1. Rapid Inhibition Profiling in Bacillus subtilis to Identify the Mechanism of Action of New Antimicrobials.

    ACS Chemical Biology 11(8):2222 (2016) PMID 27193499

    Increasing antimicrobial resistance has become a major public health crisis. New antimicrobials with novel mechanisms of action (MOA) are desperately needed. We previously developed a method, bacterial cytological profiling (BCP), which utilizes fluorescence microscopy to rapidly identify the MO...
  2. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.
    Mingxun Wang, Jeremy Carver, Vanessa Phelan, Laura M Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen, Jeramie Watrous, Clifford A Kapono, Tal Luzzatto-Knaan, Carla Porto, Amina Bouslimani, Alexey V Melnik, Michael J Meehan, Wei-Ting Liu, Max Crüsemann, Paul D Boudreau, Eduardo Esquenazi, Mario Sandoval-Calderón, Roland D Kersten, Laura A Pace, Robert A Quinn, Katherine R Duncan, Hsu, Dimitrios J Floros, Ronnie Gavilan, Karin Kleigrewe, Trent Northen, Rachel J Dutton, Delphine Parrot, Erin Carlson, Bertrand Aigle, Charlotte F Michelsen, Lars Jelsbak, Christian Sohlenkamp, Pavel Pevzner, Anna Edlund, Jeffrey McLean, Jörn Piel, Brian T Murphy, Lena Gerwick, Liaw, Yu-Liang Yang, Hans-Ulrich Humpf, Maria Maansson, Robert A Keyzers, Amy C Sims, Andrew R Johnson, Ashley M Sidebottom, Brian E Sedio, Andreas Klitgaard, Charles B Larson, Cristopher A Boya P, Daniel Torres-Mendoza, David J Gonzalez, Denise B Silva, Lucas Marques, Daniel P Demarque, Egle Pociute, Ellis C O'Neill, Enora Briand, Eric J N Helfrich, Eve A Granatosky, Evgenia Glukhov, Florian Ryffel, Hailey Houson, Hosein Mohimani, Jenan Kharbush, Yi Zeng, Julia A Vorholt, Kenji L Kurita, Pep Charusanti, Kerry L McPhail, Kristian Fog Nielsen, Lisa Vuong, Maryam Elfeki, Matthew F Traxler, Niclas Engene, Nobuhiro Koyama, Oliver B Vining, Ralph Baric, Ricardo Silva, Samantha J Mascuch, Sophie Tomasi, Stefan Jenkins, Venkat Macherla, Thomas Hoffman, Vinayak Agarwal, Philip G Williams, Jingqui Dai, Ram Neupane, Joshua Gurr, Andrés M C Rodríguez, Anne Lamsa, Chen Zhang, Kathleen Dorrestein, Brendan M Duggan, Jehad Almaliti, Pierre-Marie Allard, Prasad Phapale, Louis-Felix Nothias, Theodore Alexandrov, Marc Litaudon, Jean-Luc Wolfender, Jennifer E Kyle, Thomas O Metz, Tyler Peryea, Dac-Trung Nguyen, Danielle VanLeer, Paul Shinn, Ajit Jadhav, Rolf Müller, Katrina M Waters, Wenyuan Shi, Xueting Liu, Lixin Zhang, Rob Knight, Paul R Jensen, Bernhard Ø Palsson, Kit Pogliano, Roger G Linington, Marcelino Gutiérrez, Norberto P Lopes, William H Gerwick, Bradley S Moore, Pieter C Dorrestein, and Nuno Bandeira

    Nature Biotechnology 34(8):828 (2016) PMID 27504778

    The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques...
  3. Phosphorylation of spore coat proteins by a family of atypical protein kinases.

    PNAS 113(25):E3482 (2016) PMID 27185916 PMCID PMC4922149

    The modification of proteins by phosphorylation occurs in all life forms and is catalyzed by a large superfamily of enzymes known as protein kinases. We recently discovered a family of secretory pathway kinases that phosphorylate extracellular proteins. One member, family with sequence similarit...
  4. Reticulons Regulate the ER Inheritance Block during ER Stress.

    Developmental Cell 37(3):279 (2016) PMID 27117666 PMCID PMC4911346

    Segregation of functional organelles during the cell cycle is crucial to generate healthy daughter cells. In Saccharomyces cerevisiae, ER stress causes an ER inheritance block to ensure cells inherit a functional ER. Here, we report that formation of tubular ER in the mother cell, the first step...
  5. Application of bacterial cytological profiling to crude natural product extracts reveals the antibacterial arsenal of Bacillus subtilis.

    Journal of Antibiotics 69(5):353 (2016) PMID 26648120

    Although most clinically used antibiotics are derived from natural products, identifying new antibacterial molecules from natural product extracts is difficult due to the complexity of these extracts and the limited tools to correlate biological activity with specific molecules. Here, we show th...
  6. Fatty acid-releasing activities in Sinorhizobium meliloti include unusual diacylglycerol lipase.

    Environmental Microbiology 17(9):3391 (2015) PMID 25711932 PMCID PMC4914366

    Phospholipids are well known for their membrane-forming properties and thereby delimit any cell from the exterior world. In addition, membrane phospholipids can act as precursors for signals and other biomolecules during their turnover. Little is known about phospholipid signalling, turnover and...
  7. Bacillithiol: a key protective thiol in Staphylococcus aureus.

