Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila
The posttranscriptional addition of nucleotides to the 3' end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. Here, we show that in flies, 3' terminal RNA uridylation triggers the processive, 3'-to-5' exoribonucleolytic decay via the RNase II/R enzyme CG16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. Together with the TUTase Tailor, dmDis3l2 forms the cytoplasmic, terminal RNA uridylation-mediated processing (TRUMP) complex that functionally cooperates in the degradation of structured RNA. RNA immunoprecipitation and high-throughput sequencing reveals a...
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Reimao-Pinto, M. M., Manzenreither, R. A., Burkard, T. R., Sledz, P., Jinek, M., Mechtler, K., Ameres, S. L. Tags: RNA Biology Articles Source Type: research

MicroRNA-34/449 controls mitotic spindle orientation during mammalian cortex development
Correct orientation of the mitotic spindle determines the plane of cellular cleavage and is crucial for organ development. In the developing cerebral cortex, spindle orientation defects result in severe neurodevelopmental disorders, but the precise mechanisms that control this important event are not fully understood. Here, we use a combination of high-content screening and mouse genetics to identify the miR-34/449 family as key regulators of mitotic spindle orientation in the developing cerebral cortex. By screening through all cortically expressed miRNAs in HeLa cells, we show that several members of the miR-34/449 famil...
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Fededa, J. P., Esk, C., Mierzwa, B., Stanyte, R., Yuan, S., Zheng, H., Ebnet, K., Yan, W., Knoblich, J. A., Gerlich, D. W. Tags: Cell Adhesion, Polarity & Cytoskeleton, Neuroscience, RNA Biology Articles Source Type: research

T-lymphoid progenitors - we know what they are, but know not what they may be
This study not only supports that the lymphoid fate of early T-cell progenitors is not yet fully stabilized but also shows that under oncogenic conditions, this multilineage plasticity potential of T-lymphoid progenitors can lead to transdifferentiation into myeloid leukemia. While gene expression profiles suggest that approximately 5% of all AML cases originate from T-lymphoid progenitors, novel treatment strategies targeting JAK2/STAT3 signaling might open new avenues for this AML cohort. (Source: EMBO Journal)
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Bullinger, L. Tags: Cancer, Development & Differentiation, Immunology News [amp ] Views Source Type: research

Molecular requirements of the B-cell antigen receptor for sensing monovalent antigens
How the B-cell antigen receptor (BCR) is activated upon interaction with its cognate antigen or with anti-BCR antibodies is not fully understood. We have recently shown that B-cell activation is accompanied by the opening of the pre-organized BCR oligomers, an observation that strengthens the role of receptor reorganization in signalling. We have now analysed the BCR oligomer opening and signalling upon treatment with different monovalent stimuli. Our results indicate that monovalent antigens are able to disturb and open the BCR oligomer, but that this requires the presence and activity of the Src family kinase (SFK) Lyn. ...
Source: EMBO Journal - November 1, 2016 Category: Molecular Biology Authors: Volkmann, C., Brings, N., Becker, M., Hobeika, E., Yang, J., Reth, M. Tags: Immunology Articles Source Type: research

A Golgi rhomboid protease Rbd2 recruits Cdc48 to cleave yeast SREBP
Hypoxic growth of fungi requires sterol regulatory element-binding protein (SREBP) transcription factors, and human opportunistic fungal pathogens require SREBP activation for virulence. Proteolytic release of fission yeast SREBPs from the membrane in response to low oxygen requires the Golgi membrane-anchored Dsc E3 ligase complex. Using genetic interaction arrays, we identified Rbd2 as a rhomboid family protease required for SREBP proteolytic processing. Rbd2 is an active, Golgi-localized protease that cleaves the transmembrane segment of the TatA rhomboid model substrate. Epistasis analysis revealed that the Dsc E3 liga...
Source: EMBO Journal - November 1, 2016 Category: Molecular Biology Authors: Hwang, J., Ribbens, D., Raychaudhuri, S., Cairns, L., Gu, H., Frost, A., Urban, S., Espenshade, P. J. Tags: Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence
During development, hematopoietic stem cells (HSCs) emerge from aortic endothelial cells (ECs) through an intermediate stage called hemogenic endothelium by a process known as endothelial-to-hematopoietic transition (EHT). While Notch signaling, including its upstream regulator Vegf, is known to regulate this process, the precise molecular control and temporal specificity of Notch activity remain unclear. Here, we identify the zebrafish transcriptional regulator evi1 as critically required for Notch-mediated EHT. In vivo live imaging studies indicate that evi1 suppression impairs EC progression to hematopoietic fate a...
Source: EMBO Journal - November 1, 2016 Category: Molecular Biology Authors: Konantz, M., Alghisi, E., Müller, J. S., Lenard, A., Esain, V., Carroll, K. J., Kanz, L., North, T. E., Lengerke, C. Tags: Development & Differentiation, Signal Transduction, Stem Cells Articles Source Type: research

