Now showing items 1-20 of 29

    • ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing 

      Pritchard, Justin R.; Chao, Michael C.; Abel, Sören; Davis, Brigid M.; Baranowski, Catherine; Zhang, Yanjia J.; Rubin, Eric J.; Waldor, Matthew K. (Public Library of Science, 2014)
      Transposon-insertion sequencing (TIS) is a powerful approach for deciphering genetic requirements for bacterial growth in different conditions, as it enables simultaneous genome-wide analysis of the fitness of thousands ...
    • Benzoic Acid-Inducible Gene Expression in Mycobacteria 

      Dragset, Marte S.; Barczak, Amy K.; Kannan, Nisha; Mærk, Mali; Flo, Trude H.; Valla, Svein; Rubin, Eric J.; Steigedal, Magnus (Public Library of Science, 2015)
      Conditional expression is a powerful tool to investigate the role of bacterial genes. Here, we adapt the Pseudomonas putida-derived positively regulated XylS/Pm expression system to control inducible gene expression in ...
    • Compound-gene interaction mapping reveals distinct roles for Staphylococcus aureus teichoic acids 

      Santa Maria, J. P.; Sadaka, A.; Moussa, S; Brown, Stephanie Michelle; Zhang, Yanjia Jason; Rubin, Eric Joseph; Gilmore, Michael S.; Walker, Susan Saks (Proceedings of the National Academy of Sciences, 2014)
      Staphylococcus aureus contains two distinct teichoic acid (TA) polymers, lipoteichoic acid (LTA) and wall teichoic acid (WTA), which are proposed to play redundant roles in regulating cell division. To gain insight into ...
    • Compounds targeting disulfide bond forming enzyme DsbB of Gram-negative bacteria 

      Landeta, Cristina; Blazyk, Jessica L.; Hatahet, Feras; Meehan, Brian M.; Eser, Markus; Myrick, Alissa; Bronstain, Ludmila; Minami, Shoko; Arnold, Holly; Ke, Na; Rubin, Eric J.; Furie, Barbara C.; Furie, Bruce; Beckwith, Jon; Dutton, Rachel; Boyd, Dana (2015)
      In bacteria, disulfide bonds confer stability on many proteins exported to the cell envelope or beyond. These proteins include numerous bacterial virulence factors. Thus, bacterial enzymes that promote disulfide bond ...
    • Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis 

      DeJesus, Michael A.; Gerrick, Elias R.; Xu, Weizhen; Park, Sae Woong; Long, Jarukit E.; Boutte, Cara C.; Rubin, Eric J.; Schnappinger, Dirk; Ehrt, Sabine; Fortune, Sarah M.; Sassetti, Christopher M.; Ioerger, Thomas R. (American Society for Microbiology, 2017)
      ABSTRACT For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to ...
    • Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug Resistant Mycobacterium tuberculosis 

      Farhat, Maha R; Shapiro, B Jesse; Kieser, Karen J; Sultana, Razvan; Jacobson, Karen R; Victor, Thomas C; Warren, Robin M; Streicher, Elizabeth M; Calver, Alistair; Sloutsky, Alex; Kaur, Devinder; Posey, Jamie E; Plikaytis, Bonnie; Oggioni, Marco R; Gardy, Jennifer L; Johnston, James C; Rodrigues, Mabel; Tang, Patrick K C; Kato-Maeda, Midori; Borowsky, Mark L; Muddukrishna, Bhavana; Kreiswirth, Barry N; Kurepina, Natalia; Galagan, James; Gagneux, Sebastien; Birren, Bruce; Rubin, Eric J; Lander, Eric S; Sabeti, Pardis C; Murray, Megan (2013)
      Mycobacterium tuberculosis is successfully evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including the genetic changes favored by selection in resistant ...
    • Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis 

