Escherichia coli str. K-12 substr. MG1655

Summary

Alias: Escherichia coli MG1655, Escherichia coli str. K12 substr. MG1655, Escherichia coli str. MG1655, Escherichia coli strain MG1655

Top Publications

  1. pmc Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter
    L M Guzman
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Bacteriol 177:4121-30. 1995
  2. ncbi Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant
    P P Cherepanov
    Universitat Oldenburg, Germany
    Gene 158:9-14. 1995
  3. pmc Molecular basis of bacterial outer membrane permeability revisited
    Hiroshi Nikaido
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 3202, USA
    Microbiol Mol Biol Rev 67:593-656. 2003
  4. pmc An efficient recombination system for chromosome engineering in Escherichia coli
    D Yu
    Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 97:5978-83. 2000
  5. ncbi Prokaryotic toxin-antitoxin stress response loci
    Kenn Gerdes
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Nat Rev Microbiol 3:371-82. 2005
  6. pmc The acetate switch
    Alan J Wolfe
    Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
    Microbiol Mol Biol Rev 69:12-50. 2005
  7. ncbi Multistability in the lactose utilization network of Escherichia coli
    Ertugrul M Ozbudak
    Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 427:737-40. 2004
  8. pmc The TetR family of transcriptional repressors
    Juan L Ramos
    Department of Plant Biochemistry and Molecular and Cellular Biology, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
    Microbiol Mol Biol Rev 69:326-56. 2005
  9. ncbi Two-component signal transduction
    A M Stock
    Center for Advanced Biotechnology and Medicine and Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Annu Rev Biochem 69:183-215. 2000
  10. pmc Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein
    Maria A Schumacher
    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97201 3098, USA
    EMBO J 21:3546-56. 2002

Research Grants

  1. GENETIC CONTROL OF NITRATE RESPIRATION IN E. COLI
    Valley J Stewart; Fiscal Year: 2010
  2. Novel Approaches for the Control of Microbial Pathogens
    JOSEPH F LUTKENHAUS; Fiscal Year: 2010
  3. Glucose Signaling: Regulation of Enzyme Activity
    DONALD PETTIGREW; Fiscal Year: 2006
  4. IMP Dehydrogenase and the Hydra of Cancer Chemotherapy
    GEORGE MARKHAM; Fiscal Year: 2008
  5. SCREEN DEVELOPMENT FOR ANTIMICROBIAL PRODRUGS
    Kim Lewis; Fiscal Year: 2009
  6. BASIC MECHANISMS OF ION CHANNEL FUNCTION
    Christopher Miller; Fiscal Year: 2009
  7. The Nature of Bacterial Uncultivability
    Kim Lewis; Fiscal Year: 2008
  8. Structural studies on the Initiator protein, IBP39.
    Maria Schumacher; Fiscal Year: 2008
  9. MECHANISMS OF CHAPERONE FUNCTION IN THE LENS
    Hassane McHaourab; Fiscal Year: 2008
  10. X-Ray Crystallographic Studies of N4 RNA Polymerases
    Katsuhiko Murakami; Fiscal Year: 2008

Patents

  1. Method for producing useful substance
  2. Method for producing useful substance
  3. IMPROVING ACTIVITY OF FE-S CLUSTER REQUIRING PROTEINS
  4. Method for producing L-amino acid
  5. Method for producing L-amino acid
  6. Method for producing useful substance
  7. Method for producing useful substance
  8. Method for producing L-amino acid
  9. Method for producing target substance
  10. A cell with reduced ppGppase activity