PRC2 preserves intestinal progenitors and restricts secretory lineage commitment
Chromatin modifications shape cell heterogeneity by activating and repressing defined sets of genes involved in cell proliferation, differentiation and development. Polycomb-repressive complexes (PRCs) act synergistically during development and differentiation by maintaining transcriptional repression of common genes. PRC2 exerts this activity by catalysing H3K27 trimethylation. Here, we show that in the intestinal epithelium PRC2 is required to sustain progenitor cell proliferation and the correct balance between secretory and absorptive lineage differentiation programs. Using genetic models, we show that PRC2 activity is...
Source: EMBO Journal - November 1, 2016 Category: Molecular Biology Authors: Chiacchiera, F., Rossi, A., Jammula, S., Zanotti, M., Pasini, D. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Stem Cells Articles Source Type: research

Aneuploid embryonic stem cells exhibit impaired differentiation and increased neoplastic potential
Aneuploidy leads to severe developmental defects in mammals and is also a hallmark of cancer. However, whether aneuploidy is a driving cause or a consequence of tumor formation remains controversial. Paradoxically, existing studies based on aneuploid yeast and mouse fibroblasts have shown that aneuploidy is usually detrimental to cellular fitness. Here, we examined the effects of aneuploidy on mouse embryonic stem (ES) cells by generating a series of cell lines that each carries an extra copy of single chromosomes, including trisomy 6, 8, 11, 12, or 15. Most of these aneuploid cell lines had rapid proliferation rates and e...
Source: EMBO Journal - November 1, 2016 Category: Molecular Biology Authors: Zhang, M., Cheng, L., Jia, Y., Liu, G., Li, C., Song, S., Bradley, A., Huang, Y. Tags: Cancer, Development & Differentiation, Stem Cells Articles Source Type: research

Polycomb-dependent control of cell fate in adult tissue
Epigenetic control of gene expression in adult tissues is crucial to maintain organ function and homeostasis. A report in this issue of The EMBO Journal (Chiacchiera et al, 2016b), together with another one published in Gastroenterology (Koppens et al, 2016), unveils how chromatin repressive complex PRC2 controls the equilibrium between secretory and absorptive fates in the intestine. PRC2 controls proliferation of cells within the crypt and at the same time represses the transcription factor Atoh1, thus favoring the generation of enterocytes versus secretory cell types in the adult intestine. (Source: EMBO Journal)
Source: EMBO Journal - November 1, 2016 Category: Molecular Biology Authors: Vizan, P., Beringer, M., Di Croce, L. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells News [amp ] Views Source Type: research

Too much to differentiate: aneuploidy promotes proliferation and teratoma formation in embryonic stem cells
Aneuploidy, or an uneven number of chromosomes, has mostly detrimental consequences in eukaryotic cells, which include impaired proliferation as well as compromised DNA replication and protein folding. Unexpectedly, a new study published in this issue of The EMBO Journal shows that in murine embryonic stem cells aneuploidy does not interfere with proliferation, but rather hinders their differentiation capacity, thus propelling the formation of poorly differentiated teratomas. (Source: EMBO Journal)
Source: EMBO Journal - November 1, 2016 Category: Molecular Biology Authors: Storchova, Z. Tags: Cancer, Development & Differentiation, Stem Cells News [amp ] Views Source Type: research

The hVps34-SGK3 pathway alleviates sustained PI3K/Akt inhibition by stimulating mTORC1 and tumour growth
(Source: EMBO Journal)
Source: EMBO Journal - October 15, 2016 Category: Molecular Biology Authors: Bago, R., Sommer, E., Castel, P., Crafter, C., Bailey, F. P., Shpiro, N., Baselga, J., Cross, D., Eyers, P. A., Alessi, D. R. Tags: Corrigendum Source Type: research

The effects of proteasomal inhibition on synaptic proteostasis
Synaptic function crucially depends on uninterrupted synthesis and degradation of synaptic proteins. While much has been learned on synaptic protein synthesis, little is known on the routes by which synaptic proteins are degraded. Here we systematically studied how inhibition of the ubiquitin-proteasome system (UPS) affects the degradation rates of thousands of neuronal and synaptic proteins. We identified a group of proteins, including several proteins related to glutamate receptor trafficking, whose degradation rates were significantly slowed by UPS inhibition. Unexpectedly, however, degradation rates of most synaptic pr...
Source: EMBO Journal - October 15, 2016 Category: Molecular Biology Authors: Hakim, V., Cohen, L. D., Zuchman, R., Ziv, T., Ziv, N. E. Tags: Neuroscience, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

An essential step of kinetochore formation controlled by the SNARE protein Snap29
The kinetochore is an essential structure that mediates accurate chromosome segregation in mitosis and meiosis. While many of the kinetochore components have been identified, the mechanisms of kinetochore assembly remain elusive. Here, we identify a novel role for Snap29, an unconventional SNARE, in promoting kinetochore assembly during mitosis in Drosophila and human cells. Snap29 localizes to the outer kinetochore and prevents chromosome mis-segregation and the formation of cells with fragmented nuclei. Snap29 promotes accurate chromosome segregation by mediating the recruitment of Knl1 at the kinetochore and ensuring st...
Source: EMBO Journal - October 15, 2016 Category: Molecular Biology Authors: Morelli, E., Mastrodonato, V., Beznoussenko, G. V., Mironov, A. A., Tognon, E., Vaccari, T. Tags: Cell Cycle, Membrane & Intracellular Transport Articles Source Type: research

