hupB

Summary

Gene Symbol: hupB
Description: HU, DNA-binding transcriptional regulator, beta subunit
Alias: ECK0434, JW0430, dpeA, hopD
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. ncbi The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids
    Anna Balandina
    Laboratoire de Physiologie Bacterienne, CNRS UPR 9073, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    J Biol Chem 277:27622-8. 2002
  2. pmc The Escherichia coli histone-like protein HU affects DNA initiation, chromosome partitioning via MukB, and cell division via MinCDE
    A Jaffe
    Institut Jacques Monod Centre National de la Recherche Scientifique, Universite Paris 7, France
    J Bacteriol 179:3494-9. 1997
  3. pmc Repressor induced site-specific binding of HU for transcriptional regulation
    T Aki
    Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 4255, USA
    EMBO J 16:3666-74. 1997
  4. pmc The binding motif recognized by HU on both nicked and cruciform DNA
    D Kamashev
    Laboratoire de Physiologie Bacterienne, CNRS, UPR 9073, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    EMBO J 18:5434-44. 1999
  5. pmc Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid
    T Ali Azam
    Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
    J Bacteriol 181:6361-70. 1999
  6. ncbi Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate
    B D Lavoie
    Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
    Cell 85:761-71. 1996
  7. ncbi Protein HU binds specifically to kinked DNA
    A Pontiggia
    Istituto Scientifico Ospedale San Raffaele, Milano, Italy
    Mol Microbiol 7:343-50. 1993
  8. ncbi DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA
    E Bonnefoy
    Institut de Biologie Physico Chimique, Paris, France
    J Mol Biol 242:116-29. 1994
  9. pmc Evidence for involvement of proteins HU and RpoS in transcription of the osmoresponsive proU operon in Escherichia coli
    D Manna
    Centre for Cellular and Molecular Biology, Hyderabad, India
    J Bacteriol 176:5378-84. 1994
  10. ncbi HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps
    B Castaing
    Groupe Reparation des lesions Radio et Chimio Induites, URA 147, CNRS, Institut Gustave Roussy, Villejuif, France
    J Biol Chem 270:10291-6. 1995

Research Grants

  1. Repair of Clustered DNA Damages
    YOKE KOW; Fiscal Year: 2008
  2. Repair of Clustered DNA Damages
    Yoke W Kow; Fiscal Year: 2010

Scientific Experts

  • John van Noort
  • Remus Th Dame
  • Nicholas Delihas
  • C J Dorman
  • Kathleen Sandman
  • Jacques Oberto
  • Junseock Koh
  • YOKE KOW
  • J Rouviere-Yaniv
  • Nicole A Becker
  • Sankar Adhya
  • Dmitri Kamashev
  • Ishita Mukerji
  • Ana I Prieto
  • Kristi Wojtuszewski
  • Norbert Garnier
  • Anna Balandina
  • Josette Rouviere-Yaniv
  • O V Preobrazhenskaia
  • Matej Butala
  • Hongkai Bi
  • T A Azam
  • D Kamashev
  • Luke Czapla
  • James M Benevides
  • Sundari Chodavarapu
  • Jason D Kahn
  • L James Maher
  • Tumpa Sarkar
  • Fusheng Guo
  • Bertrand Castaing
  • Franck Coste
  • Ashley B Williams
  • T Aki
  • Martijn S Luijsterburg
  • Akio Kuroda
  • A Balandina
  • Sudeshna Kar
  • Szabolcs Semsey
  • A Ishihama
  • Kerren K Swinger
  • Haribabu Arthanari
  • Mitsumasa Hashimoto
  • Jean Ramstein
  • Giuseppe Lia
  • Nancy Trun
  • Valorie T Ryan
  • V L Karpov
  • Pilar Morales
  • Mara Giangrossi
  • L Claret
  • Christina Kahramanoglou
  • H Lee
  • Gillian M Fraser
  • Ruhi M Ali
  • Nicholas M Luscombe
  • Aswin S N Seshasayee
  • Karine Loth
  • Rafal Augustyniak
  • Christian Damblon
  • Virginie Nadan
  • N Perez
  • S Adhya
  • Stephen J W Busby
  • David J Lee
  • Toshihiko Fukamachi
  • Hiromi Saito
  • Lianle Sun
  • Hiroshi Kobayashi
  • Jon M Kaguni
  • T Ali Azam
  • George J Thomas
  • David Swigon
  • E V Krolenko
  • Magdalena M Felczak
  • Jessica Kawakami
  • Jessica Danahy
  • Josette Rouvière Yaniv
  • Paola B Arimondo
  • Alexey K Mazur
  • Wilma K Olson
  • Iulia Vitoc
  • Patricia L Foster
  • Nicholas V Hud
  • H Ohtake
  • K Nomura
  • N Takiguchi
  • Maarten C Noom
  • Gijs J L Wuite
  • J Kato

Detail Information

Publications80

  1. ncbi The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids
    Anna Balandina
    Laboratoire de Physiologie Bacterienne, CNRS UPR 9073, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    J Biol Chem 277:27622-8. 2002
    ....
