rho factor

Summary

Summary: A protein which effects termination of RNA synthesis during the genetic transcription process by dissociating the ternary transcription complex RNA;-RNA POLYMERASE DNA at the termination of a gene.

Top Publications

  1. pmc Bacterial transcription terminators: the RNA 3'-end chronicles
    Jason M Peters
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    J Mol Biol 412:793-813. 2011
  2. doi 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
  3. ncbi Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading
    Emmanuel Skordalakes
    Department of Molecular and Cell Biology, University of California, Berkeley, 239 Hildebrand Hall, 3206, Berkeley, CA 94720, USA
    Cell 114:135-46. 2003
  4. pmc Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complex
    Jisha Chalissery
    Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
    J Mol Biol 371:855-72. 2007
  5. doi Interaction with the nascent RNA is a prerequisite for the recruitment of Rho to the transcription elongation complex in vitro
    B Sudha Kalyani
    Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, Nampally, Hyderabad 500 001, India
    J Mol Biol 413:548-60. 2011
  6. doi Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA
    Dipak Dutta
    Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India
    J Biol Chem 283:20243-51. 2008
  7. pmc Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho
    D J Jin
    Department of Bacteriology, University of Wisconsin, Madison 53706
    Proc Natl Acad Sci U S A 89:1453-7. 1992
  8. pmc Running in reverse: the structural basis for translocation polarity in hexameric helicases
    Nathan D Thomsen
    Department of Molecular and Cell Biology, Quantitative Biosciences Institute, University of California, Berkeley, CA 94720, USA
    Cell 139:523-34. 2009
  9. ncbi Rho-dependent termination and ATPases in transcript termination
    John P Richardson
    Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
    Biochim Biophys Acta 1577:251-260. 2002
  10. pmc Rho-dependent transcription termination: more questions than answers
    Sharmistha Banerjee
    Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
    J Microbiol 44:11-22. 2006

Scientific Experts

Detail Information

Publications146 found, 100 shown here

  1. pmc Bacterial transcription terminators: the RNA 3'-end chronicles
    Jason M Peters
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    J Mol Biol 412:793-813. 2011
    ..In this review, we consider the current state of knowledge about bacterial termination mechanisms and the relationship between terminator sequence and steps in the termination mechanism...
  2. doi 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
    ..Transcription can be terminated by Rho factor, an essential protein in enterobacteria...
  3. ncbi Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading
    Emmanuel Skordalakes
    Department of Molecular and Cell Biology, University of California, Berkeley, 239 Hildebrand Hall, 3206, Berkeley, CA 94720, USA
    Cell 114:135-46. 2003
    In bacteria, one of the major transcriptional termination mechanisms requires a RNA/DNA helicase known as the Rho factor. We have determined two structures of Rho complexed with nucleic acid recognition site mimics in both free and ..
  4. pmc Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complex
    Jisha Chalissery
    Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
    J Mol Biol 371:855-72. 2007
    ..The rate of ATP hydrolysis regulates the processivity of translocation along the RNA and is directly correlated with the efficiency of RNA release. NusG improves the speed of RNA release and is not involved in any other step...
  5. doi Interaction with the nascent RNA is a prerequisite for the recruitment of Rho to the transcription elongation complex in vitro
    B Sudha Kalyani
    Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, Nampally, Hyderabad 500 001, India
    J Mol Biol 413:548-60. 2011
    ..We concluded that the nascent RNA loading of Rho and its interaction with the rut site are mandatory and prerequisites for its recruitment to the EC under in vitro experimental conditions...
  6. doi Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA
    Dipak Dutta
    Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India
    J Biol Chem 283:20243-51. 2008
    ....
  7. pmc Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho
    D J Jin
    Department of Bacteriology, University of Wisconsin, Madison 53706
    Proc Natl Acad Sci U S A 89:1453-7. 1992
    ....
  8. pmc Running in reverse: the structural basis for translocation polarity in hexameric helicases
    Nathan D Thomsen
    Department of Molecular and Cell Biology, Quantitative Biosciences Institute, University of California, Berkeley, CA 94720, USA
    Cell 139:523-34. 2009
    ..For a video summary of this article, see the PaperFlick file with the Supplemental Data available online...
  9. ncbi Rho-dependent termination and ATPases in transcript termination
    John P Richardson
    Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
    Biochim Biophys Acta 1577:251-260. 2002
    ..Actions of the Rho structure in the channel on the 3' segment that are coupled to ATP hydrolysis pull the RNA from its contacts with the template and RNA polymerase, thus causing termination of its synthesis...
  10. pmc Rho-dependent transcription termination: more questions than answers
    Sharmistha Banerjee
    Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
    J Microbiol 44:11-22. 2006
    ..An attempt has also been made to understand the physiology of Rho in the light of its phylogeny...
  11. ncbi The RNA-binding domain of transcription termination factor rho: isolation, characterization, and determination of sequence limits
    D Modrak
    Department of Chemistry, Indiana University, Bloomington 47405
    Biochemistry 33:8292-9. 1994
    ..Thus, the results show that this fragment, which contains an RNP1 sequence motif, will be a good model for future physical-chemical studies of the protein-RNA interactions of rho...