Amyloid precursor protein maintains constitutive and adaptive plasticity of dendritic spines in adult brain by regulating D-serine homeostasis
Dynamic synapses facilitate activity-dependent remodeling of neural circuits, thereby providing the structural substrate for adaptive behaviors. However, the mechanisms governing dynamic synapses in adult brain are still largely unknown. Here, we demonstrate that in the cortex of adult amyloid precursor protein knockout (APP-KO) mice, spine formation and elimination were both reduced while overall spine density remained unaltered. When housed under environmental enrichment, APP-KO mice failed to respond with an increase in spine density. Spine morphology was also altered in the absence of APP. The underlying mechanism of t...
Source: EMBO Journal - October 15, 2016 Category: Molecular Biology Authors: Zou, C., Crux, S., Marinesco, S., Montagna, E., Sgobio, C., Shi, Y., Shi, S., Zhu, K., Dorostkar, M. M., Müller, U. C., Herms, J. Tags: Neuroscience Articles Source Type: research

TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs
Uridylation of various cellular RNA species at the 3' end has been generally linked to RNA degradation. In mammals, uridylated pre-let-7 miRNAs and mRNAs are targeted by the 3' to 5' exoribonuclease DIS3L2. Mutations in DIS3L2 have been associated with Perlman syndrome and with Wilms tumor susceptibility. Using in vivo cross-linking and immunoprecipitation (CLIP) method, we discovered the DIS3L2-dependent cytoplasmic uridylome of human cells. We found a broad spectrum of uridylated RNAs including rRNAs, snRNAs, snoRNAs, tRNAs, vault, 7SL, Y RNAs, mRNAs, lncRNAs, and transcripts from pseudogenes. The unifying features ...
Source: EMBO Journal - October 15, 2016 Category: Molecular Biology Authors: Ustianenko, D., Pasulka, J., Feketova, Z., Bednarik, L., Zigackova, D., Fortova, A., Zavolan, M., Vanacova, S. Tags: RNA Biology Articles Source Type: research

Contribution of intertwined loop to membrane association revealed by Zika virus full-length NS1 structure
The association of Zika virus (ZIKV) infections with microcephaly and neurological diseases has highlighted an emerging public health concern. Here, we report the crystal structure of the full-length ZIKV nonstructural protein 1 (NS1), a major host-interaction molecule that functions in flaviviral replication, pathogenesis, and immune evasion. Of note, a long intertwined loop is observed in the wing domain of ZIKV NS1, and forms a hydrophobic "spike", which can contribute to cellular membrane association. For different flaviviruses, the amino acid sequences of the "spike" are variable but their common c...
Source: EMBO Journal - October 15, 2016 Category: Molecular Biology Authors: Xu, X., Song, H., Qi, J., Liu, Y., Wang, H., Su, C., Shi, Y., Gao, G. F. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

Pore formation by GSDMD is the effector mechanism of pyroptosis
Pyroptosis is a unique, pro-inflammatory form of lytic cell death that is initiated by the activation of inflammatory caspases. The caspase substrate gasdermin D (GSDMD) plays a critical function in pyroptosis, yet the precise mode of action of this molecule in cell death execution remained unclear. Several recent reports, including a The EMBO Journal article, show that the caspase-matured N-terminal fragment of GSDMD is recruited to lipid membranes to form pore-like structures, which constitutes the key effector mechanism of pyroptotic cell death. (Source: EMBO Journal)
Source: EMBO Journal - October 15, 2016 Category: Molecular Biology Authors: Gaidt, M. M., Hornung, V. Tags: Autophagy & Cell Death, Immunology News [amp ] Views Source Type: research

Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging
Centrioles are essential for the formation of centrosomes and cilia. While numerical and/or structural centrosomes aberrations are implicated in cancer, mutations in centriolar and centrosomal proteins are genetically linked to ciliopathies, microcephaly, and dwarfism. The evolutionarily conserved mechanisms underlying centrosome biogenesis are centered on a set of key proteins, including Plk4, Sas-6, and STIL, whose exact levels are critical to ensure accurate reproduction of centrioles during cell cycle progression. However, neither the intracellular levels of centrosomal proteins nor their stoichiometry within centrosom...
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Bauer, M., Cubizolles, F., Schmidt, A., Nigg, E. A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics Resource Source Type: research

Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator
In budding yeast, the monopolin complex mediates sister kinetochore cross-linking and co-orientation in meiosis I. The CK1 kinase Hrr25 is critical for sister kinetochore co-orientation, but its roles are not well understood. Here, we present the structures of Hrr25 and its complex with the monopolin subunit Mam1. Hrr25 possesses a "central domain" that packs tightly against the kinase C-lobe, adjacent to the binding site for Mam1. Together, the Hrr25 central domain and Mam1 form a novel, contiguous embellishment to the Hrr25 kinase domain that affects Hrr25 conformational dynamics and enzyme kinetics. Mam1 binds...
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Ye, Q., Ur, S. N., Su, T. Y., Corbett, K. D. Tags: Cell Cycle, Structural Biology Articles Source Type: research

