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  • Continuous directed evolution of proteins with improved soluble expression
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-20
    Tina Wang, Ahmed H. Badran, Tony P. Huang, David R. Liu

    We report the development of soluble expression phage-assisted continuous evolution (SE-PACE), a system for rapidly evolving proteins with increased soluble expression. Through use of a PACE-compatible AND gate that uses a split-intein pIII, SE-PACE enables two simultaneous positive selections to evolve proteins with improved expression while maintaining their desired activities. In as little as three days, SE-PACE evolved several antibody fragments with >5-fold improvement in expression yield while retaining binding activity. We also developed an activity-independent form of SE-PACE to correct folding-defective variants of maltose-binding protein (MBP) and to evolve variants of the eukaryotic cytidine deaminase APOBEC1 with improved expression properties. These evolved APOBEC1 variants were found to improve the expression and apparent activity of Cas9-derived base editors when used in place of the wild-type cytidine deaminase. Together, these results suggest that SE-PACE can be applied to a wide variety of proteins to rapidly improve their soluble expression.

    更新日期:2018-08-20
  • O-GlcNAc modification of eIF4GI acts as a translational switch in heat shock response
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-20
    Xingqian Zhang, Xin Erica Shu, Shu-Bing Qian

    Heat shock response (HSR) is an ancient signaling pathway leading to thermoprotection of nearly all living organisms. Emerging evidence suggests that intracellular O-linked β-N-acetylglucosamine (O-GlcNAc) serves as a molecular ‘thermometer’ by reporting ambient temperature fluctuations. Whether and how O-GlcNAc modification regulates HSR remains unclear. Here we report that, upon heat shock stress, the key translation initiation factor eIF4GI undergoes dynamic O-GlcNAcylation at the N-terminal region. Without O-GlcNAc modification, the preferential translation of stress mRNAs is impaired. Unexpectedly, stress mRNAs are entrapped within stress granules (SGs) that are no longer dissolved during stress recovery. Mechanistically, we show that stress-induced eIF4GI O-GlcNAcylation repels poly(A)-binding protein 1 and promotes SG disassembly, thereby licensing stress mRNAs for selective translation. Using various eIF4GI mutants created by CRISPR/Cas9, we demonstrate that eIF4GI acts as a translational switch via reversible O-GlcNAcylation. Our study reveals a central mechanism linking heat stress sensing, protein remodeling, SG dynamics and translational reprogramming.

    更新日期:2018-08-20
  • Author Correction: Mitochondrial DNA repair and replication proteins revealed by targeted chemical probes
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-20
    Simon Wisnovsky, Sae Rin Jean, Shana O Kelley

    Author Correction: Mitochondrial DNA repair and replication proteins revealed by targeted chemical probes Author Correction: Mitochondrial DNA repair and replication proteins revealed by targeted chemical probes, Published online: 20 August 2018; doi:10.1038/s41589-018-0040-5 Author Correction: Mitochondrial DNA repair and replication proteins revealed by targeted chemical probes

    更新日期:2018-08-20
  • TA gets a PG rating
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-17
    Mirella Bucci

    TA gets a PG rating TA gets a PG rating, Published online: 17 August 2018; doi:10.1038/s41589-018-0126-0 TA gets a PG rating

    更新日期:2018-08-18
  • ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-17
    Alla Peselis, Alexander Serganov

    The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognate ligand ppGpp, a second messenger involved in stress response, or PRPP, a precursor in purine biosynthesis. Both RNAs adopt similar structures and contain a conserved core previously observed in the guanidine-specific ykkC riboswitch. However, ppGpp and PRPP riboswitches uniquely employ an additional helical element that joins the ends of the ligand-sensing domains and creates a tunnel for direct and Mg2+-mediated binding of ligands. Mutational and footprinting experiments highlight the importance of conserved nucleotides forming the tunnel and long-distance contacts for ligand binding and genetic response. Our work provides new insights into the specificity of riboswitches and gives a unique opportunity for future studies of RNA evolution.

    更新日期:2018-08-18
  • Stuck on you
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-17
    Caitlin Deane

    Stuck on you Stuck on you, Published online: 17 August 2018; doi:10.1038/s41589-018-0124-2 Stuck on you

    更新日期:2018-08-18
  • Allosteric mechanisms underlie GPCR signaling to SH3-domain proteins through arrestin
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-17
    Fan Yang, Peng Xiao, Chang-xiu Qu, Qi Liu, Liu-yang Wang, Zhi-xin Liu, Qing-tao He, Chuan Liu, Jian-ye Xu, Rui-rui Li, Meng-jing Li, Qing Li, Xu-zhen Guo, Zhao-ya Yang, Dong-fang He, Fan Yi, Ke Ruan, Yue-mao Shen, Xiao Yu, Jin-peng Sun, Jiangyun Wang

    Signals from 800 G-protein-coupled receptors (GPCRs) to many SH3 domain-containing proteins (SH3-CPs) regulate important physiological functions. These GPCRs may share a common pathway by signaling to SH3-CPs via agonist-dependent arrestin recruitment rather than through direct interactions. In the present study, 19F-NMR and cellular studies revealed that downstream of GPCR activation engagement of the receptor-phospho-tail with arrestin allosterically regulates the specific conformational states and functional outcomes of remote β-arrestin 1 proline regions (PRs). The observed NMR chemical shifts of arrestin PRs were consistent with the intrinsic efficacy and specificity of SH3 domain recruitment, which was controlled by defined propagation pathways. Moreover, in vitro reconstitution experiments and biophysical results showed that the receptor–arrestin complex promoted SRC kinase activity through an allosteric mechanism. Thus, allosteric regulation of the conformational states of β-arrestin 1 PRs by GPCRs and the allosteric activation of downstream effectors by arrestin are two important mechanisms underlying GPCR-to-SH3-CP signaling.

