[ASAP] <italic toggle=”yes”>Vibrio natriegens</italic>: An Alternative Expression System for the High-Yield Production of Isotopically Labeled Proteins

June 13th, 2019 by Walter Becker*, Florian Wimberger, and Klaus Zangger*

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Biochemistry
DOI: 10.1021/acs.biochem.9b00403

April 2019 Newsletter Released

June 12th, 2019 by Šileikyte, J., Blachly–Dyson, E., Sewell, R., Carpi, A., Menabo, R., Di Lisa, F., Ricchelli, F., Bernardi, P., Forte, M.

The April newsletter was just released. BIOL members should have received it in their email. You can find the newsletter here.

  • Posted in DBC News
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[ASAP] Characterization of Acyl Carrier Protein-Dependent Glycosyltransferase in Mitomycin C Biosynthesis

June 11th, 2019 by Hai P. Nguyen† and Kenichi Yokoyama*†‡

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Biochemistry
DOI: 10.1021/acs.biochem.9b00379

[ASAP] Design of a Protein Motif Responsive to Tyrosine Nitration and an Encoded Turn-Off Sensor of Tyrosine Nitration

June 11th, 2019 by Andrew R. Urmey and Neal J. Zondlo*

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Biochemistry
DOI: 10.1021/acs.biochem.9b00334

DNA duplex recognition activates Exo1 nuclease activity [DNA and Chromosomes]

June 10th, 2019 by Yuxi Li, Jiangchuan Shen, Hengyao Niu

Exonuclease 1 (Exo1) is an evolutionarily conserved eukaryotic nuclease that plays a multifaceted role in maintaining genome stability. The biochemical attributes of Exo1 have been extensively characterized via conventional assays. However, the key step governing its activation remains elusive. Extending upon a previous finding that Exo1 can digest a randomly selected ssDNA, but not a poly dT oligonucleotide and using purified recombinant Exo1 and nuclease and electrophoretic mobility shift assays, here we determined that DNA hairpins with a stem size of 4 bp or longer are able to activate Exo1-mediated digestion of ssDNA. We further provide evidence suggesting that Exo1 uses an evolutionarily conserved residue, Lys-185. This residue interacted with the phosphate group bridging the third and fourth nucleotide on the digestion strand of the substrate DNA for duplex recognition, critical for Exo1 activation on not only ssDNA, but also dsDNA. Additionally, the defect of an exo1-K185A mutant in duplex digestion was partially rescued by longer overhanging DNA. However, we noted that the enhanced Exo1 nuclease activity by longer overhanging DNA is largely eliminated by replication protein A (RPA), likely due to the previously reported RPA activity that strips Exo1 off the ssDNA. We conclude that duplex DNA contact by Exo1 is a general mechanism that controls its activation and that this mechanism is particularly important for digestion of duplex DNA whose nascent ssDNA is bound by RPA.

BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

June 10th, 2019 by William Farnaby

Nature Chemical Biology, Published online: 10 June 2019; doi:10.1038/s41589-019-0294-6

A structure-based design allows the development of a potent PROTAC to degrade BAF ATPase subunits SMARCA2 and SMARCA4 via recruitment of E3 ubiquitin ligase VHL and induce cancer cell death.
  • Posted in Nat Chem Biol, Publications
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Author Correction: Mitochondrial metabolism promotes adaptation to proteotoxic stress

June 4th, 2019 by Peter Tsvetkov

Nature Chemical Biology, Published online: 04 June 2019; doi:10.1038/s41589-019-0315-5

Author Correction: Mitochondrial metabolism promotes adaptation to proteotoxic stress
  • Posted in Nat Chem Biol, Publications
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Mitochondrial metabolism promotes adaptation to proteotoxic stress

May 27th, 2019 by Peter Tsvetkov

Nature Chemical Biology, Published online: 27 May 2019; doi:10.1038/s41589-019-0291-9

Mitochondrial energy metabolism regulates proteotoxic stress tolerance, exposing a newly discovered sensitivity to the small molecule elesclomol, which induces FDX1-mediated, copper-dependent cell death.

Unraveling the role of the transcriptional regulator VirS in low pH-induced responses of Mycobacterium tuberculosis and identification of VirS inhibitors [Microbiology]

May 24th, 2019 by Swati Singh, Nikita Goswami, Anil K. Tyagi, Garima Khare

The ability of Mycobacterium tuberculosis to respond and adapt to various stresses such as oxygen/nitrogen radicals and low pH inside macrophages is critical for the persistence of this human pathogen inside its host. We have previously shown that an AraC/XylS-type transcriptional regulator, VirS, which is induced in low pH, is involved in remodeling the architecture of the bacterial cell envelope. However, how VirS influences gene expression to coordinate these pH responses remains unclear. Here, using a genetic biosensor of cytoplasmic pH, we demonstrate that VirS is required for the intracellular pH maintenance in response to acidic stress and inside acidified macrophages. Furthermore, we observed that VirS plays an important role in blocking phagosomal–lysosomal fusions. Transcriptomics experiments revealed that VirS affects the expression of genes encoding metabolic enzymes, cell-wall envelope proteins, efflux pumps, ion transporters, detoxification enzymes, and transcriptional regulators expressed under low-pH stress. Employing electrophoretic mobility-shift assays, DNA footprinting, and in silico analysis, we identified a DNA sequence to which VirS binds and key residues in VirS required for its interaction with DNA. A significant role of VirS in M. tuberculosis survival in adverse conditions suggested it as a potential anti-mycobacterial drug target. To that end, we identified VirS inhibitors in a virtual screen; the top hit compounds inhibited its DNA-binding activity and also M. tuberculosis growth in vitro and inside macrophages. Our findings establish that VirS mediates M. tuberculosis responses to acidic stress and identify VirS-inhibiting compounds that may form the basis for developing more effective anti-mycobacterial agents.
  • Posted in Journal of Biological Chemistry, Publications
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[ASAP] Fluorescence-Activated Droplet Sorting for Single-Cell Directed Evolution

May 22nd, 2019 by Derek Vallejo, Ali Nikoomanzar, Brian M. Paegel, John C. Chaput

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ACS Synthetic Biology
DOI: 10.1021/acssynbio.9b00103