  12. doi Suppression of in vivo Rho-dependent transcription termination defects: evidence for kinetically controlled steps
    Rajesh Shashni
    Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad, India
    Microbiology 158:1468-81. 2012
    ..Finally, these results indicated that one of the major roles of NusG in in vivo Rho-dependent termination is to enhance the speed of RNA release from the EC...
  13. ncbi Mutational analysis and secondary structure model of the RNP1-like sequence motif of transcription termination factor Rho
    A Martinez
    Department of Chemistry, Indiana University, Bloomington, 47405, USA
    J Mol Biol 257:895-908. 1996
    ....
  14. ncbi Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli
    R Harinarayanan
    Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
    J Mol Biol 332:31-46. 2003
    ....
  15. pmc Compromised factor-dependent transcription termination in a nusA mutant of Escherichia coli: spectrum of termination efficiencies generated by perturbations of Rho, NusG, NusA, and H-NS family proteins
    Shivalika Saxena
    Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001, India
    J Bacteriol 193:3842-50. 2011
    ....
  16. ncbi The antibiotic bicyclomycin affects the secondary RNA binding site of Escherichia coli transcription termination factor Rho
    A Magyar
    Department of Biochemical and Biophysical Sciences, University of Houston, Houston, Texas 77204 5934, USA
    J Biol Chem 271:25369-74. 1996
    ..The data suggested that the antibiotic binds to Rho, influencing the secondary RNA binding (tracking) site on Rho and slows the tracking of Rho toward the bound RNA polymerase...
  17. ncbi A consensus motif common to all Rho-dependent prokaryotic transcription terminators
    P Alifano
    Dipartimento di Biologia e Patologia Cellulare e Molecolare, Universita di Napoli, Italy
    Cell 64:553-63. 1991
    ....
  18. doi Interaction surface of bacteriophage P4 protein Psu required for complex formation with the transcription terminator Rho
    Bibhusita Pani
    Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, Tuljaguda, Nampally, Hyderabad 500001, India
    J Mol Biol 389:647-60. 2009
    ..We propose that the globular N-terminal domain of Psu confers structural integrity to the functionally important C-terminal tail, which interacts directly with the hexameric Rho...
  19. pmc Evidence supporting a tethered tracking model for helicase activity of Escherichia coli Rho factor
    E J Steinmetz
    Department of Biochemistry, University of Rochester Medical Center, NY 14642
    Proc Natl Acad Sci U S A 91:1401-5. 1994
    ..DNA helix. This "tethered tracking" model is consistent with other properties of Rho factor, including the presence of two classes of RNA binding sites on the Rho hexamer and the 1:1 stoichiometry in the ..
  20. pmc Mechanism of inhibition of Rho-dependent transcription termination by bacteriophage P4 protein Psu
    Bibhusita Pani
    Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
    J Biol Chem 281:26491-500. 2006
    ..We propose that Psu inhibits Rho-dependent termination by slowing down the translocation of Rho along the RNA because of its slow ATPase activity...
  21. pmc Prediction of rho-independent transcriptional terminators in Escherichia coli
    E A Lesnik
    Ibis Therapeutics, 2292 Faraday Avenue, Carlsbad, CA 92008, USA
    Nucleic Acids Res 29:3583-94. 2001
    ....
  22. ncbi Dual role of boxB RNA motif in the mechanisms of termination/antitermination at the lambda tR1 terminator revealed in vivo
    Erwann Vieu
    Centre de Biophysique Moleculaire, CNRS, rue Charles Sadron, 45071 Orleans, France
    J Mol Biol 339:1077-87. 2004
    ....
  23. pmc Reduced Rho-dependent transcription termination permits NusA-independent growth of Escherichia coli
    C Zheng
    Department of Microbiology and Immunology, University of Michigan, Ann Arbor 48109 0620
    Proc Natl Acad Sci U S A 91:7543-7. 1994
    ..Thus, NusA-dependent coupling should be less important in a mutant with low Rho activity. The fact that E. coli grows without NusA argues that NusA should be considered an accessory factor rather than a subunit of RNA polymerase...
  24. ncbi The transcription termination factor Rho is required for oxidative stress survival in Caulobacter crescentus
    Valéria C S Italiani
    Depto de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Avenida Prof Lineu Prestes, 1374, 05508 900 Sao Paulo, SP, Brazil
    Mol Microbiol 44:181-94. 2002
    ..These results indicate that the Rho factor is essential for an efficient response to certain stresses in Caulobacter.
  25. ncbi Analysis of tryptophanase operon expression in vitro: accumulation of TnaC-peptidyl-tRNA in a release factor 2-depleted S-30 extract prevents Rho factor action, simulating induction
    Feng Gong
    Department of Biological Sciences, Stanford University, Stanford, California 94305 5020, USA
    J Biol Chem 277:17095-100. 2002
    ..This ribosome remains stalled at the tna stop codon and blocks the access of Rho factor to the tna transcript, thereby preventing transcription termination...
