SHLD2/FAM35A co-operates with REV7 to coordinate DNA double-strand break repair pathway choice
DNA double-strand breaks (DSBs) can be repaired by two major pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). DNA repair pathway choice is governed by the opposing activities of 53BP1, in complex with its effectors RIF1 and REV7, and BRCA1. However, it remains unknown how the 53BP1/RIF1/REV7 complex stimulates NHEJ and restricts HR to the S/G2 phases of the cell cycle. Using a mass spectrometry (MS)-based approach, we identify 11 high-confidence REV7 interactors and elucidate the role of SHLD2 (previously annotated as FAM35A and RINN2) as an effector of REV7 in the NHEJ pathway. FAM35A depleti...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Findlay, S., Heath, J., Luo, V. M., Malina, A., Morin, T., Coulombe, Y., Djerir, B., Li, Z., Samiei, A., Simo-Cheyou, E., Karam, M., Bagci, H., Rahat, D., Grapton, D., Lavoie, E. G., Dove, C., Khaled, H., Kuasne, H., Mann, K. K., Klein, K. O., Greenwood, Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Queuosine-modified tRNAs confer nutritional control of protein translation
Global protein translation as well as translation at the codon level can be regulated by tRNA modifications. In eukaryotes, levels of tRNA queuosinylation reflect the bioavailability of the precursor queuine, which is salvaged from the diet and gut microbiota. We show here that nutritionally determined Q-tRNA levels promote Dnmt2-mediated methylation of tRNA Asp and control translational speed of Q-decoded codons as well as at near-cognate codons. Deregulation of translation upon queuine depletion results in unfolded proteins that trigger endoplasmic reticulum stress and activation of the unfolded protein response, both in...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Tuorto, F., Legrand, C., Cirzi, C., Federico, G., Liebers, R., Müller, M., Ehrenhofer-Murray, A. E., Dittmar, G., Gröne, H.-J., Lyko, F. Tags: Metabolism, Protein Biosynthesis & Quality Control, RNA Biology Articles Source Type: research

Deficiency in the nuclear long noncoding RNA Charme causes myogenic defects and heart remodeling in mice
Myogenesis is a highly regulated process that involves the conversion of progenitor cells into multinucleated myofibers. Besides proteins and miRNAs, long noncoding RNAs (lncRNAs) have been shown to participate in myogenic regulatory circuitries. Here, we characterize a murine chromatin-associated muscle-specific lncRNA, Charme, which contributes to the robustness of the myogenic program in vitro and in vivo. In myocytes, Charme depletion triggers the disassembly of a specific chromosomal domain and the downregulation of myogenic genes contained therein. Notably, several Charme-sensitive genes are associated...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Ballarino, M., Cipriano, A., Tita, R., Santini, T., Desideri, F., Morlando, M., Colantoni, A., Carrieri, C., Nicoletti, C., Musaro, A., Carroll, D. O., Bozzoni, I. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, RNA Biology, Vascular Biology & Angiogenesis Articles Source Type: research

Zika virus elicits inflammation to evade antiviral response by cleaving cGAS via NS1-caspase-1 axis
Viral infection triggers host innate immune responses, which primarily include the activation of type I interferon (IFN) signaling and inflammasomes. Here, we report that Zika virus (ZIKV) infection triggers NLRP3 inflammasome activation, which is further enhanced by viral non-structural protein NS1 to benefit its replication. NS1 recruits the host deubiquitinase USP8 to cleave K11-linked poly-ubiquitin chains from caspase-1 at Lys134, thus inhibiting the proteasomal degradation of caspase-1. The enhanced stabilization of caspase-1 by NS1 promotes the cleavage of cGAS, which recognizes mitochondrial DNA release and initiat...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Zheng, Y., Liu, Q., Wu, Y., Ma, L., Zhang, Z., Liu, T., Jin, S., She, Y., Li, Y.-P., Cui, J. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

One-step CRISPR/Cas9 method for the rapid generation of human antibody heavy chain knock-in mice
Here, we describe a one-step, in vivo CRISPR/Cas9 nuclease-mediated strategy to generate knock-in mice. We produced knock-in (KI) mice wherein a 1.9-kb DNA fragment bearing a pre-arranged human B-cell receptor heavy chain was recombined into the native murine immunoglobulin locus. Our methodology relies on Cas9 nuclease-induced double-stranded breaks directed by two sgRNAs to occur within the specific target locus of fertilized oocytes. These double-stranded breaks are subsequently repaired via homology-directed repair by a plasmid-borne template containing the pre-arranged human immunoglobulin heavy chain. To validat...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Lin, Y.-C., Pecetta, S., Steichen, J. M., Kratochvil, S., Melzi, E., Arnold, J., Dougan, S. K., Wu, L., Kirsch, K. H., Nair, U., Schief, W. R., Batista, F. D. Tags: Genetics, Gene Therapy & Genetic Disease, Immunology Resource Source Type: research

DCAF13 promotes pluripotency by negatively regulating SUV39H1 stability during early embryonic development
Mammalian oocytes and zygotes have the unique ability to reprogram a somatic cell nucleus into a totipotent state. SUV39H1/2-mediated histone H3 lysine-9 trimethylation (H3K9me3) is a major barrier to efficient reprogramming. How SUV39H1/2 activities are regulated in early embryos and during generation of induced pluripotent stem cells (iPSCs) remains unclear. Since expression of the CRL4 E3 ubiquitin ligase in oocytes is crucial for female fertility, we analyzed putative CRL4 adaptors (DCAFs) and identified DCAF13 as a novel CRL4 adaptor that is essential for preimplantation embryonic development. Dcaf13 is expressed from...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Zhang, Y.-L., Zhao, L.-W., Zhang, J., Le, R., Ji, S.-Y., Chen, C., Gao, Y., Li, D., Gao, S., Fan, H.-Y. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, Stem Cells Articles Source Type: research