Detail Information

Publications127 found, 100 shown here

  1. pmc Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter
    L M Guzman
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Bacteriol 177:4121-30. 1995
    ..We have exploited the tight regulation of the PBAD promoter to study the phenotypes of null mutations of essential genes and explored the use of pBAD vectors as an expression system...
  2. ncbi Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant
    P P Cherepanov
    Universitat Oldenburg, Germany
    Gene 158:9-14. 1995
    ..This system was applied in the construction of an E. coli endA deletion mutation which can be transduced by P1 to the genetic background of interest using TcR as a marker. The transductant can then be freed of the TcR if required...
  3. pmc Molecular basis of bacterial outer membrane permeability revisited
    Hiroshi Nikaido
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 3202, USA
    Microbiol Mol Biol Rev 67:593-656. 2003
    ....
  4. pmc An efficient recombination system for chromosome engineering in Escherichia coli
    D Yu
    Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 97:5978-83. 2000
    ..This system will be especially useful for the engineering of large bacterial plasmids such as those from bacterial artificial chromosome libraries...
  5. ncbi Prokaryotic toxin-antitoxin stress response loci
    Kenn Gerdes
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Nat Rev Microbiol 3:371-82. 2005
    ..It has been proposed that toxin-antitoxin loci function in bacterial programmed cell death, but evidence now indicates that these loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress...
  6. pmc The acetate switch
    Alan J Wolfe
    Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
    Microbiol Mol Biol Rev 69:12-50. 2005
    ..Next, the way in which cells regulate AMP-ACS activity through reversible acetylation is described. Finally, the "acetate switch" as it exists in selected eubacteria, archaea, and eukaryotes, including humans, is described...
  7. ncbi Multistability in the lactose utilization network of Escherichia coli
    Ertugrul M Ozbudak
    Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 427:737-40. 2004
    ..The phase diagram thus serves as a sensitive probe of molecular interactions and as a powerful tool for rational network design...
  8. pmc The TetR family of transcriptional repressors
    Juan L Ramos
    Department of Plant Biochemistry and Molecular and Cellular Biology, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
    Microbiol Mol Biol Rev 69:326-56. 2005
    ..Information related to the TetR family of regulators has been updated in a database that can be accessed at www.bactregulators.org...
  9. ncbi Two-component signal transduction
    A M Stock
    Center for Advanced Biotechnology and Medicine and Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Annu Rev Biochem 69:183-215. 2000
    ..Thus detailed analyses of a relatively small number of representative proteins provide a foundation for understanding this large family of signaling proteins...
  10. pmc Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein
    Maria A Schumacher
    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97201 3098, USA
    EMBO J 21:3546-56. 2002
    ..Such binding suggests a mechanism for Hfq function...
  11. pmc Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli
    Iris Keren
    Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115
    J Bacteriol 186:8172-80. 2004
    ..The function of these specialized dormant cells is to ensure the survival of the population in the presence of lethal factors...
  12. pmc Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity
    Harald Weber
    Institut fur Biologie, Mikrobiologie, Freie Universitat Berlin, Königin Luise Str 12 16a, 14195 Berlin, Germany
    J Bacteriol 187:1591-603. 2005
    ..Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation...
  13. doi Structural and mechanistic determinants of c-di-GMP signalling
    Tilman Schirmer
    Biozentrum, University of Basel, Klingelbergstrasse 50, CH 4056 Basel, Switzerland
    Nat Rev Microbiol 7:724-35. 2009
    ..Here, we review recent data on the structure and functional properties of the protein families that are involved in c-di-GMP signalling and discuss the mechanistic implications...
  14. pmc Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli
    Franziska Mika
    Institut für Biologie Mikrobiologie, Freie Universitat Berlin, 14195 Berlin, Germany
    Mol Microbiol 84:51-65. 2012
    ..Thus, antagonistic regulation of csgD and RprA at the mRNA level integrates cell envelope stress signals with global gene expression during stationary phase and biofilm formation...
  15. ncbi The Y-family of DNA polymerases
    H Ohmori
    Mol Cell 8:7-8. 2001
  16. pmc Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
    Byung Kwan Cho
    Department of Bioengineering, University of California San Diego, La Jolla, California 92093 0412, USA
    Genome Res 18:900-10. 2008
    ..These novel results provide new insight into how Fis modulates DNA topology at a genome scale and thus advance our understanding of the architectural bases of the E. coli nucleoid...
  17. ncbi Mechanisms and functions of DNA mismatch repair
    Guo Min Li
    Graduate Center for Toxicology and Markey Cancer Center, Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
    Cell Res 18:85-98. 2008
    ....
  18. ncbi Optimality and evolutionary tuning of the expression level of a protein
    Erez Dekel
    Department of Molecular Cell Biology and Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel
    Nature 436:588-92. 2005
    ..Thus, protein expression from the lac operon seems to be a solution of a cost-benefit optimization problem, and can be rapidly tuned by evolution to function optimally in new environments...
  19. ncbi A synthetic oscillatory network of transcriptional regulators
    M B Elowitz
    Department of Molecular Biology and Physics, Princeton University, New Jersey 08544, USA
    Nature 403:335-8. 2000
    ..Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks...
  20. pmc SSB as an organizer/mobilizer of genome maintenance complexes
    Robert D Shereda
    Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
    Crit Rev Biochem Mol Biol 43:289-318. 2008
    ..Similar themes to those highlighted in this review are evident in all biological systems...
  21. pmc Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli
    Claude Sauter
    European Molecular Biology Laboratory, Structural and Computational Biology Programme, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:4091-8. 2003
    ..Finally, a detailed structural comparison shows that the Sm-fold is remarkably well conserved in bacteria, Archaea and Eukarya, and represents a universal and modular building unit for oligomeric RNA binding proteins...
  22. ncbi Bacterial persistence as a phenotypic switch
    Nathalie Q Balaban
    Laboratory of Living Matter and Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 305:1622-5. 2004
    ..Inherent heterogeneity of bacterial populations may be important in adaptation to fluctuating environments and in the persistence of bacterial infections...
  23. pmc Translational control and target recognition by Escherichia coli small RNAs in vivo
    Johannes H Urban
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Nucleic Acids Res 35:1018-37. 2007
    ..We expect our GFP fusion approach to be applicable to sRNA targets of other bacteria, and also demonstrate that Vibrio RyhB sRNA represses a Vibrio sodB fusion when co-expressed in E.coli...
  24. pmc DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide
    M Zheng
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    J Bacteriol 183:4562-70. 2001
    ..These results expand our understanding of the oxidative stress response and raise interesting questions regarding the nature of other regulators that modulate gene expression in response to hydrogen peroxide...
  25. pmc RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Genes Dev 19:2176-86. 2005
    ..The formation of ribonucleoprotein complexes containing RNases could be a general way by which small RNAs destabilize target mRNAs in both prokaryotes and eukaryotes...
  26. pmc The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA
    Toby J Soper
    Program in Cellular, Molecular, Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218 2685, USA
    RNA 14:1907-17. 2008
    ..Once base-pairing between DsrA and rpoS mRNA is established, interactions between Hfq and the mRNA may stabilize the RNA complex by removing Hfq from the sRNA...
  27. pmc Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit
    Richard A Wing
