Dalmatian: spotting the difference in cohesin protectors
The cohesin complex prevents separation of chromosomes following their duplication until the appropriate time during cell division. In vertebrates, establishment and maintenance of cohesin-dependent linkages depend on two distinct proteins, sororin and shugoshin. New findings published in The EMBO Journal show that in Drosophila, the function of both of these cohesin regulators is carried out by a single hybrid protein, Dalmatian. (Source: EMBO Journal)
Source: EMBO Journal - June 1, 2017 Category: Molecular Biology Authors: Marston, A. L. Tags: Cell Cycle News [amp ] Views Source Type: research

Judging a tumor cell by its cover: a matter of mitochondrial contact sites
Glioblastoma is a highly aggressive brain tumor constituted by glioma stem cell and differentiated cell populations with distinct susceptibility to cytotoxic T lymphocytes crucial for tumor immune surveillance. In this issue of The EMBO Journal, Bassoy et al (2017) show that the surface expression of certain glycans that favor recognition and killing by T cells depends on mitochondrial contacts with the endoplasmic reticulum, extending the function of this interface even to immune recognition. (Source: EMBO Journal)
Source: EMBO Journal - June 1, 2017 Category: Molecular Biology Authors: Lakshminarayanan, S., Scorrano, L. Tags: Cancer, Immunology, Metabolism News [amp ] Views Source Type: research

Endothelial basement membrane laminin 511 is essential for shear stress response
(Source: EMBO Journal)
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Di Russo, J., Luik, A.-L., Yousif, L., Budny, S., Oberleithner, H., Hofschröer, V., Klingauf, J., van Bavel, E., Bakker, E. N., Hellstrand, P., Bhattachariya, A., Albinsson, S., Pincet, F., Hallmann, R., Sorokin, L. M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Vascular Biology & Angiogenesis Corrigenda Source Type: research

Osteopontin attenuates aging-associated phenotypes of hematopoietic stem cells
(Source: EMBO Journal)
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Guidi, N., Sacma, M., Ständker, L., Soller, K., Marka, G., Eiwen, K., Weiss, J. M., Kirchhoff, F., Weil, T., Cancelas, J. A., Florian, M. C., Geiger, H. Tags: Ageing, Cell Adhesion, Polarity & Cytoskeleton, Stem Cells Corrigenda Source Type: research

Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs
NEAT1_2 long noncoding RNA (lncRNA) is the molecular scaffold of paraspeckle nuclear bodies. Here, we report an improved RNA extraction method: extensive needle shearing or heating of cell lysate in RNA extraction reagent improved NEAT1_2 extraction by 20-fold (a property we term "semi-extractability"), whereas using a conventional method NEAT1_2 was trapped in the protein phase. The improved extraction method enabled us to estimate that approximately 50 NEAT1_2 molecules are present in a single paraspeckle. Another architectural lncRNA, IGS16, also exhibited similar semi-extractability. A comparison of RNA-seq d...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Chujo, T., Yamazaki, T., Kawaguchi, T., Kurosaka, S., Takumi, T., Nakagawa, S., Hirose, T. Tags: Methods & Resources, Protein Biosynthesis & Quality Control, RNA Biology Source Type: research

USP49 negatively regulates tumorigenesis and chemoresistance through FKBP51-AKT signaling
The AKT pathway is a fundamental signaling pathway that mediates multiple cellular processes, such as cell proliferation and survival, angiogenesis, and glucose metabolism. We recently reported that the immunophilin FKBP51 is a scaffolding protein that can enhance PHLPP-AKT interaction and facilitate PHLPP-mediated dephosphorylation of AKT at Ser473, negatively regulating AKT activation. However, the regulation of FKBP51-PHLPP-AKT pathway remains unclear. Here we report that a deubiquitinase, USP49, is a new regulator of the AKT pathway. Mechanistically, USP49 deubiquitinates and stabilizes FKBP51, which in turn enhances P...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Luo, K., Li, Y., Yin, Y., Li, L., Wu, C., Chen, Y., Nowsheen, S., Hu, Q., Zhang, L., Lou, Z., Yuan, J. Tags: Cancer, Post-translational Modifications, Proteolysis & Proteomics, Signal Transduction Articles Source Type: research