Parkinson's disease: convergence on synaptic homeostasis
Parkinson's disease, the second most common neurodegenerative disorder, affects millions of people globally. There is no cure, and its prevalence will double by 2030. In recent years, numerous causative genes and risk factors for Parkinson's disease have been identified and more than half appear to function at the synapse. Subtle synaptic defects are thought to precede blunt neuronal death, but the mechanisms that are dysfunctional at synapses are only now being unraveled. Here, we review recent work and propose a model where different Parkinson proteins interact in a cell compartment-specific manner at the synapse where t...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Soukup, S.-F., Vanhauwaert, R., Verstreken, P. Tags: Molecular Biology of Disease, Neuroscience Review Source Type: research

Error-free DNA damage tolerance pathway is facilitated by the Irc5 translocase through cohesin
DNA damage tolerance (DDT) mechanisms facilitate replication resumption and completion when DNA replication is blocked by bulky DNA lesions. In budding yeast, template switching (TS) via the Rad18/Rad5 pathway is a favored DDT pathway that involves usage of the sister chromatid as a template to bypass DNA lesions in an error-free recombination-like process. Here, we establish that the Snf2 family translocase Irc5 is a novel factor that promotes TS and averts single-stranded DNA persistence during replication. We demonstrate that, during replication stress, Irc5 enables replication progression by assisting enrichment of coh...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Litwin, I., Bakowski, T., Szakal, B., Pilarczyk, E., Maciaszczyk-Dziubinska, E., Branzei, D., Wysocki, R. Tags: Cell Cycle, DNA Replication, Repair & Recombination Articles Source Type: research

TRIM16 controls assembly and degradation of protein aggregates by modulating the p62-NRF2 axis and autophagy
Sequestration of protein aggregates in inclusion bodies and their subsequent degradation prevents proteostasis imbalance, cytotoxicity, and proteinopathies. The underlying molecular mechanisms controlling the turnover of protein aggregates are mostly uncharacterized. Herein, we show that a TRIM family protein, TRIM16, governs the process of stress-induced biogenesis and degradation of protein aggregates. TRIM16 facilitates protein aggregate formation by positively regulating the p62-NRF2 axis. We show that TRIM16 is an integral part of the p62-KEAP1-NRF2 complex and utilizes multiple mechanisms for stabilizing NRF2. Under ...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Jena, K. K., Kolapalli, S. P., Mehto, S., Nath, P., Das, B., Sahoo, P. K., Ahad, A., Syed, G. H., Raghav, S. K., Senapati, S., Chauhan, S., Chauhan, S. Tags: Autophagy & Cell Death, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling
Multi-subunit cullin-RING ligases (CRLs) are the largest family of ubiquitin E3 ligases in humans. CRL activity is tightly regulated to prevent unintended substrate degradation or autocatalytic degradation of CRL subunits. Using a proteomics strategy, we discovered that CRL4AMBRA1 (CRL substrate receptor denoted in superscript) targets Elongin C (ELOC), the essential adapter protein of CRL5 complexes, for polyubiquitination and degradation. We showed that the ubiquitin ligase function of CRL4AMBRA1 is required to disrupt the assembly and attenuate the ligase activity of human CRL5SOCS3 and HIV-1 CRL5VIF complexes as AMBRA1...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Chen, S.-H., Jang, G. M., Hüttenhain, R., Gordon, D. E., Du, D., Newton, B. W., Johnson, J. R., Hiatt, J., Hultquist, J. F., Johnson, T. L., Liu, Y.-L., Burton, L. A., Ye, J., Reichermeier, K. M., Stroud, R. M., Marson, A., Debnath, J., Gross, J. Tags: Autophagy & Cell Death, Post-translational Modifications, Proteolysis & Proteomics, Systems & Computational Biology Articles Source Type: research

MIWI2 targets RNAs transcribed from piRNA-dependent regions to drive DNA methylation in mouse prospermatogonia
Argonaute/Piwi proteins can regulate gene expression via RNA degradation and translational regulation using small RNAs as guides. They also promote the establishment of suppressive epigenetic marks on repeat sequences in diverse organisms. In mice, the nuclear Piwi protein MIWI2 and Piwi-interacting RNAs (piRNAs) are required for DNA methylation of retrotransposon sequences and some other sequences. However, its underlying molecular mechanisms remain unclear. Here, we show that piRNA-dependent regions are transcribed at the stage when piRNA-mediated DNA methylation takes place. MIWI2 specifically interacts with RNAs from t...
Source: EMBO Journal - September 14, 2018 Category: Molecular Biology Authors: Watanabe, T., Cui, X., Yuan, Z., Qi, H., Lin, H. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Development & Differentiation, RNA Biology Articles Source Type: research

