Nature Chemical Biology Contents: September 2012 Volume 8 Number 9, pp 738 - 805

TABLE OF CONTENTS September 2012 Volume 8, Issue 9 Research Highlights News and Views Brief Communications Articles Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement The Open Innovation Pavilion has a fresh set of Challenges that need a winning solution from biologists like you. Submit a proposed solution for any of our open Challenges for a chance to win up to $1 million! View all open Challenges by clicking here. Click here to see stories from past Solvers.   Research Highlights Top Regulation: Positively alarming | Virology: Cholesterol manipulation | Proteomics: Cross-talking modifications | Synthetic biology: Beta testing | Drug resistance: The stroma's contribution | Iron-sulfur clusters: MMS to the nucleus | Prodrug activation: Glutaredoxin family tree | Immunity: FetA gets fat News and Views Top Peroxidasin: Tying the collagen-sulfilimine knot   pp740 - 741 Stephen J Weiss doi:10.1038/nchembio.1050 Type IV collagen, a major constituent of basement membranes, contains an unusual intermolecular sulfilimine crosslink whose route of biosynthesis has remained undefined. An oxidative triad consisting of peroxidasin, H2O2 and halide is now shown to drive sulfilimine generation in vivo. See also: Article by Bhave et al. Glycosyltransferases: Carb loading strategy is spot on   pp741 - 742 Jeffrey C Gildersleeve doi:10.1038/nchembio.1049 Glycosyltransferases, enzymes that catalyze glycosidic bond formation, are one of the most important but least well-characterized protein families found in nature. A new label-free, high-throughput glycan array-based strategy enables rapid profiling of tens of thousands of potential glycosyltransferase reactions. See also: Article by Ban et al. Membranes: First steps to rafts?   pp743 - 744 John R Silvius doi:10.1038/nchembio.1045 Single-molecule observations reveal that lipid- and protein-based interactions jointly contribute to the interactions among glycosylphosphatidylinositol-anchored proteins in membranes. Understanding these interactions will help to refine long-evolving (and still debated) models of 'raft' domains in biological membranes. See also: Article by Suzuki et al. Chemical Biology JOBS of the week Tenure Track Faculty Positions in Chemical Biology University of California San Francisco Chemical Science, Molecular Biology or Biochemistry Graduate – KTP Associate Queen’s University Belfast Postdoctoral position as Synthetic Chemist in Organic Chemistry and Chemical Biology Institut de Recerca Biomedica - IRB Lectureship in Chemical Biology University of York PhD position in Biophysics / Chemical Biology Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland More Science jobs from Chemical Biology EVENT 13th Tetrahedron Symposium (Asia) – Challenges in Bioorganic & Organic Medicinal Chemistry 27-30 November 2012 UK More science events from Brief Communications Top Caspase-1 activity is required to bypass macrophage apoptosis upon Salmonella infection   pp745 - 747 Aaron W Puri, Petr Broz, Aimee Shen, Denise M Monack and Matthew Bogyo doi:10.1038/nchembio.1023 AWP28, an activity-based probe for caspase-1, reveals that caspase-1 is required to bypass apoptosis for pyroptotic cell death during bacterial infection of macrophages. Expanding the genetic code of Drosophila melanogaster    pp748 - 750 Ambra Bianco, Fiona M Townsley, Sebastian Greiss, Kathrin Lang and Jason W Chin doi:10.1038/nchembio.1043 Genetic code expansion by ribosomal incorporation of non-natural amino acids has provided a useful approach for site-specific protein modification. This approach has now been extended to the model organism Drosophila melanogaster, permitting the introduction of non-standard amino acids into proteins within specific cell and tissue types and across developmental stages. Chemical compounds Articles Top AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation   pp751 - 758 Christopher S