    更新日期:2018-08-18
  • A ribonucleotide trap
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-17
    Yiyun Song

    A ribonucleotide trap A ribonucleotide trap, Published online: 17 August 2018; doi:10.1038/s41589-018-0127-z A ribonucleotide trap

    更新日期:2018-08-18
  • Mimicking cross-α amyloids
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-17
    Meytal Landau

    Mimicking cross-α amyloids Mimicking cross-α amyloids, Published online: 17 August 2018; doi:10.1038/s41589-018-0118-0 The design of spiraling cross-α amyloid-like structures reveals fascinating supermolecular fibrils of diverse compactness and stability. The small sequence variations governing cross-α self-assembly properties concur with amyloids being basic building blocks of life and natural targets for microbial structural mimicry.

    更新日期:2018-08-18
  • Catch and identify your prey
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-17
    Karin Kuehnel

    Catch and identify your prey Catch and identify your prey, Published online: 17 August 2018; doi:10.1038/s41589-018-0125-1 Catch and identify your prey

    更新日期:2018-08-18
  • An optical sensor to monitor dynamics of extracellular glycine
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-08-17
    Dmitri A. Rusakov

    An optical sensor to monitor dynamics of extracellular glycine An optical sensor to monitor dynamics of extracellular glycine, Published online: 17 August 2018; doi:10.1038/s41589-018-0123-3 A computational design approach was used to develop a genetically encoded FRET-based optical sensor that is aimed at monitoring extracellular glycine levels in brain tissue with the sensitivity and resolution to discern differences in dendritic spine and shaft environment and concentration dynamics upon afferent stimulation.

    更新日期:2018-08-18
  • Designed peptides that assemble into cross-α amyloid-like structures
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-30
    Shao-Qing Zhang, Hai Huang, Junjiao Yang, Huong T. Kratochvil, Marco Lolicato, Yanxin Liu, Xiaokun Shu, Lijun Liu, William F. DeGrado

    Amyloids adopt ‘cross-β’ structures composed of long, twisted fibrils with β-strands running perpendicular to the fibril axis. Recently, a toxic peptide was proposed to form amyloid-like cross-α structures in solution, with a planar bilayer-like assembly observed in the crystal structure. Here we crystallographically characterize designed peptides that assemble into spiraling cross-α amyloid-like structures, which resemble twisted β-amyloid fibrils. The peptides form helical dimers, stabilized by packing of small and apolar residues, and the dimers further assemble into cross-α amyloid-like fibrils with superhelical pitches ranging from 170 Å to 200 Å. When a small residue that appeared critical for packing was converted to leucine, it resulted in structural rearrangement to a helical polymer. Fluorescently tagged versions of the designed peptides form puncta in mammalian cells, which recover from photobleaching with markedly different kinetics. These structural folds could be potentially useful for directing in vivo protein assemblies with predetermined spacing and stabilities.

    更新日期:2018-07-31
  • Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-30
    William H. Zhang, Michel K. Herde, Joshua A. Mitchell, Jason H. Whitfield, Andreas B. Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, Polina E. Gulakova, Daniel Minge, Björn Breithausen, Susanne Schoch, Harald Janovjak, Colin J. Jackson, Christian Henneberger

    Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli.

    更新日期:2018-07-31
  • A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-30
    Esther Braselmann, Aleksandra J. Wierzba, Jacob T. Polaski, Mikołaj Chromiński, Zachariah E. Holmes, Sheng-Ting Hung, Dilara Batan, Joshua R Wheeler, Roy Parker, Ralph Jimenez, Dorota Gryko, Robert T. Batey, Amy E. Palmer

    RNAs directly regulate a vast array of cellular processes, emphasizing the need for robust approaches to fluorescently label and track RNAs in living cells. Here, we develop an RNA imaging platform using the cobalamin riboswitch as an RNA tag and a series of probes containing cobalamin as a fluorescence quencher. This highly modular ‘Riboglow’ platform leverages different colored fluorescent dyes, linkers and riboswitch RNA tags to elicit fluorescence turn-on upon binding RNA. We demonstrate the ability of two different Riboglow probes to track mRNA and small noncoding RNA in live mammalian cells. A side-by-side comparison revealed that Riboglow outperformed the dye-binding aptamer Broccoli and performed on par with the gold standard RNA imaging system, the MS2-fluorescent protein system, while featuring a much smaller RNA tag. Together, the versatility of the Riboglow platform and ability to track diverse RNAs suggest broad applicability for a variety of imaging approaches.

    更新日期:2018-07-31
  • Gramibactin is a bacterial siderophore with a diazeniumdiolate ligand system
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-30
    Ron Hermenau, Keishi Ishida, Sofia Gama, Bianca Hoffmann, Michel Pfeifer-Leeg, Winfried Plass, Jan Frieder Mohr, Thomas Wichard, Hans-Peter Saluz, Christian Hertweck

    Genome mining and chemical analyses revealed that rhizosphere bacteria (Paraburkholderia graminis) produce a new type of siderophore, gramibactin, a lipodepsipeptide that efficiently binds iron with a logβ value of 27.6. Complexation-induced proton NMR chemical shifts show that the unusual N-nitrosohydroxylamine (diazeniumdiolate) moieties participate in metal binding. Gramibactin biosynthesis genes are conserved in numerous plant-associated bacteria associated with rice, wheat, and maize, which may utilize iron from the complex.

    更新日期:2018-07-31
  • Dopamine gets lit
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-17
    Mirella Bucci

    Dopamine gets lit Dopamine gets lit, Published online: 17 July 2018; doi:10.1038/s41589-018-0111-7 Dopamine gets lit

    更新日期:2018-07-18
  • A remote control for switching
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-17
    Marc Vendrell

    A remote control for switching A remote control for switching, Published online: 17 July 2018; doi:10.1038/s41589-018-0107-3 Calcium channels are crucial regulators of a broad range of biological processes. A photoswitchable chemical probe allows the opening and closing of these channels with unprecedented temporal resolution, providing new opportunities to study calcium-dependent signaling pathways in real time.