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 382:859-69. 2008
    ..Finally, superimposing a recent structure of the clamp bound to DNA on this Pol IIIalpha complex with DNA places a loop of the beta-binding domain into the appropriate clamp cleft and supports a mechanism of polymerase switching...
  28. ncbi CsrA post-transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli
    Xin Wang
    Department of Microbiology and Immunology, Emory University School of Medicine, 3105 Rollins Research Center, 1510 Clifton Road N E, Atlanta, GA 30322, USA
    Mol Microbiol 56:1648-63. 2005
    ..These studies define the crucial mechanisms, though not the only means, by which the Csr system influences biofilm formation...
  29. pmc Effect of RyhB small RNA on global iron use in Escherichia coli
    Eric Massé
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    J Bacteriol 187:6962-71. 2005
    ..Our results demonstrate the broad effects of a single noncoding RNA on iron homeostasis...
  30. pmc Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110
    Koji Hayashi
    Division of Genome Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi Pref, Japan
    Mol Syst Biol 2:2006.0007. 2006
    ..Errors in the original MG1655 sequence (<1 per 13,000 bases) were mostly within portions sequenced with out-dated technology based on radioactive chemistry...
  31. pmc Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli
    Christina Kahramanoglou
    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    Nucleic Acids Res 39:2073-91. 2011
    ..Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques...
  32. pmc Structure of the SSB-DNA polymerase III interface and its role in DNA replication
    Aimee H Marceau
    Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706 1532, USA
    EMBO J 30:4236-47. 2011
    ..Destabilization of the χ/SSB complex in vivo produces cells with temperature-dependent cell cycle defects that appear to arise from replisome instability...
  33. ncbi The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli
    Uwe Sauer
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    J Biol Chem 279:6613-9. 2004
    ..metabolism with an extraordinary flexibility to cope with varying catabolic and anabolic demands, which raises two general questions: why do only a few bacteria contain both isoforms, and how do other organisms manage NADPH metabolism?..
  34. pmc Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs
    Peter J Mikulecky
    Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, USA
    Nat Struct Mol Biol 11:1206-14. 2004
    ..Our model explains how Hfq can simultaneously bind a ncRNA and its mRNA target to facilitate the strand displacement reaction required for Hfq-dependent translational regulation...
  35. pmc Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes
    Deo Prakash Pandey
    Department of Biochemistry and Molecular Biology, University of Southern Denmark DK 5230 Odense M, Denmark
    Nucleic Acids Res 33:966-76. 2005
    ....
  36. ncbi Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli
    Tao Wu
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    Cell 121:235-45. 2005
    ..These genetic interactions suggest a role for YfgL, one of the lipoprotein components of the protein assembly complex, in a homeostatic control mechanism that coordinates the overall OM assembly process...
  37. pmc N6-methyl-adenine: an epigenetic signal for DNA-protein interactions
    Didier Wion
    INSERM U318, CHU Michallon, Universite Joseph Fourier, 38043 Grenoble, France
    Nat Rev Microbiol 4:183-92. 2006
    ..In alpha-proteobacteria, CcrM methylation regulates the cell cycle in Caulobacter, Rhizobium and Agrobacterium, and has a role in Brucella abortus infection...
  38. pmc Persisters: a distinct physiological state of E. coli
    Devang Shah
    Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115, USA
    BMC Microbiol 6:53. 2006
    ..Recent progress in understanding persisters is encouraging, but the main obstacle in understanding their nature was our inability to isolate these elusive cells from a wild-type population since their discovery in 1944...
  39. ncbi The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability
    R Lange
    Department of Biology, University of Konstanz, Germany
    Genes Dev 8:1600-12. 1994
    ....
  40. pmc AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants
    H Okusu
    Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
    J Bacteriol 178:306-8. 1996
    ..This experiment identified the AcrAB system as the major pump responsible for making the Mar mutants resistant to many agents, including tetracycline, chloramphenicol, ampicillin, nalidixic acid, and rifampin...
  41. ncbi Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli
    B L Wei
    Department of Molecular Biology and Immunology, University of North Texas Health Science Center at Fort Worth, 3500 Camp Bowie Blvd, Fort Worth, TX 76107 2699, USA
    Mol Microbiol 40:245-56. 2001
    ..Thus, CsrA stimulates flhDC gene expression by a post-transcriptional mechanism reminiscent of its function in the repression of glycogen biosynthesis...
  42. pmc DNA as a nutrient: novel role for bacterial competence gene homologs
    S E Finkel
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 1340, USA
    J Bacteriol 183:6288-93. 2001
    ..Homologs of these E. coli genes are present in many members of the gamma subclass of Proteobacteria, suggesting that the mechanisms for consumption of DNA may have been widely conserved during evolution...
  43. ncbi The HtrA family of proteases: implications for protein composition and cell fate
    Tim Clausen
    Max Planck Institut fur Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, 82152 Martinsried, Germany
    Mol Cell 10:443-55. 2002
    ..Here, we discuss the properties and roles of this ATP-independent protease chaperone system in protein metabolism and cell fate...
  44. doi (p)ppGpp: still magical?
    Katarzyna Potrykus
    Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 2785, USA
    Annu Rev Microbiol 62:35-51. 2008
    ..Many basic questions still exist. This review tries to focus on some issues that linger even for the most widely characterized bacterial strains...
  45. pmc Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check
    Nam Ky Tonthat
    Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    EMBO J 30:154-64. 2011
    ..Thus, the combined data reveal how SlmA derails Z-ring formation at the correct place and time to effect NO...
  46. doi Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Tokyo, Japan
    FEMS Microbiol Lett 312:160-8. 2010
    ..The possible interplay between three activators was analysed in detail...
  47. ncbi A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator
    S Altuvia
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell 90:43-53. 1997
    ..Our results suggest that the oxyS RNA acts as a regulator that integrates adaptation to hydrogen peroxide with other cellular stress responses and helps to protect cells against oxidative damage...
  48. ncbi GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility
    Roger Simm
    Microbiology and Tumorbiology Center MTC, Karolinska Institutet, Box 280, SE 171 77 Stockholm, Sweden
    Mol Microbiol 53:1123-34. 2004
    ..Thus, the data suggest that c-di-GMP is a novel global second messenger in bacteria the metabolism of which is controlled by GGDEF and EAL domain proteins...
  49. ncbi DNA mismatch repair
    Thomas A Kunkel
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Annu Rev Biochem 74:681-710. 2005
    ..Emphasis is on structure-function studies of MMR proteins, on how mismatches are recognized, on the process by which the newly replicated strand is identified, and on excision of the replication error...
  50. pmc Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli
    Christopher J Cardinale
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Science 320:935-8. 2008
    ..Deletion of the cryptic rac prophage in wild-type E. coli increases bicyclomycin resistance and permits deletion of nusG. Thus, Rho termination, supported by NusA and NusG, is required to suppress the toxic activity of foreign genes...
  51. doi Structural basis for the regulated protease and chaperone function of DegP
    Tobias Krojer
    Research Institute for Molecular Pathology IMP, Dr Bohrgasse 7, A 1030 Vienna, Austria
    Nature 453:885-90. 2008
    ..Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases...
  52. pmc Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli
    Christina Pesavento
    Institut für Biologie Mikrobiologie, Freie Universitat Berlin, 14195 Berlin, Germany
    Genes Dev 22:2434-46. 2008
    ..In summary, these data reveal the logic and sequence of molecular events underlying the motile-to-adhesive "lifestyle" switch in E. coli...