Tunneling nanotubes spread fibrillar {alpha}-synuclein by intercellular trafficking of lysosomes
Synucleinopathies such as Parkinson's disease are characterized by the pathological deposition of misfolded α-synuclein aggregates into inclusions throughout the central and peripheral nervous system. Mounting evidence suggests that intercellular propagation of α-synuclein aggregates may contribute to the neuropathology; however, the mechanism by which spread occurs is not fully understood. By using quantitative fluorescence microscopy with co-cultured neurons, here we show that α-synuclein fibrils efficiently transfer from donor to acceptor cells through tunneling nanotubes (TNTs) inside lysosomal vesicl...
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Abounit, S., Bousset, L., Loria, F., Zhu, S., de Chaumont, F., Pieri, L., Olivo-Marin, J.-C., Melki, R., Zurzolo, C. Tags: Membrane & Intracellular Transport, Neuroscience Articles Source Type: research

NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation
Mitochondrial gene expression uses a non-universal genetic code in mammals. Besides reading the conventional AUG codon, mitochondrial (mt-)tRNAMet mediates incorporation of methionine on AUA and AUU codons during translation initiation and on AUA codons during elongation. We show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt-tRNAMet to methylate cytosine 34 (C34) at the wobble position. NSUN3 specifically recognises the anticodon stem loop (ASL) of the tRNA, explaining why a mutation that compromises ASL basepairing leads to disease. We further identify ALKBH1/ABH1 as the dioxygenase ...
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Haag, S., Sloan, K. E., Ranjan, N., Warda, A. S., Kretschmer, J., Blessing, C., Hübner, B., Seikowski, J., Dennerlein, S., Rehling, P., Rodnina, M. V., Höbartner, C., Bohnsack, M. T. Tags: Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal-to-zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by post-transcriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs, this pathway does not fully explain mRNA clearance. We investigated how codon identity and translation affect mRNA stability during development and homeostasis. We show that the codon triplet contains translation-dependent regulatory information that influences ...
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Bazzini, A. A., del Viso, F., Moreno-Mateos, M. A., Johnstone, T. G., Vejnar, C. E., Qin, Y., Yao, J., Khokha, M. K., Giraldez, A. J. Tags: Development & Differentiation, Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

The plant-specific CDKB1-CYCB1 complex mediates homologous recombination repair in Arabidopsis
Upon DNA damage, cyclin-dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology-dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant-specific B1-type CDKs (CDKB1s) and the class of B1-type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1-C...
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Weimer, A. K., Biedermann, S., Harashima, H., Roodbarkelari, F., Takahashi, N., Foreman, J., Guan, Y., Pochon, G., Heese, M., Van Damme, D., Sugimoto, K., Koncz, C., Doerner, P., Umeda, M., Schnittger, A. Tags: Cell Cycle, DNA Replication, Repair & Recombination, Plant Biology Articles Source Type: research

Methionine on the rise: how mitochondria changed their codon usage
The tRNA specific for methionine (tRNAMet) of human mitochondria contains a formyl-cytosine at the wobble position of the anticodon to facilitate its binding to AUG, AUA and (in one instance) to AUU. In this issue of The EMBO Journal, Haag et al identify a two-step enzyme pathway facilitating the modification of the tRNA. Sequential reactions of the methyltransferase NSUN3 and the dioxygenase ALKBH1/ABH1 are important to render the tRNA as able to recognize the non-canonical methionine codons AUA and AUUs, a property critical for efficient protein synthesis in human mitochondria. (Source: EMBO Journal)
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Boos, F., Wollin, M., Herrmann, J. M. Tags: Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research

A code within a code: how codons influence mRNA stability
The genetic code was deciphered more than 50 years ago, but we are only now becoming aware of a second, hidden code. It is the concept of "codon optimality" that enters the scene of developmental and homeostatic gene expression, linking translation rates, mRNA stability, and tRNA abundance. Both at the biological and methodological levels, work by Giraldez and colleagues in this issue of The EMBO Journal paves the way for further analyses of such key regulatory mechanisms. (Source: EMBO Journal)
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Martinez, J., Zagrovic, B. Tags: Development & Differentiation, Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research

A plant solution to the CDK conundrum in the DNA damage response
To cope with DNA damage, proliferating cells have evolved sophisticated mechanisms including cell cycle arrest and activation of DNA repair. Paradoxically, various DNA damage response pathways are promoted by cyclin-dependent kinase (CDK) activity, while cell cycle remains arrested. New work in The EMBO Journal shows that plant cells have evolved intricate ways to resolve this dilemma, by utilizing distinct and specialized CDKs for cell cycle progression and homologous recombination. (Source: EMBO Journal)
Source: EMBO Journal - October 3, 2016 Category: Molecular Biology Authors: Desvoyes, B., Gutierrez, C. Tags: Cell Cycle, DNA Replication, Repair & Recombination, Plant Biology News [amp ] Views Source Type: research