  26. pmc Structure of rho factor: an RNA-binding domain and a separate region with strong similarity to proven ATP-binding domains
    A J Dombroski
    Department of Biochemistry, University of Rochester Medical Center, NY 14642
    Proc Natl Acad Sci U S A 85:2538-42. 1988
    ..The implications of discrete domains for RNA and nucleotide binding are discussed in the context of requirements for specific interactions between RNA-binding and ATP-hydrolysis sites during transcription termination...
  27. ncbi Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures
    Y d'Aubenton Carafa
    C N R S Centre de Génétique Moleculaire, Laboratoire associé à l Université Pierre et Marie Curie, Gif sur Yvette, France
    J Mol Biol 216:835-58. 1990
    ..It also predicts with reasonable accuracy the in vitro termination efficiency of known rho-independent terminators, as well as predicting the existence of 35 as yet uncharacterized terminators...
  28. ncbi Transcription termination factor rho has three distinct structural domains
    J W Dolan
    Department of Chemistry, Indiana University, Bloomington 47405
    J Biol Chem 265:5747-54. 1990
    ..This result plus the finding that ADP and ATP inhibit the cleavage in the linker between the two domains indicate that those domains interact intimately in spite of their functional distinctions...
  29. ncbi Transcription termination factor rho can displace streptavidin from biotinylated RNA
    Annie Schwartz
    CNRS UPR4301, Centre de Biophysique Moleculaire, rue Charles Sadron, 45071 Orleans Cedex 2, France
    J Biol Chem 282:31469-76. 2007
    ..Although the ring-shaped Rho factor exhibits in vitro RNA-dependent ATPase and directional RNA-DNA helicase activities, the actual molecular ..
  30. ncbi Physical properties of the Escherichia coli transcription termination factor rho. 2. Quaternary structure of the rho hexamer
    J Geiselmann
    Institute of Molecular Biology, University of Oregon, Eugene 97403
    Biochemistry 31:121-32. 1992
    ..Fluorescence energy transfer data are presented and integrated with data from the literature to arrive at a self-consistent model for the quaternary structure of the rho hexamer...
  31. doi A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase
    Annie Schwartz
    Centre Nationale de la Recherche Scientifique CNRS UPR4301, Centre de Biophysique Moleculaire, Orleans, France
    Nat Struct Mol Biol 16:1309-16. 2009
    The bacterial Rho factor is a ring-shaped ATP-dependent helicase that tracks along RNA transcripts and disrupts RNA-DNA duplexes and transcription complexes in its path...
  32. ncbi Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis
    C J Ingham
    School of Biological Sciences, Nottingham University, UK
    Mol Microbiol 31:651-63. 1999
    ..This contrasts with E. coli in which NusG is essential but NusA becomes dispensable if Rho terminates transcription less efficiently...
  33. pmc Expression of bacterial Rho factor in yeast identifies new factors involved in the functional interplay between transcription and mRNP biogenesis
    Christine Mosrin-Huaman
    Centre de Biophysique Moleculaire, UPR 4301 du CNRS, rue Charles Sadron, Orleans cedex 2, France
    Mol Cell Biol 29:4033-44. 2009
    ..The assay is based on the perturbation of gene expression induced by the bacterial Rho factor, an RNA-dependent helicase/translocase that acts as a competitor at one or several steps of mRNP biogenesis in ..
  34. ncbi The structural basis for terminator recognition by the Rho transcription termination factor
    C E Bogden
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Massachusetts 02142, USA
    Mol Cell 3:487-93. 1999
    ..Dimerization of symmetric subunits on an asymmetric ligand is developed as a model for allosteric control in the action of the intact Rho hexamer...
  35. ncbi RNA passes through the hole of the protein hexamer in the complex with the Escherichia coli Rho factor
    B R Burgess
    Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
    J Biol Chem 276:4182-9. 2001
    ..These data are consistent with binding of the rut region of RNA around the crown, with its 3'-segment passing through the center of the Rho hexamer...
  36. ncbi Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor
    Emmanuel Skordalakes
    Department of Molecular and Cell Biology, University of California, Berkeley, 327B Hildebrand Hall 3206, Berkeley, CA 94720, USA
    Cell 127:553-64. 2006
    ..The structure explains the molecular effects of numerous mutations and provides new insights into the links between substrate recognition, ATP turnover, and coordinated strand movement...
  37. ncbi Mechanochemistry of transcription termination factor Rho
    Joshua L Adelman
    Biophysics Graduate Group, University of California, Berkeley, Berkeley, California 94720, USA
    Mol Cell 22:611-21. 2006
    ....
  38. ncbi Elongation factor NusG interacts with termination factor rho to regulate termination and antitermination of transcription
    J Li
    Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
    Genes Dev 7:161-72. 1993
    ..Therefore, the interaction of NusG with rho is important both for rho-dependent termination and for antitermination by N at rho-dependent terminators...
  39. ncbi Mutations in the rho transcription termination factor that affect RNA tracking
    Yi Xu
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204 5001, USA
    J Biol Chem 277:30023-30. 2002
    ....
