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

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

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

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

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

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

The balance of Id3 and E47 determines neural stem/precursor cell differentiation into astrocytes
Adult neural stem/precursor cells (NSPCs) of the subventricular zone (SVZ) are an endogenous source for neuronal replacement in CNS disease. However, adult neurogenesis is compromised after brain injury in favor of a glial cell fate, which is mainly attributed to changes in the NSPC environment. Yet, it is unknown how this unfavorable extracellular environment translates into a transcriptional program altering NSPC differentiation. Here, we show that genetic depletion of the transcriptional regulator Id3 decreased the number of astrocytes generated from SVZ-derived adult NSPCs in the cortical lesion area after traumatic br...
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Bohrer, C., Pfurr, S., Mammadzada, K., Schildge, S., Plappert, L., Hils, M., Pous, L., Rauch, K. S., Dumit, V. I., Pfeifer, D., Dengjel, J., Kirsch, M., Schachtrup, K., Schachtrup, C. Tags: Neuroscience Articles Source Type: research

H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein
Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in the creation of a rigid, densely packed heterochromatic network that is inaccessible to the transcription machinery. Here, we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population that rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to the maintenance of heterochromatin domains. In the abse...
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Stunnenberg, R., Kulasegaran-Shylini, R., Keller, C., Kirschmann, M. A., Gelman, L., Bühler, M. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, Transcription Articles Source Type: research

Immunomodulatory activity of extracellular Hsp70 mediated via paired receptors Siglec-5 and Siglec-14
The intracellular chaperone heat-shock protein 70 (Hsp70) can be secreted from cells, but its extracellular role is unclear, as the protein has been reported to both activate and suppress the innate immune response. Potential immunomodulatory receptors on myelomonocytic lineage cells that bind extracellular Hsp70 are not well defined. Siglecs are Ig-superfamily lectins on mammalian leukocytes that recognize sialic acid-bearing glycans and thereby modulate immune responses. Siglec-5 and Siglec-14, expressed on monocytes and neutrophils, share identical ligand-binding domains but have opposing signaling functions. Based...
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Fong, J. J., Sreedhara, K., Deng, L., Varki, N. M., Angata, T., Liu, Q., Nizet, V., Varki, A. Tags: Immunology Articles Source Type: research

Alu element-containing RNAs maintain nucleolar structure and function
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a function...
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Caudron-Herger, M., Pankert, T., Seiler, J., Nemeth, A., Voit, R., Grummt, I., Rippe, K. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, RNA Biology, Transcription Articles Source Type: research

Complement activation, regulation, and molecular basis for complement-related diseases
We present an integrated and updated view of complement based on structural and functional data and describe the new roles attributed to complement. Finally, we discuss how the structural and mechanistic understanding of the complement system rationalizes the genetic defects conferring uncontrolled activation or other undesirable effects of complement. (Source: EMBO Journal)
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Bajic, G., Degn, S. E., Thiel, S., Andersen, G. R. Tags: Immunology Review Source Type: research

Siglecs take a TOLL on inflammation: deciphering the Hsp70 riddle
The manuscript by Fong et al (2015) in this issue of The EMBO Journal addresses an ongoing question in immunology: are extracellular HSPs endogenous inflammatory signals or are they in fact built-in inhibitors of those same functions? In a highly original series of experiments, they identify novel Hsp70 receptors in monocytes as members of the Siglec family. Even more significantly, two Siglec family members transmitted divergent responses to Hsp70, with Siglec-5 dampening inflammation while Siglec-14 triggering the inflammatory cascade. These findings therefore go some way in addressing the open question: is Hsp70 pr...
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Calderwood, S. K., Murshid, A. Tags: Immunology News [amp ] Views Source Type: research

Assembly of the nucleolus: in need of revision
Our current view of the nucleolus has been shaped by the concept that the organization of this prominent compartment within the nucleus is primarily dictated by its function, the making of ribosome subunits. Whether ribosome biogenesis is framed by a dedicated nucleolar scaffold has remained unclear. In this issue of The EMBO Journal, Caudron-Herger and colleagues present evidence for a nucleolar skeleton composed of non-coding RNA enriched in Alu repeat elements. (Source: EMBO Journal)
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Carmo-Fonseca, M. Tags: Chromatin, Epigenetics, Genomics & Functional Genomics, RNA Biology, Transcription News [amp ] Views Source Type: research