      Zhang, Yanjia Jason; Ioerger, Thomas R.; Huttenhower, Curtis; Long, Jarukit E.; Sassetti, Christopher M.; Sacchettini, James C.; Rubin, Eric Joseph (Public Library of Science, 2012)
      Identifying genomic elements required for viability is central to our understanding of the basic physiology of bacterial pathogens. Recently, the combination of high-density mutagenesis and deep sequencing has allowed for ...
    • High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data 

      Chao, Michael C.; Pritchard, Justin R.; Zhang, Yanjia J.; Rubin, Eric J.; Livny, Jonathan; Davis, Brigid M.; Waldor, Matthew K. (Oxford University Press, 2013)
      The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial ...
    • High-Throughput Sequencing Enhanced Phage Display Identifies Peptides That Bind Mycobacteria 

      Ngubane, Nqobile A. C.; Gresh, Lionel; Ioerger, Thomas R.; Sacchettini, James C.; Zhang, Yanjia J.; Rubin, Eric J.; Pym, Alexander; Khati, Makobetsa (Public Library of Science, 2013)
      Bacterial cell wall components have been previously used as infection biomarkers detectable by antibodies. However, it is possible that the surface of the Mycobacterium tuberculosis (M. tb), the causative agent of tuberculosis ...
    • Identification of Host-Targeted Small Molecules That Restrict Intracellular Mycobacterium tuberculosis Growth 

      Stanley, Sarah A.; Barczak, Amy K.; Silvis, Melanie R.; Luo, Samantha S.; Sogi, Kimberly; Vokes, Martha; Bray, Mark-Anthony; Carpenter, Anne E.; Moore, Christopher B.; Siddiqi, Noman; Rubin, Eric J.; Hung, Deborah T. (Public Library of Science, 2014)
      Mycobacterium tuberculosis remains a significant threat to global health. Macrophages are the host cell for M. tuberculosis infection, and although bacteria are able to replicate intracellularly under certain conditions, ...
    • Identification of New Drug Targets and Resistance Mechanisms in Mycobacterium tuberculosis 

      Ioerger, Thomas R.; O’Malley, Theresa; Liao, Reiling; Guinn, Kristine M.; Hickey, Mark J.; Mohaideen, Nilofar; Murphy, Kenan C.; Boshoff, Helena I. M.; Mizrahi, Valerie; Rubin, Eric J.; Sassetti, Christopher M.; Barry, Clifton E.; Sherman, David R.; Parish, Tanya; Sacchettini, James C. (Public Library of Science, 2013)
      Identification of new drug targets is vital for the advancement of drug discovery against Mycobacterium tuberculosis, especially given the increase of resistance worldwide to first- and second-line drugs. Because traditional ...
    • Inflammatory signaling in human Tuberculosis granulomas is spatially organized 

      Marakalala, Mohlopheni J.; Raju, Ravikiran M.; Sharma, Kirti; Zhang, Yanjia J.; Eugenin, Eliseo A.; Prideaux, Brendan; Daudelin, Isaac B.; Chen, Pei-Yu; Booty, Matthew G.; Kim, Jin Hee; Eum, Seok Yong; Via, Laura E.; Behar, Samuel M.; Barry, Clifton E.; Mann, Matthias; Dartois, Véronique; Rubin, Eric J. (2016)
      Granulomas are the pathological hallmark of tuberculosis (TB). However, their function and mechanisms of formation remain poorly understood. To understand the role of granulomas in TB, we analyzed the proteomes of granulomas ...
    • Interaction and Modulation of Two Antagonistic Cell Wall Enzymes of Mycobacteria 

      Hett, Erik Christian; Chao, Michael; Rubin, Eric Joseph (Public Library of Science, 2010)
      Bacterial cell growth and division require coordinated cell wall hydrolysis and synthesis, allowing for the removal and expansion of cell wall material. Without proper coordination, unchecked hydrolysis can result in cell ...
    • Investigating the Rates and Drivers of Drug Resistance in Mycobacterium Tuberculosis 

