bacterial rna

Summary

Summary: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.

Top Publications

  1. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
  2. pmc Regulatory RNAs in bacteria
    Lauren S Waters
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
    Cell 136:615-28. 2009
  3. ncbi The Listeria transcriptional landscape from saprophytism to virulence
    Alejandro Toledo-Arana
    Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
    Nature 459:950-6. 2009
  4. pmc Pyrosequencing enumerates and contrasts soil microbial diversity
    Luiz F W Roesch
    Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 0700, USA
    ISME J 1:283-90. 2007
  5. pmc A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli
    Eric Massé
    Laboratory of Molecular Biology, National Cancer Institute, Building 37, Room 5132, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 99:4620-5. 2002
  6. ncbi A molecular view of microbial diversity and the biosphere
    N R Pace
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Science 276:734-40. 1997
  7. ncbi Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
    L Argaman
    Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, 91120, Jerusalem, Israel
    Curr Biol 11:941-50. 2001
  8. pmc ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
    Dean Laslett
    Murdoch University, Perth, Western Australia, Australia
    Nucleic Acids Res 32:11-6. 2004
  9. ncbi Quorum sensing in staphylococci
    Richard P Novick
    Kimmel Center for Biology and Medicine, New York University Medical Center, New York, New York 10016, USA
    Annu Rev Genet 42:541-64. 2008
  10. pmc Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    Jonathan A Bernstein
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:9697-702. 2002

Detail Information

Publications279 found, 100 shown here

  1. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
    ..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
  2. pmc Regulatory RNAs in bacteria
    Lauren S Waters
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
    Cell 136:615-28. 2009
    ..Here, we review the known mechanisms and roles of regulatory RNAs, highlight emerging themes, and discuss remaining questions...
  3. ncbi The Listeria transcriptional landscape from saprophytism to virulence
    Alejandro Toledo-Arana
    Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
    Nature 459:950-6. 2009
    ..Together, our data unravel successive and coordinated global transcriptional changes during infection and point to previously unknown regulatory mechanisms in bacteria...
  4. pmc Pyrosequencing enumerates and contrasts soil microbial diversity
    Luiz F W Roesch
    Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 0700, USA
    ISME J 1:283-90. 2007
    ..This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea...
  5. pmc A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli
    Eric Massé
    Laboratory of Molecular Biology, National Cancer Institute, Building 37, Room 5132, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 99:4620-5. 2002
    ....
  6. ncbi A molecular view of microbial diversity and the biosphere
    N R Pace
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Science 276:734-40. 1997
    ....
  7. ncbi Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
    L Argaman
    Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, 91120, Jerusalem, Israel
    Curr Biol 11:941-50. 2001
    ..Thus, in spite of the rising recognition that such RNAs may play key roles in bacterial physiology, many of the small RNAs known to date were discovered fortuitously...
  8. pmc ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
    Dean Laslett
    Murdoch University, Perth, Western Australia, Australia
    Nucleic Acids Res 32:11-6. 2004
    ..The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags...
  9. ncbi Quorum sensing in staphylococci
    Richard P Novick
    Kimmel Center for Biology and Medicine, New York University Medical Center, New York, New York 10016, USA
    Annu Rev Genet 42:541-64. 2008
    ..We conclude with the suggestion that agr autoactivation, unlike classical enzyme induction, can occur under suboptimal conditions and can distinguish self from non-self by inducing an exclusive and coordinated population wide response...
  10. pmc Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    Jonathan A Bernstein
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:9697-702. 2002
    ..Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability...
  11. pmc RNAMotif, an RNA secondary structure definition and search algorithm
    T J Macke
    Ibis Therapeutics, 2292 Faraday Avenue, Carlsbad, CA 92008, USA
    Nucleic Acids Res 29:4724-35. 2001
    ....
  12. pmc New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras
    Kevin E Ashelford
    Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, P O Box 915, Cardiff CF10 3TL, United Kingdom
    Appl Environ Microbiol 72:5734-41. 2006
    ..Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/...
  13. pmc Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    David H Mathews
    Center for Human Genetics and Molecular Pediatric Disease, The Aab Institute of Biomedical Sciences, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 703, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 101:7287-92. 2004
    ..For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs...
  14. pmc The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    Les Dethlefsen
    Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
    PLoS Biol 6:e280. 2008
    ..The rapid return to the pretreatment community composition is indicative of factors promoting community resilience, the nature of which deserves future investigation...
  15. ncbi Experimental approaches for the discovery and characterization of regulatory small RNA
    Cynthia Mira Sharma
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Curr Opin Microbiol 12:536-46. 2009
    ..We will also review the available toolbox for wet lab-based research, including in vivo and in vitro reporter systems, genetic methods and biochemical co-purification of sRNA interaction partners...
  16. ncbi Global analysis of small RNA and mRNA targets of Hfq
    Aixia Zhang
    Cell Biology and Metabolism Branch, National Institute of Child Health and Development, Bethesda MD 20892, USA
    Mol Microbiol 50:1111-24. 2003
    ..Thus Hfq immunoprecipitation followed by microarray analysis is a highly effective method for detecting a major class of small RNAs as well as identifying new Hfq functions...
  17. ncbi Structure of the 70S ribosome complexed with mRNA and tRNA
    Maria Selmer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 313:1935-42. 2006
    ..The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation...
  18. ncbi Recognition of cognate transfer RNA by the 30S ribosomal subunit
    J M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 292:897-902. 2001
    ..The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs...
  19. 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...
