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Nature Chemical Biology

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https://www.readbyqxmd.com/read/29769740/identification-of-a-s-aureus-virulence-factor-by-activity-based-protein-profiling-abpp
#1
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...
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769739/membrane-association-of-monotopic-phosphoglycosyl-transferase-underpins-function
#2
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...
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769738/tracking-trna-packages
#3
Achillefs N Kapanidis, Mathew Stracy
No abstract text is available yet for this article.
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769737/next-generation-biocontainment-systems-for-engineered-organisms
#4
REVIEW
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...
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769736/trna-tracking-for-direct-measurements-of-protein-synthesis-kinetics-in-live-cells
#5
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...
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769735/enzymes-emerge-by-upcycling
#6
Michael J Harms
No abstract text is available yet for this article.
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769734/nitrogen-goes-around
#7
Jianping Yu
No abstract text is available yet for this article.
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769733/buffering-transition
#8
Yiyun Song
No abstract text is available yet for this article.
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769732/functional-phosphorylation
#9
Mirella Bucci
No abstract text is available yet for this article.
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769731/slaming-transcription
#10
Grant Miura
No abstract text is available yet for this article.
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29769730/electron-handoff
#11
Caitlin Deane
No abstract text is available yet for this article.
May 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29760514/publisher-correction-evolution-of-chalcone-isomerase-from-a-noncatalytic-ancestor
#12
Miriam Kaltenbach, Jason R Burke, Mirco Dindo, Anna Pabis, Fabian S Munsberg, Avigayel Rabin, Shina C L Kamerlin, Joseph P Noel, Dan S Tawfik
In the version of this article originally published, the number for the equal contributions footnote was missing for Miriam Kaltenbach and Jason R. Burke in the author list. The error has been corrected in the PDF and print versions of this article.
May 14, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29736039/design-of-glycosylation-sites-by-rapid-synthesis-and-analysis-of-glycosyltransferases
#13
Weston Kightlinger, Liang Lin, Madisen Rosztoczy, Wenhao Li, Matthew P DeLisa, Milan Mrksich, Michael C Jewett
Glycosylation is an abundant post-translational modification that is important in disease and biotechnology. Current methods to understand and engineer glycosylation cannot sufficiently explore the vast experimental landscapes required to accurately predict and design glycosylation sites modified by glycosyltransferases. Here we describe a systematic platform for glycosylation sequence characterization and optimization by rapid expression and screening (GlycoSCORES), which combines cell-free protein synthesis and mass spectrometry of self-assembled monolayers...
May 7, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29728602/publisher-correction-a-selective-peptide-inhibitor-of-frizzled-7-receptors-disrupts-intestinal-stem-cells
#14
Aaron H Nile, Felipe de Sousa E Melo, Susmith Mukund, Robert Piskol, Simon Hansen, Lijuan Zhou, Yingnan Zhang, Yue Fu, Emily B Gogol, László G Kömüves, Zora Modrusan, Stephane Angers, Yvonne Franke, Christopher Koth, Wayne J Fairbrother, Weiru Wang, Frederic J de Sauvage, Rami N Hannoush
The version of this article originally published contained older versions of the Life Sciences Reporting Summary and the Supplementary Text and Figures. The error has been corrected in the HTML and PDF versions of the article.
May 4, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29728601/publisher-correction-direct-multiplex-imaging-and-optogenetics-of-rho-gtpases-enabled-by-near-infrared-fret
#15
Daria M Shcherbakova, Natasha Cox Cammer, Tsipora M Huisman, Vladislav V Verkhusha, Louis Hodgson
In the version of this article originally published, the values for time shown on the x axis of Figure 5c were incorrect. The error has been corrected in all versions of the paper.
May 4, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29713061/shared-strategies-for-%C3%AE-lactam-catabolism-in-the-soil-microbiome
#16
Terence S Crofts, Bin Wang, Aaron Spivak, Tara A Gianoulis, Kevin J Forsberg, Molly K Gibson, Lauren A Johnsky, Stacey M Broomall, C Nicole Rosenzweig, Evan W Skowronski, Henry S Gibbons, Morten O A Sommer, Gautam Dantas
The soil microbiome can produce, resist, or degrade antibiotics and even catabolize them. While resistance genes are widely distributed in the soil, there is a dearth of knowledge concerning antibiotic catabolism. Here we describe a pathway for penicillin catabolism in four isolates. Genomic and transcriptomic sequencing revealed β-lactamase, amidase, and phenylacetic acid catabolon upregulation. Knocking out part of the phenylacetic acid catabolon or an apparent penicillin utilization operon (put) resulted in loss of penicillin catabolism in one isolate...
April 30, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29686359/direct-multiplex-imaging-and-optogenetics-of-rho-gtpases-enabled-by-near-infrared-fret
#17
Daria M Shcherbakova, Natasha Cox Cammer, Tsipora M Huisman, Vladislav V Verkhusha, Louis Hodgson
Direct visualization and light control of several cellular processes is a challenge, owing to the spectral overlap of available genetically encoded probes. Here we report the most red-shifted monomeric near-infrared (NIR) fluorescent protein, miRFP720, and the fully NIR Förster resonance energy transfer (FRET) pair miRFP670-miRFP720, which together enabled design of biosensors compatible with CFP-YFP imaging and blue-green optogenetic tools. We developed a NIR biosensor for Rac1 GTPase and demonstrated its use in multiplexed imaging and light control of Rho GTPase signaling pathways...
April 23, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29686358/generalized-extracellular-molecule-sensor-platform-for-programming-cellular-behavior
#18
Leo Scheller, Tobias Strittmatter, David Fuchs, Daniel Bojar, Martin Fussenegger
Strategies for expanding the sensor space of designer receptors are urgently needed to tailor cell-based therapies to respond to any type of medically relevant molecules. Here, we describe a universal approach to designing receptor scaffolds that enables antibody-specific molecular input to activate JAK/STAT, MAPK, PLCG or PI3K/Akt signaling rewired to transgene expression driven by synthetic promoters. To demonstrate its scope, we equipped the GEMS (generalized extracellular molecule sensor) platform with antibody fragments targeting a synthetic azo dye, nicotine, a peptide tag and the PSA (prostate-specific antigen) biomarker, thereby covering inputs ranging from small molecules to proteins...
April 23, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29686357/evolution-of-cyclohexadienyl-dehydratase-from-an-ancestral-solute-binding-protein
#19
Ben E Clifton, Joe A Kaczmarski, Paul D Carr, Monica L Gerth, Nobuhiko Tokuriki, Colin J Jackson
The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase...
April 23, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29686356/evolution-of-chalcone-isomerase-from-a-noncatalytic-ancestor
#20
Miriam Kaltenbach, Jason R Burke, Mirco Dindo, Anna Pabis, Fabian S Munsberg, Avigayel Rabin, Shina C L Kamerlin, Joseph P Noel, Dan S Tawfik
The emergence of catalysis in a noncatalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a nonenzymatic ancestor related to the widely distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs). Ancestral inference supported the evolution of CHI from a protein lacking isomerase activity. Further, we identified four alternative founder mutations, i.e., mutations that individually instated activity, including a mutation that is not phylogenetically traceable...
April 23, 2018: Nature Chemical Biology
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