Susan Lindquist (1949–2016)

January 19th, 2017 by Tricia R Serio

Nature Chemical Biology 13, 127 (2017). doi:10.1038/nchembio.2305

Author: Tricia R Serio

Susan Lindquist passed away on 27 October 2016, far too early for those who marveled at her brilliance through her many contributions to science, for all who knew her directly, and especially for her former trainees.

Synthetic biology: Sensing with modular receptors

January 19th, 2017 by Matthew Brenner

Nature Chemical Biology 13, 131 (2017). doi:10.1038/nchembio.2290

Authors: Matthew Brenner, Jang Hwan Cho & Wilson W Wong

Sensing and responding to diverse extracellular signals is a crucial aspect of cellular decision-making that is currently lacking in the synthetic biology toolkit. The development of modular receptor platforms allows for the rewiring of cellular input–output relationships.

Super-resolution visualization of caveolae deformation in response to osmotic stress [Signal Transduction]

January 17th, 2017 by Lu Yang, Suzanne Scarlata

Caveolae are protein dense plasma membrane domains structurally composed of caveolin -1 or -3 along with other proteins. Our previous studies have shown that caveolae enhance calcium signals generated through the Gαq/phospholipase Cβ signaling pathway, and that subjecting cells to hypo-osmotic stress reverses this enhancement. In this study, we have used super-resolution fluorescence microscopy supplemented by fluorescence correlation studies to determine the structural factors that underlie this behavior. We find similar and significant populations of Gαq and one of its receptors, bradykinin type 2 receptor (β2R), as well as Gαi and its coupled 2-adrenergic receptor (βAR), localize to caveolae domains. While mild osmotic stress deforms caveolae altering interactions between caveolae and these proteins, it does not affect the general structure and the localization of caveolae components remain largely unchanged. Additionally, in contrast to calcium signals mediated through Gαq-B2R, osmotic stress does not affect cAMP signals mediated through Gαi and βAR. Structurally, we find that mild osmotic stress corresponding roughly to a pressure of 3.82 N/m2 increases the domain diameter by ~30% and increases the fluorescence intensity in the center of the domain mouth suggesting a flattening of the invagination. Approximate calculations show that caveolae in muscle tissue have the strength to handle the stress of muscle movement.

Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis

January 16th, 2017 by Matthew J Rodrigues

Nature Chemical Biology 13, 290 (2017). doi:10.1038/nchembio.2273

Authors: Matthew J Rodrigues, Volker Windeisen, Yang Zhang, Gabriela Guédez, Stefan Weber, Marco Strohmeier, Jeremiah W Hanes, Antoine Royant, Gwyndaf Evans, Irmgard Sinning, Steven E Ealick, Tadhg P Begley & Ivo Tews

  • Posted in Nat Chem Biol, Publications
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Chemical proteomics reveals ADP-ribosylation of small GTPases during oxidative stress

January 16th, 2017 by Nathan P Westcott

Nature Chemical Biology 13, 302 (2017). doi:10.1038/nchembio.2280

Authors: Nathan P Westcott, Joseph P Fernandez, Henrik Molina & Howard C Hang

  • Posted in Nat Chem Biol, Publications
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Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors

January 16th, 2017 by Ely B Porter

Nature Chemical Biology 13, 295 (2017). doi:10.1038/nchembio.2278

Authors: Ely B Porter, Jacob T Polaski, Makenna M Morck & Robert T Batey

  • Posted in Nat Chem Biol, Publications
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Designed cell consortia as fragrance-programmable analog-to-digital converters

January 16th, 2017 by Marius Müller

Nature Chemical Biology 13, 309 (2017). doi:10.1038/nchembio.2281

Authors: Marius Müller, Simon Ausländer, Andrea Spinnler, David Ausländer, Julian Sikorski, Marc Folcher & Martin Fussenegger

  • Posted in Nat Chem Biol, Publications
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Autoinhibition of the Nuclease ARTEMIS is Mediated by a Physical Interaction between Its Catalytic and C-terminal Domains [Immunology]

January 12th, 2017 by Doris Niewolik, Ingrid Peter, Carmen Butscher, Klaus Schwarz

The nuclease ARTEMIS is essential for the development of B and T lymphocytes. It is required for opening DNA hairpins generated during antigen receptor gene assembly from variable (V), diversity (D) and joining (J) subgenic elements (V(D)J recombination). As a member of the non-homologous end joining pathway it is also involved in repairing a subset of pathological DNA double-strand breaks. Loss of ARTEMIS function therefore results in radiosensitive severe combined immunodeficiency (RS-SCID). The hairpin-opening activity is dependent on the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), which can bind to and phosphorylate ARTEMIS. The ARTEMIS C-terminus is dispensable for cellular V(D)J recombination and in vitro nuclease assays with C-terminally truncated ARTEMIS show DNA PKcs-independent hairpin-opening activity. Therefore it has been postulated that ARTEMIS is regulated via autoinhibition by its C-terminus. To obtain evidence for the autoinhibition model, we performed co-immunoprecipitation experiments with combinations of ARTEMIS mutants. We show that an N-terminal fragment comprising the catalytic domain can interact both with itself and with a C-terminal fragment. Amino acid exchanges N456A+S457A+E458Q in the C-terminus of full-length ARTEMIS resulted in unmasking of the N-terminus and in increased ARTEMIS activity in cellular V(D)J recombination assays. Mutations in ARTEMIS-deficient patients impaired the interaction with the C-terminus and also affected protein stability. The interaction between the N- and C-terminal domains was not DNA-PKcs dependent and phosphomimetic mutations in the C-terminal domain did not result in unmasking of the catalytic domain. Our experiments provide strong evidence that a physical interaction between the C-terminal and catalytic domains mediates ARTEMIS autoinhibition.

MraY–antibiotic complex reveals details of tunicamycin mode of action

January 9th, 2017 by Jonna K Hakulinen

Nature Chemical Biology 13, 265 (2017). doi:10.1038/nchembio.2270

Authors: Jonna K Hakulinen, Jenny Hering, Gisela Brändén, Hongming Chen, Arjan Snijder, Margareta Ek & Patrik Johansson

The rapid increase of antibiotic resistance has created an urgent need to develop novel antimicrobial agents. Here we describe the crystal structure of the promising bacterial target phospho-N-acetylmuramoyl–pentapeptide translocase (MraY) in complex with the nucleoside antibiotic tunicamycin. The structure not only reveals the mode of action of several related natural-product antibiotics but also gives an indication on the binding mode of the MraY UDP–MurNAc–pentapeptide and undecaprenyl-phosphate substrates.

  • Posted in Nat Chem Biol, Publications
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Visualizing the secondary and tertiary architectural domains of lncRNA RepA

January 9th, 2017 by Fei Liu

Nature Chemical Biology 13, 282 (2017). doi:10.1038/nchembio.2272

Authors: Fei Liu, Srinivas Somarowthu & Anna Marie Pyle

  • Posted in Nat Chem Biol, Publications
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