  53. pmc Structural analysis of a monomeric form of the twin-arginine leader peptide binding chaperone Escherichia coli DmsD
    Charles M Stevens
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
    J Mol Biol 389:124-33. 2009
    ..coli DmsA and the most conserved regions on the surface of EcDmsD...
  54. pmc Structural analysis of substrate binding by the TatBC component of the twin-arginine protein transport system
    Michael J Tarry
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
    Proc Natl Acad Sci U S A 106:13284-9. 2009
    ..Similar TatBC-substrate complexes can be generated by an alternative in vitro reconstitution method and using a different substrate protein...
  55. doi Remnant signal peptides on non-exported enzymes: implications for the evolution of prokaryotic respiratory chains
    Bérengère Ize
    School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
    Microbiology 155:3992-4004. 2009
    ..These data highlight an intimate genetic and evolutionary link between some non-exported redox enzymes and those transported across membranes by the Tat translocation system...
  56. pmc Molecular adaptation of the DegQ protease to exert protein quality control in the bacterial cell envelope
    Justyna Sawa
    Institute of Molecular Pathology, A 1030 Vienna, Austria
    J Biol Chem 286:30680-90. 2011
    ..Furthermore, our in vitro and in vivo data imply a pH-related function of DegQ in the bacterial cell envelope...
  57. pmc The single-stranded DNA-binding protein of Escherichia coli
    R R Meyer
    Department of Biological Sciences, University of Cincinnati, Ohio 45221
    Microbiol Rev 54:342-80. 1990
    ..During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake...
  58. ncbi A large-conductance mechanosensitive channel in E. coli encoded by mscL alone
    S I Sukharev
    Laboratory of Molecular Biology, University of Wisconsin Madison 53706
    Nature 368:265-8. 1994
    ..The mscL nucleotide sequence predicts a unique protein of only 136 amino acids, with a highly hydrophobic core and very different from porins or other known proteins...
  59. pmc Coordinated regulation of amino sugar-synthesizing and -degrading enzymes in Escherichia coli K-12
    J A Plumbridge
    Institut de Biologie Physico chimique URA1139, Paris, France
    J Bacteriol 175:4951-6. 1993
    ....
  60. pmc A cycle of binding and release of the DnaK, DnaJ and GrpE chaperones regulates activity of the Escherichia coli heat shock transcription factor sigma32
    J Gamer
    Zentrum fur Molekulare Biologie, Universitat Heidelberg, Germany
    EMBO J 15:607-17. 1996
    ..These data indicate that reversible inhibition of sigma32 activity through transient association of DnaK and DnaJ is a central regulatory element of the heat shock response...
  61. ncbi The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli
    Bijoy K Mohanty
    Department of Genetics, University of Georgia, Athens, GA 30602, USA
    Mol Microbiol 54:905-20. 2004
    ..Analysis of mRNA half-lives in hfq, deltapcnB and hfq deltapcnB mutants suggests that Hfq and PAP I function in the same mRNA decay pathway...
  62. pmc Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB
    Taras Afonyushkin
    Max F Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter Dr Bohrgasse 9 4, A 1030 Vienna, Austria
    Nucleic Acids Res 33:1678-89. 2005
    ..These data are discussed in terms of a model, which accounts for the observed roles of RNase E and RNase III in sodB mRNA turnover...
  63. ncbi A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation
    Rebecca G Ponder
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Mol Cell 19:791-804. 2005
    ..Our findings reveal an RpoS-controlled switch from high-fidelity to mutagenic DSBR under stress. This limits genetic instability both in time and to localized genome regions, potentially important evolutionary strategies...
  64. pmc Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
    Alexander Serganov
    Nature 441:1167-71. 2006
    ..In addition, this structure provides insight into how folded RNAs can form precision binding pockets that rival those formed by protein genetic factors...
  65. pmc The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool
    Martijn Bekker
    Swammerdam Institute for Life Sciences Molecular Microbial Physiology, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
    J Bacteriol 192:746-54. 2010
    ..coli is modulated by the redox state of the menaquinone pool and that the ubiquinone/ubiquinol ratio in vivo surely is not the only determinant of ArcB activity...
  66. doi In situ protein folding and activation in bacterial inclusion bodies
    Nuria Gonzalez-Montalban
    Institute for Biotechnology and Biomedicine, Department of Genetics and Microbiology, Autonomous University of Barcelona and CIBER BBN Network in Bioengineering, Biomaterials and Nanomedicine, Bellaterra, 08193 Barcelona, Spain
    Biotechnol Bioeng 100:797-802. 2008
    ..In addition, in situ folding and protein activation in inclusion bodies is negatively regulated by the chaperone DnaK...
  67. doi The mechanisms of carbon catabolite repression in bacteria
    Josef Deutscher
    Laboratorie de Microbiologie et Génétique Moléculaire, INRA AgroParisTech CNRS, F 78850 Thiverval Grignon, France
    Curr Opin Microbiol 11:87-93. 2008
    ..PTS-independent CCR mechanisms are operative in several other bacteria...
  68. doi DNA apurinic-apyrimidinic site binding and excision by endonuclease IV
    Elsa D Garcin
    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB4 La Jolla, California 92037, USA
    Nat Struct Mol Biol 15:515-22. 2008
    ....
  69. pmc Functional analysis of the protein machinery required for transport of lipopolysaccharide to the outer membrane of Escherichia coli
    Paola Sperandeo
    Dipartimento di Biotecnologie e Bioscienze, Universita di Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
    J Bacteriol 190:4460-9. 2008
    ..Moreover, the location of at least one of these five proteins in every cellular compartment suggests a model for how the LPS assembly pathway is organized and ordered in space...
  70. pmc Protein exchange dynamics at chemoreceptor clusters in Escherichia coli
    Sonja Schulmeister
    Zentrum für Molekulare Biologie and Interdisziplinäres Zentrum für Wissenschaftliches Rechnen, Universitat Heidelberg, D 69120 Heidelberg, Germany
    Proc Natl Acad Sci U S A 105:6403-8. 2008
    ..Our results indicate that the rates of protein turnover at the cluster have evolved to ensure optimal performance of the chemotaxis pathway...
  71. doi Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes
    Timothy J Knowles
    Cancer Research UK Institute for Cancer Studies, School of Medicine, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
    Mol Microbiol 68:1216-27. 2008
    ..Together, this provides the first structural model of how multiple POTRA domains recruit substrates from the periplasmic solution into the outer membrane...
  72. doi Determination of the number of active GroES subunits in the fused heptamer GroES required for interactions with GroEL
    Tatsuya Nojima
    Chemical Resources Laboratory R1 7, Tokyo Institute of Technology, Yokohama, Japan
    J Biol Chem 283:18385-92. 2008
    ..These results indicate the presence of an intermediate GroEL/substrate/GroES complex in which the substrate and GroES bind to GroEL by sharing seven common binding sites...
  73. pmc Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA
    Cai Guang Yang
    Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
    Nature 452:961-5. 2008
    ..In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein...
  74. pmc Simple generation of site-directed point mutations in the Escherichia coli chromosome using Red(R)/ET(R) Recombination
    Ralf Heermann
    Ludwig Maximilians Universitat Munchen, Department Biologie I, Bereich Mikrobiologie, Maria Ward Str, 1a, D 80638 München, Germany
    Microb Cell Fact 7:14. 2008
    ..For many investigations, chromosomal systems are required rather than artificial plasmid based systems...
  75. doi Spatial regulators for bacterial cell division self-organize into surface waves in vitro
    Martin Loose
    Biotechnologisches Zentrum der Technischen Universität Dresden, Tatzberg 47 51, 01307 Dresden, Germany
    Science 320:789-92. 2008
    ..We present a reaction-diffusion model of the MinD and MinE dynamics that accounts for our experimental observations and also captures the in vivo oscillations...
  76. doi Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module
    Guang Yao Li
    Division of Signaling Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
    J Mol Biol 380:107-19. 2008
    ....