  2. pmc The Escherichia coli histone-like protein HU affects DNA initiation, chromosome partitioning via MukB, and cell division via MinCDE
    A Jaffe
    Institut Jacques Monod Centre National de la Recherche Scientifique, Universite Paris 7, France
    J Bacteriol 179:3494-9. 1997
    Escherichia coli hupA hupB double mutants, lacking both subunits (HU1 and HU2) of the histone-like protein HU, accumulate secondary mutations...
  3. pmc Repressor induced site-specific binding of HU for transcriptional regulation
    T Aki
    Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 4255, USA
    EMBO J 16:3666-74. 1997
    ..The example of gal repression provides a model for studying how a 'condensed' DNA becomes available for transcription...
  4. pmc The binding motif recognized by HU on both nicked and cruciform DNA
    D Kamashev
    Laboratoire de Physiologie Bacterienne, CNRS, UPR 9073, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    EMBO J 18:5434-44. 1999
    ..The HU binding motif present in both structures is a pair of inclined DNA helices...
  5. pmc Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid
    T Ali Azam
    Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
    J Bacteriol 181:6361-70. 1999
    ..These changes in the composition of nucleoid-associated proteins in the stationary phase are accompanied by compaction of the genome DNA and silencing of the genome functions...
  6. ncbi Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate
    B D Lavoie
    Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
    Cell 85:761-71. 1996
    ..The data, which directly localize selected HU amino acids with respect to DNA in the transpososome, were used as constraints for computer-based molecular modeling to derive the first snapshot of an HU-DNA interaction...
  7. ncbi Protein HU binds specifically to kinked DNA
    A Pontiggia
    Istituto Scientifico Ospedale San Raffaele, Milano, Italy
    Mol Microbiol 7:343-50. 1993
    ..All these properties are analogous to the properties of the mammalian chromatin protein HMG1. We suggest that HU is a prokaryotic HMG1-like protein rather than a histone-like protein...
  8. ncbi DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA
    E Bonnefoy
    Institut de Biologie Physico Chimique, Paris, France
    J Mol Biol 242:116-29. 1994
    ..These results support a model where two HU-protein dimers specifically bind to two equivalent angles present opposite each other in the four-way-junction-DNA structure with almost no dimer-dimer interactions...
  9. pmc Evidence for involvement of proteins HU and RpoS in transcription of the osmoresponsive proU operon in Escherichia coli
    D Manna
    Centre for Cellular and Molecular Biology, Hyderabad, India
    J Bacteriol 176:5378-84. 1994
    ..The dpeA locus was allelic to hupB, which along with hupA encodes the nucleoid protein HU...
  10. ncbi HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps
    B Castaing
    Groupe Reparation des lesions Radio et Chimio Induites, URA 147, CNRS, Institut Gustave Roussy, Villejuif, France
    J Biol Chem 270:10291-6. 1995
    ..Furthermore, the GDB protein is not detected in the crude extract of an E. coli double mutant strain hupA hupB that has no functional HU protein. These results led us to identify the GDB protein as the HU protein...