Statistical relevance--relevant statistics, part I
(Source: EMBO Journal)
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Klaus, B. Tags: Commentary Source Type: research

Gottfried Schatz (1936-2015)--mitochondrial pioneer and ambassador for science
(Source: EMBO Journal)
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Haucke, V., Glick, B. S. Tags: Obituary Source Type: research

Reproducibility blues
Research findings advance science only if they are significant, reliable and reproducible. Scientists and journals must publish robust data in a way that renders it optimally reproducible. Reproducibility has to be incentivized and supported by the research infrastructure but without dampening innovation. (Source: EMBO Journal)
Source: EMBO Journal - November 12, 2015 Category: Molecular Biology Authors: Pulverer, B. Tags: Editorial Source Type: research

Phospholipid methylation controls Atg32-mediated mitophagy and Atg8 recycling
Degradation of mitochondria via selective autophagy, termed mitophagy, contributes to mitochondrial quality and quantity control whose defects have been implicated in oxidative phosphorylation deficiency, aberrant cell differentiation, and neurodegeneration. How mitophagy is regulated in response to cellular physiology remains obscure. Here, we show that mitophagy in yeast is linked to the phospholipid biosynthesis pathway for conversion of phosphatidylethanolamine to phosphatidylcholine by the two methyltransferases Cho2 and Opi3. Under mitophagy-inducing conditions, cells lacking Opi3 exhibit retardation of Cho2 repressi...
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Sakakibara, K., Eiyama, A., Suzuki, S. W., Sakoh-Nakatogawa, M., Okumura, N., Tani, M., Hashimoto, A., Nagumo, S., Kondo-Okamoto, N., Kondo-Kakuta, C., Asai, E., Kirisako, H., Nakatogawa, H., Kuge, O., Takao, T., Ohsumi, Y., Okamoto, K. Tags: Autophagy & Cell Death, Metabolism, Physiology Articles Source Type: research

Disruption of adaptor protein 2{mu} (AP-2{mu}) in cochlear hair cells impairs vesicle reloading of synaptic release sites and hearing
Active zones (AZs) of inner hair cells (IHCs) indefatigably release hundreds of vesicles per second, requiring each release site to reload vesicles at tens per second. Here, we report that the endocytic adaptor protein 2μ (AP-2μ) is required for release site replenishment and hearing. We show that hair cell-specific disruption of AP-2μ slows IHC exocytosis immediately after fusion of the readily releasable pool of vesicles, despite normal abundance of membrane-proximal vesicles and intact endocytic membrane retrieval. Sound-driven postsynaptic spiking was reduced in a use-dependent manner, and the altered interspi...
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Jung, S., Maritzen, T., Wichmann, C., Jing, Z., Neef, A., Revelo, N. H., Al-Moyed, H., Meese, S., Wojcik, S. M., Panou, I., Bulut, H., Schu, P., Ficner, R., Reisinger, E., Rizzoli, S. O., Neef, J., Strenzke, N., Haucke, V., Moser, T. Tags: Neuroscience Articles Source Type: research

Suppression of miR-199a maturation by HuR is crucial for hypoxia-induced glycolytic switch in hepatocellular carcinoma
Glucose metabolic reprogramming is a hallmark of cancer. Cancer cells rapidly adjust their energy source from oxidative phosphorylation to glycolytic metabolism in order to efficiently proliferate in a hypoxic environment, but the mechanism underlying this switch is still incompletely understood. Here, we report that hypoxia potently induces the RNA-binding protein HuR to specifically bind primary miR-199a transcript to block miR-199a maturation in hepatocellular carcinoma (HCC) cells. We demonstrate that this hypoxia-suppressed miR-199a plays a decisive role in limiting glycolysis in HCC cells by targeting hexokinase-2 (H...
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Zhang, L.-F., Lou, J.-T., Lu, M.-H., Gao, C., Zhao, S., Li, B., Liang, S., Li, Y., Li, D., Liu, M.-F. Tags: Cancer, Metabolism, RNA Biology Articles Source Type: research