  40. ncbi A mutation in the ATP binding domain of rho alters its RNA binding properties and uncouples ATP hydrolysis from helicase activity
    S Pereira
    Department of Biochemistry, University of Rochester Medical Center, New York 14642, USA
    J Biol Chem 270:30401-7. 1995
    ..The single F232C mutation thus appears to uncouple the protein's ATPase activity from its helicase function, so rho can no longer harness available energy for use in subsequent reactions...
  41. ncbi Loading Rho to terminate transcription
    John P Richardson
    Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
    Cell 114:157-9. 2003
    ..The opening is wide enough to accommodate single-stranded RNA and suggests that this conformation is poised to load onto mRNA...
  42. ncbi Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-binding
    R R Wei
    Departments of Biology, Indiana University, Bloomington, 47405, USA
    J Mol Biol 314:1007-15. 2001
    ....
  43. pmc rho is not essential for viability or virulence in Staphylococcus aureus
    R S Washburn
    GlaxoSmithKline, Collegeville, Pennsylvania 19426, USA
    Antimicrob Agents Chemother 45:1099-103. 2001
    ..aureus Rho. Our results explain the lack of activity of bicyclomycin against many gram-positive bacteria and raise the possibility that the essentiality of rho may be the exception rather than the rule...
  44. ncbi Analysis of E. coli rho factor: mutations affecting secondary-site interactions
    S Pereira
    Department of Biochemistry, University of Rochester Medical Center, NY 14642, USA
    J Mol Biol 251:30-40. 1995
    ....
  45. ncbi Sequence-specific interactions in the RNA-binding domain of Escherichia coli transcription termination factor Rho
    T Kevin Hitchens
    Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
    J Biol Chem 281:33697-703. 2006
    b>Rho factor is an essential protein that causes termination of transcription in a wide variety of bacteria by an RNA-dependent helicase activity. Rho is activated by transcripts that contain a high proportion of cytidine residues...
  46. ncbi Transcription termination factor rho is an RNA-DNA helicase
    C A Brennan
    Cell 48:945-52. 1987
    E. coli rho factor can unwind a short RNA-DNA duplex in vitro...
  47. pmc Functional interactions of ligand cofactors with Escherichia coli transcription termination factor rho. II. Binding of RNA
    J Geiselmann
    Institute of Molecular Biology, University of Oregon, Eugene 97403
    Protein Sci 1:861-73. 1992
    ..Based on these features of the rho-RNA interaction and other experimental data we propose a molecular model of the interaction of rho with its cofactors...
  48. ncbi The binding of C10 oligomers to Escherichia coli transcription termination factor Rho
    Xin Chen
    Department of Biochemistry and the Fels Institute for Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
    J Biol Chem 279:16301-10. 2004
    ....
  49. ncbi Interactions of Escherichia coli transcription termination factor rho with RNA. II. Electron microscopy and nuclease protection experiments
    D G Bear
    Department of Cell Biology, University of New Mexico School of Medicine, Albuquerque 87131
    J Mol Biol 199:623-35. 1988
    ..These findings and those of the companion paper are discussed in terms of various models for the structure of the rho-RNA complex in transcription termination...
  50. ncbi Structural and functional dissections of transcription termination factor rho by random mutagenesis
    Y Miwa
    Department of Biochemistry, Kyoto University, Japan
    J Mol Biol 254:815-37. 1995
    ....
  51. ncbi Interactions of Escherichia coli transcription termination factor rho with RNA. I. Binding stoichiometries and free energies
    J A McSwiggen
    Institute of Molecular Biology, University of Oregon, Eugene 97403
    J Mol Biol 199:609-22. 1988
    ..The possible significance of these results for models of rho-dependent transcription termination is discussed in the companion paper...
  52. pmc A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript
    Smita Shankar
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Mol Cell 27:914-27. 2007
    ..Furthermore, as NusA is not required for the antipausing activity of Q(82) in vitro, we distinguish two distinct activities of antiterminators, namely antipausing and RNA occlusion, and discuss their roles in Q(82) function...
  53. pmc The Rhodobacter sphaeroides 2.4.1 rho gene: expression and genetic analysis of structure and function
    M Gomelsky
    Department of Microbiology and Molecular Genetics, The University of Texas Medical School at Houston, Texas 77030, USA
    J Bacteriol 178:1946-54. 1996
    ..The gene downstream of rho is homologous to thdF, whose product is involved in thiophene and furan oxidation...
  54. ncbi Rho factor: transcription termination in four steps
    Daniel L Kaplan
    Rockefeller University, Laboratory of DNA Replication, Box 228, 1230 York Avenue, New York, NY 10021, USA
    Curr Biol 13:R714-6. 2003
    b>Rho factor is a hexameric ring-shaped helicase which terminates transcription in Escherichia coli. Two recent crystal structures of Rho in complex with nucleic acid reveal how this helicase ring loads onto mRNA and encircles it.
  55. pmc Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene
    T Opperman
    Department of Chemistry, Indiana University, Bloomington 47405
    J Bacteriol 176:5033-43. 1994
    ..Since functionally defective mutants for E. coli Rho exist in all three of these segments, they represent important parts of Rho that have undergone adaptive evolution...