  11. ncbi Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid
    T A Azam
    Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
    Genes Cells 5:613-26. 2000
    ..The intracellular localization of these proteins in E. coli could be predicted from these data, but no attempt has been made thus far to directly observe the intracellular distribution of the DNA-binding proteins...
  12. pmc The histone-like protein HU binds specifically to DNA recombination and repair intermediates
    D Kamashev
    Laboratoire de Physiologie Bacterienne, CNRS, UPR 9073, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    EMBO J 19:6527-35. 2000
    ..Both structural motifs are recognized by HU at least 1000-fold more avidly than duplex DNA...
  13. pmc The histone-like protein HU does not obstruct movement of T7 RNA polymerase in Escherichia coli cells but stimulates its activity
    Pilar Morales
    Laboratoire de Physiologie Bactérienne CNRS, UPR 9073, Institut de Biologie Physico Chimique, 75005 Paris, France
    J Bacteriol 184:1565-70. 2002
    ..Thus, in contrast to eukaryotic nucleosomes, HU does not impair T7 RNAP activity but has a stimulatory effect. Finally, our results suggest that HU can also influence mRNA stability in vivo...
  14. ncbi HU: promoting or counteracting DNA compaction?
    Remus Thei Dame
    Laboratory of Molecular Genetics, Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P O Box 9502, 2300 RA, Leiden, The Netherlands
    FEBS Lett 529:151-6. 2002
    ..The protein is likely to play an architectural role, but instead of being responsible for DNA compaction it could be involved in antagonising compaction by other proteins such as H-NS...
  15. pmc Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping
    Giuseppe Lia
    Department of Biology, University of Milan, 20133 Milan, Italy
    Proc Natl Acad Sci U S A 100:11373-7. 2003
    ..Such topological intermediates may operate similarly in other multiprotein complexes of transcription, replication, and recombination...
  16. pmc Dual architectural roles of HU: formation of flexible hinges and rigid filaments
    John van Noort
    Molecular Biophysics, Kavli Institute of Nanoscience, Delft University of Technology, NL 2628 CJ, Delft, The Netherlands
    Proc Natl Acad Sci U S A 101:6969-74. 2004
    ..At higher HU concentrations, a rigid nucleoprotein filament is formed in which HU appears to arrange helically around the DNA without inducing significant condensation...
  17. ncbi The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin
    Remus T Dame
    Physics of Complex Systems, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
    Mol Microbiol 56:858-70. 2005
    ..Many of these new insights can be attributed to the use of recently developed biophysical techniques...
  18. pmc HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments
    E Bonnefoy
    Laboratoire de Physiologie Bacterienne, Institut de Biologie Physico Chimique, Paris, France
    EMBO J 10:687-96. 1991
    ..coli (IHF) form different structures with the same DNA fragments. Moreover, HU seems to enhance the DNA-binding capacity of IHF to a DNA fragment which does not contain its consensus sequence...
  19. pmc Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling
    Fusheng Guo
    Laboratory of Molecular Biology, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892 4264, USA
    Proc Natl Acad Sci U S A 104:4309-14. 2007
    ....
  20. pmc Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli
    Nicole A Becker
    Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St SW, Rochester, MN 55905, USA
    Nucleic Acids Res 35:3988-4000. 2007
    ..These results suggest that host nucleoid proteins can directly facilitate or inhibit DNA looping in bacteria...
  21. doi Mechanisms of specific and nonspecific binding of architectural proteins in prokaryotic gene regulation
    James M Benevides
    School of Biological Sciences, University of MissouriKansas City, 5100 Rockhill Road, Kansas City, Missouri 64110 2499, USA
    Biochemistry 47:3855-62. 2008
    ....
  22. pmc The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
    Jacques Oberto
    Laboratoire de Physiologie Bacterienne, CNRS, UPR 9073, Institut de Biologie Physico Chimique, Paris, France
    PLoS ONE 4:e4367. 2009
    ..It can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Cells lacking HU grow very poorly and display many phenotypes...