  20. pmc Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment
    Dirk Schnappinger
    Department of Microbiology and Immunology, Cornell University, 1300 York Avenue, New York, NY 10021, USA
    J Exp Med 198:693-704. 2003
    ..The microbial transcriptome thus served as a bioprobe of the MTB phagosomal environment, showing it to be nitrosative, oxidative, functionally hypoxic, carbohydrate poor, and capable of perturbing the pathogen's cell envelope...
  21. pmc Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
    Douglas W Selinger
    Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, USA
    Genome Res 13:216-23. 2003
    ..We discuss the application of subgenic resolution DNA microarray analysis to study global mechanisms of RNA transcription and processing...
  22. pmc Global gene expression in Staphylococcus aureus biofilms
    Karen E Beenken
    Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, 4301 W Markham, Little Rock, AR 72205, USA
    J Bacteriol 186:4665-84. 2004
    ..A primary theme that emerged from the analysis of these genes is that persistence within a biofilm requires an adaptive response that limits the deleterious effects of the reduced pH associated with anaerobic growth conditions...
  23. pmc Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut
    A Suau
    Laboratoire d Ecologie et Physiologie du Système Digestif, Institut National de la Recherche Agronomique, 78352 Jouy en Josas Cedex, France
    Appl Environ Microbiol 65:4799-807. 1999
    ..However, the majority of generated rDNA sequences (76%) did not correspond to known organisms and clearly derived from hitherto unknown species within this human gut microflora...
  24. pmc Genomic insights that advance the species definition for prokaryotes
    Konstantinos T Konstantinidis
    Center for Microbial Ecology, and Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824, USA
    Proc Natl Acad Sci U S A 102:2567-72. 2005
    ....
  25. 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...
  26. pmc The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins
    Ahmed Gaballa
    Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Proc Natl Acad Sci U S A 105:11927-32. 2008
    ..Thus, iron deprivation in B. subtilis activates pathways to remodel the proteome to preserve iron for the most critical cellular functions...
  27. pmc Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence
    Gilly Padalon-Brauch
    Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, 91120, Jerusalem, Israel
    Nucleic Acids Res 36:1913-27. 2008
    ..Our study suggests that the island encoded sRNA genes play an important role within the network that regulates bacterial adaptation to environmental changes and stress conditions and thus controls virulence...
  28. pmc Two GacA-dependent small RNAs modulate the quorum-sensing response in Pseudomonas aeruginosa
    Elisabeth Kay
    Département de Microbiologie Fondamentale, Universite de Lausanne, Building Biophore, CH 1015 Lausanne, Switzerland
    J Bacteriol 188:6026-33. 2006
    ..Both mutants showed increased swarming ability, azurin release, and early biofilm development...
  29. pmc DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription
    N Majdalani
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 95:12462-7. 1998
    ..We propose that DsrA pairing stimulates RpoS translation by acting as an anti-antisense RNA, freeing the translation initiation region from the cis-acting antisense RNA and allowing increased translation...
  30. ncbi Riboswitches in eubacteria sense the second messenger cyclic di-GMP
    N Sudarsan
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
    Science 321:411-3. 2008
    ..In addition, sequences matching the consensus for cyclic di-GMP riboswitches are present in the genome of a bacteriophage...
  31. ncbi The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal
    Atilio Deana
    Kimmel Center for Biology and Medicine at the Skirball Institute, and Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
    Nature 451:355-8. 2008
    ..coli not only catalyses a process functionally reminiscent of eukaryotic mRNA decapping but also bears an evolutionary relationship to the eukaryotic decapping enzyme Dcp2...
  32. ncbi An antisense RNA inhibits translation by competing with standby ribosomes
    Fabien Darfeuille
    Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S 75124 Uppsala, Sweden
    Mol Cell 26:381-92. 2007
    ..This may involve ribosome sliding to a transiently open tisB TIR. IstR-1 competes with ribosomes by base pairing to the standby site located approximately 100 nucleotides upstream...
  33. pmc Identification of small RNAs in Mycobacterium tuberculosis
    Kristine B Arnvig
    Division of Mycobacterial Research, MRC National Institute for Medical Research, London NW7 1AA, UK
    Mol Microbiol 73:397-408. 2009
    ..This is the first experimental evidence of sRNAs in M. tuberculosis and it will be important to consider the potential influence of sRNA regulation when studying the transcriptome and the proteome of M. tuberculosis during infection...
  34. pmc Positive control of swarming, rhamnolipid synthesis, and lipase production by the posttranscriptional RsmA/RsmZ system in Pseudomonas aeruginosa PAO1
    Karin Heurlier
    Institut de Microbiologie Fondamentale, Universite de Lausanne, CH 1015 Lausanne, Switzerland
    J Bacteriol 186:2936-45. 2004
    ..Overexpression of rsmZ and a null mutation in rsmA resulted in quantitatively similar, negative or positive effects on target genes, in agreement with a model that postulates titration of RsmA protein by RsmZ RNA...
  35. ncbi The riboswitch control of bacterial metabolism
    Evgeny Nudler
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Trends Biochem Sci 29:11-7. 2004
    ..Here, we summarize the recent progress in the identification and characterization of riboswitches and discuss their evolution and distribution...
  36. ncbi Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
    Verena Pfeiffer
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
    Nat Struct Mol Biol 16:840-6. 2009
    ..The discovery of CDS targeting markedly expands the sequence space for sRNA target predictions in bacteria...