  56. ncbi The molecular basis for the mode of action of bicyclomycin
    Harold Kohn
    Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7360, USA
    Curr Drug Targets Infect Disord 5:273-95. 2005
    ....
  57. ncbi Experimental analysis of Helicobacter pylori transcriptional terminators suggests this microbe uses both intrinsic and factor-dependent termination
    Andrea R Castillo
    Department of Environmental Toxicology, University of California, Santa Cruz, CA, USA
    Mol Microbiol 67:155-70. 2008
    ..In conclusion, we found that H. pylori possesses numerous Rho-dependent and intrinsic terminators including some found in intragenic regions...
  58. ncbi Regulation of rho-dependent transcription termination by NusG is specific to the Escherichia coli elongation complex
    Z Pasman
    Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
    Biochemistry 39:5573-85. 2000
    ..Thus, we conclude that NusG modulates Rho-dependent termination by interacting specifically with the RNAP of the E. coli elongation complex to render the complex more susceptible to the termination activity of Rho...
  59. ncbi Three-dimensional reconstruction of transcription termination factor rho: orientation of the N-terminal domain and visualization of an RNA-binding site
    X Yu
    Department of Biochemistry and Molecular Genetics, University of Virginia Health Sciences, Charlottesville, VA, 22908 0733, USA
    J Mol Biol 299:1279-87. 2000
    ..Although rho shares a common structural core with the F1-ATPase and other hexameric helicases, there has been a divergence in function due to rho's N-terminal domain, which has no homology to other helicases...
  60. ncbi The bicyclomycin sensitivities of 38 bicyclomycin-resistant mutants of transcription termination protein rho and the location of their mutations support a structural model of rho based on the F(1) ATPase
    K A Moyse
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    J Mol Biol 302:565-79. 2000
    ..As a whole, the bicyclomycin sensitivities of the mutants are consistent with the locations of their respective mutations in the model of Rho based on the F(1) ATPase, therefore supporting the emerging consensus model of Rho structure...
  61. ncbi Participation of Rho-dependent transcription termination in oxidative stress sensitivity caused by an rpoB mutation
    Nobuyuki Kawamura
    Laboratory of Developmental Biochemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7 3 1, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Genes Cells 10:477-87. 2005
    ..Either a multicopy supply of the rof gene or bicyclomycin, both of which inhibit the transcription termination Rho factor, suppressed the increased sensitivity to oxidative stress of the rifampicin-resistant rpoB mutation in ..
  62. pmc Suppression of factor-dependent transcription termination by antiterminator RNA
    Rodney A King
    Section on Microbial Genetics, Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 2785, USA
    J Bacteriol 185:7085-91. 2003
    ..put-mediated antitermination thus shows no apparent terminator specificity, suggesting that put inhibits a step that is common to termination at the different types of terminator...
  63. ncbi C(5)-C(5a)-modified bicyclomycins: synthesis, structure, and biochemical and biological properties
    F Vincent
    Department of Chemistry, University of Houston, Houston, Texas 77204-5641, USA
    J Org Chem 66:2251-64. 2001
    ..2.2]-bicyclic ring system. The observed biochemical activities for the C(5a)-extended conjugated bicyclomycin derivatives and the (5E) and (5Z) isomers were correlated with a structural model for the 1-rho complex...
  64. ncbi Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin
    Emmanuel Skordalakes
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Structure 13:99-109. 2005
    ..Our data explain why only certain elements of BCM have been amenable to modification and serve as a template for the design of new inhibitors...
  65. pmc Expression of the Bacillus subtilis trpEDCFBA operon is influenced by translational coupling and Rho termination factor
    H Yakhnin
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Bacteriol 183:5918-26. 2001
    ..We found that TRAP-dependent formation of the SD blocking hairpin allows Rho access to the nascent transcript, causing transcriptional polarity...
  66. ncbi Transcription attenuation associated with bacterial repetitive extragenic BIME elements
    O Espeli
    Centre de Génétique Moléculaire du CNRS, Centre National de la Recherche Scientifique, Gif sur Yvette Cedex, F 91198, France
    J Mol Biol 314:375-86. 2001
    ..This attenuation phenomenon, together with the known ability of BIMEs to stabilize upstream mRNA, reveals how dispersion of these abundant repetitive elements may affect gene regulation at the genome level...
  67. ncbi Rho's role in transcription attenuation in the tna operon of E. coli
    Feng Gong
    Department of Biological Sciences, Stanford University, Stanford, California 94305 5020, USA
    Methods Enzymol 371:383-91. 2003
  68. ncbi Active site occupancy required for catalytic cooperativity by Escherichia coli transcription termination factor Rho
    Rebecca J Browne
    Department of Biochemistry and Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
    J Biol Chem 280:13300-3. 2005
    ..They further suggest that, once the enzyme is saturated with ATP, a V(max) enzyme conformation is achieved that is stable for at least three catalytic cycles...
  69. ncbi Catalytic cooperativity among subunits of Escherichia coli transcription termination factor Rho. Kinetics and substrate structural requirements
    Rebecca J Browne
    Department of Biochemistry and Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
    J Biol Chem 280:13292-9. 2005
    ..The results reinforce the importance of catalytic cooperativity in normal Rho function and suggest that several protein conformations exist along the catalytic pathway...