  23. ncbi The Escherichia coli histone-like protein HU regulates rpoS translation
    A Balandina
    Laboratoire de Physiologie Bacterienne, CNRS, UPR 9073, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    Mol Microbiol 39:1069-79. 2001
    ..We demonstrate here that HU, an abundant DNA-binding, histone-like protein, is able specifically to recognize an RNA molecule and therefore play a role in post-transcriptional regulation...
  24. ncbi IHF and HU: flexible architects of bent DNA
    Kerren K Swinger
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
    Curr Opin Struct Biol 14:28-35. 2004
    ..These techniques include time-resolved synchrotron X-ray footprinting, differential scanning calorimetry, isothermal titration calorimetry and single-molecule experiments...
  25. ncbi Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity
    T A Azam
    Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
    J Biol Chem 274:33105-13. 1999
    ....
  26. pmc Nucleoid remodeling by an altered HU protein: reorganization of the transcription program
    Sudeshna Kar
    Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 4264, USA
    Proc Natl Acad Sci U S A 102:16397-402. 2005
    ..We propose that, as in eukaryotes, the nucleoid architecture dictates the global transcription profile and, consequently, the behavior pattern in bacteria...
  27. ncbi The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective
    Martijn S Luijsterburg
    Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
    J Struct Biol 156:262-72. 2006
    ..In this review, we provide an overview of the major nucleoid-associated proteins from a structural perspective and we discuss their possible roles in dynamically shaping the bacterial nucleoid...
  28. ncbi Native Escherichia coli HU protein is a heterotypic dimer
    J Rouviere-Yaniv
    FEBS Lett 106:297-300. 1979
  29. ncbi Regulation of HU alpha and HU beta by CRP and FIS in Escherichia coli
    L Claret
    Institute de Biologie Physico Chimique, Laboratoire de Physiologie Bacterienne, Paris, France
    J Mol Biol 263:126-39. 1996
    ..abundant DNA binding proteins of Escherichia coli, is encoded by two closely related but unlinked genes, hupA and hupB. Overproduction of one or the other of the subunits has been shown to induce the SOS response and mucoidy...
  30. ncbi Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure
    Jean Ramstein
    Centre de Biophysique Moleculaire, CNRS, Affiliated to the University of Orleans, rue Charles Sadron, 45071 Orleans Cedex 02, France
    J Mol Biol 331:101-21. 2003
    ..coli cold-shock adaptation. Besides, I(2) might be required in E.coli for the HU chain exchange, which allows the heterodimer formation from homodimers...
  31. ncbi IHF and HU stimulate assembly of pre-replication complexes at Escherichia coli oriC by two different mechanisms
    Valorie T Ryan
    Department of Biological Services, Florida Institute of Technology, 150 W University Blvd, Melbourne, Florida 32901, USA
    Mol Microbiol 46:113-24. 2002
    ..HU did not redistribute DnaA, but suppressed binding specifically at I3. These results suggest that different pathways mediated by bacterial chromatin proteins exist to regulate pre-RC assembly and unwind oriC...
  32. pmc Preferential binding of E.coli histone-like protein HU alpha to negatively supercoiled DNA
    H Shindo
    Tokyo College of Pharmacy, Japan
    Nucleic Acids Res 20:1553-8. 1992
    ..It was suggested that HU in vivo interacts preferentially with the regions deformed under torsional stress or with the metabolically active regions along DNA...
  33. ncbi Selective expression of the beta-subunit of nucleoid-associated protein HU during cold shock in Escherichia coli
    Mara Giangrossi
    Laboratory of Genetics, Department of Biology MCA, University of Camerino, Camerino MC, Italy
    Mol Microbiol 44:205-16. 2002
    Expression of Escherichia coli hupA and hupB, the structural genes encoding the most abundant nucleoid-associated proteins HUalpha and HUbeta has been studied during cold shock...