    更新日期:2018-07-18
  • 3D interaction hubs
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-17
    Yiyun Song

    3D interaction hubs 3D interaction hubs, Published online: 17 July 2018; doi:10.1038/s41589-018-0112-6 3D interaction hubs

    更新日期:2018-07-18
  • Caught in the act
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-17
    Karin Kuehnel

    Caught in the act Caught in the act, Published online: 17 July 2018; doi:10.1038/s41589-018-0110-8 Caught in the act

    更新日期:2018-07-18
  • Antigen processing movers and shakers
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-17
    Tim Elliott

    Antigen processing movers and shakers Antigen processing movers and shakers, Published online: 17 July 2018; doi:10.1038/s41589-018-0106-4 Monitoring MHC-I dynamics upon binding to its chaperone TAPBPR helps us understand how optimal peptide sequences are selected for presentation and coordinated with release of the chaperone from the ternary peptide–MHC-I–TAPBPR complex.

    更新日期:2018-07-18
  • Crowd control
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-17
    Grant Miura

    Crowd control Crowd control, Published online: 17 July 2018; doi:10.1038/s41589-018-0109-1 Crowd control

    更新日期:2018-07-18
  • Facile target validation in an animal model with intracellularly expressed monobodies
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-16
    Ankit Gupta, Jing Xu, Shirley Lee, Steven T. Tsai, Bo Zhou, Kohei Kurosawa, Michael S. Werner, Akiko Koide, Alexander J. Ruthenburg, Yali Dou, Shohei Koide

    Rapidly determining the biological effect of perturbing a site within a potential drug target could guide drug discovery efforts, but it remains challenging. Here, we describe a facile target validation approach that exploits monobodies, small synthetic binding proteins that can be fully functionally expressed in cells. We developed a potent and selective monobody to WDR5, a core component of the mixed lineage leukemia (MLL) methyltransferase complex. The monobody bound to the MLL interaction site of WDR5, the same binding site for small-molecule inhibitors whose efficacy has been demonstrated in cells but not in animals. As a genetically encoded reagent, the monobody inhibited proliferation of an MLL-AF9 cell line in vitro, suppressed its leukemogenesis and conferred a survival benefit in an in vivo mouse leukemia model. The capacity of this approach to readily bridge biochemical, structural, cellular characterization and tests in animal models may accelerate discovery and validation of druggable sites.

    更新日期:2018-07-18
  • Acetylation blocks DNA damage–induced chromatin ADP-ribosylation
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-16
    Glen Liszczak, Katharine L. Diehl, Geoffrey P. Dann, Tom W. Muir

    Recent studies report serine ADP-ribosylation on nucleosomes during the DNA damage response. We unveil histone H3 serine 10 as the primary acceptor residue for chromatin ADP-ribosylation and find that specific histone acetylation marks block this activity. Our results provide a molecular explanation for the well-documented phenomenon of rapid deacetylation at DNA damage sites and support the combinatorial application of PARP and HDAC inhibitors for the treatment of PARP-dependent cancers.

    更新日期:2018-07-18
  • PAINTing translation
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-09
    Yuichiro Mishima

    PAINTing translation PAINTing translation, Published online: 09 July 2018; doi:10.1038/s41589-018-0102-8 Establishment of the germ cell lineage requires post-transcriptional regulation of mRNAs, yet the underlying molecular mechanisms are not fully understood in vertebrates. A small-molecule inhibitor of germ cell formation reveals a noncanonical translation system used in zebrafish embryos.

    更新日期:2018-07-10
  • Noncanonical translation via deadenylated 3′ UTRs maintains primordial germ cells
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-09
    Youngnam N. Jin, Peter J. Schlueter, Nathalie Jurisch-Yaksi, Pui-Ying Lam, Shan Jin, Woong Y. Hwang, Jing-Ruey Joanna Yeh, Masaaki Yoshigi, Shao-En Ong, Monica Schenone, Christina R. Hartigan, Steven A. Carr, Randall T. Peterson

    Primordial germ cells (PGCs) form during early embryogenesis with a supply of maternal mRNAs that contain shorter poly(A) tails. How translation of maternal mRNAs is regulated during PGC development remains elusive. Here we describe a small-molecule screen with zebrafish embryos that identified primordazine, a compound that selectively ablates PGCs. Primordazine's effect on PGCs arises from translation repression through primordazine-response elements in the 3′ UTRs. Systematic dissection of primordazine's mechanism of action revealed that translation of mRNAs during early embryogenesis occurs by two distinct pathways, depending on the length of their poly(A) tails. In addition to poly(A)-tail-dependent translation (PAT), early embryos perform poly(A)-tail-independent noncanonical translation (PAINT) via deadenylated 3′ UTRs. Primordazine inhibits PAINT without inhibiting PAT, an effect that was also observed in quiescent, but not proliferating, mammalian cells. These studies reveal that PAINT is an alternative form of translation in the early embryo and is indispensable for PGC maintenance.

    更新日期:2018-07-10
  • Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-07-09
    Andrew C. McShan, Kannan Natarajan, Vlad K. Kumirov, David Flores-Solis, Jiansheng Jiang, Mareike Badstübner, Jugmohit S. Toor, Clive R. Bagshaw, Evgenii L. Kovrigin, David H. Margulies, Nikolaos G. Sgourakis

    Chaperones TAPBPR and tapasin associate with class I major histocompatibility complexes (MHC-I) to promote optimization (editing) of peptide cargo. Here, we use solution NMR to investigate the mechanism of peptide exchange. We identify TAPBPR-induced conformational changes on conserved MHC-I molecular surfaces, consistent with our independently determined X-ray structure of the complex. Dynamics present in the empty MHC-I are stabilized by TAPBPR and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized according to the global stability of the final pMHC-I product and anneal in a native-like conformation to be edited by TAPBPR. Our results demonstrate an inverse relationship between MHC-I peptide occupancy and TAPBPR binding affinity, wherein the lifetime and structural features of transiently bound peptides control the regulation of a conformational switch located near the TAPBPR binding site, which triggers TAPBPR release. These results suggest a similar mechanism for the function of tapasin in the peptide-loading complex.