  37. pmc Small untranslated RNA antitoxin in Bacillus subtilis
    Jessica M Silvaggi
    Department of Molecular and Cellular Biology, The Biological Laboratories, 16 Divinity Ave, Harvard University, Cambridge, MA 02138, USA
    J Bacteriol 187:6641-50. 2005
    ..We propose that the ratA transcript is an antisense RNA that anneals to the 3' end of the txpA mRNA, thereby triggering its degradation...
  38. ncbi Lost in translation: the influence of ribosomes on bacterial mRNA decay
    Atilio Deana
    Skirball Institute of Biomolecular Medicine and Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
    Genes Dev 19:2526-33. 2005
    ..The influence of translation on mRNA decay provides a quality-control mechanism for minimizing the use of poorly or improperly translated mRNAs as templates for the production of abnormal proteins that might be toxic to bacteria...
  39. pmc Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA
    Klas I Udekwu
    Department of Cell and Molecular Biology, Uppsala University, S 75124 Uppsala, Sweden
    Genes Dev 19:2355-66. 2005
    ..MicA requires the presence of the Hfq protein, although the mechanistic basis for this remains unclear...
  40. ncbi Determination of the regulon and identification of novel mRNA targets of Pseudomonas aeruginosa RsmA
    Anja Brencic
    Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
    Mol Microbiol 72:612-32. 2009
    ..Our work supports a model in which RsmA acts as a negative translational regulator, and where its positive effects are achieved indirectly by RsmA-mediated interference with translation of specific regulatory factors...
  41. ncbi A rough guide to the non-coding RNA world of Salmonella
    Jörg Vogel
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Mol Microbiol 71:1-11. 2009
    ..functions (and mechanisms thereof) of RNA that had remained unknown in Escherichia coli, and pioneered the use of high-throughput sequencing technology to identify the sRNA and mRNA targets of bacterial RNA-binding proteins.
  42. ncbi The role of Hfq in bacterial pathogens
    Yanjie Chao
    RNA Biology Group, Max Planck Institute for Infection Biology, Berlin, Germany
    Curr Opin Microbiol 13:24-33. 2010
    ..Hfq also facilitates post-transcriptional cross-talk between the core and variable genome regions of bacterial pathogens, and might help integrate horizontally acquired virulence genes into existing regulatory networks...
  43. ncbi Mycobacterium tuberculosis invasion of macrophages: linking bacterial gene expression to environmental cues
    Kyle H Rohde
    Cornell University, College of Veterinary Medicine, Department of Microbiology and Immunology, Ithaca, NY 14853, USA
    Cell Host Microbe 2:352-64. 2007
    ..Finally, there are marked species-specific differences in the response of Mtb and M. bovis BCG to intraphagosomal cues...
  44. ncbi Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction
    Thorleif Møller
    Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense, Campusvej 55, DK 5230 M, Odense, Denmark
    Mol Cell 9:23-30. 2002
    ..We speculate that Sm proteins in general cooperate in bimolecular RNA-RNA interaction and that protein-mediated complex formation permits small RNAs to interact with a broad range of target RNAs...
  45. 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...
  46. ncbi Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
    Rebecca K Montange
    Nature 441:1172-5. 2006
    ..Ligand binding induces the formation of a series of tertiary interactions with one of the helices, serving as a communication link between the aptamer and expression platform domains...
  47. pmc The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    Jamie J Cannone
    Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712 1095, USA
    BMC Bioinformatics 3:2. 2002
    ..This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields...
  48. ncbi Biology of trans-translation
    Kenneth C Keiler
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Annu Rev Microbiol 62:133-51. 2008
    ..Diverse bacteria require trans-translation when they execute large changes in their genetic programs, including responding to stress, pathogenesis, and differentiation...
  49. pmc Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi
    Kimberly C Tu
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Genes Dev 21:221-33. 2007
    ..Other regulators appear to be involved in control of V. harveyi qrr expression, allowing the integration of additional sensory information into the regulation of quorum-sensing gene expression...
  50. pmc Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
    Alexandra Sittka
    Max Planck Institute for Infection Biology, RNA Biology, Berlin, Germany
    PLoS Genet 4:e1000163. 2008
    ..We present a generic strategy that is ideal for the systems-level analysis of the post-transcriptional regulons of RNA-binding proteins and for sRNA discovery in a wide range of bacteria...
  51. ncbi Real-time kinetics of gene activity in individual bacteria
    Ido Golding
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Cell 123:1025-36. 2005
    ..This greatly facilitates kinetic interpretations in terms of the integer-valued random processes that produce the fluctuations...
  52. ncbi The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
    J Kenneth Wickiser
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Mol Cell 18:49-60. 2005
    ..quot; This reliance on the kinetics of ligand association and RNA polymerization speed might be common for riboswitches that utilize transcription termination mechanisms...
  53. ncbi A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome
    Verena Pfeiffer
    Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Mol Microbiol 66:1174-91. 2007
    ..This study identifies the first regulatory RNA of an enterobacterial pathogenicity island, and new roles for Hfq and HilD in SPI-1 gene expression...
  54. 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
    ....
  55. ncbi Regulation of RpoS by a novel small RNA: the characterization of RprA
    N Majdalani
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bldg 37 Room 2E 18, Bethesda, MD 20892 4255, USA
    Mol Microbiol 39:1382-94. 2001
    ..The existence of two very different small RNA regulators of RpoS translation suggests that such additional regulatory RNAs are likely to exist, both for regulation of RpoS and for regulation of other important cellular components...