Retraction: 'A pair of transposon-derived proteins regulate active DNA demethylation in Arabidopsis
(Source: EMBO Journal)
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Li, Q., Yuan, W., Wang, X., Liu, Y., Ma, X., Sun, H., Tong, J., Tian, X., Li, Y., Qian, W. Tags: Retraction Source Type: research

A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG
8-oxo-7,8-dihydroxy-2'-deoxyguanosine (8-oxo-dG) has high mutagenic potential as it is prone to mispair with deoxyadenine (dA). In order to maintain genomic integrity, post-replicative 8-oxo-dG:dA mispairs are removed through DNA polymerase lambda (Pol )-dependent MUTYH-initiated base excision repair (BER). Here, we describe seven novel crystal structures and kinetic data that fully characterize 8-oxo-dG bypass by Pol . We demonstrate that Pol has a flexible active site that can tolerate 8-oxo-dG in either the anti- or syn-conformation. Importantly, we show that discrimination against the pro-mutagenic syn-conformation occ...
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Burak, M. J., Guja, K. E., Hambardjieva, E., Derkunt, B., Garcia-Diaz, M. Tags: DNA Replication, Repair & Recombination, Structural Biology Articles Source Type: research

IGFBP1 increases {beta}-cell regeneration by promoting {alpha}- to {beta}-cell transdifferentiation
There is great interest in therapeutically harnessing endogenous regenerative mechanisms to increase the number of β cells in people with diabetes. By performing whole-genome expression profiling of zebrafish islets, we identified 11 secreted proteins that are upregulated during β-cell regeneration. We then tested the proteins' ability to potentiate β-cell regeneration in zebrafish at supraphysiological levels. One protein, insulin-like growth factor (Igf) binding-protein 1 (Igfbp1), potently promoted β-cell regeneration by potentiating α- to β-cell transdifferentiation. Using various inhibit...
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Lu, J., Liu, K.-C., Schulz, N., Karampelias, C., Charbord, J., Hilding, A., Rautio, L., Bertolino, P., Östenson, C.-G., Brismar, K., Andersson, O. Tags: Molecular Biology of Disease, Signal Transduction, Stem Cells Articles Source Type: research

Loss of FBXO7 (PARK15) results in reduced proteasome activity and models a parkinsonism-like phenotype in mice
Mutations in the FBXO7 (PARK15) gene have been implicated in a juvenile form of parkinsonism termed parkinsonian pyramidal syndrome (PPS), characterized by Parkinsonian symptoms and pyramidal tract signs. FBXO7 (F-box protein only 7) is a subunit of the SCF (SKP1/cullin-1/F-box protein) E3 ubiquitin ligase complex, but its relevance and function in neurons remain to be elucidated. Here, we report that the E3 ligase FBXO7-SCF binds to and ubiquitinates the proteasomal subunit PSMA2. In addition, we show that FBXO7 is a proteasome-associated protein involved in proteasome assembly. In FBXO7 knockout mice, we find reduced pro...
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Vingill, S., Brockelt, D., Lancelin, C., Tatenhorst, L., Dontcheva, G., Preisinger, C., Schwedhelm-Domeyer, N., Joseph, S., Mitkovski, M., Goebbels, S., Nave, K.-A., Schulz, J. B., Marquardt, T., Lingor, P., Stegmüller, J. Tags: Neuroscience, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Golgi membrane-associated degradation pathway in yeast and mammals
In conclusion, GOMED is activated by the disruption of PI(4)P-dependent anterograde trafficking in autophagy-deficient yeast and mammalian cells. (Source: EMBO Journal)
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Yamaguchi, H., Arakawa, S., Kanaseki, T., Miyatsuka, T., Fujitani, Y., Watada, H., Tsujimoto, Y., Shimizu, S. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Metabolism Articles Source Type: research

Natural underlying mtDNA heteroplasmy as a potential source of intra-person hiPSC variability
Functional variability among human clones of induced pluripotent stem cells (hiPSCs) remains a limitation in assembling high-quality biorepositories. Beyond inter-person variability, the root cause of intra-person variability remains unknown. Mitochondria guide the required transition from oxidative to glycolytic metabolism in nuclear reprogramming. Moreover, mitochondria have their own genome (mitochondrial DNA [mtDNA]). Herein, we performed mtDNA next-generation sequencing (NGS) on 84 hiPSC clones derived from a cohort of 19 individuals, including mitochondrial and non-mitochondrial patients. The analysis of mtDNA varian...
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Perales-Clemente, E., Cook, A. N., Evans, J. M., Roellinger, S., Secreto, F., Emmanuele, V., Oglesbee, D., Mootha, V. K., Hirano, M., Schon, E. A., Terzic, A., Nelson, T. J. Tags: Stem Cells Articles Source Type: research