Distinct preoptic-BST nuclei dissociate paternal and infanticidal behavior in mice
Paternal behavior is not innate but arises through social experience. After mating and becoming fathers, male mice change their behavior toward pups from infanticide to paternal care. However, the precise brain areas and circuit mechanisms connecting these social behaviors are largely unknown. Here we demonstrated that the c-Fos expression pattern in the four nuclei of the preoptic-bed nuclei of stria terminalis (BST) region could robustly discriminate five kinds of previous social behavior of male mice (parenting, infanticide, mating, inter-male aggression, solitary control). Specifically, neuronal activation in the centr...
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Tsuneoka, Y., Tokita, K., Yoshihara, C., Amano, T., Esposito, G., Huang, A. J., Yu, L. M., Odaka, Y., Shinozuka, K., McHugh, T. J., Kuroda, K. O. Tags: Neuroscience Articles Source Type: research

Dysregulated miRNA biogenesis downstream of cellular stress and ALS-causing mutations: a new mechanism for ALS
Interest in RNA dysfunction in amyotrophic lateral sclerosis (ALS) recently aroused upon discovering causative mutations in RNA-binding protein genes. Here, we show that extensive down-regulation of miRNA levels is a common molecular denominator for multiple forms of human ALS. We further demonstrate that pathogenic ALS-causing mutations are sufficient to inhibit miRNA biogenesis at the Dicing step. Abnormalities of the stress response are involved in the pathogenesis of neurodegeneration, including ALS. Accordingly, we describe a novel mechanism for modulating microRNA biogenesis under stress, involving stress granule for...
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Emde, A., Eitan, C., Liou, L.-L., Libby, R. T., Rivkin, N., Magen, I., Reichenstein, I., Oppenheim, H., Eilam, R., Silvestroni, A., Alajajian, B., Ben-Dov, I. Z., Aebischer, J., Savidor, A., Levin, Y., Sons, R., Hammond, S. M., Ravits, J. M., Möll Tags: Neuroscience, RNA Biology Articles Source Type: research

Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions
Acetylation is frequently detected on mitochondrial enzymes, and the sirtuin deacetylase SIRT3 is thought to regulate metabolism by deacetylating mitochondrial proteins. However, the stoichiometry of acetylation has not been studied and is important for understanding whether SIRT3 regulates or suppresses acetylation. Using quantitative mass spectrometry, we measured acetylation stoichiometry in mouse liver tissue and found that SIRT3 suppressed acetylation to a very low stoichiometry at its target sites. By examining acetylation changes in the liver, heart, brain, and brown adipose tissue of fasted mice, we found that SIRT...
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Weinert, B. T., Moustafa, T., Iesmantavicius, V., Zechner, R., Choudhary, C. Tags: Metabolism, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

NSMCE2 suppresses cancer and aging in mice independently of its SUMO ligase activity
The SMC5/6 complex is the least understood of SMC complexes. In yeast, smc5/6 mutants phenocopy mutations in sgs1, the BLM ortholog that is deficient in Bloom's syndrome (BS). We here show that NSMCE2 (Mms21, in Saccharomyces cerevisiae), an essential SUMO ligase of the SMC5/6 complex, suppresses cancer and aging in mice. Surprisingly, a mutation that compromises NSMCE2-dependent SUMOylation does not have a detectable impact on murine lifespan. In contrast, NSMCE2 deletion in adult mice leads to pathologies resembling those found in patients of BS. Moreover, and whereas NSMCE2 deletion does not have a detectable impact on ...
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Jacome, A., Gutierrez-Martinez, P., Schiavoni, F., Tenaglia, E., Martinez, P., Rodriguez-Acebes, S., Lecona, E., Murga, M., Mendez, J., Blasco, M. A., Fernandez-Capetillo, O. Tags: DNA Replication, Repair & Recombination, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

MicroRNAs in ALS: small pieces to the puzzle
MicroRNAs have emerged as crucial regulators of neuronal function, suggesting that aberrant microRNA expression might contribute to pathologies of the nervous system. In this issue of The EMBO Journal, Emde et al (2015) report a global decrease in microRNAs as common hallmark of different forms of amyotrophic lateral sclerosis (ALS). Strikingly, enhancing microRNA biogenesis has beneficial effects on the neuromuscular function in mouse models of ALS. Thus, the microRNA pathway represents a promising novel target for therapeutic intervention in neurodegeneration. (Source: EMBO Journal)
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Bicker, S., Schratt, G. Tags: Neuroscience, RNA Biology News [amp ] Views Source Type: research