STARD3 mediates endoplasmic reticulum-to-endosome cholesterol transport at membrane contact sites
StAR-related lipid transfer domain-3 (STARD3) is a sterol-binding protein that creates endoplasmic reticulum (ER)–endosome contact sites. How this protein, at the crossroad between sterol uptake and synthesis pathways, impacts the intracellular distribution of this lipid was ill-defined. Here, by using in situ cholesterol labeling and quantification, we demonstrated that STARD3 induces cholesterol accumulation in endosomes at the expense of the plasma membrane. STARD3-mediated cholesterol routing depends both on its lipid transfer activity and its ability to create ER–endosome contacts. Corroborating this,...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Wilhelm, L. P., Wendling, C., Vedie, B., Kobayashi, T., Chenard, M.-P., Tomasetto, C., Drin, G., Alpy, F. Tags: Membrane & Intracellular Transport Articles Source Type: research

The SAC1 domain in synaptojanin is required for autophagosome maturation at presynaptic terminals
Presynaptic terminals are metabolically active and accrue damage through continuous vesicle cycling. How synapses locally regulate protein homeostasis is poorly understood. We show that the presynaptic lipid phosphatase synaptojanin is required for macroautophagy, and this role is inhibited by the Parkinson's disease mutation R258Q. Synaptojanin drives synaptic endocytosis by dephosphorylating PI(4,5)P2, but this function appears normal in SynaptojaninRQ knock-in flies. Instead, R258Q affects the synaptojanin SAC1 domain that dephosphorylates PI(3)P and PI(3,5)P2, two lipids found in autophagosomal membranes. Using advance...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Vanhauwaert, R., Kuenen, S., Masius, R., Bademosi, A., Manetsberger, J., Schoovaerts, N., Bounti, L., Gontcharenko, S., Swerts, J., Vilain, S., Picillo, M., Barone, P., Munshi, S. T., de Vrij, F. M., Kushner, S. A., Gounko, N. V., Mandemakers, W., Bonifat Tags: Autophagy & Cell Death, Neuroscience Articles Source Type: research

let-7 regulates radial migration of new-born neurons through positive regulation of autophagy
During adult neurogenesis, newly formed olfactory bulb (OB) interneurons migrate radially to integrate into specific layers of the OB. Despite the importance of this process, the intracellular mechanisms that regulate radial migration remain poorly understood. Here, we find that microRNA (miRNA) let-7 regulates radial migration by modulating autophagy in new-born neurons. Using Argonaute2 immunoprecipitation, we performed global profiling of miRNAs in adult-born OB neurons and identified let-7 as a highly abundant miRNA family. Knockdown of let-7 in migrating neuroblasts prevented radial migration and led to an immature mo...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Petri, R., Pircs, K., Jönsson, M. E., Akerblom, M., Brattas, P. L., Klussendorf, T., Jakobsson, J. Tags: Development & Differentiation, Neuroscience Articles Source Type: research

A second Wpl1 anti-cohesion pathway requires dephosphorylation of fission yeast kleisin Rad21 by PP4
We report here that Wpl1 anti-cohesion function includes an additional mechanism. A genetic screen uncovered that Protein Phosphatase 4 (PP4) mutants allowed cell survival in the complete absence of Eso1. PP4 co-immunoprecipitated Wpl1 and cohesin and Wpl1 triggered Rad21 de-phosphorylation in a PP4-dependent manner. Relevant residues were identified and mapped within the central domain of Rad21. Phospho-mimicking alleles dampened Wpl1 anti-cohesion activity, while alanine mutants were neutral indicating that Rad21 phosphorylation would shelter cohesin from Wpl1 unless erased by PP4. Experiments in post-replicative cells l...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Birot, A., Eguienta, K., Vazquez, S., Claverol, S., Bonneu, M., Ekwall, K., Javerzat, J.-P., Vaur, S. Tags: Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Hypoxia enhances antibody-dependent dengue virus infection
Dengue virus (DENV) has been found to replicate in lymphoid organs such as the lymph nodes, spleen, and liver in post-mortem analysis. These organs are known to have low oxygen levels (~0.5–4.5% O2) due to the vascular anatomy. However, how physiologically low levels of oxygen affect DENV infection via hypoxia-induced changes in the immune response remains unknown. Here, we show that monocytes adapted to 3% O2 show greater susceptibility to antibody-dependent enhancement of DENV infection. Low oxygen level induces HIF1α-dependent upregulation of fragment crystallizable gamma receptor IIA (FcRIIA) as well as HIF...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Gan, E. S., Cheong, W. F., Chan, K. R., Ong, E. Z., Chai, X., Tan, H. C., Ghosh, S., Wenk, M. R., Ooi, E. E. Tags: Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Fatty acid synthesis is critical for stem cell pluripotency via promoting mitochondrial fission
Pluripotent stem cells are known to display distinct metabolic phenotypes than their somatic counterparts. While accumulating studies are focused on the roles of glucose and amino acid metabolism in facilitating pluripotency, little is known regarding the role of lipid metabolism in regulation of stem cell activities. Here, we show that fatty acid (FA) synthesis activation is critical for stem cell pluripotency. Our initial observations demonstrated enhanced lipogenesis in pluripotent cells and during cellular reprogramming. Further analysis indicated that de novo FA synthesis controls cellular reprogramming and embryonic ...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Wang, L., Zhang, T., Wang, L., Cai, Y., Zhong, X., He, X., Hu, L., Tian, S., Wu, M., Hui, L., Zhang, H., Gao, P. Tags: Metabolism, Stem Cells Articles Source Type: research