  56. pmc Defining the normal bacterial flora of the oral cavity
    Jørn A Aas
    Institute of Oral Biology, University of Oslo, Postbox 1052 Blindern, 0316 Oslo, Norway
    J Clin Microbiol 43:5721-32. 2005
    ..It is important to fully define the human microflora of the healthy oral cavity before we can understand the role of bacteria in oral disease...
  57. ncbi Extraction of high-quality bacterial RNA from infected leaf tissue for bacterial in planta gene expression analysis by multiplexed fluorescent Northern hybridization
    Alexander Schenk
    Jacobs University Bremen, School of Engineering and Sciences, Campus Ring 1, 28759 Bremen, Germany
    Mol Plant Pathol 9:227-35. 2008
    ..The method was assessed regarding its sensitivity and might by useful for studying a variety of plant-microbe interactions...
  58. ncbi The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis
    Karine Prévost
    Departement de Biochimie, Groupe ARN, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
    Mol Microbiol 64:1260-73. 2007
    ..This is demonstrated by growth assays in which shikimate or the siderophore enterochelin correct the growth defect observed for a ryhB mutant in iron-limited media...
  59. ncbi RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli
    Jean François Jacques
    Departement de Biochimie, Faculte de Medecine et des Sciences de la Sante, Groupe ARN Université de Sherbrooke, Sherbrooke, Quebec, Canada
    Mol Microbiol 62:1181-90. 2006
    ..Overall, our data demonstrate that, by regulating synthesis of nonessential iron-using proteins, the small RNA RyhB ensures that the iron is directed towards the iron-requiring enzymes that are indispensable...
  60. pmc A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
    Timothy T Perkins
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    PLoS Genet 5:e1000569. 2009
    ..Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome...
  61. pmc Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci
    R A Lease
    Molecular Genetics Program, Wadsworth Center, New York State Department of Health, and School of Public Health, State University of New York at Albany, P O Box 22002, Albany, New York 12201 2002, USA
    Proc Natl Acad Sci U S A 95:12456-61. 1998
    ..Sequences within DsrA complementary to three additional genes, argR, ilvIH, and rbsD, suggest that DsrA is a riboregulator of gene expression that acts coordinately via RNA:RNA interactions at multiple loci...
  62. ncbi 6S RNA regulates E. coli RNA polymerase activity
    K M Wassarman
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell 101:613-23. 2000
    ..We show 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. Our results suggest that the interaction of 6S RNA with RNA polymerase modulates sigma70-holoenzyme activity...
  63. ncbi SAR11 clade dominates ocean surface bacterioplankton communities
    Robert M Morris
    Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
    Nature 420:806-10. 2002
    ..Although the biogeochemical role of the SAR11 clade remains uncertain, these data support the conclusion that this microbial group is among the most successful organisms on Earth...
  64. 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...
  65. pmc TargetRNA: a tool for predicting targets of small RNA action in bacteria
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    Nucleic Acids Res 36:W109-13. 2008
    ..The predictive performance of TargetRNA has been validated experimentally in several bacterial organisms. TargetRNA is freely available at http://snowwhite.wellesley.edu/targetRNA...
  66. ncbi 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...
  67. ncbi Interaction of the Bacillus stearothermophilus ribosomal protein S15 with its 5'-translational operator mRNA
    L G Scott
    Department of Molecular Biology and Skaggs Institute for Chemical Biology, MB33, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 314:413-22. 2001
    ..The BS15 mRNA and 16 S rRNA binding sites share a common secondary structure yet have little sequence identity. The mRNA and rRNA may in fact present similar if not identical structural elements that confer BS15 recognition...
  68. pmc Three small RNAs jointly ensure secondary metabolism and biocontrol in Pseudomonas fluorescens CHA0
    Elisabeth Kay
    Département de Microbiologie Fondamentale, Universite de Lausanne, CH 1015 Lausanne, Switzerland
    Proc Natl Acad Sci U S A 102:17136-41. 2005
    ..This differential expression is assumed to facilitate fine tuning of GacS/A-controlled cell population density-dependent regulation in P. fluorescens...
  69. pmc Microbial community gene expression in ocean surface waters
    Jorge Frias-Lopez
    Departments of Civil and Environmental Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 105:3805-10. 2008
    ..Thus, microbial community transcriptomic analyses revealed not only indigenous gene- and taxon-specific expression patterns but also gene categories undetected in previous DNA-based metagenomic surveys...
  70. pmc Evidence for a major role of antisense RNAs in cyanobacterial gene regulation
    Jens Georg
    Faculty of Biology and Freiburg Initiative in Systems Biology, University of Freiburg, Freiburg 79104, Germany
    Mol Syst Biol 5:305. 2009
    ..Extrapolated to the whole genome, approximately 10% of all genes in Synechocystis are influenced by asRNAs. Thus, chromosomally encoded asRNAs may have an important function in eubacterial regulatory networks...
  71. ncbi CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae
    Derrick H Lenz
    Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544 1014, USA
    Mol Microbiol 58:1186-202. 2005
    ..The VarS/VarA-CsrA/BCD system converges with the V. cholerae quorum-sensing systems to regulate the expression of the Qrr sRNAs, and thus, the entire quorum-sensing regulon...
  72. ncbi An overview of RNAs with regulatory functions in gram-positive bacteria
    Pascale Romby
    Architecture et Reactivite de l ARN, Universite de Strasbourg, CNRS, IBMC, 15 rue Rene Descartes, 67084, Strasbourg, France
    Cell Mol Life Sci 67:217-37. 2010
    ..Information on their various functions and modes of action has been well documented for gram-negative bacteria. Here, we summarize the current knowledge of regulatory RNAs in gram-positive bacteria...