    更新日期:2018-07-10
  • Publisher Correction: The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-27
    Suzana Markolovic, Qinqin Zhuang, Sarah E. Wilkins, Charlotte D. Eaton, Martine I. Abboud, Maximiliano J. Katz, Helen E. McNeil, Robert K. Leśniak, Charlotte Hall, Weston B. Struwe, Rebecca Konietzny, Simon Davis, Ming Yang, Wei Ge, Justin L. P. Benesch, Benedikt M. Kessler, Peter J. Ratcliffe, Matthew E. Cockman, Roman Fischer, Pablo Wappner, Rasheduzzaman Chowdhury, Mathew L. Coleman, Christopher J. Schofield

    Publisher Correction: The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPasesPublisher Correction: The Jumonji-C oxygenase JMJD7 catalyzes (3<i>S</i>)-lysyl hydroxylation of TRAFAC GTPases, Published online: 27 June 2018; doi:10.1038/s41589-018-0104-6Publisher Correction: The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases

    更新日期:2018-06-28
  • Designing microbial consortia with defined social interactions
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-25
    Wentao Kong, David R. Meldgin, James J. Collins, Ting Lu

    Designer microbial consortia are an emerging frontier in synthetic biology that enable versatile microbiome engineering. However, the utilization of such consortia is hindered by our limited capacity in rapidly creating ecosystems with desired dynamics. Here we present the development of synthetic communities through social interaction engineering that combines modular pathway reconfiguration with model creation. Specifically, we created six two-strain consortia, each possessing a unique mode of interaction, including commensalism, amensalism, neutralism, cooperation, competition and predation. These consortia follow distinct population dynamics with characteristics determined by the underlying interaction modes. We showed that models derived from two-strain consortia can be used to design three- and four-strain ecosystems with predictable behaviors and further extended to provide insights into community dynamics in space. This work sheds light on the organization of interacting microbial species and provides a systematic framework—social interaction programming—to guide the development of synthetic ecosystems for diverse purposes.

    更新日期:2018-06-27
  • Sarpagan bridge enzyme has substrate-controlled cyclization and aromatization modes
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-25
    Thu-Thuy T. Dang, Jakob Franke, Ines Soares Teto Carqueijeiro, Chloe Langley, Vincent Courdavault, Sarah E. O’Connor

    Cyclization reactions that create complex polycyclic scaffolds are hallmarks of alkaloid biosynthetic pathways. We present the discovery of three homologous cytochrome P450s from three monoterpene indole alkaloid-producing plants (Rauwolfia serpentina, Gelsemium sempervirens and Catharanthus roseus) that provide entry into two distinct alkaloid classes, the sarpagans and the β-carbolines. Our results highlight how a common enzymatic mechanism, guided by related but structurally distinct substrates, leads to either cyclization or aromatization.

    更新日期:2018-06-27
  • Cleavage of a carbon–fluorine bond by an engineered cysteine dioxygenase
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-25
    Jiasong Li, Wendell P. Griffith, Ian Davis, Inchul Shin, Jiangyun Wang, Fahui Li, Yifan Wang, Daniel J. Wherritt, Aimin Liu

    Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93–Tyr157 cross-linked cofactor. Here, we investigated this Cys–Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a genetic method. The catalytically active variants were obtained with a thioether bond between Cys93 and the halogen-substituted Tyr157, and we determined the crystal structures of both wild-type and engineered CDO variants in the purely uncross-linked form and with a mature cofactor. Along with mass spectrometry and 19F NMR, these data indicated that the enzyme could catalyze oxidative C–F or C–Cl bond cleavage, resulting in a substantial conformational change of both Cys93 and Tyr157 during cofactor assembly. These findings provide insights into the mechanism of Cys–Tyr cofactor biogenesis and may aid the development of bioinspired aromatic carbon–halogen bond activation.

    更新日期:2018-06-27
  • Unraveling the rewired network
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-25
    Vinayak Palve, Brent M. Kuenzi, Uwe Rix

    Unraveling the rewired networkUnraveling the rewired network, Published online: 25 June 2018; doi:10.1038/s41589-018-0083-7Adaptive survival signaling can promote resistance to individual kinase inhibitors. A new study used a pathway-based approach to characterize shared kinome-wide rewiring mechanisms across multiple kinase inhibitors and developed rational drug-combination approaches that target cross-talk between two signaling pathways.

    更新日期:2018-06-27
  • Kinome rewiring reveals AURKA limits PI3K-pathway inhibitor efficacy in breast cancer
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-25
    Hayley J. Donnella, James T. Webber, Rebecca S. Levin, Roman Camarda, Olga Momcilovic, Nora Bayani, Khyati N. Shah, James E. Korkola, Kevan M. Shokat, Andrei Goga, John D. Gordan, Sourav Bandyopadhyay

    Dysregulation of the PI3K-AKT-mTOR signaling network is a prominent feature of breast cancers. However, clinical responses to drugs targeting this pathway have been modest, possibly because of dynamic changes in cellular signaling that drive resistance and limit drug efficacy. Using a quantitative chemoproteomics approach, we mapped kinome dynamics in response to inhibitors of this pathway and identified signaling changes that correlate with drug sensitivity. Maintenance of AURKA after drug treatment was associated with resistance in breast cancer models. Incomplete inhibition of AURKA was a common source of therapy failure, and combinations of PI3K, AKT or mTOR inhibitors with the AURKA inhibitor MLN8237 were highly synergistic and durably suppressed mTOR signaling, resulting in apoptosis and tumor regression in vivo. This signaling map identifies survival factors whose presence limits the efficacy of targeted therapies and reveals new drug combinations that may unlock the full potential of PI3K–AKT–mTOR pathway inhibitors in breast cancer.

    更新日期:2018-06-27
  • Metabolic engineering of a carbapenem antibiotic synthesis pathway in Escherichia coli
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-25
    Helena Shomar, Sophie Gontier, Niels J. F. van den Broek, Héctor Tejeda Mora, Marek J. Noga, Peter-Leon Hagedoorn, Gregory Bokinsky

    Carbapenems, a family of β-lactam antibiotics, are among the most powerful bactericidal compounds in clinical use. However, as rational engineering of native carbapenem-producing microbes is not currently possible, the present carbapenem supply relies upon total chemical synthesis of artificial carbapenem derivatives. To enable access to the full diversity of natural carbapenems, we have engineered production of a simple carbapenem antibiotic within Escherichia coli. By increasing concentrations of precursor metabolites and identifying a reducing cofactor of a bottleneck enzyme, we improved productivity by 60-fold over the minimal pathway and surpassed reported titers obtained from carbapenem-producing Streptomyces species. We stabilized E. coli metabolism against antibacterial effects of the carbapenem product by artificially inhibiting membrane synthesis, which further increased antibiotic productivity. As all known naturally occurring carbapenems are derived from a common intermediate, our engineered strain provides a platform for biosynthesis of tailored carbapenem derivatives in a genetically tractable and fast-growing species.