  77. doi Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity
    Martin Overgaard
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Mol Microbiol 69:841-57. 2008
    ..A mutational analysis of the operator sites showed that RelE in excess counteracted cooperative binding of the RelB(2)*RelE complexes to the operator sites. Thus, RelE controls relBE transcription by conditional cooperativity...
  78. doi Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate
    S Meyer
    Department of Structural Biology, Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, Dortmund 44227, Germany
    J Mol Biol 380:532-47. 2008
    ..We propose a model for the interaction between GidA and MnmE, which is supported by site-directed mutagenesis. Our data suggest that this interaction is modulated and potentially regulated by the switch function of the G domain of MnmE...
  79. pmc Regulation by nucleoid-associated proteins at the Escherichia coli nir operon promoter
    Douglas F Browning
    School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
    J Bacteriol 190:7258-67. 2008
    ..Differences in the upstream IHF and Fis binding sites at the nir promoter in related enteric bacteria fix the level of nir operon expression under anaerobic growth conditions...
  80. doi GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites
    Angela Tramonti
    Istituto di Biologia e Patologia Molecolari, CNR, Sapienza Universita di Roma, Roma, Italy
    Mol Microbiol 70:965-82. 2008
    ..The presence of five GadX/GadW-specific binding sites in the AFI suggests that GadX and GadW may act as H-NS counter-silencers...
  81. pmc CDD: specific functional annotation with the Conserved Domain Database
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D205-10. 2009
    ....
  82. doi Molecular basis for regulation of the heat shock transcription factor sigma32 by the DnaK and DnaJ chaperones
    Fernanda Rodriguez
    Zentrum fur Molekulare Biologie der Universitat Heidelberg, DKFZ ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
    Mol Cell 32:347-58. 2008
    ....
  83. pmc Transforming DNA uptake gene orthologs do not mediate spontaneous plasmid transformation in Escherichia coli
    Dongchang Sun
    Centre National de la Recherche Scientifique, LMGM UMR5100, F 31000 Toulouse, France
    J Bacteriol 191:713-9. 2009
    ..Our data together, with previous reports that HofQ is required for the use of dsDNA as a carbon source, suggest the existence of two routes for DNA entry, at least across the outer membrane of E. coli...
  84. pmc Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death
    Michael A Kohanski
    Department of Biomedical Engineering, Center for BioDynamics, and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Cell 135:679-90. 2008
    ....
  85. pmc PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution
    Jonathan M Guberman
    Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
    PLoS Comput Biol 4:e1000233. 2008
    ....
  86. doi Role of the sRNA GcvB in regulation of cycA in Escherichia coli
    Sarah C Pulvermacher
    Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
    Microbiology 155:106-14. 2009
    ..However, mutations predicted to disrupt base-pairing between cycA mRNA and GcvB did not alter expression of cycA : : lacZ. A model for GcvB function in cell physiology is discussed...
  87. pmc Contact-dependent growth inhibition causes reversible metabolic downregulation in Escherichia coli
    S K Aoki
    Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA
    J Bacteriol 191:1777-86. 2009
    ..Consistent with the observed decrease in Deltap, the phage shock response was induced in cells undergoing CDI but not in recovering cells, based on analysis of levels of pspA mRNA...
  88. pmc FtsZ condensates: an in vitro electron microscopy study
    David Popp
    ERATO Actin Filament Dynamics Project, Japan Science and Technology Corporation, c o RIKEN Harima Institute at Spring 8, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Biopolymers 91:340-50. 2009
    ..We shed light on the molecular arrangement of FtsZ filaments within these suprastructures using high resolution electron microscopy...
  89. pmc The oligomerization of OxyR in Escherichia coli
    Gwendowlyn S Knapp
    Department of Biochemistry and Biophysics, Texas A and M University, 2128 TAMU, College Station, Texas 77843 2128, USA
    Protein Sci 18:101-7. 2009
    ..We compared the properties of these hot spots to those described in the literature from other systems. The hot spots identified in this study are not especially conserved amongst a set of OxyR orthologs...
  90. pmc Identification of stable S-adenosylmethionine (SAM) analogues derivatised with bioorthogonal tags: effect of ligands on the affinity of the E. coli methionine repressor, MetJ, for its operator DNA
    Catherine Joce
    School of Chemistry, University of Leeds, Leeds, UKLS2 9JT, UK
    Org Biomol Chem 7:635-8. 2009
    ..The efficient synthesis of a range of stable SAM mimetics, and their ability to promote the binding of the E. coli methionine repressor (MetJ) to its operator DNA, is described...
  91. doi Maturation and degradation of ribosomal RNA in bacteria
    Murray P Deutscher
    Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, USA
    Prog Mol Biol Transl Sci 85:369-91. 2009
    ..The second focus of this review is to describe these degradative reactions, the RNases that carry them out, and the conditions that initiate the turnover process...
  92. pmc Bowl-shaped oligomeric structures on membranes as DegP's new functional forms in protein quality control
    Qing Tao Shen
    Department of Biological Sciences and Biotechnology, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China
    Proc Natl Acad Sci U S A 106:4858-63. 2009
    ..Our findings imply that DegP might regulate its dual roles during protein quality control, depending on its assembly state in the narrow bacterial envelope...
  93. pmc DinB upregulation is the sole role of the SOS response in stress-induced mutagenesis in Escherichia coli
    Rodrigo S Galhardo
    Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 3411, USA
    Genetics 182:55-68. 2009
    ....
  94. pmc Kinetic behavior of the major multidrug efflux pump AcrB of Escherichia coli
    Keiji Nagano
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 106:5854-8. 2009
    ..For the very hydrophilic cefazolin there was little sign of efflux...
  95. pmc Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA
    Kazuyuki Fujimitsu
    Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812 8582, Japan
    Genes Dev 23:1221-33. 2009
    ..Our findings reveal a novel regulatory pathway that promotes the initiation of chromosomal replication via DnaA reactivation...
  96. pmc The conserved C-terminal tail of FtsZ is required for the septal localization and division inhibitory activity of MinC(C)/MinD
    Bang Shen
    Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
    Mol Microbiol 72:410-24. 2009
    ..This binding displaces FtsA and/or ZipA, and more importantly, positions MinC(N) near the FtsZ polymers making it a more effective inhibitor...
  97. doi Multiple chaperonins in bacteria--why so many?
    Peter A Lund
    School of Biosciences, University of Birmingham, Birmingham, UK
    FEMS Microbiol Rev 33:785-800. 2009
    ....
  98. pmc The crystal structure of the TolB box of colicin A in complex with TolB reveals important differences in the recruitment of the common TolB translocation portal used by group A colicins
    Ying Zhang
    Institute of Infection, Immunity and Inflammation, School of Molecular Medical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Mol Microbiol 75:623-36. 2010
    ..coli cells...
  99. pmc A conserved haem redox and trafficking pathway for cofactor attachment
    Cynthia L Richard-Fogal
    Department of Biology, Washington University, St Louis, MO 63130, USA
    EMBO J 28:2349-59. 2009
    ....
  100. pmc Escherichia coli unsaturated fatty acid synthesis: complex transcription of the fabA gene and in vivo identification of the essential reaction catalyzed by FabB
    Youjun Feng
    Department of Microbiology, University of Illinois, Urbana, Illinois 61801, USA
    J Biol Chem 284:29526-35. 2009
    ..These data indicate that the key reaction in UFA synthesis catalyzed by FabB is elongation of the cis-3-decenoyl-ACP produced by FabA...
  101. doi Induction kinetics of a conditional pH stress response system in Escherichia coli
    Georg Fritz
    Arnold Sommerfeld Center for Theoretical Physics, Ludwig Maximilians Universitat Munchen, Germany
    J Mol Biol 393:272-86. 2009
    ..Furthermore, the analysis puts causal constraints on the precise mechanism of signal transduction via the regulatory protein CadC...