  73. ncbi Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level
    Kai Papenfort
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Res Microbiol 160:278-87. 2009
    ..This review summarizes how and when several such regulators (CyaR, DsrA, GcvB, OmrAB, RNAIII, RybB, RyhB) act upon multiple targets...
  74. pmc Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E
    Kazushi Suzuki
    Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
    Genes Dev 20:2605-17. 2006
    ..Thus, these studies demonstrate a novel process for the selective targeting of RNA molecules for degradation by RNase E and a novel function for a GGDEF-EAL protein...
  75. pmc Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis
    Jessica M Silvaggi
    Department of Molecular and Cellular Biology, The Biological Laboratories, 16 Divinity Ave, Harvard University, Cambridge, MA 02138, USA
    J Bacteriol 188:532-41. 2006
    ..Our results indicate that the full repertoire of sporulation-specific gene expression involves the activation of multiple genes for small, noncoding RNAs...
  76. pmc Initiation of RNA decay in Escherichia coli by 5' pyrophosphate removal
    Helena Celesnik
    Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 27:79-90. 2007
    ..Moreover, these results reveal a striking parallel between the mechanisms of mRNA decay in prokaryotic and eukaryotic organisms...
  77. pmc The RNA binding protein Hfq interacts specifically with tRNAs
    Taewoo Lee
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    RNA 14:514-23. 2008
    ..We infer that tRNA binding and reduced fidelity are linked by a role for Hfq in tRNA modification...
  78. pmc Bacterial flora-typing with targeted, chip-based Pyrosequencing
    Andreas Sundquist
    Department of Computer Science, Stanford University, Stanford, CA 94305, USA
    BMC Microbiol 7:108. 2007
    ..In particular, classifying the microbial content of samples by sequencing the < 1,600 bp 16S rRNA gene will be affected by such limitations...
  79. pmc Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator
    Thomas A Geissmann
    Institut Jacques Monod, CNRS Universités Paris 6 et Paris 7, Paris, France
    EMBO J 23:396-405. 2004
    ..Thus, Hfq is a critical chaperone in vivo and in vitro, changing the folding of the target mRNA to make it subject to the small RNA regulator...
  80. pmc Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon
    P Seksik
    INRA, CR de Jouy en Josas, 78352 Jouy en Josas, France
    Gut 52:237-42. 2003
    ..We investigated potential differences in the faecal microflora between patients with colonic CD in remission (n=9), patients with active colonic CD (n=8), and healthy volunteers (n=16) using culture independent techniques...
  81. ncbi Hfq structure, function and ligand binding
    Richard G Brennan
    Department of Biochemistry and Molecular Biology, Unit 1000 University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard Houston, TX 77030 4009, USA
    Curr Opin Microbiol 10:125-33. 2007
    ..Fluorescence resonance energy transfer (FRET) studies directly demonstrated the role of Hfq as a chaperone that facilitates the interaction between sRNAs and target mRNAs. There are still, however, some unresolved questions...
  82. 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...
  83. ncbi Group A streptococcal growth phase-associated virulence factor regulation by a novel operon (Fas) with homologies to two-component-type regulators requires a small RNA molecule
    B Kreikemeyer
    Department of Medical Microbiology and Hygiene, University Hospital Ulm, Robert-Koch-Str. 8, D-89081 Ulm, Germany
    Mol Microbiol 39:392-406. 2001
    ..Thus, despite structural and functional similarities between fas and agr, to date the fas operon appears not to be involved in group A streptococcal (GAS) quorum-sensing regulation...
  84. pmc A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi
    Kimberly C Tu
    Department of Molecular Biology, Howard Hughes Medical Institute, Princeton, NJ 08544 1014, USA
    Mol Microbiol 70:896-907. 2008
    ..Our results suggest that feedback is essential for optimizing the dynamics of the transitions between individual and group behaviours...
  85. pmc Identification of Mycobacterium tuberculosis RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS)
    J E Graham
    Department of Biology, Washington University, St Louis, MO 63130, USA
    Proc Natl Acad Sci U S A 96:11554-9. 1999
    ..tuberculosis genes expressed in response to host interaction, will allow the study of gene expression in a variety of microorganisms, including expression resulting from interaction with human tissues in natural disease states...
  86. ncbi Structures of the bacterial ribosome at 3.5 A resolution
    Barbara S Schuwirth
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Science 310:827-34. 2005
    ....
  87. pmc The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
    J R Cole
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 33:D294-6. 2005
    ..The RDP-II email address for questions or comments is rdpstaff@msu.edu...
  88. ncbi Structure and mechanism of a metal-sensing regulatory RNA
    Charles E Dann
    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Cell 130:878-92. 2007
    ..Given the distribution of this RNA element, it may constitute a common mode for bacterial metal ion regulation, and its discovery suggests the possibility of additional RNA-based metal sensors in modern and primordial organisms...
  89. ncbi Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling
    Joanna C Betts
    Respiratory Pathogens, GlaxoSmithKline, Stevenage, Herts, UK
    Mol Microbiol 43:717-31. 2002
    ..Thus, we have generated a model with which we can search for agents active against persistent M. tuberculosis and revealed a number of potential targets expressed under these conditions...
  90. ncbi Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA
    Richard A Lease
    T C Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 2865, USA
    J Mol Biol 344:1211-23. 2004
    ..rpoS RNA complex. We conclude that recognition of rpoS mRNA is stimulated by binding of Hfq to free DsrA sRNA, followed by release of Hfq from the sRNA.mRNA complex...