    更新日期:2018-06-27
  • The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-18
    Suzana Markolovic, Qinqin Zhuang, Sarah E. Wilkins, Charlotte D. Eaton, Martine I. Abboud, Maximiliano J. Katz, Helen E. McNeil, Robert K. Leśniak, Charlotte Hall, Weston B. Struwe, Rebecca Konietzny, Simon Davis, Ming Yang, Wei Ge, Justin L. P. Benesch, Benedikt M. Kessler, Peter J. Ratcliffe, Matthew E. Cockman, Roman Fischer, Pablo Wappner, Rasheduzzaman Chowdhury, Mathew L. Coleman, Christopher J. Schofield

    Biochemical, structural and cellular studies reveal Jumonji-C (JmjC) domain-containing 7 (JMJD7) to be a 2-oxoglutarate (2OG)-dependent oxygenase that catalyzes (3S)-lysyl hydroxylation. Crystallographic analyses reveal JMJD7 to be more closely related to the JmjC hydroxylases than to the JmjC demethylases. Biophysical and mutation studies show that JMJD7 has a unique dimerization mode, with interactions between monomers involving both N- and C-terminal regions and disulfide bond formation. A proteomic approach identifies two related members of the translation factor (TRAFAC) family of GTPases, developmentally regulated GTP-binding proteins 1 and 2 (DRG1/2), as activity-dependent JMJD7 interactors. Mass spectrometric analyses demonstrate that JMJD7 catalyzes Fe(ii)- and 2OG-dependent hydroxylation of a highly conserved lysine residue in DRG1/2; amino-acid analyses reveal that JMJD7 catalyzes (3S)-lysyl hydroxylation. The functional assignment of JMJD7 will enable future studies to define the role of DRG hydroxylation in cell growth and disease.

    更新日期:2018-06-18
  • The anti-staphylococcal lipolanthines are ribosomally synthesized lipopeptides
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-18
    Vincent Wiebach, Andi Mainz, Mary-Ann J. Siegert, Natalia A. Jungmann, Guillaume Lesquame, Sophie Tirat, Assia Dreux-Zigha, Jozsef Aszodi, Dominique Le Beller, Roderich D. Süssmuth

    The potent antibacterial lanthipeptide microvionin, isolated from a culture of Microbacterium arborescens, exhibits a new triamino-dicarboxylic acid moiety, termed avionin, and an unprecedented N-terminal guanidino fatty acid. We identified the corresponding biosynthetic gene cluster and reconstituted central steps of avionin biosynthesis in vitro. Genome mining and isolation of nocavionin from Nocardia terpenica revealed a widespread distribution of this lanthipeptide class, termed lipolanthines, which may be useful as future antimicrobial drugs.

    更新日期:2018-06-18
  • Vitamin B12 import is all about timing
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-18
    Lutz Schmitt

    Vitamin B12 import is all about timing Vitamin B12 import is all about timing, Published online: 18 June 2018; doi:10.1038/s41589-018-0087-3 Single-molecule techniques combined with molecular dynamics simulations allowed visualization of a surprisingly high level of conformational homogeneity in the transport cycle of an ABC import system, BtuCD-F, and revealed an unexpected tight coupling of distinct conformational states responsible for vitamin B12 binding, transport and release.

    更新日期:2018-06-18
  • Tricks for taking up residence
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-18
    Mirella Bucci

    Tricks for taking up residence Tricks for taking up residence, Published online: 18 June 2018; doi:10.1038/s41589-018-0094-4 Tricks for taking up residence

    更新日期:2018-06-18
  • Scavenging of superoxide by a membrane-bound superoxide oxidase
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-18
    Camilla A. K. Lundgren, Dan Sjöstrand, Olivier Biner, Matthew Bennett, Axel Rudling, Ann-Louise Johansson, Peter Brzezinski, Jens Carlsson, Christoph von Ballmoos, Martin Högbom

    Superoxide is a reactive oxygen species produced during aerobic metabolism in mitochondria and prokaryotes. It causes damage to lipids, proteins and DNA and is implicated in cancer, cardiovascular disease, neurodegenerative disorders and aging. As protection, cells express soluble superoxide dismutases, disproportionating superoxide to oxygen and hydrogen peroxide. Here, we describe a membrane-bound enzyme that directly oxidizes superoxide and funnels the sequestered electrons to ubiquinone in a diffusion-limited reaction. Experiments in proteoliposomes and inverted membranes show that the protein is capable of efficiently quenching superoxide generated at the membrane in vitro. The 2.0 Å crystal structure shows an integral membrane di-heme cytochrome b poised for electron transfer from the P-side and proton uptake from the N-side. This suggests that the reaction is electrogenic and contributes to the membrane potential while also conserving energy by reducing the quinone pool. Based on this enzymatic activity, we propose that the enzyme family be denoted superoxide oxidase (SOO).

    更新日期:2018-06-18
  • Please hold for chaperones
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-18
    Caitlin Deane

    Please hold for chaperones Please hold for chaperones, Published online: 18 June 2018; doi:10.1038/s41589-018-0092-6 Please hold for chaperones

    更新日期:2018-06-18
  • Single-molecule probing of the conformational homogeneity of the ABC transporter BtuCD
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-18
    Min Yang, Nurit Livnat Levanon, Burçin Acar, Burcu Aykac Fas, Gal Masrati, Jessica Rose, Nir Ben-Tal, Turkan Haliloglu, Yongfang Zhao, Oded Lewinson

    ATP-binding cassette (ABC) transporters use the energy of ATP hydrolysis to move molecules through cellular membranes. They are directly linked to human diseases, cancer multidrug resistance, and bacterial virulence. Very little is known of the conformational dynamics of ABC transporters, especially at the single-molecule level. Here, we combine single-molecule spectroscopy and a novel molecular simulation approach to investigate the conformational dynamics of the ABC transporter BtuCD. We observe a single dominant population of molecules in each step of the transport cycle and tight coupling between conformational transitions and ligand binding. We uncover transient conformational changes that allow substrate to enter the transporter. This is followed by a ‘squeezing’ motion propagating from the extracellular to the intracellular side of the translocation cavity. This coordinated sequence of events provides a mechanism for the unidirectional transport of vitamin B12 by BtuCD.