Acetyl-ed question in mitochondrial biology?
Lysine acetylation on numerous mitochondrial proteins, targeted by the sirtuin deacylase SIRT3, has been proposed to play a major role in regulating diverse mitochondrial functions, particularly in the liver. A new study by Weinert, Choudhary, and colleagues, in this issue of The EMBO Journal, finds that the absolute levels of hepatic mitochondrial protein acetylation in wild-type mice are extremely low and may be insufficient to exert regulatory effects. (Source: EMBO Journal)
Source: EMBO Journal - November 3, 2015 Category: Molecular Biology Authors: Lombard, D. B., Dash, B. P., Kumar, S. Tags: Metabolism, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

Retraction: 'An endogenous, systemic RNAi pathway in plants'
(Source: EMBO Journal)
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Dunoyer, P., Brosnan, C. A., Schott, G., Wang, Y., Jay, F., Alioua, A., Himber, C., Voinnet, O. Tags: Retractions Source Type: research

Retraction: 'Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana'
(Source: EMBO Journal)
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Brigneti, G., Voinnet, O., Li, W.-X., Ji, L.-H., Ding, S.-W., Baulcombe, D. C. Tags: Retractions Source Type: research

Differential effects of viral silencing suppressors on siRNA and miRNA loading support the existence of two distinct cellular pools of ARGONAUTE1
(Source: EMBO Journal)
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Schott, G., Mari-Ordonez, A., Himber, C., Alioua, A., Voinnet, O., Dunoyer, P. Tags: Corrigenda Source Type: research

Nuclear import of CaMV P6 is required for infection and suppression of the RNA silencing factor DRB4
(Source: EMBO Journal)
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Haas, G., Azevedo, J., Moissiard, G., Geldreich, A., Himber, C., Bureau, M., Fukuhara, T., Keller, M., Voinnet, O. Tags: Corrigenda Source Type: research

Two classes of short interfering RNA in RNA silencing
(Source: EMBO Journal)
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Hamilton, A., Voinnet, O., Chappell, L., Baulcombe, D. Tags: Corrigenda Source Type: research

Postmitotic diversification of olfactory neuron types is mediated by differential activities of the HMG-box transcription factor SOX-2
Diversification of neuron classes is essential for functions of the olfactory system, but the underlying mechanisms that generate individual olfactory neuron types are only beginning to be understood. Here we describe a role of the highly conserved HMG-box transcription factor SOX-2 in postmitotic specification and alternative differentiation of the Caenorhabditis elegans AWC and AWB olfactory neurons. We show that SOX-2 partners with different transcription factors to diversify postmitotic olfactory cell types. SOX-2 functions cooperatively with the OTX/OTD transcription factor CEH-36 to specify an AWC "ground state,...
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Alqadah, A., Hsieh, Y.-W., Vidal, B., Chang, C., Hobert, O., Chuang, C.-F. Tags: Development & Differentiation, Transcription Articles Source Type: research

Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition
Many bacteria use small RNAs (sRNAs) and the RNA chaperone Hfq to regulate mRNA stability and translation. Hfq, a ring-shaped homohexamer, has multiple faces that can bind both sRNAs and their mRNA targets. We find that Hfq has at least two distinct ways in which it interacts with sRNAs; these different binding properties have strong effects on the stability of the sRNA in vivo and the sequence requirements of regulated mRNAs. Class I sRNAs depend on proximal and rim Hfq sites for stability and turn over rapidly. Class II sRNAs are more stable and depend on the proximal and distal Hfq sites for stabilization. Using de...
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Schu, D. J., Zhang, A., Gottesman, S., Storz, G. Tags: Microbiology, Virology & Host Pathogen Interaction, RNA Biology Articles Source Type: research