Self-organized developmental patterning and differentiation in cerebral organoids
Cerebral organoids recapitulate human brain development at a considerable level of detail, even in the absence of externally added signaling factors. The patterning events driving this self-organization are currently unknown. Here, we examine the developmental and differentiative capacity of cerebral organoids. Focusing on forebrain regions, we demonstrate the presence of a variety of discrete ventral and dorsal regions. Clearing and subsequent 3D reconstruction of entire organoids reveal that many of these regions are interconnected, suggesting that the entire range of dorso-ventral identities can be generated within cont...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Renner, M., Lancaster, M. A., Bian, S., Choi, H., Ku, T., Peer, A., Chung, K., Knoblich, J. A. Tags: Development & Differentiation Articles Source Type: research

Cancer cell metabolism: the essential role of the nonessential amino acid, glutamine
Biochemistry textbooks and cell culture experiments seem to be telling us two different things about the significance of external glutamine supply for mammalian cell growth and proliferation. Despite the fact that glutamine is a nonessential amino acid that can be synthesized by cells from glucose-derived carbons and amino acid-derived ammonia, most mammalian cells in tissue culture cannot proliferate or even survive in an environment that does not contain millimolar levels of glutamine. Not only are the levels of glutamine in standard tissue culture media at least ten-fold higher than other amino acids, but glutamine is a...
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Zhang, J., Pavlova, N. N., Thompson, C. B. Tags: Cancer, Metabolism Review Source Type: research

Revealing the inner workings of organoids
The mechanisms by which human stem cells self-organise into brain-like tissues in 3D organoid culture are poorly understood. In this issue of The EMBO Journal, Renner and Lancaster et al demonstrate that in the absence of external stimuli, human cerebral organoids develop large forebrain structures that display specific landmarks of spatial and temporal patterning, including signalling centres producing known morphogens. The generation of cerebral organoids is therefore likely to reflect normal brain development. (Source: EMBO Journal)
Source: EMBO Journal - May 15, 2017 Category: Molecular Biology Authors: Dias, C., Guillemot, F. Tags: Development & Differentiation News [amp ] Views Source Type: research

The retinoblastoma homolog RBR1 mediates localization of the repair protein RAD51 to DNA lesions in Arabidopsis
The retinoblastoma protein (Rb), which typically functions as a transcriptional repressor of E2F-regulated genes, represents a major control hub of the cell cycle. Here, we show that loss of the Arabidopsis Rb homolog RETINOBLASTOMA-RELATED 1 (RBR1) leads to cell death, especially upon exposure to genotoxic drugs such as the environmental toxin aluminum. While cell death can be suppressed by reduced cell-proliferation rates, rbr1 mutant cells exhibit elevated levels of DNA lesions, indicating a direct role of RBR1 in the DNA-damage response (DDR). Consistent with its role as a transcriptional repressor, we find that RBR1 d...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Biedermann, S., Harashima, H., Chen, P., Heese, M., Bouyer, D., Sofroni, K., Schnittger, A. Tags: Cell Cycle, DNA Replication, Repair & Recombination, Plant Biology Articles Source Type: research

Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control
The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic H2AX-labelled DNA damage foci in an ATM- and ATR-dependent manner. These H2AX-labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co-localise with RBR foci. RBR and AtBRCA1 physically interact in vitro and in planta...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Horvath, B. M., Kourova, H., Nagy, S., Nemeth, E., Magyar, Z., Papdi, C., Ahmad, Z., Sanchez-Perez, G. F., Perilli, S., Blilou, I., Pettko-Szandtner, A., Darula, Z., Meszaros, T., Binarova, P., Bogre, L., Scheres, B. Tags: Cell Cycle, DNA Replication, Repair & Recombination, Plant Biology Articles Source Type: research

