Genomes and Genes
Gene Symbol: hupB
Description: HU, DNA-binding transcriptional regulator, beta subunit
Alias: ECK0434, JW0430, dpeA, hopD
Species: Escherichia coli str. K-12 substr. MG1655
- Kamashev D, Rouviere Yaniv J. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J. 2000;19:6527-35 pubmed..Both structural motifs are recognized by HU at least 1000-fold more avidly than duplex DNA. ..
- Guo F, Adhya S. Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling. Proc Natl Acad Sci U S A. 2007;104:4309-14 pubmed
- Rouviere Yaniv J, Kjeldgaard N. Native Escherichia coli HU protein is a heterotypic dimer. FEBS Lett. 1979;106:297-300 pubmed
- Shindo H, Furubayashi A, Shimizu M, Miyake M, Imamoto F. Preferential binding of E.coli histone-like protein HU alpha to negatively supercoiled DNA. Nucleic Acids Res. 1992;20:1553-8 pubmed..It was suggested that HU in vivo interacts preferentially with the regions deformed under torsional stress or with the metabolically active regions along DNA. ..
- Azam T, Ishihama A. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem. 1999;274:33105-13 pubmed
- Lia G, Bensimon D, Croquette V, Allemand J, Dunlap D, Lewis D, et al. Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc Natl Acad Sci U S A. 2003;100:11373-7 pubmed..Such topological intermediates may operate similarly in other multiprotein complexes of transcription, replication, and recombination. ..
- Claret L, Rouviere Yaniv J. Regulation of HU alpha and HU beta by CRP and FIS in Escherichia coli. J Mol Biol. 1996;263:126-39 pubmed..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...
- Pontiggia A, Negri A, Beltrame M, Bianchi M. Protein HU binds specifically to kinked DNA. Mol Microbiol. 1993;7:343-50 pubmed..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. ..
- Bonnefoy E, Takahashi M, Yaniv J. DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J Mol Biol. 1994;242:116-29 pubmed..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. ..
- Castaing B, Zelwer C, Laval J, Boiteux S. HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps. J Biol Chem. 1995;270:10291-6 pubmed..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...
- Dame R. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol. 2005;56:858-70 pubmed..Many of these new insights can be attributed to the use of recently developed biophysical techniques. ..
- Swinger K, Rice P. IHF and HU: flexible architects of bent DNA. Curr Opin Struct Biol. 2004;14:28-35 pubmed..These techniques include time-resolved synchrotron X-ray footprinting, differential scanning calorimetry, isothermal titration calorimetry and single-molecule experiments. ..
- van Noort J, Verbrugge S, Goosen N, Dekker C, Dame R. Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc Natl Acad Sci U S A. 2004;101:6969-74 pubmed..At higher HU concentrations, a rigid nucleoprotein filament is formed in which HU appears to arrange helically around the DNA without inducing significant condensation. ..
- Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol. 1999;181:6361-70 pubmed..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. ..
- Azam T, Hiraga S, Ishihama A. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells. 2000;5:613-26 pubmed..coli could be classified into two groups. One group proteins was distributed uniformly within the nucleoid, but the other group of proteins showed an irregular distribution, forming immuno-stained spots or clumps. ..
- Ramstein J, Hervouet N, Coste F, Zelwer C, Oberto J, Castaing B. Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure. J Mol Biol. 2003;331:101-21 pubmed..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. ..
- Giangrossi M, Giuliodori A, Gualerzi C, Pon C. Selective expression of the beta-subunit of nucleoid-associated protein HU during cold shock in Escherichia coli. Mol Microbiol. 2002;44:205-16 pubmedExpression 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...
- Kamashev D, Balandina A, Rouviere Yaniv J. The binding motif recognized by HU on both nicked and cruciform DNA. EMBO J. 1999;18:5434-44 pubmed..The HU binding motif present in both structures is a pair of inclined DNA helices. ..
- Balandina A, Claret L, Hengge Aronis R, Rouviere Yaniv J. The Escherichia coli histone-like protein HU regulates rpoS translation. Mol Microbiol. 2001;39:1069-79 pubmed..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. ..
- Luijsterburg M, Noom M, Wuite G, Dame R. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol. 2006;156:262-72 pubmed..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. ..
- Manna D, Gowrishankar J. Evidence for involvement of proteins HU and RpoS in transcription of the osmoresponsive proU operon in Escherichia coli. J Bacteriol. 1994;176:5378-84 pubmed..The dpeA locus was allelic to hupB, which along with hupA encodes the nucleoid protein HU...
- Rouviere Yaniv J, Yaniv M, Germond J. E. coli DNA binding protein HU forms nucleosomelike structure with circular double-stranded DNA. Cell. 1979;17:265-74 pubmed..The circular SV40 DNA is condensed by a ratio of 2.0-2.5 relative to naked DNA. This is similar to the ratio (2.4) measured for chromatin formed by reassociation of relaxed SV40 DNA with the four core histones. ..