  34. pmc A functional assay in Escherichia coli to detect non-assisted interaction between galactose repressor dimers
    N Perez
    Equipe Interactions à Distance, CNRS UMR 8532, Institut Gustave Roussy PR2, 39 rue Camille Desmoulins, 94 805 Villejuif Cedex, France
    Nucleic Acids Res 28:3600-4. 2000
    ..Furthermore, the assay may be generalised to detection of rather weak cooperative interactions between DNA-bound proteins...
  35. ncbi Construction and characterization of the deletion mutant of hupA and hupB genes in Escherichia coli
    M Wada
    Laboratory of Molecular Genetics, RIKEN Tsukuba Life Science Center, Ibaraki, Japan
    J Mol Biol 204:581-91. 1988
    Insertion and deletion mutations of the hupB and hupA genes, which encode the HU-1 and HU-2 proteins, respectively, of Escherichia coli, have been constructed in vitro and transferred to the hup loci on the bacterial chromosome...
  36. pmc HU, the major histone-like protein of E. coli, modulates the binding of IHF to oriC
    E Bonnefoy
    Laboratoire de Physiologie Bacterienne, Institut de Biologie Physico Chimique, Paris, France
    EMBO J 11:4489-96. 1992
    ..In addition, we show that HU can modulate the binding of IHF to its specific oriC site. Depending on the relative concentrations of HU and IHF, HU is able either to activate or to inhibit the binding of IHF to oriC...
  37. pmc Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12
    Ana I Prieto
    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    Nucleic Acids Res 40:3524-37. 2012
    ..Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms...
  38. pmc Alterations of the outer membrane composition in Escherichia coli lacking the histone-like protein HU
    E Painbeni
    Unité Propre de Recherche 7090, Centre National de la Recherche Scientifique, Laboratoire de Physiologie Bacterienne, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    Proc Natl Acad Sci U S A 94:6712-7. 1997
    ..These findings demonstrate a novel link between a bacterial chromosomal protein and the outer membrane composition...
  39. ncbi Promoters and autogenous control of the Escherichia coli hupA and hupB genes
    K Kohno
    Department of Molecular Genetics, Kyoto Pharmaceutical University, Japan
    J Mol Biol 213:27-36. 1990
    Three start sites and a single start site for transcription of the hupB and hupA genes, respectively, have been identified in Escherichia coli...
  40. pmc DNA trajectory in the Gal repressosome
    Szabolcs Semsey
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genes Dev 18:1898-907. 2004
    ..In this structure the center of the HU-binding site is located at the apex of the DNA loop. The approach reported here can be used to distinguish between otherwise indistinguishable DNA trajectories in complex nucleoprotein machines...
  41. pmc The HU-DNA binding interaction probed with UV resonance Raman spectroscopy: structural elements of specificity
    Kristi Wojtuszewski
    Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459 0175, USA
    Protein Sci 13:2416-28. 2004
    ..These and other results suggest that protein-induced bending plays an important role in HU site-specific binding and supports a model of a mutually induced fit...
  42. ncbi [Assays on comparing the local concentration of HU protein in the different regions of Escherichia coli genomic DNA]
    O V Preobrazhenskaia
    Mol Biol (Mosk) 39:678-86. 2005
    ..coli genome: oriC region, promoter and structural regions of hupA and hupB genes coding two different subunits of HU, and structural parts of dps and glgS genes which are active only in ..
  43. ncbi HU and IHF: similarities and differences. In Escherichia coli, the lack of HU is not compensated for by IHF
    F Boubrik
    Laboratoire de Physiologie Bacterienne, Institut de Biologie Physico Chimique, Paris
    Res Microbiol 142:239-47. 1991
    ....
  44. pmc Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines
    Tumpa Sarkar
    School of Chemistry and Biochemistry, Parker H Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332 0400, USA
    Nucleic Acids Res 35:951-61. 2007
    ..Our demonstration that HU governs DNA condensation in vitro also suggests a mechanism by which HU could act as an architectural protein for bacterial chromosome compaction and organization in vivo...
  45. pmc The Escherichia coli histone-like protein HU has a role in stationary phase adaptive mutation
    Ashley B Williams
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Genetics 177:723-35. 2007
    ..Additionally, HU mutations inhibit growth-dependent mutations without a reduction in the level of Pol IV. These effects of HU mutations on adaptive mutation and on growth-dependent mutations reveal novel functions for HU in mutagenesis...
