Nature Chemical Biology Contents: May 2014 Volume 10 No 5 pp 319 - 406

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TABLE OF CONTENTS May 2014 Volume 10, Issue 5 Commentary Research Highlights News and Views Perspective Brief Communication Articles Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nature Structural & Molecular Biology  FOCUS ON UBIQUITIN  Ubiquitin and ubiquitin-like proteins have central roles in regulating cellular processes and homeostasis. This Focus examines our understanding of the ubiquitination reaction and the mechanisms by which ubiquitin and related modifications affect key cellular functions. Produced with support from  Takeda    Commentary Top Engineering synergy in biotechnology   pp319 - 322 Jens Nielsen, Martin Fussenegger, Jay Keasling, Sang Yup Lee, James C Liao et al. doi:10.1038/nchembio.1519 Biotechnology is a central focus in efforts to provide sustainable solutions for the provision of fuels, chemicals and materials. On the basis of a recent open discussion, we summarize the development of this field, highlighting the distinct but complementary approaches provided by metabolic engineering and synthetic biology for the creation of efficient cell factories to convert biomass and other feedstocks to desired chemicals. Research Highlights Top Metal regulation: Iron clad delivery | Immunology: Interfering with Interferon | Plant innate immunity: Tussling over tyrosine | Peptides: A synthetic step change | Cell biology: Just the two of us | Apoptosis: A channel off-target | Natural products: A painful discovery | Kinase regulation: Switching GSK3 off News and Views Top Metabolism: Pathogens love the poison   pp326 - 327 Stéphane Ménage and Ina Attrée doi:10.1038/nchembio.1505 Itaconate is a metabolite secreted by activated macrophages that inhibits pathogen growth. Some pathogens use itaconate degradation enzymes to promote their survival and infectivity, highlighting metabolic pathways to be considered in host-pathogen interactions. Pluripotency: Citrullination unravels stem cells   pp327 - 328 Daniel J Slade, Venkataraman Subramanian and Paul R Thompson doi:10.1038/nchembio.1504 Maintenance of the pluripotent stem cell state is regulated by the post-translational modification of histones. The discovery that citrullination of the linker histone H1 is critical to this process represents a new role for the protein arginine deiminases in development. Labeling: Palladium brings proteins to life   pp328 - 330 Kun Qian and Yujun George Zheng doi:10.1038/nchembio.1507 A bioorthogonal decaging strategy, mediated by small-molecule palladium compounds, can recover the lysine-dependent activity of cellular proteins. This activation technique could be generally applicable for controlling and probing function of a protein target in living cells. Chemical Biology JOBS of the week Post-Doctoral Fellowship In Biomedical Research Oklahoma State University Postdoctoral Fellowship Moffitt Cancer Center & Research Institute Postdoc in musselinspired multifunctional hydrogel materials Aarhus University Doctoral Studentship In Biology Lund University More Science jobs from Chemical Biology EVENT Chemical Biology Discussion Group Year-End Symposium 3 June 2014 New York, USA More science events from Perspective Top Rethinking biological activation of methane and conversion to liquid fuels   pp331 - 339 Chad A Haynes and Ramon Gonzalez doi:10.1038/nchembio.1509 Methane is an energy resource that is currently being wasted through emissions, venting and flaring during petroleum extraction. Recent discoveries regarding the basis of enzyme function and microbial metabolism provide the foundation for new thinking about how to reclaim this resource through bioconversion. Brief Communication Top Structural basis for hijacking siderophore receptors by antimicrobial lasso peptides   pp340 - 342 Indran Mathavan, Séverine Zirah, Shahid Mehmood, Hassanul G Choudhury, Christophe Goulard et al. doi:10.1038/nchembio.1499 Lasso peptides are antimicrobial bacterial peptides that hijack outer membrane siderophores to kill target cells. The structural and biochemical basis of antimicrobial lasso peptide MccJ25 binding to siderophore FhuA explains why these peptides have a narrow range of target species. Articles Top Target identification for a Hedgehog pathway inhibitor reveals the receptor GPR39   pp343 - 349 Frederic Bassilana, Adam Carlson, Jennifer A DaSilva, Bianka Grosshans, Solange Vidal et al. doi:10.1038/nchembio.1481 A new small-molecule inhibitor of the Hedgehog signaling pathway acts independently of Smoothened (Smo). Rather than acting through Smo, which is a GPCR-like protein of the pathway, the compound acts through the orphan GPCR GPR39, with the level of GPR39 activation correlating with Hh pathway inhibition. Chemical compounds Golgi sorting regulates organization and activity of GPI proteins at apical membranes   pp350 - 357 Simona Paladino, Stéphanie Lebreton, Simona Tivodar, Fabio Formiggini, Giulia Ossato et al. doi:10.1038/nchembio.1495 High-resolution microscopy and biochemistry show that homoclusters of GPI-anchored proteins (GPI-APs) in the Golgi arrive at the apical membrane of polarized cells and then coalesce into larger heteroclusters. Therefore, sorting at the Golgi determines organization of GPI-APs at the plasma membrane. G-quadruplexes regulate Epstein-Barr virus–encoded nuclear antigen 1 mRNA translation   pp358 - 364 Pierre Murat, Jie Zhong, Lea Lekieffre, Nathan P Cowieson, Jennifer L Clancy et al. doi:10.1038/nchembio.1479 Biophysical analysis reveals that conserved G-rich sequences within the mRNAs of gammaherpesvirus genome maintenance proteins (GMPs) form G-quadruplexes (G4). Stabilization of mRNA G4 motifs represses GMP translation, whereas destabilization enhances translation, suggesting that these RNA elements are cis-acting translational regulators of proteins involved in viral latency. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark   pp365 - 370 Lunzhi Dai, Chao Peng, Emilie Montellier, Zhike Lu, Yue Chen et al. doi:10.1038/nchembio.1497 Histone post-translational modifications are important regulators of chromatin structure and gene expression. Lysine 2-hydroxisobutyrylation sites, discovered by MS and validated by chemical synthesis, are found in active chromatin and associated with male germ cell differentiation. Chemical compounds Bacterial itaconate degradation promotes pathogenicity   pp371 - 377 Jahminy Sasikaran, Michał Ziemski, Piotr K Zadora, Angela Fleig and Ivan A Berg doi:10.1038/nchembio.1482 Host cells respond to bacterial infection by producing itaconate, an inhibitor of bacterial metabolism, among other strategies. Biochemical characterization now defines genes known to be important for bacterial virulence as a new pathway that degrades itaconate into metabolic building blocks. Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase   pp378 - 385 Stefan Frielingsdorf, Johannes Fritsch, Andrea Schmidt, Mathias Hammer, Julia Löwenstein et al. doi:10.1038/nchembio.1500 Certain oxygen-tolerant hydrogenases contain a unique [4Fe-3S] cluster near the catalytic site, but the role of this cofactor is not fully understood. Crystallographic, spectroscopic and computational data now provide evidence for redox-dependent transformations of this cluster, potentially explaining how specialized hydrogenases can safely reduce inhibitory O2. Design of activated serine–containing catalytic triads with atomic-level accuracy   pp386 - 391 Sridharan Rajagopalan, Chu Wang, Kai Yu, Alexandre P Kuzin, Florian Richter et al. doi:10.1038/nchembio.1498 De novo enzyme designs have generally tried to optimize multiple aspects of enzyme function simultaneously. Focusing only on positioning of active site residues to generate a nucleophilic serine as assessed by activity-based protein profiling now leads to a successful intermediate design. Bioretrosynthetic construction of a didanosine biosynthetic pathway   pp392 - 399 William R Birmingham, Chrystal A Starbird, Timothy D Panosian, David P Nannemann, T M Iverson et al. doi:10.1038/nchembio.1494 Bioretrosynthesis is meant to simplify construction of metabolic pathways by screening only for the final desired product. This approach, aided by protein design and crystallography, is now used to synthesize an antiretroviral nucleoside analog and surprisingly identifies a new enzyme function. Chemical compounds Amphotericin forms an extramembranous and fungicidal sterol sponge   pp400 - 406 Thomas M Anderson, Mary C Clay, Alexander G Cioffi, Katrina A Diaz, Grant S Hisao et al. doi:10.1038/nchembio.1496 NMR structural data and biophysical and biological experiments show that the antifungal compound amphotericin is toxic because it acts as a sterol sponge by interacting with ergosterol on the fungal membrane and extracting it from within the membrane to the surface of the membrane. Top Advertisement BRAND NEW: Discounts on lab equipment Exclusive prices and information - all in one place! Check our listings before you buy.  VISIT MARKETPLACE TODAY      Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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