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June 2018 Volume 14, Issue 6

Research Highlights
News & Views
Brief Communications

Research Highlights


Electron handoff    p525
Caitlin Deane

SLAMing transcription    p525
Grant Miura

Functional phosphorylation    p525
Mirella Bucci

Buffering transition    p525
Yiyun Song

Nature Chemical Biology
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News & Views


Enzymes emerge by upcycling    pp526 - 527
Michael J. Harms

Nitrogen goes around    pp527 - 528
Jianping Yu

Tracking tRNA packages    pp528 - 529
Achillefs N. Kapanidis & Mathew Stracy

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Next-generation biocontainment systems for engineered organisms    pp530 - 537
Jeong Wook Lee, Clement T. Y. Chan, Shimyn Slomovic & James J. Collins

Synthetic biology offers innovative approaches for engineering biological systems, but also supports the development of biocontainment strategies that ensure the safe application of genetically modified organisms.



Brief Communications


Membrane association of monotopic phosphoglycosyl transferase underpins function    pp538 - 541
Leah C. Ray, Debasis Das, Sonya Entova, Vinita Lukose, Andrew J. Lynch et al.

The structure of a monotopic polyprenol phosphate phosphoglycosyl transferase, PglC, reveals how it interacts with the bacterial membrane and coordinates a reaction between membrane-embedded and soluble substrates during glycoconjugate assembly.





Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein    pp542 - 547
Ben E. Clifton, Joe A. Kaczmarski, Paul D. Carr, Monica L. Gerth, Nobuhiko Tokuriki et al.

Ancestral protein reconstruction, with structural and biochemical analysis, illustrates the evolution of a solute-binding protein to cyclohexadienyl dehydratase through incorporation of a catalytic residue and gradual reshaping of the binding site.



Evolution of chalcone isomerase from a noncatalytic ancestor    pp548 - 555
Miriam Kaltenbach, Jason R. Burke, Mirco Dindo, Anna Pabis, Fabian S. Munsberg et al.

Ancestral sequence inference, directed evolution, structural analysis, NMR, and molecular dynamics simulations illuminate how enantioselective activity arises during the evolutionary trajectory of chalcone isomerase from a noncatalytic ancestor.



Shared strategies for β-lactam catabolism in the soil microbiome    pp556 - 564
Terence S. Crofts, Bin Wang, Aaron Spivak, Tara A. Gianoulis, Kevin J. Forsberg et al.

A β-lactamase, a novel type of amidase, and the phenylacetic acid catabolon comprise a catabolic pathway, revealed by genomic and transcriptomic analysis, that enables multiple soil bacteria to use β-lactam antibiotics as a carbon source.



Dynamic coupling between conformations and nucleotide states in DNA gyrase    pp565 - 574
Aakash Basu, Matthew Hobson, Paul Lebel, Louis E. Fernandes, Elsa M. Tretter et al.

Single-molecule measurements of DNA gyrase activity reveal conformational dynamics coupling ATP consumption to DNA supercoiling.


The cyanobacterial ornithine–ammonia cycle involves an arginine dihydrolase    pp575 - 581
Hao Zhang, Yujie Liu, Xiaoqun Nie, Lixia Liu, Qiang Hua et al.

An ornithine–ammonia cycle involving an arginine dihydrolase was identified in cyanobacteria. This cycle serves as a conduit in the nitrogen storage-and-remobilization machinery and enables cellular adaptation to nitrogen fluctuations.



A selective peptide inhibitor of Frizzled 7 receptors disrupts intestinal stem cells    pp582 - 590
Aaron H. Nile, Felipe de Sousa e Melo, Susmith Mukund, Robert Piskol, Simon Hansen et al.

A phage-derived peptide selectively binds to the Frizzled 7 CRD resulting in disruption of the dimer interface and impairing Wnt/β-catenin stem signaling in intestinal organoids.



Direct multiplex imaging and optogenetics of Rho GTPases enabled by near-infrared FRET    pp591 - 600


The monomeric near-infrared (NIR) fluorescent protein miRFP720 enables development of fully NIR Förster resonance energy transfer (FRET) biosensors compatible with CFP–YFP FRET biosensors and blue–green optogenetic tools without optical cross-talk.



Genome-wide mutant profiling predicts the mechanism of a Lipid II binding antibiotic    pp601 - 608
Marina Santiago, Wonsik Lee, Antoine Abou Fayad, Kathryn A. Coe, Mithila Rajagopal et al.

Use of a combined Tn-seq and machine-learning approach for predicting mechanisms and targets of antibiotic action in Staphylococcus aureus shows that the natural product lysocin E (LysE) binds Lipid II on the cell surface and damages the membrane.



Identification of a S. aureus virulence factor by activity-based protein profiling (ABPP)    pp609 - 617
Christian S. Lentz, Jessica R. Sheldon, Lisa A. Crawford, Rachel Cooper, Megan Garland et al.

ABP profiling identifies uncharacterized S. aureus serine hydrolases, including the surface-localized FphB, which processes lipid ester substrates and is required for infection in vivo. An FphB inhibitor reduces in vivo bacterial load.



tRNA tracking for direct measurements of protein synthesis kinetics in live cells    pp618 - 626
Ivan L. Volkov, Martin Lindén, Javier Aguirre Rivera, Ka-Weng Ieong, Mikhail Metelev et al.

Combination of single-molecule tracking experiments and machine-learning approaches to monitor diffusional state transitions between ribosome-bound and free tRNAs allows codon resolution measurements of translation kinetics.



Design of glycosylation sites by rapid synthesis and analysis of glycosyltransferases    pp627 - 635
Weston Kightlinger, Liang Lin, Madisen Rosztoczy, Wenhao Li, Matthew P. DeLisa et al.

The GlycoSCORES method, which involves cell-free protein expression and substrate-site profiling of glycosyltransferase enzymes by SAMDI–MS, enables the identification of glycosylation tags for glycoengineering efforts.



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