MIM through MOM: the awakening of Bax and Bak pores
The mechanism whereby mitochondrial DNA (mtDNA) is released into the cytosol and activates the cGAS/STING inflammatory pathway during Bax/Bax-mediated apoptosis is unknown. In this issue, Riley et al (2018) report that widening of Bax and Bak pores on the mitochondrial outer membrane (MOM) during apoptosis allows the extrusion of the mitochondrial inner membrane (MIM) into the cytosol and its permeabilization to release mtDNA independently of caspases. In this scenario, Bax and Bak emerge as key modulators of the apoptotic immunogenic response. (Source: EMBO Journal)
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Cosentino, K., Garcia-Saez, A. J. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Signal Transduction News [amp ] Views Source Type: research

Hip to the Game: YAP/TAZ is required for nonmelanoma skin cancers
Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the two most common skin cancers found in humans. These cancers can acquire drug resistance and pose considerable medical burdens to clinics and patients if left untreated. Two recent studies show that active Hippo signaling plays a critical role in initiating BCC and SCC tumorigenesis, providing new opportunities to develop therapies against these skin malignancies. (Source: EMBO Journal)
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Miranda, M. M., Lowry, W. E. Tags: Cancer, Signal Transduction News [amp ] Views Source Type: research

Small molecule inhibitors reveal an indispensable scaffolding role of RIPK2 in NOD2 signaling
RIPK2 mediates inflammatory signaling by the bacteria-sensing receptors NOD1 and NOD2. Kinase inhibitors targeting RIPK2 are a proposed strategy to ameliorate NOD-mediated pathologies. Here, we reveal that RIPK2 kinase activity is dispensable for NOD2 inflammatory signaling and show that RIPK2 inhibitors function instead by antagonizing XIAP-binding and XIAP-mediated ubiquitination of RIPK2. We map the XIAP binding site on RIPK2 to the loop between β2 and β3 of the N-lobe of the kinase, which is in close proximity to the ATP-binding pocket. Through characterization of a new series of ATP pocket-binding RIPK2 inhi...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Hrdinka, M., Schlicher, L., Dai, B., Pinkas, D. M., Bufton, J. C., Picaud, S., Ward, J. A., Rogers, C., Suebsuwong, C., Nikhar, S., Cuny, G. D., Huber, K. V., Filippakopoulos, P., Bullock, A. N., Degterev, A., Gyrd-Hansen, M. Tags: Autophagy & Cell Death, Immunology Articles Source Type: research

ER-to-lysosome-associated degradation of proteasome-resistant ATZ polymers occurs via receptor-mediated vesicular transport
Maintenance of cellular proteostasis relies on efficient clearance of defective gene products. For misfolded secretory proteins, this involves dislocation from the endoplasmic reticulum (ER) into the cytosol followed by proteasomal degradation. However, polypeptide aggregation prevents cytosolic dislocation and instead activates ill-defined lysosomal catabolic pathways. Here, we describe an ER-to-lysosome-associated degradation pathway (ERLAD) for proteasome-resistant polymers of alpha1-antitrypsin Z (ATZ). ERLAD involves the ER-chaperone calnexin (CNX) and the engagement of the LC3 lipidation machinery by the ER-resident ...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Fregno, I., Fasana, E., Bergmann, T. J., Raimondi, A., Loi, M., Solda, T., Galli, C., D'Antuono, R., Morone, D., Danieli, A., Paganetti, P., van Anken, E., Molinari, M. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Mitochondrial inner membrane permeabilisation enables mtDNA release during apoptosis
During apoptosis, pro-apoptotic BAX and BAK are activated, causing mitochondrial outer membrane permeabilisation (MOMP), caspase activation and cell death. However, even in the absence of caspase activity, cells usually die following MOMP. Such caspase-independent cell death is accompanied by inflammation that requires mitochondrial DNA (mtDNA) activation of cGAS-STING signalling. Because the mitochondrial inner membrane is thought to remain intact during apoptosis, we sought to address how matrix mtDNA could activate the cytosolic cGAS-STING signalling pathway. Using super-resolution imaging, we show that mtDNA is efficie...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Riley, J. S., Quarato, G., Cloix, C., Lopez, J., O'Prey, J., Pearson, M., Chapman, J., Sesaki, H., Carlin, L. M., Passos, J. F., Wheeler, A. P., Oberst, A., Ryan, K. M., Tait, S. W. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Signal Transduction Articles Source Type: research

Rtt105 functions as a chaperone for replication protein A to preserve genome stability
Generation of single-stranded DNA (ssDNA) is required for the template strand formation during DNA replication. Replication Protein A (RPA) is an ssDNA-binding protein essential for protecting ssDNA at replication forks in eukaryotic cells. While significant progress has been made in characterizing the role of the RPA–ssDNA complex, how RPA is loaded at replication forks remains poorly explored. Here, we show that the Saccharomyces cerevisiae protein regulator of Ty1 transposition 105 (Rtt105) binds RPA and helps load it at replication forks. Cells lacking Rtt105 exhibit a dramatic reduction in RPA loading at replica...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Li, S., Xu, Z., Xu, J., Zuo, L., Yu, C., Zheng, P., Gan, H., Wang, X., Li, L., Sharma, S., Chabes, A., Li, D., Wang, S., Zheng, S., Li, J., Chen, X., Sun, Y., Xu, D., Han, J., Chan, K., Qi, Z., Feng, J., Li, Q. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