  70. ncbi Identification of a structural element that is essential for two functions of transcription factor NusG
    Lislott V Richardson
    Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
    Biochim Biophys Acta 1729:135-40. 2005
    ..This finding suggests that the mini-domain serves as a structural element for an interaction rather than as a site for residue-specific contacts...
  71. ncbi How Rho exerts its muscle on RNA
    John P Richardson
    Department of Chemistry, Indiana University, Bloomington, Indiana 47408, USA
    Mol Cell 22:711-2. 2006
    b>Rho factor in bacteria terminates transcription by using energy from ATP hydrolysis to forcefully dissociate the transcripts from RNA polymerase...
  72. pmc Mutations in the ATP-binding domain of Escherichia coli rho factor affect transcription termination in vivo
    A J Dombroski
    Department of Biochemistry, University of Rochester Medical Center, New York 14642
    J Bacteriol 172:2477-84. 1990
    ..the environment of the cell confirmed that transcription termination in vivo is indeed related to the ability of rho factor to properly hydrolyze nucleoside triphosphates, as would be predicted from results in vitro...
  73. pmc Ribosomal RNA antitermination in vitro: requirement for Nus factors and one or more unidentified cellular components
    C L Squires
    Department of Biological Sciences, Columbia University, New York, NY 10027
    Proc Natl Acad Sci U S A 90:970-4. 1993
    ..The DNA template requirements were the same as those previously established in vivo; transcription of a wild-type boxA sequence is both necessary and sufficient to promote RNA polymerase modification into a terminator-resistant form...
  74. ncbi Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin
    C L Chan
    Department of Biology, Washington University, St Louis, MO 63130
    J Mol Biol 233:25-42. 1993
    ..We suggest that electrostatic interaction between the pause hairpin and RNA polymerase, rather than disruption of an RNA:DNA heteroduplex, delays elongation at the his leader pause site...
  75. ncbi Kinetics of the RNA-DNA helicase activity of Escherichia coli transcription termination factor rho. 1. Characterization and analysis of the reaction
    K M Walstrom
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Biochemistry 36:7980-92. 1997
    ..Thus, rho can recycle and function as a catalytic helicase under reaction conditions resembling those found in the cell...
  76. ncbi Kinetics of the RNA-DNA helicase activity of Escherichia coli transcription termination factor rho. 2. Processivity, ATP consumption, and RNA binding
    K M Walstrom
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
    Biochemistry 36:7993-8004. 1997
    ..The implications of these results for models of rho helicase function and for the role of rho in termination are discussed...
  77. pmc Bicyclomycin sensitivity and resistance affect Rho factor-mediated transcription termination in the tna operon of Escherichia coli
    C Yanofsky
    Department of Biological Sciences, Stanford University, California 94305 5020, USA
    J Bacteriol 177:4451-6. 1995
    The growth-inhibiting drug bicyclomycin, known to be an inhibitor of Rho factor activity in Escherichia coli, was shown to increase basal level expression of the tryptophanase (tna) operon and to allow growth of a tryptophan auxotroph on ..
  78. ncbi NusG alters rho-dependent termination of transcription in vitro independent of kinetic coupling
    K W Nehrke
    Department of Biochemistry, University of Rochester Medical Center, NY 14642
    Gene Expr 3:119-33. 1993
    ..With the well-characterized trp t' terminator of E. coli, and no other proteins than E. coli RNA polymerase and rho factor, nusG causes a proximal shift in the terminated RNA endpoints, compared to the endpoints generated by rho alone...
  79. ncbi Bicyclomycin and dihydrobicyclomycin inhibition kinetics of Escherichia coli rho-dependent transcription termination factor ATPase activity
    H G Park
    Department of Chemistry, University of Houston, Texas 77204, USA
    Arch Biochem Biophys 323:447-54. 1995
    ..The observed loss of ATPase activity upon prolonged incubation of rho with excess purified bicyclomycin is attributed to the covalent modification of the protein by the antibiotic at multiple sites...
  80. ncbi An Escherichia coli gene (yaeO) suppresses temperature-sensitive mutations in essential genes by modulating Rho-dependent transcription termination
    S Pichoff
    Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, Toulouse, France
    Mol Microbiol 29:859-69. 1998
    ..Our data indicate that the suppression is not caused by overexpression of the mutated genes, but presumably by indirect stabilization of the mutated proteins...
  81. ncbi Mutations in an RNP1 consensus sequence of Rho protein reduce RNA binding affinity but facilitate helicase turnover
    C A Brennan
    Department of Biochemistry, University of Rochester, New York 14642
    J Biol Chem 266:17296-305. 1991
    ..Our results indicate that several different components of RNA interaction are required for rho activity and support a role for the RNP1 consensus region of rho in at least one specific aspect of RNA binding...
  82. pmc Structure of the DNA distal to the gene for ribosomal protein S20 in Escherichia coli K12: presence of a strong terminator and an IS1 element
    G A Mackie
    Nucleic Acids Res 14:6965-81. 1986
    ..Thus it seems unlikely that the distal copy of IS1 plays any role in the termination or stability of mRNA transcribed from the gene for S20...