  91. ncbi A glycine-dependent riboswitch that uses cooperative binding to control gene expression
    Maumita Mandal
    Department of Molecular, Cellular, and Developmental Biology, Yale University, Post Office Box 208103, New Haven, CT 06520 8103, USA
    Science 306:275-9. 2004
    ..Thus, riboswitches perform key regulatory roles and exhibit complex performance characteristics that previously had been observed only with protein factors...
  92. pmc Coding-sequence determinants of gene expression in Escherichia coli
    Grzegorz Kudla
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 324:255-8. 2009
    ..In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness...
  93. ncbi FourU: a novel type of RNA thermometer in Salmonella
    Torsten Waldminghaus
    Lehrstuhl für Biologie der Mikroorganismen, Ruhr Universitat Bochum, 44780 Bochum, Germany
    Mol Microbiol 65:413-24. 2007
    ....
  94. ncbi Reconstituting bacterial RNA repair and modification in vitro
    Chio Mui Chan
    Department of Biochemistry, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Science 326:247. 2009
    ..Thus, unlike eukaryotic Hen1 involved in RNA interference, the bacterial Hen1 is part of an RNA repair and modification system...
  95. ncbi Bacterial RNA is recognized by different sets of immunoreceptors
    Florian Eberle
    Department of Hygiene and Medical Microbiology, University of Heidelberg, Heidelberg, Germany
    Eur J Immunol 39:2537-47. 2009
    ..Here we show that bacterial RNA is a potent trigger for type-I IFN secretion in human PBMC...
  96. ncbi Synthesis-mediated release of a small RNA inhibitor of RNA polymerase
    Karen M Wassarman
    Department of Bacteriology, University of Wisconsin Madison, Madison, WI 53706, USA
    Science 314:1601-3. 2006
    ..In vivo, 6S RNA-directed RNA synthesis occurs during outgrowth from the stationary phase and likely is responsible for liberating RNAP from 6S RNA in response to nutrient availability...
  97. pmc Patterns and implications of gene gain and loss in the evolution of Prochlorococcus
    Gregory C Kettler
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Genet 3:e231. 2007
    ....
  98. ncbi Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions
    Yoshiho Ikeuchi
    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 8656, Japan
    Mol Cell 21:97-108. 2006
    ....
  99. ncbi The small RNA regulators of Escherichia coli: roles and mechanisms*
    Susan Gottesman
    Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA
    Annu Rev Microbiol 58:303-28. 2004
    ..The promoters of these small RNAs are tightly regulated, frequently as part of well-understood regulons. Lessons learned from the study of small RNAs in E. coli can be applied to finding these important regulators in other organisms...
  100. ncbi Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
    Yanmei Shi
    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 459:266-9. 2009
    ....
  101. pmc Structural insights into amino acid binding and gene control by a lysine riboswitch
    Alexander Serganov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 455:1263-7. 2008
    ....

Research Grants62

  1. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  2. Therapeutics for Drug-Resistant Bacteria: Myxopyronins
    Richard H Ebright; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Myxopyronin (Myx) is an ?-pyrone antibiotic that inhibits bacterial RNA polymerase (RNAP) through interactions with the RNAP "switch region," a structural element that mediates conformational changes ..
  3. Transcriptional Regulation by a Deacetylase, CobB, in a Periodontopathogen
    DAVID J KOLODRUBETZ; Fiscal Year: 2013
    ..any bacterium, that lysine-acetylation of transcriptional regulatory proteins plays a key role in modulating bacterial RNA expression...
  4. Nucleic Acid Enzymes and Nucleic Acids Studied at the Molecular Level
    Steven M Block; Fiscal Year: 2013
    ..Consequently, we can record from single bacterial RNA polymerase (RNAP) molecules as these step from base to base along DNA...
  5. Comprehensive Mapping and Annotation of the E. coli Transcriptome
    Barry L Wanner; Fiscal Year: 2010
    ..These studies will be carried out with methods developed by our consultant Jay C. Hinton for isolation of bacterial RNA from mice (and infected cell cultures) for preparation of cDNAs for deep sequencing...
  6. INTER AND INTRAMOLECULAR COMMUNICATIONS IN TRANSCRIPTION
    Tomasz Heyduk; Fiscal Year: 2012
    ..In aim 1 we will determine the role of conserved nontemplate -7 thymine in promoter melting by bacterial RNA polymerase...
  7. Therapeutics for Drug-Resistant Bacteria: Pseudouridimycins
    Richard H Ebright; Fiscal Year: 2013
    ..by applicant): We have discovered the first nucleoside-analog inhibitor (NAI) that selectively inhibits bacterial RNA polymerase (RNAP): pseudouridimycin (PUM). PUM is produced by Streptomyces sp...
  8. BACTERIAL TRANSCRIPTION COMPLEXES
    Richard H Ebright; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): This proposal focuses on transcription initiation and elongation by bacterial RNA polymerase (RNAP)...
  9. Structure-based mutational analysis of RNA polymerase
    KONSTANTIN V SEVERINOV; Fiscal Year: 2010
    ..We focus on bacterial RNA polymerase (RNAP), the enzyme of transcription and a validated antibiotic target...
  10. Macrophage transcriptional responses to Legionella pneumophila
    Russell E Vance; Fiscal Year: 2013
    ..pneumophila may translocate bacterial RNA into the host cell cytosol. Even if a non-RNA ligand from L...