KIF13A-regulated RhoB plasma membrane localization governs membrane blebbing and blebby amoeboid cell migration
In conclusion, KIF13A-mediated endosomal trafficking modulates RhoB plasma membrane localization to control membrane blebbing and blebby amoeboid migration. (Source: EMBO Journal)
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Gong, X., Didan, Y., Lock, J. G., Strömblad, S. Tags: Cell Adhesion, Polarity & Cytoskeleton, Membrane & Intracellular Transport Articles Source Type: research

Luteinizing hormone signaling restricts hematopoietic stem cell expansion during puberty
In this study, we identified an extrinsic mechanism by which HSC number and functions are regulated during mouse puberty. We found that the HSC number in postnatal bone marrow reached homeostasis at 4 weeks after birth. Luteinizing hormone, but not downstream sex hormones, was involved in regulating HSC homeostasis during this period. Expression of luteinizing hormone receptor (Lhcgr) is highly restricted in HSCs and multipotent progenitor cells in the hematopoietic hierarchy. When Lhcgr was deleted, HSCs continued to expand even after 4 weeks after birth, leading to abnormally elevated hematopoiesis and leukocyt...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Peng, Y. J., Yu, H., Hao, X., Dong, W., Yin, X., Lin, M., Zheng, J., Zhou, B. O. Tags: Cancer, Physiology, Stem Cells Articles Source Type: research

Neuregulin 3 promotes excitatory synapse formation on hippocampal interneurons
Hippocampal GABAergic interneurons are crucial for cortical network function and have been implicated in psychiatric disorders. We show here that Neuregulin 3 (Nrg3), a relatively little investigated low-affinity ligand, is a functionally dominant interaction partner of ErbB4 in parvalbumin-positive (PV) interneurons. Nrg3 and ErbB4 are located pre- and postsynaptically, respectively, in excitatory synapses on PV interneurons in vivo. Additionally, we show that ablation of Nrg3 results in a similar phenotype as the one described for ErbB4 ablation, including reduced excitatory synapse numbers on PV interneurons, alter...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Müller, T., Braud, S., Jüttner, R., Voigt, B. C., Paulick, K., Sheean, M. E., Klisch, C., Gueneykaya, D., Rathjen, F. G., Geiger, J. R., Poulet, J. F., Birchmeier, C. Tags: Neuroscience Articles Source Type: research

YAP-TEAD signaling promotes basal cell carcinoma development via a c-JUN/AP1 axis
The mammalian Hippo signaling pathway, through its effectors YAP and TAZ, coerces epithelial progenitor cell expansion for appropriate tissue development or regeneration upon damage. Its ability to drive rapid tissue growth explains why many oncogenic events frequently exploit this pathway to promote cancer phenotypes. Indeed, several tumor types including basal cell carcinoma (BCC) show genetic aberrations in the Hippo (or YAP/TAZ) regulators. Here, we uncover that while YAP is dispensable for homeostatic epidermal regeneration, it is required for BCC development. Our clonal analyses further demonstrate that the few emerg...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Maglic, D., Schlegelmilch, K., Dost, A. F., Panero, R., Dill, M. T., Calogero, R. A., Camargo, F. D. Tags: Cancer, Signal Transduction, Transcription Articles Source Type: research

Staphylococcus aureus virulence attenuation and immune clearance mediated by a phage lysin-derived protein
New anti-infective approaches are much needed to control multi-drug-resistant (MDR) pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA). Here, we found for the first time that a recombinant protein derived from the cell wall binding domain (CBD) of the bacteriophage lysin PlyV12, designated as V12CBD, could attenuate S. aureus virulence and enhance host immune defenses via multiple manners. After binding with V12CBD, S. aureus became less invasive to epithelial cells and more susceptible to macrophage killing. The expressions of multiple important virulence genes of S. aureus were reduced 2...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Yang, H., Xu, J., Li, W., Wang, S., Li, J., Yu, J., Li, Y., Wei, H. Tags: Immunology, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research

Seipin regulates lipid homeostasis by ensuring calcium-dependent mitochondrial metabolism
Seipin, the gene that causes Berardinelli-Seip congenital lipodystrophy type 2 (BSCL2), is important for adipocyte differentiation and lipid homeostasis. Previous studies in Drosophila revealed that Seipin promotes ER calcium homeostasis through the Ca2+-ATPase SERCA, but little is known about the events downstream of perturbed ER calcium homeostasis that lead to decreased lipid storage in Drosophila dSeipin mutants. Here, we show that glycolytic metabolites accumulate and the downstream mitochondrial TCA cycle is impaired in dSeipin mutants. The impaired TCA cycle further leads to a decreased level of citrate, a critical ...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Ding, L., Yang, X., Tian, H., Liang, J., Zhang, F., Wang, G., Wang, Y., Ding, M., Shui, G., Huang, X. Tags: Membrane & Intracellular Transport, Metabolism Articles Source Type: research

