Rapid movement and transcriptional re-localization of human cohesin on DNA
The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA. It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three-dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown. Here, we used single-molecule imaging to show that cohesin can diffuse rapidly on DNA i...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Davidson, I. F., Goetz, D., Zaczek, M. P., Molodtsov, M. I., Huis in 't Veld, P. J., Weissmann, F., Litos, G., Cisneros, D. A., Ocampo-Hafalla, M., Ladurner, R., Uhlmann, F., Vaziri, A., Peters, J.-M. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

Bimodal behaviour of interfollicular epidermal progenitors regulated by hair follicle position and cycling
Interfollicular epidermal (IFE) homeostasis is a major physiological process allowing maintenance of the skin barrier function. Despite progress in our understanding of stem cell populations in different hair follicle compartments, cellular mechanisms of IFE maintenance, in particular, whether a hierarchy of progenitors exists within this compartment, have remained controversial. We here used multicolour lineage tracing with Brainbow transgenic labels activated in the epidermis to track individual keratinocyte clones. Two modes of clonal progression could be observed in the adult murine dorsal skin. Clones attached to hair...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Roy, E., Neufeld, Z., Cerone, L., Wong, H. Y., Hodgson, S., Livet, J., Khosrotehrani, K. Tags: Development & Differentiation, Stem Cells, Systems & Computational Biology Articles Source Type: research

The diverse and expanding role of mass spectrometry in structural and molecular biology
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen–deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology in...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Lössl, P., van de Waterbeemd, M., Heck, A. J. Tags: Methods & Resources, Post-translational Modifications, Proteolysis & Proteomics, Transcription Review Source Type: research

Zika virus NS1, a pathogenicity factor with many faces
Recent publications in The EMBO Journal (Xu et al, 2016) and in Nature Structural & Molecular Biology (Brown et al, 2016) report crystal structures of the Zika virus (ZIKV) NS1 protein. The structures reveal unique surface properties that help explain the specificity of anti-ZIKV NS1 antibodies. Possible functions of this multifaceted pathogenicity factor are discussed here on the basis of the structures and cautious extrapolation from other flaviviruses. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Hilgenfeld, R. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology News [amp ] Views Source Type: research

Bimodal skin progenitors--a matter of place and time
The skin carries out specialist functions such as barrier formation and thermoregulation. The mode of cellular replenishment of the surface epithelium that forms the outermost layer during steady-state homeostasis is a subject of intensive investigations. A detailed analysis of the interfollicular epidermis reported in this issue of The EMBO Journal (Roy et al, 2016) reveals that hair follicles in their growth phase influence cellular behaviour of epithelial cells in their immediate proximity. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Ulyanchenko, S., Jensen, K. B. Tags: Development & Differentiation, Stem Cells, Systems & Computational Biology News [amp ] Views Source Type: research

Susan Lee Lindquist (1949-2016)--pioneer in the study of cellular protein folding and disease
(Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Hartl, F.-U. Tags: Obituary Source Type: research

Preprint Deja Vu
Twenty-five years ago, in August 1991, I spent a couple of afternoons at Los Alamos National Laboratory writing some simple software that enabled a small group of physicists to share drafts of their articles via automated email transactions with a central repository. Within a few years, the site migrated to the nascent WorldWideWeb as arXiv.org, and experienced both expansion in coverage and heavy growth in usage that continues to this day. In 1998, I gave a talk to a group of biologists—including David Lipman, Pat Brown, and Michael Eisen—at a meeting at Cold Spring Harbor Laboratory (CSHL) to describe th...
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Ginsparg, P. Tags: Commentary Source Type: research

Preparing for Preprints
Preprints reduce delays in sharing research results and increase the amount and diversity of data available to the scientific community. Support of this communication mechanism through appropriate policies by journals, funders and institutions will encourage community engagement. Widespread adoption would benefit both individual scientists and research, and it might improve publishing in scientific journals. Preprints are one step towards an Open Science future. (Source: EMBO Journal)
Source: EMBO Journal - December 14, 2016 Category: Molecular Biology Authors: Pulverer, B. Tags: Editorial Source Type: research

Sulfatase modifying factor 1 trafficking through the cells: from endoplasmic reticulum to the endoplasmic reticulum
(Source: EMBO Journal)
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Zito, E., Buono, M., Pepe, S., Settembre, C., Annunziata, I., Surace, E. M., Dierks, T., Monti, M., Cozzolino, M., Pucci, P., Ballabio, A., Cosma, M. P. Tags: Corrigendum Source Type: research