Formation of the transition zone by Mks5/Rpgrip1L establishes a ciliary zone of exclusion (CIZE) that compartmentalises ciliary signalling proteins and controls PIP2 ciliary abundance
Cilia are thought to harbour a membrane diffusion barrier within their transition zone (TZ) that compartmentalises signalling proteins. How this "ciliary gate" assembles and functions remains largely unknown. Contrary to current models, we present evidence that Caenorhabditis elegans MKS-5 (orthologue of mammalian Mks5/Rpgrip1L/Nphp8 and Rpgrip1) may not be a simple structural scaffold for anchoring> 10 different proteins at the TZ, but instead, functions as an assembly factor. This activity is needed to form TZ ultrastructure, which comprises Y-shaped axoneme-to-membrane connectors. Coiled-coil and C2 do...
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Jensen, V. L., Li, C., Bowie, R. V., Clarke, L., Mohan, S., Blacque, O. E., Leroux, M. R. Tags: Cell Adhesion, Polarity & Cytoskeleton Articles Source Type: research

Notch signaling regulates gastric antral LGR5 stem cell function
The major signaling pathways regulating gastric stem cells are unknown. Here we report that Notch signaling is essential for homeostasis of LGR5+ antral stem cells. Pathway inhibition reduced proliferation of gastric stem and progenitor cells, while activation increased proliferation. Notch dysregulation also altered differentiation, with inhibition inducing mucous and endocrine cell differentiation while activation reduced differentiation. Analysis of gastric organoids demonstrated that Notch signaling was intrinsic to the epithelium and regulated growth. Furthermore, in vivo Notch manipulation affected the efficienc...
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Demitrack, E. S., Gifford, G. B., Keeley, T. M., Carulli, A. J., VanDussen, K. L., Thomas, D., Giordano, T. J., Liu, Z., Kopan, R., Samuelson, L. C. Tags: Development & Differentiation Articles Source Type: research

Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis
We describe the 1.8 Å crystal structure of human parkin in its fully inhibited state and identify the key interfaces to maintain parkin inhibition. We identify the phosphoubiquitin-binding interface, provide a model for the phosphoubiquitin–parkin complex and show how phosphorylation of the Ubl domain primes parkin for optimal phosphoubiquitin binding. Furthermore, we demonstrate that the addition of phosphoubiquitin leads to displacement of the Ubl domain through loss of structure, unveiling a ubiquitin-binding site used by the E2~Ub conjugate, thus leading to active parkin. We find the role of the Ubl do...
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Kumar, A., Aguirre, J. D., Condos, T. E., Martinez-Torres, R. J., Chaugule, V. K., Toth, R., Sundaramoorthy, R., Mercier, P., Knebel, A., Spratt, D. E., Barber, K. R., Shaw, G. S., Walden, H. Tags: Molecular Biology of Disease, Post-translational Modifications, Proteolysis & Proteomics, Structural Biology Articles Source Type: research

A Ubl/ubiquitin switch in the activation of Parkin
Mutations in Parkin and PINK1 cause an inherited early-onset form of Parkinson's disease. The two proteins function together in a mitochondrial quality control pathway whereby PINK1 accumulates on damaged mitochondria and activates Parkin to induce mitophagy. How PINK1 kinase activity releases the auto-inhibited ubiquitin ligase activity of Parkin remains unclear. Here, we identify a binding switch between phospho-ubiquitin (pUb) and the ubiquitin-like domain (Ubl) of Parkin as a key element. By mutagenesis and SAXS, we show that pUb binds to RING1 of Parkin at a site formed by His302 and Arg305. pUb binding promotes disen...
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Sauve, V., Lilov, A., Seirafi, M., Vranas, M., Rasool, S., Kozlov, G., Sprules, T., Wang, J., Trempe, J.-F., Gehring, K. Tags: Molecular Biology of Disease, Post-translational Modifications, Proteolysis & Proteomics, Structural Biology Articles Source Type: research

