of the Mediator complex physically associates with the heterodimeric RNF20/40 E3-ligase complex to facilitate the monoubiquitylation of histone H2B on gene bodies of actively transcribed...
Source: EMBO Journal - December 2, 2015 Category: Molecular Biology Authors: Streubel, G., Bracken, A. P. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Post-translational Modifications, Proteolysis & Proteomics, Transcription News [amp ] Views Source Type: research

The cis-regulatory code of Hox function in Drosophila
(Source: EMBO Journal)
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Sorge, S., Ha, N., Polychronidou, M., Friedrich, J., Bezdan, D., Kaspar, P., Schaefer, M. H., Ossowski, S., Henz, S. R., Mundorf, J., Rätzer, J., Papagiannouli, F., Lohmann, I. Tags: Corrigendum Source Type: research

Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1
Mutations in the PTEN-induced kinase 1 (PINK1) are causative of autosomal recessive Parkinson's disease (PD). We have previously reported that PINK1 is activated by mitochondrial depolarisation and phosphorylates serine 65 (Ser65) of the ubiquitin ligase Parkin and ubiquitin to stimulate Parkin E3 ligase activity. Here, we have employed quantitative phosphoproteomics to search for novel PINK1-dependent phosphorylation targets in HEK (human embryonic kidney) 293 cells stimulated by mitochondrial depolarisation. This led to the identification of 14,213 phosphosites from 4,499 gene products. Whilst most phosphosites were unaf...
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Lai, Y.-C., Kondapalli, C., Lehneck, R., Procter, J. B., Dill, B. D., Woodroof, H. I., Gourlay, R., Peggie, M., Macartney, T. J., Corti, O., Corvol, J.-C., Campbell, D. G., Itzen, A., Trost, M., Muqit, M. M. Tags: Membrane & Intracellular Transport, Methods & Resources, Post-translational Modifications, Proteolysis & Proteomics Source Type: research

Alzheimer's disease-causing proline substitutions lead to presenilin 1 aggregation and malfunction
This study also points at ER chaperones as targets for the development of counter-neurodegeneration therapies. (Source: EMBO Journal)
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Ben-Gedalya, T., Moll, L., Bejerano-Sagie, M., Frere, S., Cabral, W. A., Friedmann-Morvinski, D., Slutsky, I., Burstyn-Cohen, T., Marini, J. C., Cohen, E. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research