    Expert Review of Anti-infective Therapy 13(9):1089 (2015) PMID 26184907 PMCID PMC4914364

    Bacillithiol is a low-molecular-weight thiol analogous to glutathione and is found in several Firmicutes, including Staphylococcus aureus. Since its discovery in 2009, bacillithiol has been a topic of interest because it has been found to contribute to resistance during oxidative stress and deto...
  8. Visualization and functional dissection of coaxial paired SpoIIIE channels across the sporulation septum.

    eLife 4:e06474 (2015) PMID 25950186 PMCID PMC4423119

    SpoIIIE is a membrane-anchored DNA translocase that localizes to the septal midpoint to mediate chromosome translocation and membrane fission during Bacillus subtilis sporulation. Here we use cell-specific protein degradation and quantitative photoactivated localization microscopy in strains wit...
  9. Bistable forespore engulfment in Bacillus subtilis by a zipper mechanism in absence of the cell wall.

    PLoS computational biology 10(10):e1003912 (2014) PMID 25356555 PMCID PMC4214620

    To survive starvation, the bacterium Bacillus subtilis forms durable spores. The initial step of sporulation is asymmetric cell division, leading to a large mother-cell and a small forespore compartment. After division is completed and the dividing septum is thinned, the mother cell engulfs the ...
  10. Purification and characterization of the Staphylococcus aureus bacillithiol transferase BstA.

    Biochimica et Biophysica Acta 1840(9):2851 (2014) PMID 24821014 PMCID PMC4802972

    Gram-positive bacteria in the phylum Firmicutes synthesize the low molecular weight thiol bacillithiol rather than glutathione or mycothiol. The bacillithiol transferase YfiT from Bacillus subtilis was identified as a new member of the recently discovered DinB/YfiT-like Superfamily. Based on str...
  11. Impact of a transposon insertion in phzF2 on the specialized metabolite production and interkingdom interactions of Pseudomonas aeruginosa.

    Journal of Bacteriology 196(9):1683 (2014) PMID 24532776 PMCID PMC3993319

    In microbiology, gene disruption and subsequent experiments often center on phenotypic changes caused by one class of specialized metabolites (quorum sensors, virulence factors, or natural products), disregarding global downstream metabolic effects. With the recent development of mass spectromet...
  12. In Vivo Assembly and Arrangement of the DNA Translocase SpoIIIE During Chromosome Segregation and Membrane Fission in B. Subtilis

    Biophysical Journal 106(2):226a (2014)

  13. MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus.

    Journal of Antibiotics 67(1):99 (2014) PMID 24149839 PMCID PMC3919142

    Most (75%) of the anti-infectives that save countless lives and enormously improve quality of life originate from microbes found in nature. Herein, we described a global visualization of the detectable molecules produced from a single microorganism, which we define as the 'molecular network' of ...
  14. Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules.

    PNAS 110(40):16169 (2013) PMID 24046367 PMCID PMC3791758

    Identifying the mechanism of action for antibacterial compounds is essential for understanding how bacteria interact with one another and with other cell types and for antibiotic discovery efforts, but determining a compound's mechanism of action remains a serious challenge that limits both basi...
  15. The SpoIIQ landmark protein has different requirements for septal localization and immobilization.

    Molecular Microbiology 89(6):1053 (2013) PMID 23859254 PMCID PMC3901584

    Bacillus subtilis sporulation depends on the forespore membrane protein SpoIIQ, which interacts with the mother cell protein SpoIIIAH at the septum to localize other sporulation proteins. It has remained unclear how SpoIIQ localizes. We demonstrate that localization of SpoIIQ is achieved by two ...
  16. MS/MS networking guided analysis of molecule and gene cluster families.

    PNAS 110(28):E2611 (2013) PMID 23798442 PMCID PMC3710860

    The ability to correlate the production of specialized metabolites to the genetic capacity of the organism that produces such molecules has become an invaluable tool in aiding the discovery of biotechnologically applicable molecules. Here, we accomplish this task by matching molecular families w...
  17. Visualization of pinholin lesions in vivo.

    PNAS 110(22):E2054 (2013) PMID 23671069 PMCID PMC3670314

    Lambdoid phage 21 uses a pinholin-signal anchor release endolysin strategy to effect temporally regulated host lysis. In this strategy, the pinholin S(21)68 accumulates harmlessly in the bilayer until suddenly triggering to form lethal membrane lesions, consisting of S(21)68 heptamers with centr...
  18. Peptidoglycan transformations during Bacillus subtilis sporulation.

    Molecular Microbiology 88(4):673 (2013) PMID 23531131 PMCID PMC3893088

    While vegetative Bacillus subtilis cells and mature spores are both surrounded by a thick layer of peptidoglycan (PG, a polymer of glycan strands cross-linked by peptide bridges), it has remained unclear whether PG surrounds prespores during engulfment. To clarify this issue, we generated a slen...
  19. Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles.

    Molecular Microbiology 88(3):577 (2013) PMID 23560716 PMCID PMC3641587

    Bacteriophages represent a majority of all life forms, and the vast, dynamic population with early origins is reflected in their enormous genetic diversity. A large number of bacteriophage genomes have been sequenced. They are replete with novel genes without known relatives. We know little abou...
  20. Primer on agar-based microbial imaging mass spectrometry.

    Journal of Bacteriology 194(22):6023 (2012) PMID 22821974 PMCID PMC3486372

    Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry (IMS) applied directly to microbes on agar-based medium captures global information about microbial molecules, allowing for direct correlation of chemotypes to phenotypes. This tool was developed to ...