Thursday, November 25, 2010

Hot off the presses! Nov 24 Cell

The Nov 24 issue of the Cell is now up on Pubget (About Cell): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

  • In This Issue
    - cell 143(5):653, 655 (2010)
  • Select: Cell Cycle
    - cell 143(5):657, 659 (2010)
    The phases of the cell cycle must be exquisitely timed and tightly regulated in order to ensure proper chromosome replication and segregation and cell division. New findings described in this issue's Select address key regulatory events in the cell cycle and reveal potential clinical outcomes of errors in these processes.
  • ER Sheets Get Roughed Up
    - cell 143(5):665-666 (2010)
    The molecular machinery that shapes the endoplasmic reticulum's (ER's) membrane into ordered networks of "smooth" tubules and "rough" sheets is poorly defined. Shibata et al. (2010) now report that sheet-inducing proteins, such as Climp-63, are enriched in the "rough" ER by their association with membrane-bound ribosomes, whereas curvature-inducing proteins localize at highly bent edges of membrane sheets.
  • SIRT3 in Calorie Restriction: Can You Hear Me Now?
    - cell 143(5):667-668 (2010)
    Caloric restriction decreases oxidative damage and extends life span in many organisms. Someya et al. (2010) show that the sirtuin SIRT3 mediates the protective effects of caloric restriction on age-related hearing loss by promoting the mitochondrial antioxidant system through the regulation of isocitrate dehydrogenase 2 (Idh2).
  • ATP Consumption Promotes Cancer Metabolism
    - cell 143(5):669-671 (2010)
    Cancer cells metabolize glucose by aerobic glycolysis, a phenomenon known as the Warburg effect. Fang et al. (2010) show that the endoplasmic reticulum enzyme ENTPD5 promotes ATP consumption and favors aerobic glycolysis. The findings suggest that nutrient uptake in cancer cells is limited by ATP and satisfies energy requirements other than ATP production.
  • Glycomics Hits the Big Time
    - cell 143(5):672-676 (2010)
    Cells run on carbohydrates. Glycans, sequences of carbohydrates conjugated to proteins and lipids, are arguably the most abundant and structurally diverse class of molecules in nature. Recent advances in glycomics reveal the scope and scale of their functional roles and their impact on human disease.
  • What Determines the Specificity and Outcomes of Ubiquitin Signaling?
    - cell 143(5):677-681 (2010)
    Ubiquitin signals and ubiquitin-binding domains are implicated in almost every cellular process, but how is their functionality achieved in cells? We assess recent advances in monitoring the dynamics and specificity of ubiquitin networks in vivo and discuss challenges ahead. PaperClip (2885 K)
  • Ubiquitin: Same Molecule, Different Degradation Pathways
    - cell 143(5):682-685 (2010)
    Ubiquitin is a common demoninator in the targeting of substrates to all three major protein degradation pathways in mammalian cells: the proteasome, the lysosome, and the autophagosome. The factors that direct a substrate toward a particular route of degradation likely include ubiquitin chain length and linkage type, which may favor interaction with particular receptors or confer differential susceptibility to deubiquitinase activities associated with each pathway.
  • Will the Ubiquitin System Furnish as Many Drug Targets as Protein Kinases?
    - cell 143(5):686-693 (2010)
    Protein phosphorylation and protein ubiquitination regulate most aspects of cell life, and defects in these control mechanisms cause cancer and many other diseases. In the past decade, protein kinases have become one of the most important classes of drug targets for the pharmaceutical industry. In contrast, drug discovery programs that target components of the ubiquitin system have lagged behind. In this Perspective, we discuss the reasons for the delay in this pipeline, the drugs targeting the ubiquitin system that have been developed, and new approaches that may popularize this area of drug discovery in the future.