A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit {beta}5i
Inhibition of the immunoproteasome subunit β5i alleviates autoimmune diseases in preclinical studies and represents a promising new anti-inflammatory therapy. However, the lack of structural data on the human immunoproteasome still hampers drug design. Here, we systematically determined the potency of seven α' β' epoxyketone inhibitors with varying N-caps and P3-stereochemistry for mouse/human β5c/β5i and found pronounced differences in their subunit and species selectivity. Using X-ray crystallography, the compounds were analyzed for their modes of binding to chimeric yeast proteasomes that incor...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Huber, E. M., Heinemeyer, W., de Bruin, G., Overkleeft, H. S., Groll, M. Tags: Chemical Biology, Post-translational Modifications, Proteolysis & Proteomics Resource Source Type: research

The MMS22L-TONSL heterodimer directly promotes RAD51-dependent recombination upon replication stress
Homologous recombination (HR) is a key pathway that repairs DNA double-strand breaks (DSBs) and helps to restart stalled or collapsed replication forks. How HR supports replication upon genotoxic stress is not understood. Using in vivo and in vitro approaches, we show that the MMS22L–TONSL heterodimer localizes to replication forks under unperturbed conditions and its recruitment is increased during replication stress in human cells. MMS22L–TONSL associates with replication protein A (RPA)-coated ssDNA, and the MMS22L subunit directly interacts with the strand exchange protein RAD51. MMS22L is require...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Piwko, W., Mlejnkova, L. J., Mutreja, K., Ranjha, L., Stafa, D., Smirnov, A., Brodersen, M. M., Zellweger, R., Sturzenegger, A., Janscak, P., Lopes, M., Peter, M., Cejka, P. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

CLPP coordinates mitoribosomal assembly through the regulation of ERAL1 levels
Despite being one of the most studied proteases in bacteria, very little is known about the role of ClpXP in mitochondria. We now present evidence that mammalian CLPP has an essential role in determining the rate of mitochondrial protein synthesis by regulating the level of mitoribosome assembly. Through a proteomic approach and the use of a catalytically inactive CLPP, we produced the first comprehensive list of possible mammalian ClpXP substrates involved in the regulation of mitochondrial translation, oxidative phosphorylation, and a number of metabolic pathways. We further show that the defect in mitoribosomal assembly...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Szczepanowska, K., Maiti, P., Kukat, A., Hofsetz, E., Nolte, H., Senft, K., Becker, C., Ruzzenente, B., Hornig-Do, H.-T., Wibom, R., Wiesner, R. J., Krüger, M., Trifunovic, A. Tags: Metabolism, Post-translational Modifications, Proteolysis & Proteomics, Protein Biosynthesis & Quality Control Articles Source Type: research

RKIP and TBK1 form a positive feedback loop to promote type I interferon production in innate immunity
This study reveals a previously unrecognized positive feedback loop between RKIP and TBK1 that is essential for type I interferon production in anti-viral innate immunity. (Source: EMBO Journal)
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Gu, M., Liu, Z., Lai, R., Liu, S., Lin, W., Ouyang, C., Ye, S., Huang, H., Wang, X. Tags: Immunology Articles Source Type: research

Hair cell synaptic dysfunction, auditory fatigue and thermal sensitivity in otoferlin Ile515Thr mutants
The multi-C2 domain protein otoferlin is required for hearing and mutated in human deafness. Some OTOF mutations cause a mild elevation of auditory thresholds but strong impairment of speech perception. At elevated body temperature, hearing is lost. Mice homozygous for one of these mutations, OtofI515T/I515T, exhibit a moderate hearing impairment involving enhanced adaptation to continuous or repetitive sound stimulation. In OtofI515T/I515T inner hair cells (IHCs), otoferlin levels are diminished by 65%, and synaptic vesicles are enlarged. Exocytosis during prolonged stimulation is strongly reduced. This indicates that oto...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Strenzke, N., Chakrabarti, R., Al-Moyed, H., Müller, A., Hoch, G., Pangrsic, T., Yamanbaeva, G., Lenz, C., Pan, K.-T., Auge, E., Geiss-Friedlander, R., Urlaub, H., Brose, N., Wichmann, C., Reisinger, E. Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Inactivation of the type I interferon pathway reveals long double-stranded RNA-mediated RNA interference in mammalian cells
RNA interference (RNAi) elicited by long double-stranded (ds) or base-paired viral RNA constitutes the major mechanism of antiviral defence in plants and invertebrates. In contrast, it is controversial whether it acts in chordates. Rather, in vertebrates, viral RNAs induce a distinct defence system known as the interferon (IFN) response. Here, we tested the possibility that the IFN response masks or inhibits antiviral RNAi in mammalian cells. Consistent with that notion, we find that sequence-specific gene silencing can be triggered by long dsRNAs in differentiated mouse cells rendered deficient in components of the IFN pa...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Maillard, P. V., Van der Veen, A. G., Deddouche-Grass, S., Rogers, N. C., Merits, A., Reis e Sousa, C. Tags: Immunology, RNA Biology Articles Source Type: research

