Genomes and Genes
Gene Symbol: hupA
Description: HU, DNA-binding transcriptional regulator, alpha subunit
Alias: ECK3992, JW3964
Species: Escherichia coli str. K-12 substr. MG1655
- Rouviere Yaniv J, Kjeldgaard N. Native Escherichia coli HU protein is a heterotypic dimer. FEBS Lett. 1979;106:297-300 pubmed
- Becker N, Kahn J, Maher L. Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli. Nucleic Acids Res. 2007;35:3988-4000 pubmed..These results suggest that host nucleoid proteins can directly facilitate or inhibit DNA looping in bacteria. ..
- Wery M, Woldringh C, Rouviere Yaniv J. HU-GFP and DAPI co-localize on the Escherichia coli nucleoid. Biochimie. 2001;83:193-200 pubmed..We show that DAPI and HU-GFP colocalize on the E. coli nucleoid. HU, therefore, can be considered as a natural tracer of DNA in the living bacterial cell. ..
- 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. ..
- 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
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- Oberto J, Nabti S, Jooste V, Mignot H, Rouviere Yaniv J. The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction. PLoS ONE. 2009;4:e4367 pubmed publisher..The uniform chromosomal distribution of the many operons regulated by HU strongly suggests that the transcriptional and nucleoid architectural functions of HU constitute two aspects of a unique protein-DNA interaction mechanism. ..
- Broyles S, Pettijohn D. Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch. J Mol Biol. 1986;187:47-60 pubmed..Another distinction is that HU-DNA complexes are less stable, having a dissociation half-life of 0.6 min in 50 mM-NaCl. This last property may explain prior difficulties in detecting prokaryotic nucleosome-like structures. ..
- Bonnefoy E, Rouviere Yaniv J. HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J. 1991;10:687-96 pubmed..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. ..
- Balandina A, Kamashev D, Rouviere Yaniv J. The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids. J Biol Chem. 2002;277:27622-8 pubmed
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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...
- 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
- 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. ..
- 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. ..
- Dame R, Goosen N. HU: promoting or counteracting DNA compaction?. FEBS Lett. 2002;529:151-6 pubmed..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. ..
- 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...
- 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. ..
- Aki T, Adhya S. Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J. 1997;16:3666-74 pubmed..The example of gal repression provides a model for studying how a 'condensed' DNA becomes available for transcription. ..
- Jaffe A, Vinella D, D Ari R. The Escherichia coli histone-like protein HU affects DNA initiation, chromosome partitioning via MukB, and cell division via MinCDE. J Bacteriol. 1997;179:3494-9 pubmedEscherichia coli hupA hupB double mutants, lacking both subunits (HU1 and HU2) of the histone-like protein HU, accumulate secondary mutations...
- Kar S, Choi E, Guo F, Dimitriadis E, Kotova S, Adhya S. Right-handed DNA supercoiling by an octameric form of histone-like protein HU: modulation of cellular transcription. J Biol Chem. 2006;281:40144-53 pubmed..In vivo, HUalpha(E38K,V42L) shows altered association and distribution patterns with the genetic loci whose transcription are differentially affected in the mutant strain. ..
- Wojtuszewski K, Mukerji I. The HU-DNA binding interaction probed with UV resonance Raman spectroscopy: structural elements of specificity. Protein Sci. 2004;13:2416-28 pubmed..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. ..
- 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...
- 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
- Dai Y, Li L, Roser D, Long S. Detection and identification of low-mass peptides and proteins from solvent suspensions of Escherichia coli by high performance liquid chromatography fractionation and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom. 1999;13:73-8 pubmed..coli. The methodologies reported here should be very useful in searching for unique biomarkers for bacterial discrimination. ..
- 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. ..
- 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. ..
- Struve C, Forestier C, Krogfelt K. Application of a novel multi-screening signature-tagged mutagenesis assay for identification of Klebsiella pneumoniae genes essential in colonization and infection. Microbiology. 2003;149:167-76 pubmed..Transposon insertion sites in attenuated mutants were, among others, in genes encoding well-known K. pneumoniae virulence factors such as lipopolysaccharide and capsule, as well as in genes of unknown function...
- 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. ..
- 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. ..
- 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
- 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. ..
- 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. ..
- 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...
- 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. ..
- 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
- 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...
- Becker N, Kahn J, Maher L. Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation. Nucleic Acids Res. 2008;36:4009-21 pubmed publisher..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. ..
- Butala M, Busby S, Lee D. DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes. Nucleic Acids Res. 2009;37:e37 pubmed publisher..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...
- 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
- 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. ..
- 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 ..
- 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. ..
- 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. ..
- 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 pubmedThe gene hupA encoding the HU-2 (HU-alpha) protein of Escherichia coli was mapped between rpoBC at 90 min and metA at 90.5 min on the K-12 genome by plasmid integration and P1-mediated transduction studies...
- Giacoia G. Cocaine babies in Oklahoma. J Okla State Med Assoc. 1990;83:64-7 pubmed..Recreational use of cocaine has resulted in a dramatic increase in the incidence of fetal exposure to cocaine. Increased awareness by health professionals is needed to determine the extent of the problem in Oklahoma. ..
- 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
- 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...
- 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
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- Chodavarapu S, Felczak M, Kaguni J. Two forms of ribosomal protein L2 of Escherichia coli that inhibit DnaA in DNA replication. Nucleic Acids Res. 2011;39:4180-91 pubmed publisher..Both forms of L2 also inhibit the unwinding of oriC by DnaA. These in vitro results raise the possibility that one or both forms of L2 modulate DnaA function in vivo to regulate the frequency of initiation. ..
- 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. ..
- 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. ..