    更新日期:2018-06-18
  • Stabilizing synapsis
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-18
    Yiyun Song

    Stabilizing synapsis Stabilizing synapsis, Published online: 18 June 2018; doi:10.1038/s41589-018-0095-3 Stabilizing synapsis

    更新日期:2018-06-18
  • Plasticity in binding confers selectivity in ligand-induced protein degradation
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-11
    Radosław P. Nowak, Stephen L. DeAngelo, Dennis Buckley, Zhixiang He, Katherine A. Donovan, Jian An, Nozhat Safaee, Mark P. Jedrychowski, Charles M. Ponthier, Mette Ishoey, Tinghu Zhang, Joseph D. Mancias, Nathanael S. Gray, James E. Bradner, Eric S. Fischer

    Heterobifunctional small-molecule degraders that induce protein degradation through ligase-mediated ubiquitination have shown considerable promise as a new pharmacological modality. However, we currently lack a detailed understanding of the molecular basis for target recruitment and selectivity, which is critically required to enable rational design of degraders. Here we utilize a comprehensive characterization of the ligand-dependent CRBN–BRD4 interaction to demonstrate that binding between proteins that have not evolved to interact is plastic. Multiple X-ray crystal structures show that plasticity results in several distinct low-energy binding conformations that are selectively bound by ligands. We demonstrate that computational protein–protein docking can reveal the underlying interprotein contacts and inform the design of a BRD4 selective degrader that can discriminate between highly homologous BET bromodomains. Our findings that plastic interprotein contacts confer selectivity for ligand-induced protein dimerization provide a conceptual framework for the development of heterobifunctional ligands.

    更新日期:2018-06-12
  • Linkers for protein degradation
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-11
    Philip P. Chamberlain

    Linkers for protein degradation Linkers for protein degradation, Published online: 11 June 2018; doi:10.1038/s41589-018-0057-9 The ability to subvert E3 ubiquitin ligases with small-molecule drugs offers tremendous promise for drug discovery. A new study demonstrates how structural and computational techniques can engineer and exploit unnatural protein–protein interfaces to design selective protein degraders.

    更新日期:2018-06-12
  • Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-11
    Benoit Castrec, Cyril Dian, Sarah Ciccone, Coralie L. Ebert, Willy V. Bienvenut, Jean-Pierre Le Caer, Jean-Marc Steyaert, Carmela Giglione, Thierry Meinnel

    An organism’s entire protein modification repertoire has yet to be comprehensively mapped. N-myristoylation (MYR) is a crucial eukaryotic N-terminal protein modification. Here we mapped complete Homo sapiens and Arabidopsis thaliana myristoylomes. The crystal structures of human modifier NMT1 complexed with reactive and nonreactive target-mimicking peptide ligands revealed unexpected binding clefts and a modifier recognition pattern. This information allowed integrated mapping of myristoylomes using peptide macroarrays, dedicated prediction algorithms, and in vivo mass spectrometry. Global MYR profiling at the genomic scale identified over a thousand novel, heterogeneous targets in both organisms. Surprisingly, MYR involved a non-negligible set of overlapping targets with N-acetylation, and the sequence signature marks for a third proximal acylation—S-palmitoylation—were genomically imprinted, allowing recognition of sequences exhibiting both acylations. Together, the data extend the N-end rule concept for Gly-starting proteins to subcellular compartmentalization and reveal the main neighbors influencing protein modification profiles and consequent cell fate.

    更新日期:2018-06-12
  • Copper regulates rest-activity cycles through the locus coeruleus-norepinephrine system
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-04
    Tong Xiao, Cheri M. Ackerman, Elizabeth C Carroll, Shang Jia, Adam Hoagland, Jefferson Chan, Bao Thai, Christine S. Liu, Ehud Y. Isacoff, Christopher J. Chang

    The unusually high demand for metals in the brain, along with insufficient understanding of how their dysregulation contributes to neurological diseases, motivates the study of how inorganic chemistry influences neural circuitry. We now report that the transition metal copper is essential for regulating rest–activity cycles and arousal. Copper imaging and gene expression analysis in zebrafish identifies the locus coeruleus–norepinephrine (LC-NE) system, a vertebrate-specific neuromodulatory circuit critical for regulating sleep, arousal, attention, memory and emotion, as a copper-enriched unit with high levels of copper transporters CTR1 and ATP7A and the copper enzyme dopamine β-hydroxylase (DBH) that produces NE. Copper deficiency induced by genetic disruption of ATP7A, which loads copper into DBH, lowers NE levels and hinders LC function as manifested by disruption in rest–activity modulation. Moreover, LC dysfunction caused by copper deficiency from ATP7A disruption can be rescued by restoring synaptic levels of NE, establishing a molecular CTR1–ATP7A–DBH–NE axis for copper-dependent LC function.

    更新日期:2018-06-05
  • Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-04
    Jianchao Li, Ruichi Zhu, Keyu Chen, Hui Zheng, Hongyu Zhao, Chongzhen Yuan, Hong Zhang, Chao Wang, Mingjie Zhang

    The mammalian Atg8 family proteins are central drivers of autophagy and contain six members, classified into the LC3 and GABARAP subfamilies. Due to their high sequence similarity and consequent functional overlaps, it is difficult to delineate specific functions of Atg8 proteins in autophagy. Here we discover a super-strong GABARAP-selective inhibitory peptide harbored in 270/480 kDa ankyrin-G and a super-potent pan-Atg8 inhibitory peptide from 440 kDa ankyrin-B. Structural studies elucidate the mechanism governing the Atg8 binding potency and selectivity of the peptides, reveal a general Atg8-binding sequence motif, and allow development of a more GABARAP-selective inhibitory peptide. These peptides effectively blocked autophagy when expressed in cultured cells. Expression of these ankyrin-derived peptides in Caenorhabditis elegans also inhibited autophagy, causing accumulation of the p62 homolog SQST-1, delayed development and shortened life span. Thus, these genetically encodable autophagy inhibitory peptides can be used to occlude autophagy spatiotemporally in living animals.