Atypical APC/C-dependent degradation of Mcl-1 provides an apoptotic timer during mitotic arrest
The initiation of apoptosis in response to the disruption of mitosis provides surveillance against chromosome instability. Here, we show that proteolytic destruction of the key regulator Mcl-1 during an extended mitosis requires the anaphase-promoting complex or cyclosome (APC/C) and is independent of another ubiquitin E3 ligase, SCFFbw7. Using live-cell imaging, we show that the loss of Mcl-1 during mitosis is dependent on a D box motif found in other APC/C substrates, while an isoleucine-arginine (IR) C-terminal tail regulates the manner in which Mcl-1 engages with the APC/C, converting Mcl-1 from a Cdc20-dependent and c...
Source: EMBO Journal - September 3, 2018 Category: Molecular Biology Authors: Allan, L. A., Skowyra, A., Rogers, K. I., Zeller, D., Clarke, P. R. Tags: Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Functional patchworking at the plasma membrane
Lipids and proteins are not evenly distributed within the plasma membrane (PM), but instead segregate laterally into many specialized microdomains whose functional relevance is not clear. In this issue, Busto et al (2018) demonstrate that substrate flux through a nutrient transporter drives the lateral relocation of the transporter between specific microdomains at the yeast PM, suggesting that regulating the lateral plasma membrane compartmentalization for individual proteins could be a general process for cellular response to environmental conditions. (Source: EMBO Journal)
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Leon, S., Teis, D. Tags: Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Astrocytic NF-{kappa}B brings the best and worst out of microglia
The role of astrocytes and microglia in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) remains incompletely understood. In this issue of The EMBO Journal, Alami et al (2018) employ a sophisticated genetic system that allows precise temporal control of NF-B activation in astrocytes to demonstrate that the timing of astrocyte activation is a key determinant of disease progression. Their results suggest that astrocyte activation drives microglia proliferation and that this can amplify not only the protective microglial effects in the presymptomatic phase of ALS, but also the detrimental microglial...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Dokalis, N., Prinz, M. Tags: Molecular Biology of Disease, Neuroscience News [amp ] Views Source Type: research

Lateral plasma membrane compartmentalization links protein function and turnover
Biological membranes organize their proteins and lipids into nano- and microscale patterns. In the yeast plasma membrane (PM), constituents segregate into a large number of distinct domains. However, whether and how this intricate patchwork contributes to biological functions at the PM is still poorly understood. Here, we reveal an elaborate interplay between PM compartmentalization, physiological function, and endocytic turnover. Using the methionine permease Mup1 as model system, we demonstrate that this transporter segregates into PM clusters. Clustering requires sphingolipids, the tetraspanner protein Nce102, and signa...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Busto, J. V., Elting, A., Haase, D., Spira, F., Kuhlman, J., Schäfer-Herte, M., Wedlich-Söldner, R. Tags: Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Targeting prohibitins at the cell surface prevents Th17-mediated autoimmunity
T helper (Th)17 cells represent a unique subset of CD4+ T cells and are vital for clearance of extracellular pathogens including bacteria and fungi. However, Th17 cells are also involved in orchestrating autoimmunity. By employing quantitative surface proteomics, we found that the evolutionarily conserved prohibitins (PHB1/2) are highly expressed on the surface of both murine and human Th17 cells. Increased expression of PHBs at the cell surface contributed to enhanced CRAF/MAPK activation in Th17 cells. Targeting surface-expressed PHBs on Th17 cells with ligands such as Vi polysaccharide (Typhim vaccine) inhibited CRAF-MA...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Buehler, U., Schulenburg, K., Yurugi, H., Solman, M., Abankwa, D., Ulges, A., Tenzer, S., Bopp, T., Thiede, B., Zipp, F., Rajalingam, K. Tags: Immunology Articles Source Type: research

Substrate relay in an Hsp70-cochaperone cascade safeguards tail-anchored membrane protein targeting
Membrane proteins are aggregation-prone in aqueous environments, and their biogenesis poses acute challenges to cellular protein homeostasis. How the chaperone network effectively protects integral membrane proteins during their post-translational targeting is not well understood. Here, biochemical reconstitutions showed that the yeast cytosolic Hsp70 is responsible for capturing newly synthesized tail-anchored membrane proteins (TAs) in the soluble form. Moreover, direct interaction of Hsp70 with the cochaperone Sgt2 initiates a sequential series of TA relays to the dedicated TA targeting factor Get3. In contrast to direc...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Cho, H., Shan, S.-o. Tags: Membrane & Intracellular Transport, Protein Biosynthesis & Quality Control Articles Source Type: research

Acidic cell elongation drives cell differentiation in the Arabidopsis root
In multicellular systems, the control of cell size is fundamental in regulating the development and growth of the different organs and of the whole organism. In most systems, major changes in cell size can be observed during differentiation processes where cells change their volume to adapt their shape to their final function. How relevant changes in cell volume are in driving the differentiation program is a long-standing fundamental question in developmental biology. In the Arabidopsis root meristem, characteristic changes in the size of the distal meristematic cells identify cells that initiated the differentiation prog...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Pacifici, E., Di Mambro, R., Dello Ioio, R., Costantino, P., Sabatini, S. Tags: Development & Differentiation, Plant Biology, Signal Transduction Articles Source Type: research

A temporally dynamic Foxp3 autoregulatory transcriptional circuit controls the effector Treg programme
Regulatory T cells (Treg) are negative regulators of the immune response; however, it is poorly understood whether and how Foxp3 transcription is induced and regulated in the periphery during T-cell responses. Using Foxp3-Timer of cell kinetics and activity (Tocky) mice, which report real-time Foxp3 expression, we show that the flux of new Foxp3 expressors and the rate of Foxp3 transcription are increased during inflammation. These persistent dynamics of Foxp3 transcription determine the effector Treg programme and are dependent on a Foxp3 autoregulatory transcriptional circuit. Persistent Foxp3 transcriptional activity co...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Bending, D., Paduraru, A., Ducker, C. B., Prieto Martin, P., Crompton, T., Ono, M. Tags: Immunology, Transcription Articles Source Type: research