  46. doi Escherichia coli DnaA interacts with HU in initiation at the E. coli replication origin
    Sundari Chodavarapu
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 1319, USA
    Mol Microbiol 67:781-92. 2008
    ..The greater activity of the alpha dimer of HU at oriC may stimulate initiation during early log phase compared with the lesser activity of the alphabeta heterodimer or the beta dimer...
  47. pmc DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA--protein complex on intact, linear duplex DNA
    Junseock Koh
    Program in Biophysics, University of Wisconsin, Madison WI 53706, USA
    J Mol Biol 383:324-46. 2008
    ..In particular, it explains how HU condenses or extends DNA depending on the relative concentrations of HU and DNA...
  48. doi HU participates in expression of a specific set of genes required for growth and survival at acidic pH in Escherichia coli
    Hongkai Bi
    Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
    Curr Microbiol 58:443-8. 2009
    ..histone-like Escherichia coli protein, HU, is composed of alpha and beta subunits respectively encoded by hupA and hupB in Escherichia coli...
  49. pmc DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes
    Matej Butala
    School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
    Nucleic Acids Res 37:e37. 2009
    ..We illustrate the method by investigating the proteins bound to the colicin K gene regulatory region, either before or after induction of the colicin K gene promoter...
  50. doi Nucleoid-associated proteins and bacterial physiology
    Charles J Dorman
    Department of Microbiology, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland
    Adv Appl Microbiol 67:47-64. 2009
    ....
  51. doi An alternative flexible conformation of the E. coli HUβ₂ protein: structural, dynamics, and functional aspects
    Norbert Garnier
    Centre de Biophysique Moléculaire CNRS, UPR4301, University of Orleans, rue Charles Sadron, 45071 Orleans Cedex 02, France
    Eur Biophys J 40:117-29. 2011
    ..On the basis of these data, a realistic 3D model is proposed for the major I₂ conformation of EcHUβ₂. This model is in agreement with previous experimental data...
  52. pmc Nonspecific DNA binding and bending by HUαβ: interfaces of the three binding modes characterized by salt-dependent thermodynamics
    Junseock Koh
    Program in Biophysics, University of Wisconsin Madison, Madison, WI 53706, USA
    J Mol Biol 410:241-67. 2011
    ..Structural models consistent with the observed Sk(i) values are proposed...
  53. pmc Effects of HU binding on the equilibrium cyclization of mismatched, curved, and normal DNA
    Haribabu Arthanari
    Chemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut, USA
    Biophys J 86:1625-31. 2004
    ..These results have been considered along with those previously obtained to refine a model for the interaction of HU with duplex DNA...
  54. ncbi Cloning and sequencing of the HU-2 gene of Escherichia coli
    Y Kano
    Laboratory of Molecular Genetics, RIKEN Tsukuba Life Science Center, Ibaraki, Japan
    Mol Gen Genet 209:408-10. 1987
    ..The nucleotide sequence has a possible promoter and a typical ribosomal binding site upstream of the translation initiation codon (AUG) and a possible rho-independent terminater site downstream of the termination codon (UAA) of the gene...
  55. ncbi Primary structures of two homologous ribosome-associated DNA-binding proteins of Escherichia coli
    L Mende
    FEBS Lett 96:395-8. 1978
  56. ncbi Genetic characterization of the gene hupB encoding the HU-1 protein of Escherichia coli
    Y Kano
    Gene 45:37-44. 1986
    The gene hupB encoding the HU-1(HU beta) protein of Escherichia coli was mapped between proC at min 9 and minA at min 10 on the K-12 genome by plasmid integration and chromosome transfer studies...
  57. ncbi Complete amino-acid sequences of DNA-binding proteins HU-1 and HU-2 from Escherichia coli
    B Laine
    Eur J Biochem 103:447-61. 1980
    ..No sequence homology could be established between the proteins HU-1 and HU-2 and any one of the five histones from different eukaryotes...