  • Pathogen-Mediated Posttranslational Modifications: A Re-emerging Field
    - cell 143(5):694-702 (2010)
    Posttranslational modifications are increasingly recognized as key strategies used by bacterial and viral pathogens to modulate host factors critical for infection. A number of recent studies illustrate how pathogens use these posttranslational modifications to target central signaling pathways in the host cell, such as the NF-kB and MAP kinase pathways, which are essential for pathogens' replication, propagation, and evasion from host immune responses. These discoveries open new avenues for investigating the fundamental mechanisms of pathogen infection and the development of new therapeutics.
  • Modifications of Small RNAs and Their Associated Proteins
    - cell 143(5):703-709 (2010)
    Small regulatory RNAs and their associated proteins are subject to diverse modifications that can impinge on their abundance and function. Some of the modifications are under the influence of cellular signaling, thus contributing to the dynamic regulation of RNA silencing.
  • The ER UDPase ENTPD5 Promotes Protein N-Glycosylation, the Warburg Effect, and Proliferation in the PTEN Pathway
    - cell 143(5):711-724 (2010)
    PI3K and PTEN lipid phosphatase control the level of cellular phosphatidylinositol (3,4,5)-trisphosphate, an activator of AKT kinases that promotes cell growth and survival. Mutations activating AKT are commonly observed in human cancers. We report here that ENTPD5, an endoplasmic reticulum (ER) enzyme, is upregulated in cell lines and primary human tumor samples with active AKT. ENTPD5 hydrolyzes UDP to UMP to promote protein N-glycosylation and folding in ER. Knockdown of ENTPD5 in PTEN null cells causes ER stress and loss of growth factor receptors. ENTPD5, together with cytidine monophosphate kinase-1 and adenylate kinase-1, constitute an ATP hydrolysis cycle that converts ATP to AMP, resulting in a compensatory increase in aerobic glycolysis known as the Warburg effect. The growth of PTEN null cells is inhibited both in vitro and in mouse xenograft tumor models. ENTPD5 is therefore an integral part of the PI3K/PTEN regulatory loop and a potential target for antica! ncer therapy.
  • Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome
    - cell 143(5):725-736 (2010)
    Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or zero H2A.Z molecules. SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products. The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction. Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B, and deposition of H2A.Z-H2B. These results suggest that! the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction.
  • Sororin Mediates Sister Chromatid Cohesion by Antagonizing Wapl
    - cell 143(5):737-749 (2010)
    Sister chromatid cohesion is essential for chromosome segregation and is mediated by cohesin bound to DNA. Cohesin-DNA interactions can be reversed by the cohesion-associated protein Wapl, whereas a stably DNA-bound form of cohesin is thought to mediate cohesion. In vertebrates, Sororin is essential for cohesion and stable cohesin-DNA interactions, but how Sororin performs these functions is unknown. We show that DNA replication and cohesin acetylation promote binding of Sororin to cohesin, and that Sororin displaces Wapl from its binding partner Pds5. In the absence of Wapl, Sororin becomes dispensable for cohesion. We propose that Sororin maintains cohesion by inhibiting Wapl's ability to dissociate cohesin from DNA. Sororin has only been identified in vertebrates, but we show that many invertebrate species contain Sororin-related proteins, and that one of these, Dalmatian, is essential for cohesion in Drosophila. The mechanism we describe here may therefore be widel! y conserved among different species.
  • Nonenzymatic Rapid Control of GIRK Channel Function by a G Protein-Coupled Receptor Kinase
    - cell 143(5):750-760 (2010)
    G protein-coupled receptors (GPCRs) respond to agonists to activate downstream enzymatic pathways or to gate ion channel function. Turning off GPCR signaling is known to involve phosphorylation of the GPCR by GPCR kinases (GRKs) to initiate their internalization. The process, however, is relatively slow and cannot account for the faster desensitization responses required to regulate channel gating. Here, we show that GRKs enable rapid desensitization of the G protein-coupled potassium channel (GIRK/Kir3.x) through a mechanism independent of their kinase activity. On GPCR activation, GRKs translocate to the membrane and quench channel activation by competitively binding and titrating G protein βγ subunits away from the channel. Of interest, the ability of GRKs to effect this rapid desensitization depends on the receptor type. The findings thus reveal a stimulus-specific, phosphorylation-independent mechanism for rapidly downregulating GPCR activity at the effector lev! el.