A high-throughput method to identify trans-activation domains within transcription factor sequences
Even though transcription factors (TFs) are central players of gene regulation and have been extensively studied, their regulatory trans-activation domains (tADs) often remain unknown and a systematic functional characterization of tADs is lacking. Here, we present a novel high-throughput approach tAD-seq to functionally test thousands of candidate tADs from different TFs in parallel. The tADs we identify by pooled screening validate in individual luciferase assays, whereas neutral regions do not. Interestingly, the tADs are found at arbitrary positions within the TF sequences and can contain amino acid (e.g., glutamine) r...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Arnold, C. D., Nemcko, F., Woodfin, A. R., Wienerroither, S., Vlasova, A., Schleiffer, A., Pagani, M., Rath, M., Stark, A. Tags: Methods & Resources, Systems & Computational Biology, Transcription Source Type: research

Cdc48/p97 segregase is modulated by cyclin-dependent kinase to determine cyclin fate during G1 progression
Cells sense myriad signals during G1, and a rapid response to prevent cell cycle entry is of crucial importance for proper development and adaptation. Cln3, the most upstream G1 cyclin in budding yeast, is an extremely short-lived protein subject to ubiquitination and proteasomal degradation. On the other hand, nuclear accumulation of Cln3 depends on chaperones that are also important for its degradation. However, how these processes are intertwined to control G1-cyclin fate is not well understood. Here, we show that Cln3 undergoes a challenging ubiquitination step required for both degradation and full activation. Segrega...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Parisi, E., Yahya, G., Flores, A., Aldea, M. Tags: Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Cezanne/OTUD7B is a cell cycle-regulated deubiquitinase that antagonizes the degradation of APC/C substrates
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase and key regulator of cell cycle progression. Since APC/C promotes the degradation of mitotic cyclins, it controls cell cycle-dependent oscillations in cyclin-dependent kinase (CDK) activity. Both CDKs and APC/C control a large number of substrates and are regulated by analogous mechanisms, including cofactor-dependent activation. However, whereas substrate dephosphorylation is known to counteract CDK, it remains largely unknown whether deubiquitinating enzymes (DUBs) antagonize APC/C substrate ubiquitination during mitosis. Here, we demonstrate that...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Bonacci, T., Suzuki, A., Grant, G. D., Stanley, N., Cook, J. G., Brown, N. G., Emanuele, M. J. Tags: Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

NF-{kappa}B activation in astrocytes drives a stage-specific beneficial neuroimmunological response in ALS
Astrocytes are involved in non-cell-autonomous pathogenic cascades in amyotrophic lateral sclerosis (ALS); however, their role is still debated. We show that astrocytic NF-B activation drives microglial proliferation and leukocyte infiltration in the SOD1 (G93A) ALS model. This response prolongs the presymptomatic phase, delaying muscle denervation and decreasing disease burden, but turns detrimental in the symptomatic phase, accelerating disease progression. The transition corresponds to a shift in the microglial phenotype showing two effects that can be dissociated by temporally controlling NF-B activation. While NF-B ac...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Ouali Alami, N., Schurr, C., Olde Heuvel, F., Tang, L., Li, Q., Tasdogan, A., Kimbara, A., Nettekoven, M., Ottaviani, G., Raposo, C., Röver, S., Rogers-Evans, M., Rothenhäusler, B., Ullmer, C., Fingerle, J., Grether, U., Knuesel, I., Boeck Tags: Molecular Biology of Disease, Neuroscience Articles Source Type: research

Myc and the Tip60 chromatin remodeling complex control neuroblast maintenance and polarity in Drosophila
Stem cells establish cortical polarity and divide asymmetrically to simultaneously maintain themselves and generate differentiating offspring cells. Several chromatin modifiers have been identified as stemness factors in mammalian pluripotent stem cells, but whether these factors control stem cell polarity and asymmetric division has not been investigated so far. We addressed this question in Drosophila neural stem cells called neuroblasts. We identified the Tip60 chromatin remodeling complex and its interaction partner Myc as regulators of genes required for neuroblast maintenance. Knockdown of Tip60 complex members resul...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Rust, K., Tiwari, M. D., Mishra, V. K., Grawe, F., Wodarz, A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Chromatin, Epigenetics, Genomics & Functional Genomics, Stem Cells Articles Source Type: research

RIM-binding proteins recruit BK-channels to presynaptic release sites adjacent to voltage-gated Ca2+-channels
The active zone of presynaptic nerve terminals organizes the neurotransmitter release machinery, thereby enabling fast Ca2+-triggered synaptic vesicle exocytosis. BK-channels are Ca2+-activated large-conductance K+-channels that require close proximity to Ca2+-channels for activation and control Ca2+-triggered neurotransmitter release by accelerating membrane repolarization during action potential firing. How BK-channels are recruited to presynaptic Ca2+-channels, however, is unknown. Here, we show that RBPs (for RIM-binding proteins), which are evolutionarily conserved active zone proteins containing SH3- and FN3-domains,...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Sclip, A., Acuna, C., Luo, F., Südhof, T. C. Tags: Membrane & Intracellular Transport, Neuroscience, Physiology Articles Source Type: research