A covalently bound inhibitor triggers EZH2 degradation through CHIP-mediated ubiquitination
Enhancer of zeste homolog 2 (EZH2) has been characterized as a critical oncogene and a promising drug target in human malignant tumors. The current EZH2 inhibitors strongly suppress the enhanced enzymatic function of mutant EZH2 in some lymphomas. However, the recent identification of a PRC2- and methyltransferase-independent role of EZH2 indicates that a complete suppression of all oncogenic functions of EZH2 is needed. Here, we report a unique EZH2-targeting strategy by identifying a gambogenic acid (GNA) derivative as a novel agent that specifically and covalently bound to Cys668 within the EZH2-SET domain, triggering E...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Wang, X., Cao, W., Zhang, J., Yan, M., Xu, Q., Wu, X., Wan, L., Zhang, Z., Zhang, C., Qin, X., Xiao, M., Ye, D., Liu, Y., Han, Z., Wang, S., Mao, L., Wei, W., Chen, W. Tags: Cancer, Chromatin, Epigenetics, Genomics & Functional Genomics, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

MTCL1 plays an essential role in maintaining Purkinje neuron axon initial segment
In this study, we demonstrate that in vivo knockdown of microtubule cross-linking factor 1 (MTCL1) in cerebellar Purkinje cells causes loss of axonal polarity coupled with AnkG mislocalization. MTCL1 lacking MT-stabilizing activity failed to restore these defects, and stable MT bundles spanning the AIS were disorganized in knockdown cells. Interestingly, during early postnatal development, colocalization of MTCL1 with these stable MT bundles was observed prominently in the axon hillock and proximal axon. These results indicate that MTCL1-mediated formation of stable MT bundles is crucial for maintenance of AnkG locali...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Satake, T., Yamashita, K., Hayashi, K., Miyatake, S., Tamura-Nakano, M., Doi, H., Furuta, Y., Shioi, G., Miura, E., Takeo, Y. H., Yoshida, K., Yahikozawa, H., Matsumoto, N., Yuzaki, M., Suzuki, A. Tags: Neuroscience Articles Source Type: research

miR-31 mutants reveal continuous glial homeostasis in the adult Drosophila brain
The study of adult neural cell production has concentrated on neurogenesis. The mechanisms controlling adult gliogenesis are still poorly understood. Here, we provide evidence for a homeostatic process that maintains the population of glial cells in the Drosophila adult brain. Flies lacking microRNA miR-31a start adult life with a normal complement of glia, but transiently lose glia due to apoptosis. miR-31a expression identifies a subset of predominantly gliogenic adult neural progenitor cells. Failure to limit expression of the predicted E3 ubiquitin ligase, Rchy1, in these cells results in glial loss. After an initial d...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Foo, L. C., Song, S., Cohen, S. M. Tags: Development & Differentiation, Neuroscience Articles Source Type: research

Sex-specific, reciprocal regulation of ER{alpha} and miR-22 controls muscle lipid metabolism in male mice
Control of energy homeostasis and metabolism is achieved by integrating numerous pathways, and miRNAs are involved in this process by regulating expression of multiple target genes. However, relatively little is known about the posttranscriptional processing of miRNAs and a potential role for the precursors they derive from. Here, we demonstrate that mature miRNA-22 is more abundant in muscle from male mice relative to females and that this enables sex-specific regulation of muscular lipid metabolism and body weight by repressing estrogen receptor alpha (ERα) expression. We found that the ERα adjusts its own ac...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Schweisgut, J., Schutt, C., Wüst, S., Wietelmann, A., Ghesquiere, B., Carmeliet, P., Dröse, S., Korach, K. S., Braun, T., Boettger, T. Tags: Metabolism, RNA Biology Articles Source Type: research