  83. pmc Premature termination of in vivo transcription of a gene encoding a branched-chain amino acid transport protein in Escherichia coli
    R M Williamson
    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor 48109 0606
    J Bacteriol 174:1777-82. 1992
    ..repression of the LIV-I genes and harbor a temperature-sensitive allele for either leucyl-tRNA synthetase or Rho factor. Analysis of mRNA synthesis by DNA-RNA hybridization in the various mutant strains indicated that both shortages ..
  84. ncbi Evidence for the location of bicyclomycin binding to the Escherichia coli transcription termination factor Rho
    I Riba
    Michael Barber Centre for Mass Spectrometry, UMIST, P O Box 88, Manchester M60 1QD, United Kingdom
    J Biol Chem 273:34033-41. 1998
    ..These findings provide the first structural information concerning the site of Bcm binding in Rho...
  85. pmc Rho-dependent transcription termination in the tryptophanase operon leader region of Escherichia coli K-12
    V Stewart
    J Bacteriol 166:217-23. 1986
    ..In vivo termination appeared to occur at the rho-dependent termination sites identified in vitro. Transcription pausing analyses correlated sites of pausing in tnaL with sites of rho-dependent termination...
  86. ncbi The C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase is required for efficient rho-dependent transcription termination
    M Kainz
    Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI, 53706, USA
    J Mol Biol 284:1379-90. 1998
    ..We conclude that the alphaCTD is a target for interactions with NusA that influence both termination and pausing, but in addition it participates in rho-dependent transcription termination in a NusA-independent manner...
  87. pmc Autogenous regulation of the gene for transcription termination factor rho in Escherichia coli: localization and function of its attenuators
    Y Matsumoto
    J Bacteriol 166:945-58. 1986
    ..Brown, B. Albrechtsen, S. Pedersen, and P. Klemm, J. Mol. Biol. 162:283-298, 1982; C.-J. Lim, D. Geraghty, and J. A. Fuchs, J. Bacteriol. 163:311-316, 1985; B.J. Wallace and S.R. Kushner, Gene 32:399-408, 1984)...
  88. ncbi Reproducing tna operon regulation in vitro in an S-30 system. Tryptophan induction inhibits cleavage of TnaC peptidyl-tRNA
    F Gong
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    J Biol Chem 276:1974-83. 2001
    ..Catabolite repression regulates transcription initiation, whereas excess tryptophan induces antitermination at Rho factor-dependent termination sites in the leader region of the operon...
  89. pmc Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis in Escherichia coli K-12
    Y Yang
    Department of Microbiology and Molecular Genetics, University of Texas Houston Medical School, 77030 1501, USA
    J Bacteriol 180:1814-21. 1998
    ..pdxY is completely cotranscribed with tyrS, but about 92% of tyrS transcripts terminate at a putative Rho-factor-dependent attenuator located in the tyrS-pdxY intercistronic region...
  90. ncbi Analysis of the cbhE' plasmid gene from acute disease-causing isolates of Coxiella burnetii
    M F Minnick
    Department of Microbiology, Washington State University, Pullman 99164 4233
    Gene 103:113-8. 1991
    ..CbhE is predominantly hydrophilic with a predicted pI of 4.43. The function of CbhE is unknown. No nt or aa sequences with homology to cbhE' or CbhE, respectively, were found in searches of a number of data bases...
  91. pmc Evidence suggesting cis action by the TnaC leader peptide in regulating transcription attenuation in the tryptophanase operon of Escherichia coli
    K Gish
    Department of Biological Sciences, Stanford University, California 94305 5020, USA
    J Bacteriol 177:7245-54. 1995
    ..Elevated levels of tryptophan induce transcription antitermination at one or more Rho factor-dependent termination sites in the leader region of the operon...
  92. ncbi Characterization and expression of the cbbE' gene of Coxiella burnetii
    M F Minnick
    Department of Microbiology, Washington State University, Pullman 99164 4233
    J Gen Microbiol 136:1099-107. 1990
    ..burnetii, and is absent in chromosomal DNA and plasmids (QpH1, QpDG) from other isolates of C. burnetii. A search of various DNA and amino acid sequence data bases revealed no homologies to cbbE'...
  93. pmc tRNA(Trp) translation of leader peptide codon 12 and other factors that regulate expression of the tryptophanase operon
    P Gollnick
    Department of Biological Sciences, Stanford University, California 94305 5020
    J Bacteriol 172:3100-7. 1990
    ..Deletion of a potential site for Rho factor utilization just beyond tnaC also results in partial constitutive expression...
  94. ncbi A Rho-dependent phase-variable transcription terminator controls expression of the FimE recombinase in Escherichia coli
    Susan A Joyce
    Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
    Mol Microbiol 45:1107-17. 2002
    ..In the absence of Rho factor, fimE mRNA is equally stable in phase ON and phase OFF cells, and the levels of FimE recombinase are also equal.