The MRX complex regulates Exo1 resection activity by altering DNA end structure
Homologous recombination is triggered by nucleolytic degradation (resection) of DNA double-strand breaks (DSBs). DSB resection requires the Mre11-Rad50-Xrs2 (MRX) complex, which promotes the activity of Exo1 nuclease through a poorly understood mechanism. Here, we describe the Mre11-R10T mutant variant that accelerates DSB resection compared to wild-type Mre11 by potentiating Exo1-mediated processing. This increased Exo1 resection activity leads to a decreased association of the Ku complex to DSBs and an enhanced DSB resection in G1, indicating that Exo1 has a direct function in preventing Ku association with DSBs. Molecul...
Source: EMBO Journal - August 15, 2018 Category: Molecular Biology Authors: Gobbini, E., Cassani, C., Vertemara, J., Wang, W., Mambretti, F., Casari, E., Sung, P., Tisi, R., Zampella, G., Longhese, M. P. Tags: DNA Replication, Repair & Recombination Articles Source Type: research

Growing a gasdermin pore in membranes of pyroptotic cells
Inflammasome-activated caspase-1, caspase-11, caspase-4, and caspase-5 cleave GSDMD to unleash its N-terminal gasdermin-N domain (GSDMDNterm) that perforates the plasma membrane to execute pyroptosis and stimulate inflammation. The mechanism underlying GSDMDNterm pore formation is unclear. Mulvihill et al use high-resolution atomic force microscopy (AFM) to analyze the dynamic pore formation process of GSDMDNterm. GSDMDNterm protomers are inserted into the lipid membrane to assemble arc- or slit-shaped oligomers that can incorporate additional protomers and grow into large and stable ring-shaped oligomers to form pore...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Ding, J., Shao, F. Tags: Autophagy & Cell Death, Immunology News [amp ] Views Source Type: research

A wobbly road to drug resistance in melanoma: tRNA-modifying enzymes in translation reprogramming
Alterations in transcript-specific translation are emerging as a driver of cellular transformation and cancer etiology. A new study provides evidence for enhanced codon-dependent translation of hypoxia-inducible factor 1α in promoting glycolytic metabolism and drug resistance in melanoma cells. This specialized translation reprogramming relies, in part, on mTORC2-mediated phosphorylation of enzymes modifying the wobble position of the transfer RNA anticodon. (Source: EMBO Journal)
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: McMahon, M., Ruggero, D. Tags: Cancer, Molecular Biology of Disease News [amp ] Views Source Type: research

Proteolytic ectodomain shedding of membrane proteins in mammals--hardware, concepts, and recent developments
Proteolytic removal of membrane protein ectodomains (ectodomain shedding) is a post-translational modification that controls levels and function of hundreds of membrane proteins. The contributing proteases, referred to as sheddases, act as important molecular switches in processes ranging from signaling to cell adhesion. When deregulated, ectodomain shedding is linked to pathologies such as inflammation and Alzheimer's disease. While proteases of the "a disintegrin and metalloprotease" (ADAM) and "beta-site APP cleaving enzyme" (BACE) families are widely considered as sheddases, in recent years a much b...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Lichtenthaler, S. F., Lemberg, M. K., Fluhrer, R. Tags: Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Review Source Type: research

Shelterin promotes tethering of late replication origins to telomeres for replication-timing control
DNA replication initiates at many discrete loci on eukaryotic chromosomes, and individual replication origins are regulated under a spatiotemporal program. However, the underlying mechanisms of this regulation remain largely unknown. In the fission yeast Schizosaccharomyces pombe, the telomere-binding protein Taz1, ortholog of human TRF1/TRF2, regulates a subset of late replication origins by binding to the telomere-like sequence near the origins. Here, we showed using a lacO/LacI-GFP system that Taz1-dependent late origins were predominantly localized at the nuclear periphery throughout interphase, and were localized adja...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Ogawa, S., Kido, S., Handa, T., Ogawa, H., Asakawa, H., Takahashi, T. S., Nakagawa, T., Hiraoka, Y., Masukata, H. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research

MST2 kinase suppresses rDNA transcription in response to DNA damage by phosphorylating nucleolar histone H2B
The heavily transcribed rDNA repeats that give rise to the ribosomal RNA are clustered in a unique chromatin structure, the nucleolus. Due to its highly repetitive nature and transcriptional activity, the nucleolus is considered a hotspot of genomic instability. Breaks in rDNA induce a transient transcriptional shut down to conserve energy and promote rDNA repair; however, how nucleolar chromatin is modified and impacts on rDNA repair is unknown. Here, we uncover that phosphorylation of serine 14 on histone H2B marks transcriptionally inactive nucleolar chromatin in response to DNA damage. We identified that the MST2 kinas...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Pefani, D. E., Tognoli, M. L., Pirincci Ercan, D., Gorgoulis, V., O'Neill, E. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Cilia-localized LKB1 regulates chemokine signaling, macrophage recruitment, and tissue homeostasis in the kidney
Polycystic kidney disease (PKD) and other renal ciliopathies are characterized by cysts, inflammation, and fibrosis. Cilia function as signaling centers, but a molecular link to inflammation in the kidney has not been established. Here, we show that cilia in renal epithelia activate chemokine signaling to recruit inflammatory cells. We identify a complex of the ciliary kinase LKB1 and several ciliopathy-related proteins including NPHP1 and PKD1. At homeostasis, this ciliary module suppresses expression of the chemokine CCL2 in tubular epithelial cells. Deletion of LKB1 or PKD1 in mouse renal tubules elevates CCL2 expressio...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Viau, A., Bienaime, F., Lukas, K., Todkar, A. P., Knoll, M., Yakulov, T. A., Hofherr, A., Kretz, O., Helmstädter, M., Reichardt, W., Braeg, S., Aschman, T., Merkle, A., Pfeifer, D., Dumit, V. I., Gubler, M.-C., Nitschke, R., Huber, T. B., Terzi, F Tags: Cell Adhesion, Polarity & Cytoskeleton, Immunology, Molecular Biology of Disease Articles Source Type: research

