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Nature Chemical Biology Contents: August 2017, Volume 13 No 8 pp 815 - 922

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Nature Chemical Biology


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TABLE OF CONTENTS

August 2017 Volume 13, Issue 8

Editorial
Research Highlights
News and Views
Perspective
Brief Communications
Articles
Errata

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Editorial

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Hints of hidden chemistry   p815
doi:10.1038/nchembio.2449
Biosynthetic pathways harbor diverse enzyme functions, and identifying those that catalyze unusual or synthetically challenging transformations offers new routes for biocatalytic development.

Research Highlights

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Neurodegenerative disease: Not stuck on repeat | Enzymology: Tracking off-targets | Antibacterials: PUMmeling RNAP | Biocatalysis: Achieving aminase activity


News and Views

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Redox regulation: Scaffolding H2O2 signaling   pp818 - 819
Hadley D Sikes
doi:10.1038/nchembio.2432
Peroxidases, rather than simply reducing H2O2 to water, also convey oxidation signals to proteins such as transcription factors. A new study reveals how a scaffold protein enables formation of a mixed disulfide between the peroxidase and a transcription factor.

See also: Article by Bersweiler et al.

Structural biology: Full monty of family B GPCRs   pp819 - 821
Thue W Schwartz and Thomas M Frimurer
doi:10.1038/nchembio.2438
New structures of the glucagon-like peptide-1 (GLP-1) and glucagon receptors in complex with peptide and nonpeptide ligands provide a comprehensive, detailed picture of the molecular mechanisms of action of family B GPCRs. This opens the door for true structure-based drug discovery aimed at both novel orthosteric and allosteric subsites of the receptors.

Biosynthesis: Methylating mushrooms   pp821 - 822
Albert A Bowers
doi:10.1038/nchembio.2437
The genome of the poisonous mushroom Omphalotus olearius provides a potent new biocatalytic strategy for installing backbone N-methyl amides on ribosomally synthesized peptides. This discovery could yield new biotechnologies for drug development from peptide macrocycles.

See also: Brief Communication by van der Velden et al.

Nature Chemical Biology
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Perspective

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Harnessing yeast organelles for metabolic engineering   pp823 - 832
Sarah K Hammer and José L Avalos
doi:10.1038/nchembio.2429



The organelles and subcellular compartments of yeast provide distinct environments and physical separation from the cytosol, enabling opportunities to target biosynthetic pathways to these compartments and enhance production of desirable compounds.

Brief Communications

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Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products   pp833 - 835
Niels S van der Velden, Noemi Kälin, Maximilian J Helf, J&oml;rn Piel, Michael F Freeman et al.
doi:10.1038/nchembio.2393



Characterization of the gene cluster for omphalotin biosynthesis reveals that they are ribosomally synthesized peptides whose internal α-N-methyl groups are installed by a methyltransferase fused to the precursor peptide substrate.

See also: News and Views by Bowers

A heme-dependent enzyme forms the nitrogen–nitrogen bond in piperazate   pp836 - 838
Yi-Ling Du, Hai-Yan He, Melanie A Higgins and Katherine S Ryan
doi:10.1038/nchembio.2411



Characterization of the heme-dependent enzyme KtzT reveals it to be the elusive enzyme responsible for nitrogen–nitrogen bond formation during the biosynthesis of piperazate, a building block for some nonribosomal peptide natural products.
Chemical compounds

Cpf1 proteins excise CRISPR RNAs from mRNA transcripts in mammalian cells   pp839 - 841
Guocai Zhong, Haimin Wang, Yujun Li, Mai H Tran and Michael Farzan
doi:10.1038/nchembio.2410



Cpf1 is a CRISPR effector protein that exhibits greater genome editing specificity than Cas9 nuclease. Cpf1 from two distinct bacteria selectively processes RNA polymerase II transcripts into crRNA fragments competent for genome editing.

Site-specific incorporation of phosphotyrosine using an expanded genetic code   pp842 - 844
Christian Hoppmann, Allison Wong, Bing Yang, Shuwei Li, Tony Hunter et al.
doi:10.1038/nchembio.2406



A genetically encoded unnatural amino acid analog and its acidic deprotection enable the site-specific incorporation of phosphotyrosine (pTyr) into proteins such as ubiquitin, where it can be used to study the function of this phosphorylated residue.
Chemical compounds
See also: Article by Luo et al.

Articles

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Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria   pp845 - 849
Xiaozhou Luo, Guangsen Fu, Rongsheng E Wang, Xueyong Zhu, Claudio Zambaldo et al.
doi:10.1038/nchembio.2405



A propeptide strategy increases uptake of phosphotyrosine and a nonhydrolyzable analog to facilitate their incorporation into proteins by recombinant methods, aided by a specific aminoacyl-tRNA synthetase with a reconfigured active site.
Chemical compounds
See also: Brief Communication by Hoppmann et al.

Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase   pp850 - 857
Daniel C Scott, Jared T Hammill, Jaeki Min, David Y Rhee, Michele Connelly et al.
doi:10.1038/nchembio.2386



High-throughput screening and structure-guided design identified small-molecule inhibitors that prevent the interaction between N-terminally acetylated E2 conjugating enzyme UBE2M and DCN1, an E3 ligase for the ubiquitin-like protein Nedd8.
Chemical compounds

Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis   pp858 - 866
Karine Bastard, Alain Perret, Aline Mariage, Thomas Bessonnet, Agnès Pinet-Turpault et al.
doi:10.1038/nchembio.2397



MetA and MetX are phylogenetically unrelated families of acyl-L-homoserine transferases. Experimental assignation of function and structural modeling of these families correct widespread misannotation, reveal convergence of function and uncover new functions in a subclass of MetX.
Chemical compounds

Activity-based probes for functional interrogation of retaining β-glucuronidases   pp867 - 873
Liang Wu, Jianbing Jiang, Yi Jin, Wouter W Kallemeijn, Chi-Lin Kuo et al.
doi:10.1038/nchembio.2395



Synthesis and application of activity-based probes based on cyclophellitol enabled the cellular profiling of β-glucuronidase activity and revealed an unexpected feature of endo-acting heparanase processing.
Chemical compounds

A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase   pp874 - 881
Javier Iglesias-Fernández, Susan M Hancock, Seung Seo Lee, Maola Khan, Jo Kirkpatrick et al.
doi:10.1038/nchembio.2394



Biochemical and structural analysis, combined with metadynamics simulations, illustrate how a single amino acid substitution switches a β-glycosidase from a double SN2 mechanism to a front-face SNi-like mechanism.
Chemical compounds

A mutant O-GlcNAcase enriches Drosophila developmental regulators   pp882 - 887
Nithya Selvan, Ritchie Williamson, Daniel Mariappa, David G Campbell, Robert Gourlay et al.
doi:10.1038/nchembio.2404



An inactive mutant of a bacterial O-GlcNAc hydrolase was used as an affinity reagent to enrich O-GlcNAc-modified proteins from Drosophila embryos and led to the identification, by MS-proteomics, of O-GlcNAcylated proteins involved in embryogenesis.

Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability   pp888 - 894
Stefanie Kellner, Michael S DeMott, Ching Pin Cheng, Brandon S Russell, Bo Cao et al.
doi:10.1038/nchembio.2407



Phosphorothioate (PT) DNA modifications in E. coli and Salmonella are turned over to maintain bacterial fitness through decreased susceptibility to genomic instability caused by hypochlorous-acid-mediated PT oxidation.

A scalable platform to identify fungal secondary metabolites and their gene clusters   pp895 - 901
Kenneth D Clevenger, Jin Woo Bok, Rosa Ye, Galen P Miley, Maria H Verdan et al.
doi:10.1038/nchembio.2408



Coupling the use of artificial chromosomes with metabolomics enables the high-throughput linkage of fungal natural products with their biosynthetic gene clusters. This method was used here to identify a novel polyketide-nonribosomal peptide scaffold.
Chemical compounds

Nucleation and growth of a bacterial functional amyloid at single-fiber resolution   pp902 - 908
Mike Sleutel, Imke Van den Broeck, Nani Van Gerven, Cécile Feuillie, Wim Jonckheere et al.
doi:10.1038/nchembio.2413



AFM is used to show that curli, the functional amyloid fibrils generated by bacteria, form by polar growth from a one-step nucleation of monomers into minimal fibril units without transitioning through an intermediate, non-amyloid oligomeric state.

A scaffold protein that chaperones a cysteine-sulfenic acid in H2O2 signaling   pp909 - 915
Antoine Bersweiler, Benoît D'Autréaux, Hortense Mazon, Alexandre Kriznik, Gemma Belli et al.
doi:10.1038/nchembio.2412



The H2O2-responsive transcription factor Yap1 undergoes oxidative activation mediated by the peroxidase Orp1. In vitro reconstitution of the redox relay revealed a role for the Yap1-binding protein Ybp1 in promoting the formation of a ternary complex with Orp1 and Yap1 to enable redox transfer.

See also: News and Views by Sikes

A new strategy for aromatic ring alkylation in cylindrocyclophane biosynthesis   pp916 - 921
Hitomi Nakamura, Erica E Schultz and Emily P Balskus
doi:10.1038/nchembio.2421



Cylindrocyclophane biosynthesis involves an unexpected halogenated intermediate arising from chlorination of an unactivated carbon center by a halogenase, followed by dimerization through stereospecific enzymatic alkylation of resorcinol aromatic rings.
Chemical compounds

Errata

Top

Erratum: Structural and conformational determinants of macrocycle cell permeability   p922
Björn Over, Pär Matsson, Christian Tyrchan, Per Artursson, Bradley C Doak et al.
doi:10.1038/nchembio0817-922a

Erratum: The EED protein–protein interaction inhibitor A-395 inactivates the PRC2 complex   p922
Yupeng He, Sujatha Selvaraju, Michael L Curtin, Clarissa G Jakob, Haizhong Zhu et al.
doi:10.1038/nchembio0817-922b

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