    更新日期:2018-06-05
  • Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-04
    Nan Wang, Jeffrey D. Rudolf, Liao-Bin Dong, Jerzy Osipiuk, Catherine Hatzos-Skintges, Michael Endres, Chin-Yuan Chang, Gyorgy Babnigg, Andrzej Joachimiak, George N. Phillips Jr, Ben Shen

    Acyl-coenzyme A (CoA) ligases catalyze the activation of carboxylic acids via a two-step reaction of adenylation followed by thioesterification. Here, we report the discovery of a non-adenylating acyl-CoA ligase PtmA2 and the functional separation of an acyl-CoA ligase reaction. Both PtmA1 and PtmA2, two acyl-CoA ligases from the biosynthetic pathway of platensimycin and platencin, are necessary for the two steps of CoA activation. Gene inactivation of ptmA1 and ptmA2 resulted in the accumulation of free acid and adenylate intermediates, respectively. Enzymatic and structural characterization of PtmA2 confirmed its ability to only catalyze thioesterification. Structural characterization of PtmA2 revealed it binds both free acid and adenylate substrates and undergoes the established mechanism of domain alternation. Finally, site-directed mutagenesis restored both the adenylation and complete CoA activation reactions. This study challenges the currently accepted paradigm of adenylating enzymes and inspires future investigations on functionally separated acyl-CoA ligases and their ramifications in biology.

    更新日期:2018-06-05
  • Functional assignment of multiple catabolic pathways for d-apiose
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-06-04
    Michael S. Carter, Xinshuai Zhang, Hua Huang, Jason T. Bouvier, Brian San Francisco, Matthew W. Vetting, Nawar Al-Obaidi, Jeffrey B. Bonanno, Agnidipta Ghosh, Rémi G. Zallot, Harvey M. Andersen, Steven C. Almo, John A. Gerlt

    Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind d-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for d-apiose with eleven previously unknown reactions. The new enzymes include d-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible (http://efi.igb.illinois.edu/efi-est/), so similar ‘genomic enzymology’ strategies for discovering novel pathways can be used by the community.

    更新日期:2018-06-05
  • A pathogenesis-related 10 protein catalyzes the final step in thebaine biosynthesis
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-28
    Xue Chen, Jillian M. Hagel, Limei Chang, Joseph E. Tucker, Stacey A. Shiigi, Yuora Yelpaala, Hsiang-Yun Chen, Rodrigo Estrada, Jeffrey Colbeck, Maria Enquist-Newman, Ana B. Ibáñez, Guillaume Cottarel, Genevieve M. Vidanes, Peter J. Facchini

    The ultimate step in the formation of thebaine, a pentacyclic opiate alkaloid readily converted to the narcotic analgesics codeine and morphine in the opium poppy, has long been presumed to be a spontaneous reaction. We have detected and purified a novel enzyme from opium poppy latex that is capable of the efficient formation of thebaine from (7S)-salutaridinol 7-O-acetate at the expense of labile hydroxylated byproducts, which are preferentially produced by spontaneous allylic elimination. Remarkably, thebaine synthase (THS), a member of the pathogenesis-related 10 protein (PR10) superfamily, is encoded within a novel gene cluster in the opium poppy genome that also includes genes encoding the four biosynthetic enzymes immediately upstream. THS is a missing component that is crucial to the development of fermentation-based opiate production and dramatically improves thebaine yield in engineered yeast.

    更新日期:2018-05-29
  • Computational redesign of enzymes for regio- and enantioselective hydroamination
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-21
    Ruifeng Li, Hein J. Wijma, Lu Song, Yinglu Cui, Marleen Otzen, Yu’e Tian, Jiawei Du, Tao Li, Dingding Niu, Yanchun Chen, Jing Feng, Jian Han, Hao Chen, Yong Tao, Dick B. Janssen, Bian Wu

    Introduction of innovative biocatalytic processes offers great promise for applications in green chemistry. However, owing to limited catalytic performance, the enzymes harvested from nature's biodiversity often need to be improved for their desired functions by time-consuming iterative rounds of laboratory evolution. Here we describe the use of structure-based computational enzyme design to convert Bacillus sp. YM55-1 aspartase, an enzyme with a very narrow substrate scope, to a set of complementary hydroamination biocatalysts. The redesigned enzymes catalyze asymmetric addition of ammonia to substituted acrylates, affording enantiopure aliphatic, polar and aromatic β-amino acids that are valuable building blocks for the synthesis of pharmaceuticals and bioactive compounds. Without a requirement for further optimization by laboratory evolution, the redesigned enzymes exhibit substrate tolerance up to a concentration of 300 g/L, conversion up to 99%, β-regioselectivity >99% and product enantiomeric excess >99%. The results highlight the use of computational design to rapidly adapt an enzyme to industrially viable reactions.

    更新日期:2018-05-22
  • Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-21
    Xiaoting Shu, Menghao Liu, Zhike Lu, Chenxu Zhu, Haowei Meng, Sihao Huang, Xiaoxue Zhang, Chengqi Yi

    Uracil in DNA can be generated by cytosine deamination or dUMP misincorporation; however, its distribution in the human genome is poorly understood. Here we present a selective labeling and pull-down technology for genome-wide uracil profiling and identify thousands of uracil peaks in three different human cell lines. Surprisingly, uracil is highly enriched at the centromere of the human genome. Using mass spectrometry, we demonstrate that human centromeric DNA contains a higher level of uracil. We also directly verify the presence of uracil within two centromeric uracil peaks on chromosomes 6 and 11. Moreover, centromeric uracil is preferentially localized within the binding regions of the centromere-specific histone CENP-A and can be excised by human uracil-DNA glycosylase UNG. Collectively, our approaches allow comprehensive analysis of uracil in the human genome and provide robust tools for mapping and future functional studies of uracil in DNA.