Stomaching Notch
The self-renewal and differentiation of tissue stem cells must be tightly controlled. Unrestrained self-renewal leads to over-proliferation of stem cells, which may cause tumor formation, while uncontrolled differentiation leads to depletion of the stem cell pool. In this issue of The EMBO Journal, Demitrack et al (2015) show that the Notch pathway is a key regulator of Lgr5 antral stem cell self-renewal and differentiation. Notch signaling controls the proliferation and differentiation of stem cells as well as gastric tissue growth, while uncontrolled Notch activity in stem cells leads to polyp formation. (Source: EMBO Journal)
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Yin, X., Karp, J. M. Tags: Development & Differentiation News [amp ] Views Source Type: research

pUBLically unzipping Parkin: how phosphorylation exposes a ligase bit by bit
Disposal of damaged mitochondria is tightly controlled by auto-inhibition mechanisms that keep the ubiquitin ligase Parkin in check. Several new structural studies provide insight into how PINK1-dependent phosphorylation of ubiquitin and Parkin may progressively relieve Parkin auto-inhibition. (Source: EMBO Journal)
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Dove, K. K., Klevit, R. E., Rittinger, K. Tags: Post-translational Modifications, Proteolysis & Proteomics, Structural Biology News [amp ] Views Source Type: research

When things go wrong: correcting the scientific record
A reliable scientific literature is crucial for an efficient research process. Peer review remains a highly successful quality assurance mechanism, but it does not always prevent data and image aberrations and the publication of flawed data. Journals need to be in a position to detect such problems and take proportionate action. Publishers should apply consistent policies to correcting the published literature and adopt versioning. The scientific community ought to encourage corrections. (Source: EMBO Journal)
Source: EMBO Journal - October 14, 2015 Category: Molecular Biology Authors: Pulverer, B. Tags: Editorial Source Type: research

The inner membrane histidine kinase EnvZ senses osmolality via helix-coil transitions in the cytoplasm
(Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Wang, L. C., Morgan, L. K., Godakumbura, P., Kenney, L. J., Anand, G. S. Tags: Corrigendum Source Type: research

Polynucleotide kinase-phosphatase enables neurogenesis via multiple DNA repair pathways to maintain genome stability
Polynucleotide kinase–phosphatase (PNKP) is a DNA repair factor possessing both 5'-kinase and 3'-phosphatase activities to modify ends of a DNA break prior to ligation. Recently, decreased PNKP levels were identified as the cause of severe neuropathology present in the human microcephaly with seizures (MCSZ) syndrome. Utilizing novel murine Pnkp alleles that attenuate expression and a T424GfsX48 frame-shift allele identified in MCSZ individuals, we determined how PNKP inactivation impacts neurogenesis. Mice with PNKP inactivation in neural progenitors manifest neurodevelopmental abnormalities and postnatal death. Thi...
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Shimada, M., Dumitrache, L. C., Russell, H. R., McKinnon, P. J. Tags: DNA Replication, Repair & Recombination, Neuroscience Articles Source Type: research

KIM-1-/TIM-1-mediated phagocytosis links ATG5-/ULK1-dependent clearance of apoptotic cells to antigen presentation
Phagocytosis of apoptotic cells by both professional and semi-professional phagocytes is required for resolution of organ damage and maintenance of immune tolerance. KIM-1/TIM-1 is a phosphatidylserine receptor that is expressed on epithelial cells and can transform the cells into phagocytes. Here, we demonstrate that KIM-1 phosphorylation and association with p85 results in encapsulation of phagosomes by lipidated LC3 in multi-membrane organelles. KIM-1-mediated phagocytosis is not associated with increased ROS production, and NOX inhibition does not block LC3 lipidation. Autophagy gene expression is required for efficien...
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Brooks, C. R., Yeung, M. Y., Brooks, Y. S., Chen, H., Ichimura, T., Henderson, J. M., Bonventre, J. V. Tags: Immunology, Membrane & Intracellular Transport Articles Source Type: research

Cell cycle-dependent ubiquitylation and destruction of NDE1 by CDK5-FBW7 regulates ciliary length
Primary cilia start forming within the G1 phase of the cell cycle and continue to grow as cells exit the cell cycle (G0). They start resorbing when cells re-enter the cell cycle (S phase) and are practically invisible in mitosis. The mechanisms by which cilium biogenesis and disassembly are coupled to the cell cycle are complex and not well understood. We previously identified the centrosomal phosphoprotein NDE1 as a negative regulator of ciliary length and showed that its levels inversely correlate with ciliogenesis. Here, we identify the tumor suppressor FBW7 (also known as FBXW7, CDC4, AGO, or SEL-10) as the E3 ligase t...
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Maskey, D., Marlin, M. C., Kim, S., Kim, S., Ong, E.-C., Li, G., Tsiokas, L. Tags: Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research