Research Grants63

  1. GENETIC CONTROL OF NITRATE RESPIRATION IN E. COLI
    Valley J Stewart; Fiscal Year: 2010
    ..Thus, results from the model species E. coli enhance understanding for a broad range of pathogens that significantly impact public health. ..
  2. Novel Approaches for the Control of Microbial Pathogens
    JOSEPH F LUTKENHAUS; Fiscal Year: 2010
    ..Finally, the new program has been based on our track record in which eleven investigators supported by the previous COBRE have secured a total of 16 extramural grants. Eight of the eleven have secured 12 NIH grants. ..
  3. Glucose Signaling: Regulation of Enzyme Activity
    DONALD PETTIGREW; Fiscal Year: 2006
    ..coli. ..
  4. IMP Dehydrogenase and the Hydra of Cancer Chemotherapy
    GEORGE MARKHAM; Fiscal Year: 2008
    ..These results will reveal the inner working of an essential enzyme and whether there is promise for enhancing clinical efficacy through combinations of known drugs or the discovery of novel subdomain ligands. ..
  5. SCREEN DEVELOPMENT FOR ANTIMICROBIAL PRODRUGS
    Kim Lewis; Fiscal Year: 2009
    ..RESEARCH GRANT TABLE OF CONTENTS Page Numbers Face Page 1 Description, ..
  6. BASIC MECHANISMS OF ION CHANNEL FUNCTION
    Christopher Miller; Fiscal Year: 2009
    ..abstract_text> ..
  7. The Nature of Bacterial Uncultivability
    Kim Lewis; Fiscal Year: 2008
    ..Unculturable bacteria are an enormous untapped source of potentially useful pharmaceutical compounds. Unculturable bacteria also make up most of the human oral and intestinal microflora. [unreadable] [unreadable] [unreadable]..
  8. Structural studies on the Initiator protein, IBP39.
    Maria Schumacher; Fiscal Year: 2008
    ..vaginalis suggests it is a possible target for the treatment of trichomoniasis, which afflicts over 170 million individuals each _,ear, ..
  9. MECHANISMS OF CHAPERONE FUNCTION IN THE LENS
    Hassane McHaourab; Fiscal Year: 2008
    ..Reporter group spectroscopic approaches will be used to provide insight into the structural basis of recognition and binding. ..
  10. X-Ray Crystallographic Studies of N4 RNA Polymerases
    Katsuhiko Murakami; Fiscal Year: 2008
    ..These studies will provide insights into the mechanism of transcription of the T7 bacteriophage-like single-subunit RNAP family, and specifically those enzymes in the family that require accessory factors. ..
  11. MECHANISM OF REPLICATION OF DRUG RESISTANCE FACTORS
    Deepak Bastia; Fiscal Year: 2008
    ..abstract_text> ..
  12. Phages of Burkholderia Cepacia: Biology and Therapeutics
    Ryland Young; Fiscal Year: 2009
    ..This project seeks to explore the use of these natural antibacterial agents to address this critical public health need. ..
  13. Engineering Large scale pathways from organisms to Escherichia coli
    James Liao; Fiscal Year: 2008
    ..In particular, selected projects proposed here will be used as modules in a workshop established by FRT at Ohio State and form the basis for a course (Metabolic Engineering) at UCLA. ..
  14. GENE CONTROL IN INFECTION AND LYSOGENY BY PHAGE LAMBDA
    Jeffrey Roberts; Fiscal Year: 2008
    ..We will investigate the mechanism of transcription termination and the manner in which regulatory proteins interfere with this process. ..
  15. SIGNAL SEQUENCE RECOGNITION AND PROTEIN TARGETING
    Robert Stroud; Fiscal Year: 2007
    ..These will instruct in the mechanism of replacing the role of RNA by protein, and therefore in the essence of the dynamic roles of SRP RNA and cpSRP43. ..
  16. OmpR and acid regulation of Escherichia coli fim genes
    WILLIAM SCHWAN; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  17. Plasmid-Mediated Quinolone Resistance
    George Jacoby; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  18. Non-natural Nucleoside Inhibitors of DNA Polymerases
    Anthony Berdis; Fiscal Year: 2009
    ..This knowledge will facilitate the development of new drugs as the repertoire of targets becomes more differentiated. ..
  19. Proton-coupled electron translocation in metalloenzymes
    ROBERT CUKIER; Fiscal Year: 2006
    ..Contemporaneously, we will explore PTR by simulation methodologies that we are developing, which combine quantum mechanics and molecular dynamics to quantitatively describe proton translocation. ..
  20. Biochemistry of Phenazine Production in Pseudomonas aeruginosa
    James Parsons; Fiscal Year: 2009
    ..New strategies that complement existing antimicrobial therapies clearly need to be developed to more effectively combat P. aeruginosa infections. ..
  21. TETHERED DOMAINS AS REGULATORY ELEMENTS
    Gregory Grant; Fiscal Year: 2009
    ..Our observations that PGDH from M. tuberculosis is inhibited by L-serine and that PGDH from humans is not, may provide a new focus in drug development for treatment of tuberculosis. ..
  22. Structural studies on the P1 plasmid partition apparatus
    Maria Schumacher; Fiscal Year: 2009
    ....
  23. The structural basis for APP cleavability
    Ya Ha; Fiscal Year: 2009
    ..abstract_text> ..
  24. Chemogenomic Analysis of E. coli Response to NO species
    James C Liao; Fiscal Year: 2010
    ..If hew TF targets are predicted, then the iteration continues. Otherwise, the predicted networks are verified using genetic and biochemical experiments. ..
  25. Fatty Acid Biosynthesis in Cryptosporidium parvum
    Guan Zhu; Fiscal Year: 2010
    ..3) To validate that fatty acid metabolic enzymes may serve as rational drug target in Cryptosporidium by discovering inhibitors selectively against, parasite fatty acid metabolic enzymes. ..
  26. Nitric Oxide Interaction with Red Blood Cells
    James C Liao; Fiscal Year: 2010
    ..Specific aim 2 will focus on the functional roles of this regulation using isolated porcine pulmonary and coronary microvessels. Together, these results will suggest clinical relevance and potential interventions. ..
  27. Metabolomics of the Virus-host Cell Interaction
    Joshua D Rabinowitz; Fiscal Year: 2010
    ..Such pathways, once identified, will be attractive new targets for antiviral therapy. ..
  28. Structural mechanism of DNA segregation by the pSK41 par system
    Maria Schumacher; Fiscal Year: 2010
    ..Thus, understanding the structural basis for DNA segregation by this par system will provide several points of potential therapeutic intervention against pSK41 harboring multidrug resistant S. aureus strains. ..
  29. The Electrochemistry of Diheme Cytochrome c Peroxidases
    Sean J Elliott; Fiscal Year: 2010
    ..Further, our study of triheme CCPs will elucidate the CCP machinery which is unique to pathogens such as Salmonella enterica and Yersinia pestis, providing new insights into their biochemical pathways. ..
  30. TERMINAL ENZYMES OF HEME SYNTHESIS
    Harry A Dailey; Fiscal Year: 2010
    ..3.) identify and characterize protein-protein interactions between ferrochelatase and PPO. ..
  31. MECHANISM OF TERMINATION OF DNA REPLICATION
    Deepak Bastia; Fiscal Year: 2010
    ..Finally, we wish to uncover the mode of action of the Swi1 and Swi3 proteins to determine if these act as "antisweepases". ..