A PBX1 transcriptional network controls dopaminergic neuron development and is impaired in Parkinson's disease
Pre-B-cell leukemia homeobox (PBX) transcription factors are known to regulate organogenesis, but their molecular targets and function in midbrain dopaminergic neurons (mDAn) as well as their role in neurodegenerative diseases are unknown. Here, we show that PBX1 controls a novel transcriptional network required for mDAn specification and survival, which is sufficient to generate mDAn from human stem cells. Mechanistically, PBX1 plays a dual role in transcription by directly repressing or activating genes, such as Onecut2 to inhibit lateral fates during embryogenesis, Pitx3 to promote mDAn development, and Nfe2l1 to protec...
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Villaescusa, J. C., Li, B., Toledo, E. M., Rivetti di Val Cervo, P., Yang, S., Stott, S. R., Kaiser, K., Islam, S., Gyllborg, D., Laguna-Goya, R., Landreh, M., Lönnerberg, P., Falk, A., Bergman, T., Barker, R. A., Linnarsson, S., Selleri, L., Aren Tags: Development & Differentiation, Neuroscience Articles Source Type: research

Mitochondrial DNA mutations in iPS cells: mtDNA integrity as standard iPSC selection criteria?
Somatic cells harbor random heteroplasmic mitochondrial DNA mutations, which are considered to contribute to aging. In this issue of The EMBO Journal, Perales-Clemente et al (2016) show that mtDNA mutations, present at low levels in the starting fibroblasts, become enriched in iPS cells and lead to functional defects in iPS-derived cells. In another recent study, Kang et al (2016) demonstrated that accumulation of mtDNA mutations of somatic origin in iPSCs is age related. (Source: EMBO Journal)
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Hämäläinen, R. H. Tags: Stem Cells News [amp ] Views Source Type: research

One more factor joins the plot: Pbx1 regulates differentiation and survival of midbrain dopaminergic neurons
Midbrain dopaminergic neurons have been the subject of intense research, because of their importance in pathologies such as Parkinson's disease. In this issue of The EMBO Journal, Villaescusa et al (2016) show the transcription factor Pbx1 is required for the differentiation and survival of midbrain dopaminergic neurons. Notably, Pbx1 protects from oxidative stress by inducing Nfe2l1, and the expression of both genes is reduced in dopaminergic neurons from Parkinson's patients. This is an important study, with possible implications in regenerative medicine and drug design. (Source: EMBO Journal)
Source: EMBO Journal - September 14, 2016 Category: Molecular Biology Authors: Castro, D. S. Tags: Development & Differentiation, Neuroscience News [amp ] Views Source Type: research

ER arrival sites for COPI vesicles localize to hotspots of membrane trafficking
COPI-coated vesicles mediate retrograde membrane traffic from the cis-Golgi to the endoplasmic reticulum (ER) in all eukaryotic cells. However, it is still unknown whether COPI vesicles fuse everywhere or at specific sites with the ER membrane. Taking advantage of the circumstance that the vesicles still carry their coat when they arrive at the ER, we have visualized active ER arrival sites (ERAS) by monitoring contact between COPI coat components and the ER-resident Dsl tethering complex using bimolecular fluorescence complementation (BiFC). ERAS form punctate structures near Golgi compartments, clearly distinct from ER e...
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Schröter, S., Beckmann, S., Schmitt, H. D. Tags: Membrane & Intracellular Transport Articles Source Type: research

Synaptonuclear messenger PRR7 inhibits c-Jun ubiquitination and regulates NMDA-mediated excitotoxicity
Elevated c-Jun levels result in apoptosis and are evident in neurodegenerative disorders such as Alzheimer's disease and dementia and after global cerebral insults including stroke and epilepsy. NMDA receptor (NMDAR) antagonists block c-Jun upregulation and prevent neuronal cell death following excitotoxic insults. However, the molecular mechanisms regulating c-Jun abundance in neurons are poorly understood. Here, we show that the synaptic component Proline rich 7 (PRR7) accumulates in the nucleus of hippocampal neurons following NMDAR activity. We find that PRR7 inhibits the ubiquitination of c-Jun by E3 ligase SCFFBW7 (F...
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Kravchick, D. O., Karpova, A., Hrdinka, M., Lopez-Rojas, J., Iacobas, S., Carbonell, A. U., Iacobas, D. A., Kreutz, M. R., Jordan, B. A. Tags: Neuroscience Articles Source Type: research

The hVps34-SGK3 pathway alleviates sustained PI3K/Akt inhibition by stimulating mTORC1 and tumour growth
We explore mechanisms that enable cancer cells to tolerate PI3K or Akt inhibitors. Prolonged treatment of breast cancer cells with PI3K or Akt inhibitors leads to increased expression and activation of a kinase termed SGK3 that is related to Akt. Under these conditions, SGK3 is controlled by hVps34 that generates PtdIns(3)P, which binds to the PX domain of SGK3 promoting phosphorylation and activation by its upstream PDK1 activator. Furthermore, under conditions of prolonged PI3K/Akt pathway inhibition, SGK3 substitutes for Akt by phosphorylating TSC2 to activate mTORC1. We characterise 14h, a compound that inhibits both S...
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Bago, R., Sommer, E., Castel, P., Crafter, C., Bailey, F. P., Shpiro, N., Baselga, J., Cross, D., Eyers, P. A., Alessi, D. R. Tags: Cancer, Molecular Biology of Disease, Signal Transduction Articles Source Type: research