      Gawande, Richa (2015-05-11)
      The emergence and transmission of drug resistant strains of Mycobacterium tuberculosis (Mtb) calls for urgency in understanding the barriers to effective treatment. Here we developed a chemostat cultivation system to ...
    • Lipidomic Analysis Links Mycobactin Synthase K to Iron Uptake and Virulence in M. tuberculosis 

      Madigan, Cressida A.; Martinot, Amanda Jezek; Wei, Jun-Rong; Madduri, Ashoka; Cheng, Tan-Yun; Young, David C.; Layre, Emilie; Murry, Jeffrey P.; Rubin, Eric J.; Moody, D. Branch (Public Library of Science, 2015)
      The prolonged survival of Mycobacterium tuberculosis (M. tb) in the host fundamentally depends on scavenging essential nutrients from host sources. M. tb scavenges non-heme iron using mycobactin and carboxymycobactin ...
    • Metabolic and Bactericidal Effects of Targeted Suppression of NadD and NadE Enzymes in Mycobacteria 

      Rodionova, Irina A.; Schuster, Brian M.; Guinn, Kristine M.; Sorci, Leonardo; Scott, David A.; Li, Xiaoqing; Kheterpal, Indu; Shoen, Carolyn; Cynamon, Michael; Locher, Christopher; Rubin, Eric J.; Osterman, Andrei L. (American Society of Microbiology, 2014)
      ABSTRACT Mycobacterium tuberculosis remains a major cause of death due to the lack of treatment accessibility, HIV coinfection, and drug resistance. Development of new drugs targeting previously unexplored pathways is ...
    • A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor 

      Hett, Erik Christian; Chao, Michael; Deng, Lynn L.; Rubin, Eric Joseph (Public Library of Science, 2008)
      The final stage of bacterial cell division requires the activity of one or more enzymes capable of degrading the layers of peptidoglycan connecting two recently developed daughter cells. Although this is a key step in cell ...
    • Mycobacterial Esx-3 Requires Multiple Components for Iron Acquisition 

      Siegrist, M. Sloan; Steigedal, Magnus; Ahmad, Rushdy; Mehra, Alka; Dragset, Marte S.; Schuster, Brian M.; Philips, Jennifer A.; Carr, Steven A.; Rubin, Eric J. (American Society of Microbiology, 2014)
      ABSTRACT The type VII secretion systems are conserved across mycobacterial species and in many Gram-positive bacteria. While the well-characterized Esx-1 pathway is required for the virulence of pathogenic mycobacteria and ...
    • Mycobacterial Metabolic Syndrome: LprG and Rv1410 Regulate Triacylglyceride Levels, Growth Rate and Virulence in Mycobacterium tuberculosis 

      Martinot, Amanda J.; Farrow, Mary; Bai, Lu; Layre, Emilie; Cheng, Tan-Yun; Tsai, Jennifer H.; Iqbal, Jahangir; Annand, John W.; Sullivan, Zuri A.; Hussain, M. Mahmood; Sacchettini, James; Moody, D. Branch; Seeliger, Jessica C.; Rubin, Eric J. (Public Library of Science, 2016)
      Mycobacterium tuberculosis (Mtb) mutants lacking rv1411c, which encodes the lipoprotein LprG, and rv1410c, which encodes a putative efflux pump, are dramatically attenuated for growth in mice. Here we show that loss of ...
    • \(Mycobacterium\) \(tuberculosis\) ClpP1 and ClpP2 Function Together in Protein Degradation and are Required for Viability \(in\) \(vitro\) and During Infection 

      Unnikrishnan, Meera; Krishnamoorthy, Vidhya; Raju, Ravikiran M.; Rubin, Daniel H. F.; Kandror, Olga; Akopian, Tatos; Goldberg, Alfred L.; Rubin, Eric Joseph (Public Library of Science, 2012)
      In most bacteria, Clp protease is a conserved, non-essential serine protease that regulates the response to various stresses. Mycobacteria, including \(Mycobacterium\) \(tuberculosis\) (Mtb) and \(Mycobacterium\) \(smegmatis\), ...