- Kar S, Edgar R, Adhya S. Nucleoid remodeling by an altered HU protein: reorganization of the transcription program. Proc Natl Acad Sci U S A. 2005;102:16397-402 pubmed..We propose that, as in eukaryotes, the nucleoid architecture dictates the global transcription profile and, consequently, the behavior pattern in bacteria. ..
- Morales P, Rouviere Yaniv J, Dreyfus M. The histone-like protein HU does not obstruct movement of T7 RNA polymerase in Escherichia coli cells but stimulates its activity. J Bacteriol. 2002;184:1565-70 pubmed..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. ..
- Lavoie B, Shaw G, Millner A, Chaconas G. Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate. Cell. 1996;85:761-71 pubmed..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. ..
- Kano Y, Wada M, Imamoto F. Genetic characterization of the gene hupA encoding the HU-2 protein of Escherichia coli. Gene. 1988;69:331-5 pubmed..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]. ..
- Aki T, Choy H, Adhya S. Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by GAL repressor. Genes Cells. 1996;1:179-88 pubmed..Although how HU participates in the assembly process is unknown, there may be a cooperative effect in the formation of the repression complex. ..
- Laine B, Kmiecik D, Sautiere P, Biserte G, Cohen Solal M. Complete amino-acid sequences of DNA-binding proteins HU-1 and HU-2 from Escherichia coli. Eur J Biochem. 1980;103:447-61 pubmed..No sequence homology could be established between the proteins HU-1 and HU-2 and any one of the five histones from different eukaryotes. ..
- Semsey S, Tolstorukov M, Virnik K, Zhurkin V, Adhya S. DNA trajectory in the Gal repressosome. Genes Dev. 2004;18:1898-907 pubmed..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. ..
- Czapla L, Swigon D, Olson W. Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations. J Mol Biol. 2008;382:353-70 pubmed publisher..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. ..
- Lyubchenko Y, Shlyakhtenko L, Aki T, Adhya S. Atomic force microscopic demonstration of DNA looping by GalR and HU. Nucleic Acids Res. 1997;25:873-6 pubmed..Supercoiling of DNA, which is also critical for GalR action, may stabilize the DNA loops by providing an energetically favorable geometry of the DNA. ..
- Mende L, Timm B, Subramanian R. Primary structures of two homologous ribosome-associated DNA-binding proteins of Escherichia coli. FEBS Lett. 1978;96:395-8 pubmed
- Kohno K, Wada M, Kano Y, Imamoto F. Promoters and autogenous control of the Escherichia coli hupA and hupB genes. J Mol Biol. 1990;213:27-36 pubmedThree start sites and a single start site for transcription of the hupB and hupA genes, respectively, have been identified in Escherichia coli...
- Dorman C, Hinton J, Free A. Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria. Trends Microbiol. 1999;7:124-8 pubmed..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. ..
- Trun N, Johnston D. Folding chromosomes in bacteria: examining the role of Csp proteins and other small nucleic acid-binding proteins. Curr Top Dev Biol. 2003;55:173-201 pubmed
- Garnier N, Loth K, Coste F, Augustyniak R, Nadan V, Damblon C, et al. An alternative flexible conformation of the E. coli HU?? protein: structural, dynamics, and functional aspects. Eur Biophys J. 2011;40:117-29 pubmed publisher..On the basis of these data, a realistic 3D model is proposed for the major I? conformation of EcHU??. This model is in agreement with previous experimental data. ..
- Perez N, Rehault M, Amouyal M. A functional assay in Escherichia coli to detect non-assisted interaction between galactose repressor dimers. Nucleic Acids Res. 2000;28:3600-4 pubmed..Furthermore, the assay may be generalised to detection of rather weak cooperative interactions between DNA-bound proteins. ..
- Laine B, Sautiere P, Biserte G, Cohen Solal M, Gros F, Rouviere Yaniv J. The amino- and carboxy-terminal amino acid sequences of protein HU from Escherichia coli. FEBS Lett. 1978;89:116-20 pubmed
- Bonnefoy E, Rouviere Yaniv J. HU, the major histone-like protein of E. coli, modulates the binding of IHF to oriC. EMBO J. 1992;11:4489-96 pubmed..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. ..
- Storts D, Markovitz A. Construction and characterization of mutations in hupB, the gene encoding HU-beta (HU-1) in Escherichia coli K-12. J Bacteriol. 1988;170:1541-7 pubmed..A kanamycin resistance cassette was used in the construction of insertion and deletion mutations in hupB, the gene encoding HU-beta on plasmid pJMC21...
- Bi H, Sun L, Fukamachi T, Saito H, Kobayashi H. HU participates in expression of a specific set of genes required for growth and survival at acidic pH in Escherichia coli. Curr Microbiol. 2009;58:443-8 pubmed publisher..histone-like Escherichia coli protein, HU, is composed of alpha and beta subunits respectively encoded by hupA and hupB in Escherichia coli...
- Koh J, Saecker R, Record M. DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA--protein complex on intact, linear duplex DNA. J Mol Biol. 2008;383:324-46 pubmed publisher..In particular, it explains how HU condenses or extends DNA depending on the relative concentrations of HU and DNA. ..