  32. PROTON & ELECTRON TRANSFER & ENERGY COUPLING IN SITE I
    TOMOKO NONE OHNISHI; Fiscal Year: 2010
    ..Using this new strategy, we found that both cluster N2 and flavin can generate superoxide. We will solidify this exciting finding and study its relevance to complex I function under physiological and pathological conditions. ..
  33. Chemoreception and Signal Amplification
    MICHAEL MANSON; Fiscal Year: 2005
    ..The supramolecular architecture of the receptor patch and its associated proteins will be examined using electron tomography. ..
  34. REGULATION OF PYRIMIDINE GENE EXPRESSION IN BACTERIA
    CHARLES TURNBOUGH; Fiscal Year: 2001
    ..Although these studies are done with E. coli, the work is likely to be applicable to the study of gene expression and regulation in all bacteria and probably in eukaryotes, as well. ..
  35. Studying GrpE: Protein Function, Stability, and Folding
    ANDREW MEHL; Fiscal Year: 2002
    ..Point mutants will also be created to test the function of salt bridges within the dimer interface. An internal deletion mutant is proposed that will potentially lead to only a monomer of GrpE. ..
  36. Proline uptake in staphylococcus aureus pathogenesis
    WILLIAM SCHWAN; Fiscal Year: 2002
    ..The results of this study will help us understand the role of proline transport in S. aureus infections. ..
  37. NATURAL SUBSTRATES AND INHIBITORS OF MICROBIAL MDR PUMPS
    Kim Lewis; Fiscal Year: 2002
    ..MDR inhibitors will potentiate the action of conventional antibiotics, aiding eradication of multidrug resistant human pathogens. ..
  38. STRUCTURAL & ENERGETIC PRINCIPLES OF MEMBRANE PROTEINS
    KAREN FLEMING; Fiscal Year: 2002
    ....
  39. Zeiss LSM510 META confocal-fluorescence spectroscopy
    HAROLD ERICKSON; Fiscal Year: 2003
    ..Projects for this module are proposed by two faculty from Cell Biology and two from Biochemistry. This will be the only FCS facility at Duke University, and we expect additional projects from across the campus. ..
  40. Contribution of DNA photoproducts to UV mutagenesis
    Douglas Fix; Fiscal Year: 2003
    ..Furthermore, these AREA-funded studies will provide valuable research experience for undergraduate students in the biological sciences. ..
  41. MECHANISM OF E. COLI TERMINATION FACTOR RHO
    Barbara Stitt; Fiscal Year: 2003
    ..The results will provide a better understanding of how the energy of ATP hydrolysis can be transduced to movement. ..
  42. CHARACTERIZATION OF B ANTHRACIS EXOSPORIUM PROTEINS
    CHARLES TURNBOUGH; Fiscal Year: 2004
    ..anthracis spore surface (i.e., exosporium) to create affinity-matured single chain antibodies that neutralize exosporium protein activity, then test the effects of these reagents on spore properties. ..
  43. Cryptosporidium parvum DNA replication proteins
    Guan Zhu; Fiscal Year: 2004
    ..The completion of these aims will not only prove or refute our hypothesis, but also establish a new foundation for the drug discovery targeting the parasite unique DNA mechanism machinery. ..
  44. Bacterial Cell Surfaces Gordon Conference
    Barry Rosen; Fiscal Year: 2004
    ..abstract_text> ..
  45. Transport and Metabolism of Folate Analogs in E. coli
    JACALYN GREEN; Fiscal Year: 2004
    ..coli, especially with regard to a newly identified transport protein AbgT. ..
  46. STRUCTURE BASED DRUG DESIGN
    Robert Stroud; Fiscal Year: 2004
    ..Public domain access to the structures of therapeutic targets and technology will encourage their use by major pharmaceutical companies for the better design of therapeutics. ..
  47. Nucleic Acid Gordon Research Conference
    ANNA PYLE; Fiscal Year: 2004
    ..Poster sessions and optional recreational activities will stimulate informal interactions among participants. ..
  48. THYMIDYLATE SYNTHASE
    Robert Stroud; Fiscal Year: 2001
    ..Irwin Kunts, UCSF. Some mechanistic question will be approached using NMR spectroscopy in collaboration with Dr. Thomas James, UCSF. ..
  49. NOVEL METHODS FOR DISCOVERY OF ANTI-MICROBIALS
    Kim Lewis; Fiscal Year: 2005
    ..Determination of chemical structure will be performed by a combination of MS and NMR methods. ..
  50. BIODEFENSE THERAPEUTICS FROM UNCULTURED MICROORGANISMS
    Kim Lewis; Fiscal Year: 2005
    ..Determination of chemical structure will be performed by a combination of MS and NMR methods. ..
  51. Development of a HTS system:topoisomerase targets (RMI)
    Yuk Ching Tse Dinh; Fiscal Year: 2004
    ..The screening system should also be applicable for targeting topoisomerases in pathogenic bacteria relevant for biodefense. ..
  52. ASM Conference on the New Phage Biology
    Ryland Young; Fiscal Year: 2004
    ..The site was chosen to minimize costs, facilitate travel arrangements, and to foster an interactive atmosphere which will break down disciplinary borders. ..
  53. 2005 Mechanisms of Membrane Transport Gordon Conference
    Robert Stroud; Fiscal Year: 2005
    ..abstract_text> ..
  54. Molecular Basis for Transmembrane Conduction & Signaling
    Robert Stroud; Fiscal Year: 2006
    ..A further aim is to improve crystals of the Acetylcholine receptor as a means of three-dimensional structure determination of an archetype of gating mechanisms in an archetype of neuroreceptor superfamilies. ..
  55. Automated Chip-Based Metabolomic Analysis
    James Liao; Fiscal Year: 2006
    ..abstract_text> ..
  56. Molecular mechanism of antibiotic rifampicin action
    Irina Artsimovitch; Fiscal Year: 2006
    ..Finally a set of rules for design of more potent rifamycin-like antibiotics will be formulated to achieve the long-term goal of knowledge-based creation of the new generation of antibacterial drugs. ..
  57. Substrate Recognition of a tRNA Modifying Enzyme
    George Garcia; Fiscal Year: 2006
    ..A clear understanding of the similarities and differences between the TGTs from eubacteria and human will be of significance for many reasons but most obviously for the future design of novel antibiotics. ..
  58. MUROPEPTIDE RECYCLING PATHWAY & BETA LACTAMASE INDUCTION
    James Park; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  59. Single Molecule Studies of DNA Helicases
    PIERO BIANCO; Fiscal Year: 2007
    ..abstract_text> ..
  60. Migraine Headache Treatment by Drug Aerosol Inhalation
    Joshua Rabinowitz; Fiscal Year: 2004
    ..Accomplishment of the goals of Phase II will lead directly to human clinical testing of a commercially viable device that could improve the lives of millions of people every year. ..
  61. ENZYME CATALYSIS OF ELECTRON AND GROUP TRANSFER
    PERRY FREY; Fiscal Year: 2006
    ..The contributions of beta- amino acids produced by lysine 2,3-aminomutase and arginine 2,3-aminomutase to the functions of antibiotics are not known. The beta-aminoacids may become significant in drug development. ..
  62. ENZYMATIC MECHANISMS OF SULFUR NUCLEOSIDE METABOLISM
    GEORGE MARKHAM; Fiscal Year: 2008
    ..These studies will unmask why nature conserves use of a pyruvoyl cofactor for this metabolic function instead of adopting the common pyridoxal cofactor. ..