An ATR-dependent function for the Ddx19 RNA helicase in nuclear R-loop metabolism
Coordination between transcription and replication is crucial in the maintenance of genome integrity. Disturbance of these processes leads to accumulation of aberrant DNA:RNA hybrids (R-loops) that, if unresolved, generate DNA damage and genomic instability. Here we report a novel, unexpected role for the nucleopore-associated mRNA export factor Ddx19 in removing nuclear R-loops formed upon replication stress or DNA damage. We show, in live cells, that Ddx19 transiently relocalizes from the nucleopore to the nucleus upon DNA damage, in an ATR/Chk1-dependent manner, and that Ddx19 nuclear relocalization is required to clear...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Hodroj, D., Recolin, B., Serhal, K., Martinez, S., Tsanov, N., Abou Merhi, R., Maiorano, D. Tags: DNA Replication, Repair & Recombination, RNA Biology Articles Source Type: research

Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis
We present a docking model of Rae1 bound to the B. subtilis ribosomal A-site that is consistent with this hypothesis and show that Rae1 cleaves optimally immediately upstream of a lysine codon (AAA or AAG) in vivo. (Source: EMBO Journal)
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Leroy, M., Piton, J., Gilet, L., Pellegrini, O., Proux, C., Coppee, J.-Y., Figaro, S., Condon, C. Tags: Microbiology, Virology & Host Pathogen Interaction, Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

The linear ubiquitin chain assembly complex regulates TRAIL-induced gene activation and cell death
The linear ubiquitin chain assembly complex (LUBAC) is the only known E3 ubiquitin ligase which catalyses the generation of linear ubiquitin linkages de novo. LUBAC is a crucial component of various immune receptor signalling pathways. Here, we show that LUBAC forms part of the TRAIL-R-associated complex I as well as of the cytoplasmic TRAIL-induced complex II. In both of these complexes, HOIP limits caspase-8 activity and, consequently, apoptosis whilst being itself cleaved in a caspase-8-dependent manner. Yet, by limiting the formation of a RIPK1/RIPK3/MLKL-containing complex, LUBAC also restricts TRAIL-induced necroptos...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Lafont, E., Kantari-Mimoun, C., Draber, P., De Miguel, D., Hartwig, T., Reichert, M., Kupka, S., Shimizu, Y., Taraborrelli, L., Spit, M., Sprick, M. R., Walczak, H. Tags: Autophagy & Cell Death, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Uncoupling of neurogenesis and differentiation during retinal development
Conventionally, neuronal development is regarded to follow a stereotypic sequence of neurogenesis, migration, and differentiation. We demonstrate that this notion is not a general principle of neuronal development by documenting the timing of mitosis in relation to multiple differentiation events for bipolar cells (BCs) in the zebrafish retina using in vivo imaging. We found that BC progenitors undergo terminal neurogenic divisions while in markedly disparate stages of neuronal differentiation. Remarkably, the differentiation state of individual BC progenitors at mitosis is not arbitrary but matches the differentiatio...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Engerer, P., Suzuki, S. C., Yoshimatsu, T., Chapouton, P., Obeng, N., Odermatt, B., Williams, P. R., Misgeld, T., Godinho, L. Tags: Development & Differentiation, Neuroscience Articles Source Type: research

Non-coding RNAs: the dark side of nuclear-mitochondrial communication
Mitochondria are critical hubs for the integration of several key metabolic processes implicated in cell growth and survival. They originated from bacterial ancestors through endosymbiosis, following the transfer of more than 90% of their endosymbiont genome to the host cell nucleus. Over time, a mutually beneficial symbiotic relationship has been established, which relies on continuous and elaborate signaling mechanisms between this life-essential organelle and its host. The ability of mitochondria to signal their functional state and trigger compensatory and adaptive cellular responses has long been recognized, but the u...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Vendramin, R., Marine, J.-C., Leucci, E. Tags: Metabolism, RNA Biology, Signal Transduction Review Source Type: research

Cut in translation: ribosome-dependent mRNA decay
Transcription and translation are two complex mechanisms that are tightly coupled in prokaryotic cells. Even before the completion of transcription, ribosomes attach to the nascent mRNA and initiate protein synthesis. Remarkably, recent publications have indicated an association between translation and decay of certain mRNAs. In this issue of The EMBO Journal, Leroy et al (2017) depicts a fascinating mechanism of mRNA degradation, which involves the ribosome-associated ribonuclease Rae1 in Bacillus subtilis. In a translation-dependent manner, Rae1 binds the ribosomal aminoacylation (A)-site and cleaves between specifi...
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Lalaouna, D., Masse, E. Tags: Microbiology, Virology & Host Pathogen Interaction, Protein Biosynthesis & Quality Control, RNA Biology News [amp ] Views Source Type: research