Nabel, Huijue Jia, Yu Ye, Li Shen, Hana L Goldschmidt, James T Stivers, Yi Zhang and Rahul M Kohli doi:10.1038/nchembio.1042 AID/APOBEC deaminases, which convert cytosine bases to uracils in DNA and RNA, have recently been assigned a role in epigenetic regulation as components of DNA demethylation pathways. A systematic study shows that AID/APOBEC enzymes preferentially deaminate unmodified cytosine over its C5-modified forms, calling into question the plausibility of deaminase-mediated DNA demethylation pathways. Architectural and thermodynamic principles underlying intramembrane protease function   pp759 - 768 Rosanna P Baker and Sinisa Urban doi:10.1038/nchembio.1021 Application of a new thermal light scattering technique to quantitatively analyze nearly 150 mutants of the rhomboid intramembrane protease GlpG, coupled with thermodynamic measurements and protease assays, reveals how interactions throughout the molecule collaborate to support enzyme structure and function. Discovery of glycosyltransferases using carbohydrate arrays and mass spectrometry   pp769 - 773 Lan Ban, Nicholas Pettit, Lei Li, Andreea D Stuparu, Li Cai, Wenlan Chen, Wanyi Guan, Weiqing Han, Peng George Wang and Milan Mrksich doi:10.1038/nchembio.1022 Discovery of the native activity of the ~60,000 putative glycosyltransferases remains a substantial challenge. A high-throughput, label-free method drastically speeds this process, with assays of 85 enzymes, 24 acceptors and 7 donors returning functions for four new proteins. Chemical compounds See also: News and Views by Gildersleeve Transient GPI-anchored protein homodimers are units for raft organization and function   pp774 - 783 Kenichi G N Suzuki, Rinshi S Kasai, Koichiro M Hirosawa, Yuri L Nemoto, Munenori Ishibashi, Yoshihiro Miwa, Takahiro K Fujiwara and Akihiro Kusumi doi:10.1038/nchembio.1028 Single-molecule imaging reveals that GPI-anchored proteins in the plasma membrane form homodimer rafts via ectodomain protein interactions. Raft-lipid interactions stabilize higher order oligomers, which trigger intracellular signaling upon ligand binding. See also: News and Views by Silvius Peroxidasin forms sulfilimine chemical bonds using hypohalous acids in tissue genesis   pp784 - 790 Gautam Bhave, Christopher F Cummings, Roberto M Vanacore, Chino Kumagai-Cresse, Isi A Ero-Tolliver, Mohamed Rafi, Jeong-Suk Kang, Vadim Pedchenko, Liselotte I Fessler, John H Fessler and Billy G Hudson doi:10.1038/nchembio.1038 Peroxidasin uses hypohalous acid oxidants to catalyze the formation of sulfilimine bonds in basement membranes. See also: News and Views by Weiss A stand-alone adenylation domain forms amide bonds in streptothricin biosynthesis   pp791 - 797 Chitose Maruyama, Junya Toyoda, Yasuo Kato, Miho Izumikawa, Motoki Takagi, Kazuo Shin-ya, Hajime Katano, Takashi Utagawa and Yoshimitsu Hamano doi:10.1038/nchembio.1040 A study of three synthetases involved in streptothricin biosynthesis demonstrates roles for two A domains in activating lysine, with one A domain transferring lysine to a carrier T domain and the second directly catalyzing amide bond formation to form a growing lysine oligopeptide. Chemical compounds A role for the root cap in root branching revealed by the non-auxin probe naxillin    pp798 - 805 Bert De Rybel, Dominique Audenaert, Wei Xuan, Paul Overvoorde, Lucia C Strader, Stefan Kepinski, Rebecca Hoye, Ronald Brisbois, Boris Parizot, Steffen Vanneste, Xing Liu, Alison Gilday, Ian A Graham, Long Nguyen, Leentje Jansen, Maria Fransiska Njo, Dirk Inzé, Bonnie Bartel and Tom Beeckman doi:10.1038/nchembio.1044 The plant hormone auxin affects many aspects of root development, including lateral root branching. A high-throughput screen in Arabidopsis thaliana has led to the identification of naxillin, a non-auxin chemical probe that enhances lateral root branching and has revealed an important role of the root cap in regulating this process. 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