- Arthanari H, Wojtuszewski K, Mukerji I, Bolton P. Effects of HU binding on the equilibrium cyclization of mismatched, curved, and normal DNA. Biophys J. 2004;86:1625-31 pubmed..These results have been considered along with those previously obtained to refine a model for the interaction of HU with duplex DNA. ..
- Kano Y, Ogawa T, Ogura T, Hiraga S, Okazaki T, Imamoto F. Participation of the histone-like protein HU and of IHF in minichromosomal maintenance in Escherichia coli. Gene. 1991;103:25-30 pubmedThe 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...
- Painbeni E, Caroff M, Rouviere Yaniv J. Alterations of the outer membrane composition in Escherichia coli lacking the histone-like protein HU. Proc Natl Acad Sci U S A. 1997;94:6712-7 pubmed..These findings demonstrate a novel link between a bacterial chromosomal protein and the outer membrane composition. ..
- Kano Y, Osato K, Wada M, Imamoto F. Cloning and sequencing of the HU-2 gene of Escherichia coli. Mol Gen Genet. 1987;209:408-10 pubmed
- Kamashev D, Balandina A, Mazur A, Arimondo P, Rouviere Yaniv J. HU binds and folds single-stranded DNA. Nucleic Acids Res. 2008;36:1026-36 pubmed..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. ..
- Prieto A, Kahramanoglou C, Ali R, Fraser G, Seshasayee A, Luscombe N. Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res. 2012;40:3524-37 pubmed publisher..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...
- Hashimoto M, Imhoff B, Ali M, Kow Y. HU protein of Escherichia coli has a role in the repair of closely opposed lesions in DNA. J Biol Chem. 2003;278:28501-7 pubmed..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. ..
- Kano Y, Yoshino S, Wada M, Yokoyama K, Nobuhara M, Imamoto F. Molecular cloning and nucleotide sequence of the HU-1 gene of Escherichia coli. Mol Gen Genet. 1985;201:360-2 pubmed..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. ..
- Sarkar T, Vitoc I, Mukerji I, Hud N. Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines. Nucleic Acids Res. 2007;35:951-61 pubmed..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. ..
- Ogura T, Niki H, Kano Y, Imamoto F, Hiraga S. Maintenance of plasmids in HU and IHF mutants of Escherichia coli. Mol Gen Genet. 1990;220:197-203 pubmed..1988), had mutations in the hupB gene, and that the hopD410 mutation was an ochre mutation at the 5th Gln position of HU-1...
- Williams A, Foster P. The Escherichia coli histone-like protein HU has a role in stationary phase adaptive mutation. Genetics. 2007;177:723-35 pubmed..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. ..
- Wada M, Kano Y, Ogawa T, Okazaki T, Imamoto F. Construction and characterization of the deletion mutant of hupA and hupB genes in Escherichia coli. J Mol Biol. 1988;204:581-91 pubmedInsertion 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...
- Boubrik F, Bonnefoy E, Rouviere Yaniv J. HU and IHF: similarities and differences. In Escherichia coli, the lack of HU is not compensated for by IHF. Res Microbiol. 1991;142:239-47 pubmed
- Koh J, Shkel I, Saecker R, Record M. Nonspecific DNA binding and bending by HU??: interfaces of the three binding modes characterized by salt-dependent thermodynamics. J Mol Biol. 2011;410:241-67 pubmed publisher..Structural models consistent with the observed Sk(i) values are proposed. ..
- Kuroda A, Nomura K, Takiguchi N, Kato J, Ohtake H. Inorganic polyphosphate stimulates lon-mediated proteolysis of nucleoid proteins in Escherichia coli. Cell Mol Biol (Noisy-le-grand). 2006;52:23-9 pubmed..Fusions of green fluorescent protein with HimA, Fis, HupA, and HupB were clearly associated with polyP in vivo...
- Preobrazhenskaia O, Starodubova E, Karpov V, Rouviere Yaniv J. [Assays on comparing the local concentration of HU protein in the different regions of Escherichia coli genomic DNA]. Mol Biol (Mosk). 2005;39:678-86 pubmed..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 ..
- Sandman K, Pereira S, Reeve J. Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome. Cell Mol Life Sci. 1998;54:1350-64 pubmed
- Krolenko E, Kamashev D, Balandina A, Karpov V, Rouviere Yaniv J, Preobrazhenskaia O. [Immunochemical detection of the histone-like bacterial protein Hu in covalently bound DNA-protein complexes, obtained in vitro and in vivo]. Mol Biol (Mosk). 1999;33:442-6 pubmed
- Lee H, Kim H, Kang S, Hong C, Yim J, Hwang D. Expression of the seqA gene is negatively modulated by the HU protein in Escherichia coli. Mol Gen Genet. 2001;264:931-5 pubmed..These results suggest that the HU protein functions as a negative modulator of seqA expression. ..
- Delihas N, Forst S. MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors. J Mol Biol. 2001;313:1-12 pubmed..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. ..