Dopamine signaling promotes the xenobiotic stress response and protein homeostasis
Multicellular organisms encounter environmental conditions that adversely affect protein homeostasis (proteostasis), including extreme temperatures, toxins, and pathogens. It is unclear how they use sensory signaling to detect adverse conditions and then activate stress response pathways so as to offset potential damage. Here, we show that dopaminergic mechanosensory neurons in C. elegans release the neurohormone dopamine to promote proteostasis in epithelia. Signaling through the DA receptor DOP-1 activates the expression of xenobiotic stress response genes involved in pathogenic resistance and toxin removal, and the...
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Joshi, K. K., Matlack, T. L., Rongo, C. Tags: Microbiology, Virology & Host Pathogen Interaction, Neuroscience, Protein Biosynthesis & Quality Control Articles Source Type: research

SPATA2 links CYLD to the TNF-{alpha} receptor signaling complex and modulates the receptor signaling outcomes
TNF-α is a key regulator of innate immune and proinflammatory responses. However, the composition of the TNF-α receptor-associated signaling complexes (TNF-RSC) and the architecture of the downstream signaling networks are incompletely understood. We employed quantitative mass spectrometry to demonstrate that TNF-α stimulation induces widespread protein phosphorylation and that the scope of phosphorylation expands in a temporal manner. TNF-α stimulation also induces rapid ubiquitylation of components of the TNF-RSC. Temporal analysis of the TNF-RSC composition identified SPATA2 as a novel component ...
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Wagner, S. A., Satpathy, S., Beli, P., Choudhary, C. Tags: Immunology, Post-translational Modifications, Proteolysis & Proteomics, Signal Transduction Articles Source Type: research

Autophagosome-lysosome fusion in neurons requires INPP5E, a protein associated with Joubert syndrome
Autophagy is a multistep membrane traffic pathway. In contrast to autophagosome formation, the mechanisms underlying autophagosome–lysosome fusion remain largely unknown. Here, we describe a novel autophagy regulator, inositol polyphosphate-5-phosphatase E (INPP5E), involved in autophagosome–lysosome fusion process. In neuronal cells, INPP5E knockdown strongly inhibited autophagy by impairing the fusion step. A fraction of INPP5E is localized to lysosomes, and its membrane anchoring and enzymatic activity are necessary for autophagy. INPP5E decreases lysosomal phosphatidylinositol 3,5-bisphosphate (PI(3,5)...
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Hasegawa, J., Iwamoto, R., Otomo, T., Nezu, A., Hamasaki, M., Yoshimori, T. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Molecular Biology of Disease Articles Source Type: research

Dopamine helps worms deal with stress
To maintain protein homoeostasis, animals have developed stress response pathways such as the ubiquitin proteasome system (UPS). Joshi and colleagues have demonstrated that in Caenorhabditis elegans, dopamine release from neurons acts on receptors in the epithelia to modulate protein turnover, by controlling the expression of regulators of the xenobiotic stress response. Dopamine receptor mutants challenged with pathogenic bacteria were defective in protein turnover and were also more sensitive to infection thus highlighting a role for monoamine signalling in innate immunity and stress responses. (Source: EMBO Journal)
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Chew, Y. L., Schafer, W. R. Tags: Microbiology, Virology & Host Pathogen Interaction, Neuroscience, Protein Biosynthesis & Quality Control News [amp ] Views Source Type: research

SPATA2 - Keeping the TNF signal short and sweet
In this issue of The EMBO Journal, a multi-layered global proteome resource, which comprehensively covers TNF-induced phosphorylation and ubiquitination events as well as receptor interactions, has led to identification of SPATA2 as a novel player that contributes to TNF signalling by interacting with the LUBAC ubiquitin ligase and the CYLD deubiquitylase. Loss of SPATA2 augments transcriptional activation of NF-B and limits TNF-induced necroptosis. A separate screen published in EMBO Reports corroborates these findings by showing that SPATA2 deficiency regulates CYLD activity, TNF-induced NF-B signalling and cell death. (...
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Feltham, R., Webb, A. I., Silke, J. Tags: Immunology, Post-translational Modifications, Proteolysis & Proteomics, Signal Transduction News [amp ] Views Source Type: research

Autophagosome-lysosome fusion: PIs to the rescue
Phosphoinositides (PIs), a small fraction of the cellular lipids, function in almost all cellular physiological processes and especially in intracellular membrane trafficking events. PIs play a critical role in autophagy, but only PI(3)P is well studied. In this issue of The EMBO Journal, Hasegawa et al (2016) identified INPP5E, an inositol polyphosphate 5-phosphatase, as a novel regulator of autophagy. INPP5E controls the level of PI(3,5)P2 at the lysosome and thereby locally regulates the actin cytoskeleton and autophagosome–lysosome fusion. (Source: EMBO Journal)
Source: EMBO Journal - August 31, 2016 Category: Molecular Biology Authors: Li, L., Zhong, Q. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Molecular Biology of Disease News [amp ] Views Source Type: research