TRAIL- and TNF-induced signaling complexes--so similar yet so different
TNF receptor-1 (TNFR1) and TRAIL death receptors preferentially induce pro-inflammatory or cytotoxic signaling, respectively, via distinct plasma membrane and cytosolic complexes. New studies identifying the pro-inflammatory factors TRAF2, RIP, and LUBAC in TRAIL death receptor complexes suggest that the latter are more "TNFR1-like" than anticipated and argue for revision of prevailing models of spatio-hierarchical TRAIL-induced signaling complex assembly. (Source: EMBO Journal)
Source: EMBO Journal - May 2, 2017 Category: Molecular Biology Authors: Wajant, H. Tags: Autophagy & Cell Death, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Development of LC3/GABARAP sensors containing a LIR and a hydrophobic domain to monitor autophagy
Macroautophagy allows for bulk degradation of cytosolic components in lysosomes. Overexpression of GFP/RFP-LC3/GABARAP is commonly used to monitor autophagosomes, a hallmark of autophagy, despite artifacts related to their overexpression. Here, we developed new sensors that detect endogenous LC3/GABARAP proteins at the autophagosome using an LC3-interacting region (LIR) and a short hydrophobic domain (HyD). Among HyD-LIR-GFP sensors harboring LIR motifs of 34 known LC3-binding proteins, HyD-LIR(TP)-GFP using the LIR motif from TP53INP2 allowed detection of all LC3/GABARAPs-positive autophagosomes. However, HyD-LIR(TP)-GFP ...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Lee, Y.-K., Jun, Y.-W., Choi, H.-E., Huh, Y. H., Kaang, B.-K., Jang, D.-J., Lee, J.-A. Tags: Autophagy & Cell Death Resource Source Type: research

Functional and structural insight into properdin control of complement alternative pathway amplification
We describe here a novel FP deficiency (E244K) caused by a single point mutation which results in a very low level of AP activity. Recombinant FP E244K is monomeric, fails to support bacteriolysis, and binds weakly to C3 products. We compare this to a monomeric unit excised from oligomeric FP, which is also dysfunctional in bacteriolysis but binds the AP proconvertase, C3 convertase, C3 products and partially stabilizes the convertase. The crystal structure of such a FP-convertase complex suggests that the major contact between FP and the AP convertase is mediated by a single FP thrombospondin repeat and a small region in ...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Pedersen, D. V., Roumenina, L., Jensen, R. K., Gadeberg, T. A., Marinozzi, C., Picard, C., Rybkine, T., Thiel, S., Sorensen, U. B., Stover, C., Fremeaux-Bacchi, V., Andersen, G. R. Tags: Immunology, Structural Biology Articles Source Type: research

Ataxin-3 consolidates the MDC1-dependent DNA double-strand break response by counteracting the SUMO-targeted ubiquitin ligase RNF4
The SUMO-targeted ubiquitin ligase RNF4 functions at the crossroads of the SUMO and ubiquitin systems. Here, we report that the deubiquitylation enzyme (DUB) ataxin-3 counteracts RNF4 activity during the DNA double-strand break (DSB) response. We find that ataxin-3 negatively regulates ubiquitylation of the checkpoint mediator MDC1, a known RNF4 substrate. Loss of ataxin-3 markedly decreases the chromatin dwell time of MDC1 at DSBs, which can be fully reversed by co-depletion of RNF4. Ataxin-3 is recruited to DSBs in a SUMOylation-dependent fashion, and in vitro it directly interacts with and is stimulated by recombin...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Pfeiffer, A., Luijsterburg, M. S., Acs, K., Wiegant, W. W., Helfricht, A., Herzog, L. K., Minoia, M., Böttcher, C., Salomons, F. A., van Attikum, H., Dantuma, N. P. Tags: DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Mitochondrial chaperone HSP-60 regulates anti-bacterial immunity via p38 MAP kinase signaling
Mitochondria play key roles in cellular immunity. How mitochondria contribute to organismal immunity remains poorly understood. Here, we show that HSP-60/HSPD1, a major mitochondrial chaperone, boosts anti-bacterial immunity through the up-regulation of p38 MAP kinase signaling. We first identify 16 evolutionarily conserved mitochondrial components that affect the immunity of Caenorhabditis elegans against pathogenic Pseudomonas aeruginosa (PA14). Among them, the mitochondrial chaperone HSP-60 is necessary and sufficient to increase resistance to PA14. We show that HSP-60 in the intestine and neurons is crucial for the res...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Jeong, D.-E., Lee, D., Hwang, S.-Y., Lee, Y., Lee, J.-E., Seo, M., Hwang, W., Seo, K., Hwang, A. B., Artan, M., Son, H. G., Jo, J.-H., Baek, H., Oh, Y. M., Ryu, Y., Kim, H.-J., Ha, C. M., Yoo, J.-Y., Lee, S.-J. V. Tags: Immunology, Signal Transduction Articles Source Type: research

Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA
Research into post-transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and Salmonella enterica has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ-dependent sRNAs are largely unknown. Here, we report in Salmonella Typhimurium the mode-of-action of RaiZ, a ProQ-dependent sRNA that is made fro...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Smirnov, A., Wang, C., Drewry, L. L., Vogel, J. Tags: Microbiology, Virology & Host Pathogen Interaction, Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Regulation of hypoxia responses by flavin adenine dinucleotide-dependent modulation of HIF-1{alpha} protein stability
Oxygen deprivation induces a range of cellular adaptive responses that enable to drive cancer progression. Here, we report that lysine-specific demethylase 1 (LSD1) upregulates hypoxia responses by demethylating RACK1 protein, a component of hypoxia-inducible factor (HIF) ubiquitination machinery, and consequently suppressing the oxygen-independent degradation of HIF-1α. This ability of LSD1 is attenuated during prolonged hypoxia, with a decrease in the cellular level of flavin adenine dinucleotide (FAD), a metabolic cofactor of LSD1, causing HIF-1α downregulation in later stages of hypoxia. Exogenously provide...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Yang, S.-J., Park, Y. S., Cho, J. H., Moon, B., An, H.-J., Lee, J. Y., Xie, Z., Wang, Y., Pocalyko, D., Lee, D. C., Sohn, H. A., Kang, M., Kim, J. Y., Kim, E., Park, K. C., Kim, J.-A., Yeom, Y. I. Tags: Cancer, Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

AKT-phosphorylated FOXO1 suppresses ERK activation and chemoresistance by disrupting IQGAP1-MAPK interaction
Nuclear FOXO proteins act as tumor suppressors by transcriptionally activating genes involved in apoptosis and cell cycle arrest, and these anticancer functions are inhibited by AKT-induced phosphorylation and cytoplasmic sequestration of FOXOs. We found that, after AKT-mediated phosphorylation at serine 319, FOXO1 binds to IQGAP1, a hub for activation of the MAPK pathway, and impedes IQGAP1-dependent phosphorylation of ERK1/2 (pERK1/2). Conversely, decreased FOXO1 expression increases pERK1/2 in cancer cell lines and correlates with increased pERK1/2 levels in patient specimens and disease progression. Treatment of cancer...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Pan, C.-W., Jin, X., Zhao, Y., Pan, Y., Yang, J., Karnes, R. J., Zhang, J., Wang, L., Huang, H. Tags: Cancer, Signal Transduction Articles Source Type: research

PRC2 is dispensable for HOTAIR-mediated transcriptional repression
Long non-coding RNAs (lncRNAs) play diverse roles in physiological and pathological processes. Several lncRNAs have been suggested to modulate gene expression by guiding chromatin-modifying complexes to specific sites in the genome. However, besides the example of Xist, clear-cut evidence demonstrating this novel mode of regulation remains sparse. Here, we focus on HOTAIR, a lncRNA that is overexpressed in several tumor types and previously proposed to play a key role in gene silencing through direct recruitment of Polycomb Repressive Complex 2 (PRC2) to defined genomic loci. Using genetic tools and a novel RNA-tethering s...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Portoso, M., Ragazzini, R., Brencic, Z., Moiani, A., Michaud, A., Vassilev, I., Wassef, M., Servant, N., Sargueil, B., Margueron, R. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, RNA Biology, Transcription Articles Source Type: research

Gene-body chromatin modification dynamics mediate epigenome differentiation in Arabidopsis
Heterochromatin is marked by methylation of lysine 9 on histone H3 (H3K9me). A puzzling feature of H3K9me is that this modification localizes not only in promoters but also in internal regions (bodies) of silent transcription units. Despite its prevalence, the biological significance of gene-body H3K9me remains enigmatic. Here we show that H3K9me-associated removal of H3K4 monomethylation (H3K4me1) in gene bodies mediates transcriptional silencing. Mutations in an Arabidopsis H3K9 demethylase gene IBM1 induce ectopic H3K9me2 accumulation in gene bodies, with accompanying severe developmental defects. Through suppressor scr...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Inagaki, S., Takahashi, M., Hosaka, A., Ito, T., Toyoda, A., Fujiyama, A., Tarutani, Y., Kakutani, T. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Plant Biology, Transcription Articles Source Type: research