  • Sequence-Dependent Sorting of Recycling Proteins by Actin-Stabilized Endosomal Microdomains
    - cell 143(5):761-773 (2010)
    The functional consequences of signaling receptor endocytosis are determined by the endosomal sorting of receptors between degradation and recycling pathways. How receptors recycle efficiently, in a sequence-dependent manner that is distinct from bulk membrane recycling, is not known. Here, in live cells, we visualize the sorting of a prototypical sequence-dependent recycling receptor, the beta-2 adrenergic receptor, from bulk recycling proteins and the degrading delta-opioid receptor. Our results reveal a remarkable diversity in recycling routes at the level of individual endosomes, and indicate that sequence-dependent recycling is an active process mediated by distinct endosomal subdomains distinct from those mediating bulk recycling. We identify a specialized subset of tubular microdomains on endosomes, stabilized by a highly localized but dynamic actin machinery, that mediate this sorting, and provide evidence that these actin-stabilized domains provide the physica! l basis for a two-step kinetic and affinity-based model for protein sorting into the sequence-dependent recycling pathway. PaperFlick Download this Video (37600 K)
  • Mechanisms Determining the Morphology of the Peripheral ER
    - cell 143(5):774-788 (2010)
    The endoplasmic reticulum (ER) consists of the nuclear envelope and a peripheral network of tubules and membrane sheets. The tubules are shaped by the curvature-stabilizing proteins reticulons and DP1/Yop1p, but how the sheets are formed is unclear. Here, we identify several sheet-enriched membrane proteins in the mammalian ER, including proteins that translocate and modify newly synthesized polypeptides, as well as coiled-coil membrane proteins that are highly upregulated in cells with proliferated ER sheets, all of which are localized by membrane-bound polysomes. These results indicate that sheets and tubules correspond to rough and smooth ER, respectively. One of the coiled-coil proteins, Climp63, serves as a "luminal ER spacer" and forms sheets when overexpressed. More universally, however, sheet formation appears to involve the reticulons and DP1/Yop1p, which localize to sheet edges and whose abundance determines the ratio of sheets to tubules. These proteins ! may generate sheets by stabilizing the high curvature of edges.
  • Abortive HIV Infection Mediates CD4 T Cell Depletion and Inflammation in Human Lymphoid Tissue
    - cell 143(5):789-801 (2010)
    The mechanism by which CD4 T cells are depleted in HIV-infected hosts remains poorly understood. In ex vivo cultures of human tonsil tissue, CD4 T cells undergo a pronounced cytopathic response following HIV infection. Strikingly, >95% of these dying cells are not productively infected but instead correspond to bystander cells. We now show that the death of these "bystander" cells involves abortive HIV infection. Inhibitors blocking HIV entry or early steps of reverse transcription prevent CD4 T cell death while inhibition of later events in the viral life cycle does not. We demonstrate that the nonpermissive state exhibited by the majority of resting CD4 tonsil T cells leads to accumulation of incomplete reverse transcripts. These cytoplasmic nucleic acids activate a host defense program that elicits a coordinated proapoptotic and proinflammatory response involving caspase-3 and caspase-1 activation. While this response likely evolved to protect the host, it centr! ally contributes to the immunopathogenic effects of HIV.