Hormone-induced repression of genes requires BRG1-mediated H1.2 deposition at target promoters
Eukaryotic gene regulation is associated with changes in chromatin compaction that modulate access to DNA regulatory sequences relevant for transcriptional activation or repression. Although much is known about the mechanism of chromatin remodeling in hormonal gene activation, how repression is accomplished is much less understood. Here we report that in breast cancer cells, ligand-activated progesterone receptor (PR) is directly recruited to transcriptionally repressed genes involved in cell proliferation along with the kinases ERK1/2 and MSK1. PR recruits BRG1 associated with the HP1-LSD1 complex repressor complex, which...
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Nacht, A. S., Pohl, A., Zaurin, R., Soronellas, D., Quilez, J., Sharma, P., Wright, R. H., Beato, M., Vicent, G. P. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion
Membrane fusion is essential for eukaryotic life, requiring SNARE proteins to zipper up in an α-helical bundle to pull two membranes together. Here, we show that vesicle fusion can be suppressed by phosphorylation of core conserved residues inside the SNARE domain. We took a proteomics approach using a PKCB knockout mast cell model and found that the key mast cell secretory protein VAMP8 becomes phosphorylated by PKC at multiple residues in the SNARE domain. Our data suggest that VAMP8 phosphorylation reduces vesicle fusion in vitro and suppresses secretion in living cells, allowing vesicles to dock but preventi...
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Malmersjö, S., Di Palma, S., Diao, J., Lai, Y., Pfuetzner, R. A., Wang, A. L., McMahon, M. A., Hayer, A., Porteus, M., Bodenmiller, B., Brunger, A. T., Meyer, T. Tags: Membrane & Intracellular Transport Articles Source Type: research

Macroautophagy inhibition maintains fragmented mitochondria to foster T cell receptor-dependent apoptosis
Mitochondrial dynamics and functionality are linked to the autophagic degradative pathway under several stress conditions. However, the interplay between mitochondria and autophagy upon cell death signalling remains unclear. The T-cell receptor pathway signals the so-called activation-induced cell death (AICD) essential for immune tolerance regulation. Here, we show that this apoptotic pathway requires the inhibition of macroautophagy. Protein kinase-A activation downstream of T-cell receptor signalling inhibits macroautophagy upon AICD induction. This leads to the accumulation of damaged mitochondria, which are fragmented...
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Corrado, M., Mariotti, F. R., Trapani, L., Taraborrelli, L., Nazio, F., Cianfanelli, V., Soriano, M. E., Schrepfer, E., Cecconi, F., Scorrano, L., Campello, S. Tags: Autophagy & Cell Death, Immunology Articles Source Type: research

Recruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy
Mammalian cells deploy autophagy to defend their cytosol against bacterial invaders. Anti-bacterial autophagy relies on the core autophagy machinery, cargo receptors, and "eat-me" signals such as galectin-8 and ubiquitin that label bacteria as autophagy cargo. Anti-bacterial autophagy also requires the kinase TBK1, whose role in autophagy has remained enigmatic. Here we show that recruitment of WIPI2, itself essential for anti-bacterial autophagy, is dependent on the localization of catalytically active TBK1 to the vicinity of cytosolic bacteria. Experimental manipulation of TBK1 recruitment revealed that engagem...
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Thurston, T. L., Boyle, K. B., Allen, M., Ravenhill, B. J., Karpiyevich, M., Bloor, S., Kaul, A., Noad, J., Foeglein, A., Matthews, S. A., Komander, D., Bycroft, M., Randow, F. Tags: Autophagy & Cell Death, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death
Pyroptosis is a lytic type of cell death that is initiated by inflammatory caspases. These caspases are activated within multi-protein inflammasome complexes that assemble in response to pathogens and endogenous danger signals. Pyroptotic cell death has been proposed to proceed via the formation of a plasma membrane pore, but the underlying molecular mechanism has remained unclear. Recently, gasdermin D (GSDMD), a member of the ill-characterized gasdermin protein family, was identified as a caspase substrate and an essential mediator of pyroptosis. GSDMD is thus a candidate for pyroptotic pore formation. Here, we character...
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Sborgi, L., Rühl, S., Mulvihill, E., Pipercevic, J., Heilig, R., Stahlberg, H., Farady, C. J., Müller, D. J., Broz, P., Hiller, S. Tags: Autophagy & Cell Death, Immunology Articles Source Type: research

NB-3 signaling mediates the cross-talk between post-traumatic spinal axons and scar-forming cells
Little is known about the molecules mediating the cross-talk between post-traumatic axons and scar-forming cells after spinal cord injury. We found that a sustained NB-3 induction was simultaneously present in the terminations of post-traumatic corticospinal axons and scar-forming cells at the spinal lesion site, where they were in direct contact when axons tried to penetrate the glial scar. The regrowth of corticospinal axons was enhanced in vivo with NB-3 deficiency or interruption of NB-3 trans-homophilic interactions. Biochemical, in vitro and in vivo evidence demonstrated that NB-3 homophilically intera...
Source: EMBO Journal - August 14, 2016 Category: Molecular Biology Authors: Huang, Z., Gao, Y., Sun, Y., Zhang, C., Yin, Y., Shimoda, Y., Watanabe, K., Liu, Y. Tags: Neuroscience Articles Source Type: research