And Akt-ion! IQGAP1 in control of signaling pathways
ERK signaling and Akt signaling are inversely correlated in some cancers. Yet, the precise molecular mechanism for cross-inhibition remains unclear. In this issue of The EMBO Journal, Pan et al (2017) show that when Akt is on, its phosphorylated cytoplasmic substrate FOXO1 turns off ERK activity by reshaping the Ras-ERK scaffold IQGAP1. (Source: EMBO Journal)
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Choi, S., Anderson, R. A. Tags: Cancer, Signal Transduction News [amp ] Views Source Type: research

Re-evaluating the foundations of lncRNA-Polycomb function
This study raises important questions about the role of PRC2 interactions for lncRNA-mediated functions and argues for a re-evaluation of this lncRNA–PRC2 functional paradigm. (Source: EMBO Journal)
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Blanco, M. R., Guttman, M. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, RNA Biology, Transcription News [amp ] Views Source Type: research

Non-canonical aging model systems and why we need them
Aging is one of the greatest challenges for biomedical research in the developed world. The continuing increase in lifespan without accompanying increases in health span has extreme economic and societal implications for an aging society. The majority of adult-onset diseases such as cancer, cardiovascular disease, and Alzheimer's are a direct consequence of aging, and with changing demographics, more and more people are afflicted. If we knew how to slow down the negative effects of aging, we could delay or prevent all of these diseases at once. We therefore need to understand the underlying molecular mechanisms of aging an...
Source: EMBO Journal - April 13, 2017 Category: Molecular Biology Authors: Valenzano, D. R., Aboobaker, A., Seluanov, A., Gorbunova, V. Tags: Ageing Commentary Source Type: research

Mechanism of formate-nitrite transporters by dielectric shift of substrate acidity
Bacterial formate–nitrite transporters (FNTs) regulate the metabolic flow of small, weak mono-acids. Recently, the eukaryotic PfFNT was identified as the malaria parasite's lactate transporter and novel drug target. Despite crystal data, central mechanisms of FNT gating and transport remained unclear. Here, we show elucidation of the FNT transport mechanism by single-step substrate protonation involving an invariant lysine in the periplasmic vestibule. Opposing earlier gating hypotheses and electrophysiology reports, quantification of total uptake by radiolabeled substrate indicates a permanently open conformation of...
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Wiechert, M., Beitz, E. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression
The 7SK small nuclear RNP (snRNP), composed of the 7SK small nuclear RNA (snRNA), MePCE, and Larp7, regulates the mRNA elongation capacity of RNA polymerase II (RNAPII) through controlling the nuclear activity of positive transcription elongation factor b (P-TEFb). Here, we demonstrate that the human 7SK snRNP also functions as a canonical transcription factor that, in collaboration with the little elongation complex (LEC) comprising ELL, Ice1, Ice2, and ZC3H8, promotes transcription of RNAPII-specific spliceosomal snRNA and small nucleolar RNA (snoRNA) genes. The 7SK snRNA specifically associates with a fraction of RNAPII...
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Egloff, S., Vitali, P., Tellier, M., Raffel, R., Murphy, S., Kiss, T. Tags: RNA Biology, Transcription Articles Source Type: research

The crystal structure of Zika virus NS5 reveals conserved drug targets
Zika virus (ZIKV) has emerged as major health concern, as ZIKV infection has been shown to be associated with microcephaly, severe neurological disease and possibly male sterility. As the largest protein component within the ZIKV replication complex, NS5 plays key roles in the life cycle and survival of the virus through its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent RNA polymerase (RdRp) domains. Here, we present the crystal structures of ZIKV NS5 MTase in complex with an RNA cap analogue (m7GpppA) and the free NS5 RdRp. We have identified the conserved features of ZIKV NS5 MTase and RdRp structures...
Source: EMBO Journal - April 3, 2017 Category: Molecular Biology Authors: Duan, W., Song, H., Wang, H., Chai, Y., Su, C., Qi, J., Shi, Y., Gao, G. F. Tags: Microbiology, Virology & Host Pathogen Interaction, Structural Biology Articles Source Type: research

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

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

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

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

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

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

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