  11. BACTERIAL TRANSCRIPTION COMPLEXES
    Richard H Ebright; Fiscal Year: 2012
    ABSTRACT This proposal focusses on transcription initiation and elongation by bacterial RNA polymerase (RNAP)...
  12. Targeting a novel regulatory RNA with novel antibiotics
    Jennifer V Hines; Fiscal Year: 2010
    ..We have identified a novel regulatory element in bacterial RNA, the T box system antiterminator that is an ideal target for antibacterial drug discovery...
  13. High-Throughput Identification of RNA polymerase inhibitors in vivo
    Robert Landick; Fiscal Year: 2006
    b>Bacterial RNA polymerase is both a central target in mechanistic studies of gene regulation and a highly attractive target for new antibiotic development...
  14. ARYL BRANCHED CHAIN ACYL COA ESTERS INHIBIT MYCOBACTERIU
    Samuel Silverstein; Fiscal Year: 2003
    ..antibiotics, with the exception of isoniazid (INH) and ethionamide, inhibit bacterial growth by inhibiting bacterial RNA, DNA, protein or cell wall synthesis...
  15. Antibacterial RNA Polymerase Inhibitors
    Christopher Self; Fiscal Year: 2002
    This SBIR Phase I program will design and synthesize candidate inhibitors of bacterial RNA polymerases (RNAP) as an approach to the development of novel antibacterial agents for use in treatment of infectious diseases, including ..
  16. FUNCTION OF POLYADENYLATE SEQUENCES IN BACTERIAL RNA
    NILIMA SARKAR; Fiscal Year: 2001
    ....
  17. Amplifying mRNAs for Bacterial Array Analysis
    Robert Setterquist; Fiscal Year: 2005
    ..and validate methods for (1) the purification of bacterial mRNAs from complex mixtures of host cell and bacterial RNA and (2) the global amplification of bacterial mRNAs following their purification from complex RNA mixtures...
  18. Mechanisms of RNA Decay in Bacteria
    Stanley Cohen; Fiscal Year: 2006
    ..While these investigations are intended to elucidate fundamental aspects of bacterial RNA decay, the information obtained is likely to facilitate the more efficient use of microorganisms to express ..
  19. Structure-function of RNAP inhibitor microcin J25
    Konstantin Severinov; Fiscal Year: 2006
    ..which is produced from a 58 amino acid-long McjA precursor by the action of McjB and McjC proteins targets bacterial RNA polymerase. Further research showed that Mccj25 has a unique structural fold--a threaded lasso...
  20. Novel inhibitors of M. tuberculosis RNA Polymerase
    Anthony Lynch; Fiscal Year: 2003
    ..have resulted in the discovery, characterization and optimization of a novel class of inhibitors of bacterial RNA polymerase The overall objective of this project is to establish the SAR of the Cumbre series as inhibitors of ..
  21. Function and Structure of Bacterial RNA Ligase
    Amy Raymond; Fiscal Year: 2007
    ..In addition to these in vitro experiments, I will also examine the role of this RNA ligase in vivo and use X-ray crystallography to determine the native structure. [unreadable] [unreadable]..
  22. Metabolism of M. tuberculosis: New Targets for MDR TB
    David Russell; Fiscal Year: 2004
    ..The experiments detail microarray analysis of bacterial RNA, coupled with a novel mutant screen to identify regulator elements responsible for mobilizing metabolic ..
  23. Human Gut Microflora Profiling for Population Studies
    Johanna Lampe; Fiscal Year: 2006
    ..intestinal bacteria cannot be cultured ex vivo, but several molecular methods are now available that utilize bacterial RNA and DMA to quantitate bacterial species and characterize baterial communities regardless of whether or not the ..
  24. FUNCTION OF STRUCTURES INVOLVED IN TRANSCRIPTION
    Dana Boyd; Fiscal Year: 1980
    ..The specific aims of this research are: 1) Characterization of mutant bacterial RNA polymerases to permit identification of the enzymatic step or steps affected in each mutant and to permit ..
  25. Functional Genomics Study and Database for Tuberculosis
    Li Fu; Fiscal Year: 2006
    ..Research results will advance molecular biological knowledge and benefit public health management in tuberculosis. ..
  26. Methods for characterizing noncoding RNAs in bacteria
    Brian Tjaden; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  27. IN VIVO PATHOGENESIS OF HELICOBACTER PYLORI
    James Fox; Fiscal Year: 2009
    ..pylori pathogenesis and specifically evaluate the role of regulatory T cells in limiting H. pylori-induced gastric pathology. ..
  28. X-RAY CRYSTALLOGRAPHIC STUDIES OF TAQ RNA POLYMERASE
    Seth Darst; Fiscal Year: 2008
    ..Determine the crystal structure of RNAP with the transcription elongation factor GreA/B; 5. Determine the crystal structure of T. thermophilus sigma (E) holoenzyme. ..
  29. Structural Basis for Sporulation in Bacillus
    Seth A Darst; Fiscal Year: 2010
    ..4. Structurally characterize the ?F regulatory system (?F/SpollAA/SpollAB/SpollE) controlling the initiation of Bacillus sporulation. ..
  30. Molecular mechanisms of transcription elongation
    Dmitry Vassylyev; Fiscal Year: 2009
    ..This project aims at elucidation of the detailed molecular mechanism of transcript elongation by bacterial RNA polymerase by combining the high-resolution structural analysis of elongation intermediates with the state-of-..
  31. Structure/Function of the Bacterial TRCF
    Seth Darst; Fiscal Year: 2008
    ..3. Determine the structural basis for the specific transcription termination activity of TRCF through structural studies of an RNAP ternary elongation complex (RNAP/DNA/RNA) with TRCF. ..