  58. ncbi [Immunochemical detection of the histone-like bacterial protein Hu in covalently bound DNA-protein complexes, obtained in vitro and in vivo]
    E V Krolenko
    Institute de Biologie Physico Chimique, Paris, France
    Mol Biol (Mosk) 33:442-6. 1999
  59. ncbi MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors
    N Delihas
    Department of Molecular Genetics and Microbiology School of Medicine, SUNY, Stony Brook, NY 11794 5222, USA
    J Mol Biol 313:1-12. 2001
    ..The crystal structure of one these transcriptional activators, Rob, complexed with the micF promoter has been reported. Here, we review new developments in the micF regulatory network...
  60. pmc Atomic force microscopic demonstration of DNA looping by GalR and HU
    Y L Lyubchenko
    Department of Microbiology, Arizona State University, Tempe 85287 2701, USA
    Nucleic Acids Res 25:873-6. 1997
    ..Supercoiling of DNA, which is also critical for GalR action, may stabilize the DNA loops by providing an energetically favorable geometry of the DNA...
  61. ncbi Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria
    C J Dorman
    Dept of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Ireland
    Trends Microbiol 7:124-8. 1999
    ..Thus, functional modulation of H-NS and StpA by one another and by other proteins with appropriate interaction domains is possible. This has implications for bacterial pathogenesis and adaptation to environmental stress...
  62. ncbi Genetic characterization of the gene hupA encoding the HU-2 protein of Escherichia coli
    Y Kano
    Laboratory of Molecular Genetics, Tsukuba Life Science Center, Institute of Physical and Chemical Research, Ibaraki, Japan
    Gene 69:331-5. 1988
    ..The rpoBC is located approximately 10 kb proximal to the hupA gene, and rrnE about 8 kb distal to it. Thus, the direction of hupA gene transcription is clockwise on the E. coli map [Bachmann B.J., Microbiol. Rev. 47 (1983) 180-230]...
  63. ncbi Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome
    K Sandman
    Department of Microbiology, Ohio State University, Columbus 43210, USA
    Cell Mol Life Sci 54:1350-64. 1998
    ....
  64. ncbi HU protein of Escherichia coli has a role in the repair of closely opposed lesions in DNA
    Mitsumasa Hashimoto
    Department of Radiation Oncology, Emory University, Atlanta, Georgia 30303, USA
    J Biol Chem 278:28501-7. 2003
    ..coli DNA polymerase and E. coli DNA ligase, respectively. The nick-dependent selective inhibition of endonuclease III activity by HU protein suggests that HU could play a role in reducing the formation of double strand breaks in E. coli...
  65. ncbi Folding chromosomes in bacteria: examining the role of Csp proteins and other small nucleic acid-binding proteins
    Nancy Trun
    Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
    Curr Top Dev Biol 55:173-201. 2003
  66. ncbi Molecular cloning and nucleotide sequence of the HU-1 gene of Escherichia coli
    Y Kano
    Mol Gen Genet 201:360-2. 1985
    ..The nucleotide sequence has a possible promoter and a typical ribosomal binding site upstream from the translational initiation codon (GUG) of the HU-1 gene...
  67. ncbi HU-1 mutants of Escherichia coli deficient in DNA binding
    N Goshima
    Department of Molecular Genetics, Kyoto Pharmaceutical University, Japan
    Gene 96:141-5. 1990
    We constructed four mutants of the Escherichia coli hupB gene, encoding HU-1 protein, by synthetic oligodeoxyribonucleotide-directed, site-specific mutagenesis on M13mp18 vectors...
  68. ncbi Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by GAL repressor
    T Aki
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 4255, USA
    Genes Cells 1:179-88. 1996
    ..In a purified system, GalR, nevertheless, fails to show the coordinated repression, predicting the participation of an additional factor(s) in the regulation in vivo...
  69. pmc Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations
    Luke Czapla
    Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Wright Rieman Laboratories, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
    J Mol Biol 382:353-70. 2008
    ..The local bending and undertwisting of DNA by HU, in combination with the number of bound proteins, provide a structural rationale for the condensation of DNA and the observed expression levels of reporter genes in vivo...