  95. pmc The mechanism of tryptophan induction of tryptophanase operon expression: tryptophan inhibits release factor-mediated cleavage of TnaC-peptidyl-tRNA(Pro)
    F Gong
    Department of Biological Sciences, Stanford University, Stanford, CA 94305 and Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedal, Minato ku, Tokyo 108 8639, Japan
    Proc Natl Acad Sci U S A 98:8997-9001. 2001
    ..The associated translating ribosome therefore remains attached to the leader transcript where it blocks Rho factor binding and subsequent transcription termination.
  96. pmc Ribosome recycling factor and release factor 3 action promotes TnaC-peptidyl-tRNA Dropoff and relieves ribosome stalling during tryptophan induction of tna operon expression in Escherichia coli
    Ming Gong
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    J Bacteriol 189:3147-55. 2007
    ..This stalled ribosome blocks Rho factor binding and action, preventing transcription termination in the tna operon's leader region...
  97. pmc Escherichia coli rpiA gene encoding ribose phosphate isomerase A
    B Hove-Jensen
    Department of Biological Chemistry, University Institute of Molecular Biology, Copenhagen K, Denmark
    J Bacteriol 175:5628-35. 1993
    ..within an adenylate-rich sequence following a guanylate-cytidylate-rich stem-loop structure resembling a rho factor-independent transcription terminator...
  98. ncbi Sample size calculation for multicenter randomized trial: taking the center effect into account
    Emilie Vierron
    INSERM CIC 202, Universite Francois Rabelais, Tours, CHRU de Tours, France
    Contemp Clin Trials 28:451-8. 2007
    ..This work allows for adjusting and reducing the sample size according to the magnitude of the center effect and leads to a better consistency in the conduct of multicenter randomized trials...
  99. doi A NusE:NusG complex links transcription and translation
    Björn M Burmann
    Lehrstuhl Biopolymere und Forschungszentrum für Bio Makromoleküle, Universitat Bayreuth, Universitatsstrasse 30, 95447 Bayreuth, Germany
    Science 328:501-4. 2010
    ..of transcription and translation at the ends of bacterial operons enables transcription termination by Rho factor, and competition between ribosomal NusE and Rho for NusG helps to explain why Rho cannot terminate translated ..
  100. ncbi Transcription termination: sequence and function of the rho-independent tL3 terminator in the major leftward operon of bacteriophage lambda
    K C Luk
    Gene 17:247-58. 1982
    ..Is is also active in vitro, both in the presence or absence of the rho factor. The termination point is located at 4320 bp to the left of the SL startpoint of the PL-RNA, just downstream of ..
  101. pmc Nucleotide sequence of human rho cDNA clone 12
    P Yeramian
    Nucleic Acids Res 15:1869. 1987

Research Grants37

  1. STRUCTURE AND RELATIONS OF PROTEINS AND NUCLEIC ACIDS
    PETER VON HIPPEL; Fiscal Year: 2005
    ..abstract_text> ..
  2. STRUCTURE AND RELATIONS OF PROTEINS AND NUCLEIC ACIDS
    PETER VON HIPPEL; Fiscal Year: 2007
    ....
  3. STRUCTURE AND RELATIONS OF PROTEINS AND NUCLEIC ACIDS
    PETER HANS VON HIPPEL; Fiscal Year: 2010
    ..abstract_text> ..
  4. STRUCTURE AND RELATIONS OF PROTEINS AND NUCLEIC ACIDS
    PETER VON HIPPEL; Fiscal Year: 2009
    ..abstract_text> ..
  5. Novel Methods to Identify Targets of the Neurological Agent (R)-Lacosamide
    Harold Kohn; Fiscal Year: 2009
    ..Delineation of these sites will provide a basis for understanding the mechanism of (R)-2 function and maximizing its therapeutic potential and may provide new information for the control of both neurological disorders. ..
  6. Novel Methods to Identify Targets of the Neurological Agent (R)-Lacosamide
    Harold Kohn; Fiscal Year: 2007
    ..Delineation of these sites will provide a basis for understanding the mechanism of (R)-2 function and maximizing its therapeutic potential and may provide new information for the control of both neurological disorders. ..
  7. Rho-Dependent COX-2 Expression in Intestinal Cells
    Lee Slice; Fiscal Year: 2007
    ..3) Define the role of Rho and of Protein Kinases acting upstream and downstream of Rho in COX-2 expression in intestinal epithelial cells. 4) Characterize COX-2 promoter elements that are responsive to Rho. ..
  8. Rho-Dependent COX-2 Expression in Intestinal Cells
    Lee Slice; Fiscal Year: 2007
    ..RESEARCH GRANT TABLE OF CONTENTS Page Numbers Face Page .................................................................................................................................................. 1 Description, ..
  9. Mycobacterium tuberculosis in vivo gene expression
    James Graham; Fiscal Year: 2005
    ..Understanding the roles of such differentially expressed genes will further define host-pathogen interactions in human disease, and allow development of new tools to reduce the enormous global impact of tuberculosis on mankind. ..
  10. MODE OF ACTION OF BICYCLOMYCIN
    Harold Kohn; Fiscal Year: 2003
    ..These investigations will provide the molecular basis to define novel pathways for bacterial control. ..