  • Sirt3 Mediates Reduction of Oxidative Damage and Prevention of Age-Related Hearing Loss under Caloric Restriction
    - cell 143(5):802-812 (2010)
    Caloric restriction (CR) extends the life span and health span of a variety of species and slows the progression of age-related hearing loss (AHL), a common age-related disorder associated with oxidative stress. Here, we report that CR reduces oxidative DNA damage in multiple tissues and prevents AHL in wild-type mice but fails to modify these phenotypes in mice lacking the mitochondrial deacetylase Sirt3, a member of the sirtuin family. In response to CR, Sirt3 directly deacetylates and activates mitochondrial isocitrate dehydrogenase 2 (Idh2), leading to increased NADPH levels and an increased ratio of reduced-to-oxidized glutathione in mitochondria. In cultured cells, overexpression of Sirt3 and/or Idh2 increases NADPH levels and protects from oxidative stress-induced cell death. Therefore, our findings identify Sirt3 as an essential player in enhancing the mitochondrial glutathione antioxidant defense system during CR and suggest that Sirt3-dependent mitochondrial ! adaptations may be a central mechanism of aging retardation in mammals.
  • FOXO/4E-BP Signaling in Drosophila Muscles Regulates Organism-wide Proteostasis during Aging
    - cell 143(5):813-825 (2010)
    The progressive loss of muscle strength during aging is a common degenerative event of unclear pathogenesis. Although muscle functional decline precedes age-related changes in other tissues, its contribution to systemic aging is unknown. Here, we show that muscle aging is characterized in Drosophila by the progressive accumulation of protein aggregates that associate with impaired muscle function. The transcription factor FOXO and its target 4E-BP remove damaged proteins at least in part via the autophagy/lysosome system, whereas foxo mutants have dysfunctional proteostasis. Both FOXO and 4E-BP delay muscle functional decay and extend life span. Moreover, FOXO/4E-BP signaling in muscles decreases feeding behavior and the release of insulin from producing cells, which in turn delays the age-related accumulation of protein aggregates in other tissues. These findings reveal an organism-wide regulation of proteostasis in response to muscle aging and a key role of FOXO/4E-B! P signaling in the coordination of organismal and tissue aging.
  • Reelin and Stk25 Have Opposing Roles in Neuronal Polarization and Dendritic Golgi Deployment
    - cell 143(5):826-836 (2010)
    The Reelin ligand regulates a Dab1-dependent signaling pathway required for brain lamination and normal dendritogenesis, but the specific mechanisms underlying these actions remain unclear. We find that Stk25, a modifier of Reelin-Dab1 signaling, regulates Golgi morphology and neuronal polarization as part of an LKB1-Stk25-Golgi matrix protein 130 (GM130) signaling pathway. Overexpression of Stk25 induces Golgi condensation and multiple axons, both of which are rescued by Reelin treatment. Reelin stimulation of cultured neurons induces the extension of the Golgi into dendrites, which is suppressed by Stk25 overexpression. In vivo, Reelin and Dab1 are required for the normal extension of the Golgi apparatus into the apical dendrites of hippocampal and neocortical pyramidal neurons. This demonstrates that the balance between Reelin-Dab1 signaling and LKB1-Stk25-GM130 regulates Golgi dispersion, axon specification, and dendrite growth and provides insights into the import! ance of the Golgi apparatus for cell polarization.
  • A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms
    - cell 143(5):837-847 (2010)
    Understanding the prevailing mutational mechanisms responsible for human genome structural variation requires uniformity in the discovery of allelic variants and precision in terms of breakpoint delineation. We develop a resource based on capillary end sequencing of 13.8 million fosmid clones from 17 human genomes and characterize the complete sequence of 1054 large structural variants corresponding to 589 deletions, 384 insertions, and 81 inversions. We analyze the 2081 breakpoint junctions and infer potential mechanism of origin. Three mechanisms account for the bulk of germline structural variation: microhomology-mediated processes involving short (2–20 bp) stretches of sequence (28%), nonallelic homologous recombination (22%), and L1 retrotransposition (19%). The high quality and long-range continuity of the sequence reveals more complex mutational mechanisms, including repeat-mediated inversions and gene conversion, that are most often missed by other methods, s! uch as comparative genomic hybridization, single nucleotide polymorphism microarrays, and next-generation sequencing.
  • SnapShot: The SUMO System
    - cell 143(5):848-848.e1 (2010)

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