  70. pmc Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation
    Nicole A Becker
    Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St SW, Rochester, MN 55905, USA
    Nucleic Acids Res 36:4009-21. 2008
    ..coli expressing normal levels of HU protein. Nhp6A-induced changes in the DNA length-dependence of repression efficiency suggest that Nhp6A alters DNA twist in vivo. In contrast, human HMGB2-box A derivatives did not rescue looping...
  71. ncbi The amino- and carboxy-terminal amino acid sequences of protein HU from Escherichia coli
    B Laine
    FEBS Lett 89:116-20. 1978
  72. pmc HU binds and folds single-stranded DNA
    Dmitri Kamashev
    Laboratoire de Physiologie Bacterienne, CNRS UPR 9073, Laboratoire de Biochimie Theorique, CNRS UPR 9080, Paris, France
    Nucleic Acids Res 36:1026-36. 2008
    ..Furthermore HU has a strong preference for poly(dG), while binding to poly(dA) is the weakest. HU binding to ssDNA is probably important for its capacity to cover and protect bacterial DNA both intact and carrying lesions...
  73. pmc Escherichia coli HU protein has a role in the repair of abasic sites in DNA
    Yoke W Kow
    Department of Radiation Oncology, Emory University School of Medicine, Clifton Road NE, Atlanta, GA 30322, USA
    Nucleic Acids Res 35:6672-80. 2007
    ..The function of HU protein as an AP lyase was confirmed by the ability of hupA or hupB mutations to further reduce the viability of an E...
  74. ncbi Expression of the seqA gene is negatively modulated by the HU protein in Escherichia coli
    H Lee
    Institute for Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Korea
    Mol Gen Genet 264:931-5. 2001
    ..These results suggest that the HU protein functions as a negative modulator of seqA expression...
  75. ncbi Inorganic polyphosphate stimulates lon-mediated proteolysis of nucleoid proteins in Escherichia coli
    Akio Kuroda
    Department of Molecular Biotechnology, Hiroshima University, Hiroshima, Japan
    Cell Mol Biol (Noisy-le-grand) 52:23-9. 2006
    ..Fusions of green fluorescent protein with HimA, Fis, HupA, and HupB were clearly associated with polyP in vivo...
  76. pmc Construction and characterization of mutations in hupB, the gene encoding HU-beta (HU-1) in Escherichia coli K-12
    D R Storts
    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637
    J Bacteriol 170:1541-7. 1988
    ..A kanamycin resistance cassette was used in the construction of insertion and deletion mutations in hupB, the gene encoding HU-beta on plasmid pJMC21...
  77. ncbi Participation of the histone-like protein HU and of IHF in minichromosomal maintenance in Escherichia coli
    Y Kano
    Department of Molecular Genetics, Kyoto Pharmaceutical University, Japan
    Gene 103:25-30. 1991
    The closely related Escherichia coli genes, hupA, hupB, himA and himD (hip), encode the bacterial histone-like protein subunits, HU-2, HU-1, IHF chi and IHF beta, respectively. We report here that E. coli minichromosomes [plasmids (2.7-12...
  78. ncbi Maintenance of plasmids in HU and IHF mutants of Escherichia coli
    T Ogura
    Department of Molecular Genetics, Kumamoto University Medical School, Japan
    Mol Gen Genet 220:197-203. 1990
    ..1988), had mutations in the hupB gene, and that the hopD410 mutation was an ochre mutation at the 5th Gln position of HU-1...

Research Grants2

  1. Repair of Clustered DNA Damages
    YOKE KOW; Fiscal Year: 2008
    ..Completion of these three aims is expected to provide significant understanding on how cells process tandem lesions and the biological consequences of incompletely repaired tandem lesions. ..
  2. Repair of Clustered DNA Damages
    Yoke W Kow; Fiscal Year: 2010
    ..In addition, it will provide significant insight as to the potential mechanism involved in melanoma progression. ..