  32. DEVELOPING AND IMPROVING INSTITUTIONAL ANIMAL RESOURCES
    James Fox; Fiscal Year: 2006
    ....
  33. STRUCTURAL PARAMETERS OF E COLI RNA POLYMERASE
    Seth Darst; Fiscal Year: 2001
    ....
  34. Upgrade of in-house X-ray diffraction equipment
    Seth Darst; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  35. Molecular mechanism of antibiotic rifampicin action
    Irina Artsimovitch; Fiscal Year: 2006
    Rifamycins are effective inhibitors of a wide range of bacterial RNA polymerases, earning their place as first line antibiotics in treatment of tuberculosis...
  36. Structure and function of SRP RNA
    Christian Zwieb; Fiscal Year: 2006
    ..These studies will focus on the specific features of two critical interactions and define their dynamic relationship to SRP function. [unreadable] [unreadable]..
  37. Microecology-murine gut-initiation & progression of IBD
    James Fox; Fiscal Year: 2005
    ..prior and subsequent to oral vaccination with Helicobacter spp. antigens and mucosal adjuvants, elucidate how these vaccine strategies influence microflora dynamics and impact gut cytokine responses. ..
  38. HUS Pathogenesis & clinical Outcome in an in vivo model
    James Fox; Fiscal Year: 2008
    ..We will use this model to study the pathogenesis of HUS and importantly to develop therapeutic regimens to prevent and treat EHEC disease. [unreadable] [unreadable] [unreadable] [unreadable]..
  39. Identification and characterization of non-coding RNAs in diverse bacteria
    Jonathan Livny; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  40. Helicobacter induced hepatitis and tumorigenesis
    James Fox; Fiscal Year: 2009
    ..A more complete understanding of the etiopathogenesis of hepatobiliary disease and hepatocellular carcinoma is likely to result in new strategies for treatment and prevention of these important human diseases. ..
  41. DETECTING NEONATAL SEPSIS USING MOLECULAR TECHNIQUES
    JEANNE JORDAN; Fiscal Year: 2003
    ....
  42. Mechanisms of Gene Regulation by MicroRNAs
    Joel G Belasco; Fiscal Year: 2010
    ..The proposed research should eventually be of value for understanding the etiology of diseases related to microRNA function or dysfunction and for improving the efficacy of medical therapies based on small RNA molecules. ..
  43. BORNA DISEASE VIRUS AND NEUROPSYCHIATRIC DISEASE
    WALTER LIPKIN; Fiscal Year: 2002
    ..This study will be the first to collect and process human sera and PBMC samples in clinical laboratories with no history of BDV research and dispense aliquots to a central laboratory for randomized, blinded analysis. ..
  44. SECRETION MECHANISM OF A NOVEL C. RECTUS S-LAYER PROTEIN
    David Kolodrubetz; Fiscal Year: 2002
    ..Finally, the transport mutants will be examined for the possible mis-localization of non-S-layer proteins since there are two reports of type I transport pathways transporting more than one virulence protein. ..
  45. NMR Console Upgrade and Cryoprobe
    Peter Moore; Fiscal Year: 2002
    ..There are several structural biology projects under consideration that demand this sensitivity because the molecules of interest aggregate at the concentrations required when standard probes are used. ..
  46. ROLES OF EHRLICHIAL OUTER MEMBRANE PROTEIN IN PARASITISM
    Yasuko Rikihisa; Fiscal Year: 2001
    ..Aim 5 addresses hypothesis 3 by examining the effects of immunization with the ehrlichial OMP in a mouse model of human ehrlichiosis. ..
  47. Exploring microbial diversity for novel natural products
    JULIE OLSON; Fiscal Year: 2004
    ....
  48. VACCINIA VIRUS DNA TOPOISOMERASE
    Stewart Shuman; Fiscal Year: 2006
    ..5) Biochemical and genetic characterization of the TopIB proteins from Mycobacterium avium, Mycobacterium smegmatis, and Pseudomonas aeurginosa. ..
  49. Biochemical and Structural Analysis of the Ribosome
    Mans Ehrenberg; Fiscal Year: 2007
    ..The density maps will be analyzed by manual or automated fitting of x-ray structures or by real space refinement to obtain atomic models. [unreadable] [unreadable]..
  50. Anaerobic Regulatory Pathways in a Periodontopathogen
    David Kolodrubetz; Fiscal Year: 2006
    ..Characterizing undefined, potentially new transcriptional regulatory pathways is important because the proteins involved may serve as targets for future drug development. ..
  51. Quality Control of Protein Translation
    A Wali Karzai; Fiscal Year: 2008
    ..abstract_text> ..
  52. Ambruticin for Aspergillus
    Leonard Katz; Fiscal Year: 2005
    ..Results obtained during the one year granting period will allow us to make intelligent and systematic choices of molecules for animal efficacy and IND-enabling studies in subsequent Phase II research. ..
  53. MECHANISM OF TRP GENE REGULATION BY TRAP-RNA RECOGNITION
    Paul Babitzke; Fiscal Year: 2009
    ..Genetic and biochemical experiments will be carried out to understand how the relative placement of the triplet repeats influences TRAP-mediated translation control of these three genes. ..
  54. 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. ..
  55. Biochemical and Structural Studies of RNA-Protein Complexes
    James R Williamson; Fiscal Year: 2010
    ..These studies will provide mechanistic and structural insights into common mechanisms for post-transcriptional gene regulation. ..