What's hot about otoferlin
Mutations in the otoferlin (OTOF) gene lead to profound hearing loss in humans. Interestingly, a number of missense otoferlin mutations cause hearing defects but only at higher body temperature, and the reasons for this have been elusive until now. A study published in this issue of The EMBO Journal (Strenzke et al, 2016) adds insight into the underlying mechanisms for this heat-dependent hearing loss. (Source: EMBO Journal)
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Avraham, K. B. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

Present and not reporting for duty: dsRNAi in mammalian cells
Double-stranded RNA interference (dsRNAi) represents a primary means of anti-viral defense in plants, worms, and insects, yet appears mostly supplanted by the protein-based interferon (IFN) response in vertebrates such as mammals. The degree to which dsRNAi is anti-viral in mammals has been contentious. Maillard et al (2016) find that dsRNAi retains sequence-specific silencing in mammalian cells incapable of triggering an IFN response, suggesting that dsRNAi is inhibited by the action of interferon-stimulated genes. Importantly, they observe that while dsRNA can "vaccinate" against the incoming cognate ...
Source: EMBO Journal - November 30, 2016 Category: Molecular Biology Authors: Luna, J. M., Wu, X., Rice, C. M. Tags: Immunology, RNA Biology News [amp ] Views Source Type: research

A pH- and ionic strength-dependent conformational change in the neck region regulates DNGR-1 function in dendritic cells
DNGR-1 is receptor expressed by certain dendritic cell (DC) subsets and by DC precursors in mouse. It possesses a C-type lectin-like domain (CTLD) followed by a poorly characterized neck region coupled to a transmembrane region and short intracellular tail. The CTLD of DNGR-1 binds F-actin exposed by dead cell corpses and causes the receptor to signal and potentiate cross-presentation of dead cell-associated antigens by DCs. Here, we describe a conformational change that occurs in the neck region of DNGR-1 in a pH- and ionic strength-dependent manner and that controls cross-presentation of dead cell-associated antigens. We...
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Hanc, P., Schulz, O., Fischbach, H., Martin, S. R., Kjaer, S., Reis e Sousa, C. Tags: Immunology Articles Source Type: research

Chm7 and Heh1 collaborate to link nuclear pore complex quality control with nuclear envelope sealing
The integrity of the nuclear envelope barrier relies on membrane remodeling by the ESCRTs, which seal nuclear envelope holes and contribute to the quality control of nuclear pore complexes (NPCs); whether these processes are mechanistically related remains poorly defined. Here, we show that the ESCRT-II/III chimera, Chm7, is recruited to a nuclear envelope subdomain that expands upon inhibition of NPC assembly and is required for the formation of the storage of improperly assembled NPCs (SINC) compartment. Recruitment to sites of NPC assembly is mediated by its ESCRT-II domain and the LAP2-emerin-MAN1 (LEM) family of integ...
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Webster, B. M., Thaller, D. J., Jäger, J., Ochmann, S. E., Borah, S., Lusk, C. P. Tags: Membrane & Intracellular Transport Articles Source Type: research

Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters
Mediator is a conserved, essential transcriptional coactivator complex, but its in vivo functions have remained unclear due to conflicting data regarding its genome-wide binding pattern obtained by genome-wide ChIP. Here, we used ChEC-seq, a method orthogonal to ChIP, to generate a high-resolution map of Mediator binding to the yeast genome. We find that Mediator associates with upstream activating sequences (UASs) rather than the core promoter or gene body under all conditions tested. Mediator occupancy is surprisingly correlated with transcription levels at only a small fraction of genes. Using the same approach to ...
Source: EMBO Journal - November 14, 2016 Category: Molecular Biology Authors: Grünberg, S., Henikoff, S., Hahn, S., Zentner, G. E. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

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