    更新日期:2018-05-22
  • Functional phosphorylation
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-16
    Mirella Bucci

    Functional phosphorylation Functional phosphorylation, Published online: 16 May 2018; doi:10.1038/s41589-018-0075-7 Functional phosphorylation

    更新日期:2018-05-16
  • Identification of a S. aureus virulence factor by activity-based protein profiling (ABPP)
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-16
    Christian S. Lentz, Jessica R. Sheldon, Lisa A. Crawford, Rachel Cooper, Megan Garland, Manuel R. Amieva, Eranthie Weerapana, Eric P. Skaar, Matthew Bogyo

    Serine hydrolases play diverse roles in regulating host–pathogen interactions in a number of organisms, yet few have been characterized in the human pathogen Staphylococcus aureus. Here we describe a chemical proteomic screen that identified ten previously uncharacterized S. aureus serine hydrolases that mostly lack human homologs. We termed these enzymes fluorophosphonate-binding hydrolases (FphA–J). One hydrolase, FphB, can process short fatty acid esters, exhibits increased activity in response to host cell factors, is located predominantly on the bacterial cell surface in a subset of cells, and is concentrated in the division septum. Genetic disruption of fphB confirmed that the enzyme is dispensable for bacterial growth in culture but crucial for establishing infection in distinct sites in vivo. A selective small molecule inhibitor of FphB effectively reduced infectivity in vivo, suggesting that it may be a viable therapeutic target for the treatment or management of Staphylococcus infections.

    更新日期:2018-05-16
  • Tracking tRNA packages
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-16
    Achillefs N. Kapanidis, Mathew Stracy

    Tracking tRNA packages Tracking tRNA packages, Published online: 16 May 2018; doi:10.1038/s41589-018-0066-8 Fast, single-molecule tracking microscopy monitors transitions between mobile and ribosome-bound fluorescent tRNAs to achieve nucleotide-resolution measurements of translation rates in living cells.

    更新日期:2018-05-16
  • Electron handoff
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-16
    Caitlin Deane

    Electron handoff Electron handoff, Published online: 16 May 2018; doi:10.1038/s41589-018-0073-9 Electron handoff

    更新日期:2018-05-16
  • Next-generation biocontainment systems for engineered organisms
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-16
    Jeong Wook Lee, Clement T. Y. Chan, Shimyn Slomovic, James J. Collins

    The increasing use of engineered organisms for industrial, clinical, and environmental applications poses a growing risk of spreading hazardous biological entities into the environment. To address this biosafety issue, significant effort has been invested in creating ways to confine these organisms and transgenic materials. Emerging technologies in synthetic biology involving genetic circuit engineering, genome editing, and gene expression regulation have led to the development of novel biocontainment systems. In this perspective, we highlight recent advances in biocontainment and suggest a number of approaches for future development, which may be applied to overcome remaining challenges in safeguard implementation.

    更新日期:2018-05-16
  • Buffering transition
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-16
    Yiyun Song

    Buffering transition Buffering transition, Published online: 16 May 2018; doi:10.1038/s41589-018-0076-6 Buffering transition

    更新日期:2018-05-16
  • tRNA tracking for direct measurements of protein synthesis kinetics in live cells
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-16
    Ivan L. Volkov, Martin Lindén, Javier Aguirre Rivera, Ka-Weng Ieong, Mikhail Metelev, Johan Elf, Magnus Johansson

    Our ability to directly relate results from test-tube biochemical experiments to the kinetics in living cells is very limited. Here we present experimental and analytical tools to directly study the kinetics of fast biochemical reactions in live cells. Dye-labeled molecules are electroporated into bacterial cells and tracked using super-resolved single-molecule microscopy. Trajectories are analyzed by machine-learning algorithms to directly monitor transitions between bound and free states. In particular, we measure the dwell time of tRNAs on ribosomes, and hence achieve direct measurements of translation rates inside living cells at codon resolution. We find elongation rates with tRNAPhe that are in perfect agreement with previous indirect estimates, and once fMet-tRNAfMet has bound to the 30S ribosomal subunit, initiation of translation is surprisingly fast and does not limit the overall rate of protein synthesis. The experimental and analytical tools for direct kinetics measurements in live cells have applications far beyond bacterial protein synthesis.

    更新日期:2018-05-16
  • Membrane association of monotopic phosphoglycosyl transferase underpins function
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-16
    Leah C. Ray, Debasis Das, Sonya Entova, Vinita Lukose, Andrew J. Lynch, Barbara Imperiali, Karen N. Allen

    Polyprenol phosphate phosphoglycosyl transferases (PGTs) catalyze the first membrane-committed step in assembly of essential glycoconjugates. Currently there is no structure–function information to describe how monotopic PGTs coordinate the reaction between membrane-embedded and soluble substrates. We describe the structure and mode of membrane association of PglC, a PGT from Campylobacter concisus. The structure reveals a unique architecture, provides mechanistic insight and identifies ligand-binding determinants for PglC and the monotopic PGT superfamily.

    更新日期:2018-05-16
  • Publisher Correction: Evolution of chalcone isomerase from a noncatalytic ancestor
    Nat. Chem. Biol. (IF 13.843) Pub Date : 2018-05-14
    Miriam Kaltenbach, Jason R. Burke, Mirco Dindo, Anna Pabis, Fabian S. Munsberg, Avigayel Rabin, Shina C. L. Kamerlin, Joseph P. Noel, Dan S. Tawfik

    Publisher Correction: Evolution of chalcone isomerase from a noncatalytic ancestor Publisher Correction: Evolution of chalcone isomerase from a noncatalytic ancestor, Published online: 14 May 2018; doi:10.1038/s41589-018-0079-3 Publisher Correction: Evolution of chalcone isomerase from a noncatalytic ancestor

    更新日期:2018-05-15
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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