{alpha}-synuclein assemblies sequester neuronal {alpha}3-Na+/K+-ATPase and impair Na+ gradient
Extracellular α-synuclein (α-syn) assemblies can be up-taken by neurons; however, their interaction with the plasma membrane and proteins has not been studied specifically. Here we demonstrate that α-syn assemblies form clusters within the plasma membrane of neurons. Using a proteomic-based approach, we identify the α3-subunit of Na+/K+-ATPase (NKA) as a cell surface partner of α-syn assemblies. The interaction strength depended on the state of α-syn, fibrils being the strongest, oligomers weak, and monomers none. Mutations within the neuron-specific α3-subunit are linked to rapid-...
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Shrivastava, A. N., Redeker, V., Fritz, N., Pieri, L., Almeida, L. G., Spolidoro, M., Liebmann, T., Bousset, L., Renner, M., Lena, C., Aperia, A., Melki, R., Triller, A. Tags: Neuroscience Articles Source Type: research

ESCRTs are everywhere
The ESCRT proteins are an ancient system that buds membranes and severs membrane necks from their inner face. Three "classical" functions of the ESCRTs have dominated research into these proteins since their discovery in 2001: the biogenesis of multivesicular bodies in endolysosomal sorting; the budding of HIV-1 and other viruses from the plasma membrane of infected cells; and the membrane abscission step in cytokinesis. The past few years have seen an explosion of novel functions: the biogenesis of microvesicles and exosomes; plasma membrane wound repair; neuron pruning; extraction of defective nuclear pore comp...
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Hurley, J. H. Tags: Autophagy & Cell Death, Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Review Source Type: research

Response to Heard et al
(Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Moulin, M., Voss, A. K., Thomas, T., Wong, W. W.-L., Cook, W. D., Koentgen, F., Vince, J., Silke, J., Vaux, D. L. Tags: Autophagy & Cell Death, Signal Transduction Correspondence Source Type: research

cIAP2 supports viability of mice lacking cIAP1 and XIAP
(Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Heard, K. N., Bertrand, M. J., Barker, P. A. Tags: Autophagy & Cell Death, Signal Transduction Correspondence Source Type: research

The different autophagic roads by which phagosomes travel to lysosomes
This study suggests that the autophagic machinery can regulate phagocytosis via two pathways, modification of phagosomes during LC3-associated phagocytosis (LAP) and macroautophagy of phagosomes. (Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Munz, C. Tags: Immunology, Membrane & Intracellular Transport News [amp ] Views Source Type: research

The tumor suppressor FBW7 controls ciliary length
The primary cilium provides a hub for reception of extracellular chemical and mechanical cues that influence differentiation, proliferation, and polarity, and contributes to cell cycle control. Ciliary length impacts the cilium's ability to coordinate these processes, and length control defects are linked to a number of clinically important developmental disorders. An exciting new study identifies a new mechanism of ciliary regulation based on interactions of CDK5 and the FBW7 tumor suppressor in regulating the degradation of the centrosomal protein NDE1 (Maskey et al, 2015). (Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Nikonova, A. S., Golemis, E. A. Tags: Cell Adhesion, Polarity & Cytoskeleton, Cell Cycle, Post-translational Modifications, Proteolysis & Proteomics News [amp ] Views Source Type: research

{alpha}-Synuclein oligomers pump it up!
Oligomeric forms of the Parkinson's disease-causing protein α-synuclein are suspected to mediate neurodegeneration, but the mechanisms are not understood. The present study of Shrivastava et al (2015) provides a fresh insight into this old mystery. α-Synuclein oligomers are shown by a combination of top state-of-the-art biochemical and super-resolution microscopy methods to sequester the neuronal sodium–potassium pump. Such perturbation of ion currents would ultimately lead to Ca2+ excitotoxicity. (Source: EMBO Journal)
Source: EMBO Journal - September 30, 2015 Category: Molecular Biology Authors: Kahle, P. J., Sugeno, N., Skodras, A. Tags: Neuroscience News [amp ] Views Source Type: research