RNase H2, mutated in Aicardi-Goutieres syndrome, promotes LINE-1 retrotransposition
Long INterspersed Element class 1 (LINE-1) elements are a type of abundant retrotransposons active in mammalian genomes. An average human genome contains ~100 retrotransposition-competent LINE-1s, whose activity is influenced by the combined action of cellular repressors and activators. TREX1, SAMHD1 and ADAR1 are known LINE-1 repressors and when mutated cause the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). Mutations in RNase H2 are the most common cause of AGS, and its activity was proposed to similarly control LINE-1 retrotransposition. It has therefore been suggested that increased LINE-1 activity...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Benitez-Guijarro, M., Lopez-Ruiz, C., Tarnauskaite, Z., Murina, O., Mian Mohammad, M., Williams, T. C., Fluteau, A., Sanchez, L., Vilar-Astasio, R., Garcia-Canadas, M., Cano, D., Kempen, M.-J. H., Sanchez-Pozo, A., Heras, S. R., Jackson, A. P., Reijns, M. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Immunology, Molecular Biology of Disease Articles Source Type: research

Feeding state regulates pheromone-mediated avoidance behavior via the insulin signaling pathway in Caenorhabditis elegans
Animals change sensory responses and their eventual behaviors, depending on their internal metabolic status and external food availability. However, the mechanisms underlying feeding state-dependent behavioral changes remain undefined. Previous studies have shown that Caenorhabditis elegans hermaphrodite exhibits avoidance behaviors to acute exposure of a pheromone, ascr#3 (asc-C9, C9). Here, we show that the ascr#3 avoidance behavior is modulated by feeding state via the insulin signaling pathway. Starvation increases ascr#3 avoidance behavior, and loss-of-function mutations in daf-2 insulin-like receptor gene dampen this...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Ryu, L., Cheon, Y., Huh, Y. H., Pyo, S., Chinta, S., Choi, H., Butcher, R. A., Kim, K. Tags: Cancer, Signal Transduction, Transcription Articles Source Type: research

Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles
Recent data showed that cancer cells from different tumor subtypes with distinct metastatic potential influence each other's metastatic behavior by exchanging biomolecules through extracellular vesicles (EVs). However, it is debated how small amounts of cargo can mediate this effect, especially in tumors where all cells are from one subtype, and only subtle molecular differences drive metastatic heterogeneity. To study this, we have characterized the content of EVs shed in vivo by two clones of melanoma (B16) tumors with distinct metastatic potential. Using the Cre-LoxP system and intravital microscopy, we show that c...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Steenbeek, S. C., Pham, T. V., de Ligt, J., Zomer, A., Knol, J. C., Piersma, S. R., Schelfhorst, T., Huisjes, R., Schiffelers, R. M., Cuppen, E., Jimenez, C. R., van Rheenen, J. Tags: Cancer, Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission
Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins a...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Truckenbrodt, S., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., Fornasiero, E. F., Rizzoli, S. O. Tags: Neuroscience Articles Source Type: research

Engrailed homeoprotein blocks degeneration in adult dopaminergic neurons through LINE-1 repression
We report that LINE-1 are expressed in substantia nigra ventral midbrain dopaminergic neurons, a class of neurons that degenerate in Parkinson's disease. In Engrailed-1 heterozygotes, these neurons show a progressive degeneration that starts at 6 weeks of age, coinciding with an increase in LINE-1 expression. Similarly, DNA damage and cell death, induced by an acute oxidative stress applied to embryonic midbrain neurons in culture or to adult midbrain dopaminergic neurons in vivo, are accompanied by enhanced LINE-1 expression. Reduction of LINE-1 activity through (i) direct transcriptional repression by Engrailed...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Blaudin de The, F.-X., Rekaik, H., Peze-Heidsieck, E., Massiani-Beaudoin, O., Joshi, R. L., Fuchs, J., Prochiantz, A. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Neuroscience Articles Source Type: research

The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion
Chromosome segregation depends on sister chromatid cohesion which is established by cohesin during DNA replication. Cohesive cohesin complexes become acetylated to prevent their precocious release by WAPL before cells have reached mitosis. To obtain insight into how DNA replication, cohesion establishment and cohesin acetylation are coordinated, we analysed the interaction partners of 55 human proteins implicated in these processes by mass spectrometry. This proteomic screen revealed that on chromatin the cohesin acetyltransferase ESCO2 associates with the MCM2-7 subcomplex of the replicative Cdc45-MCM-GINS helicase. The a...
Source: EMBO Journal - August 1, 2018 Category: Molecular Biology Authors: Ivanov, M. P., Ladurner, R., Poser, I., Beveridge, R., Rampler, E., Hudecz, O., Novatchkova, M., Heriche, J.-K., Wutz, G., van der Lelij, P., Kreidl, E., Hutchins, J. R., Axelsson-Ekker, H., Ellenberg, J., Hyman, A. A., Mechtler, K., Peters, J.-M. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics, DNA Replication, Repair & Recombination Articles Source Type: research