Patents18

  1. Method for producing useful substance
    Patent Number: JP2016163540-A; Date:2016-09-08
  2. Method for producing useful substance
    Patent Number: JP2016165225-A; Date:2016-09-15
  3. IMPROVING ACTIVITY OF FE-S CLUSTER REQUIRING PROTEINS
    Patent Number: JP2016171790-A; Date:2016-09-29
  4. Method for producing L-amino acid
    Patent Number: WO2014061804-A; Date:2014-04-24
  5. Method for producing L-amino acid
    Patent Number: WO2014185430-A; Date:2014-11-20
  6. Method for producing useful substance
    Patent Number: WO2015005405-A; Date:2015-01-15
  7. Method for producing useful substance
    Patent Number: WO2015005406-A; Date:2015-01-15
  8. Method for producing L-amino acid
    Patent Number: WO2015060314-A; Date:2015-04-30
  9. Method for producing target substance
    Patent Number: WO2015060391-A; Date:2015-04-30
  10. A cell with reduced ppGppase activity
    Patent Number: JP2015508647-A; Date:2015-03-23
  11. Mutant glutamate-cysteine ligase and method for producing gamma-glutamyl-valyl-glycine
    Patent Number: WO2015115612-A; Date:2015-08-06
  12. METHOD FOR PRODUCING L-AMINO ACID
    Patent Number: KR1020150099809-A; Date:2015-09-01
  13. METHOD FOR PRODUCING L-AMINO ACID
    Patent Number: EP2886651-A1; Date:2015-06-24
  14. RECOMBINANT HOST CELLS COMPRISING PHOSPHOKETOLASES
    Patent Number: KR1020130117753-A; Date:2013-10-28
  15. Biotechnological production of acrylic acid
    Patent Number: WO2009153047-A2; Date:2009-12-23
  16. IMPROVING ACTIVITY OF FE-S CLUSTER REQUIRING PROTEINS
    Patent Number: KR1020130027063-A; Date:2013-03-14
  17. IMPROVING ACTIVITY OF FE-S CLUSTER REQUIRING PROTEINS
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