Genomes and Genes
Gene Symbol: ihfB
Description: integration host factor (IHF), DNA-binding protein, beta subunit
Alias: ECK0903, JW0895, himD, hip
Species: Escherichia coli str. K-12 substr. MG1655
- Goosen N, van de Putte P. The regulation of transcription initiation by integration host factor. Mol Microbiol. 1995;16:1-7 pubmed..In addition, it summarizes the evidence indicating that IHF can stimulate transcription via a direct interaction with RNA polymerase and explores the possibility that the asymmetry of the IHF protein might reflect such an interaction. ..
- Dorman C, Higgins C. Fimbrial phase variation in Escherichia coli: dependence on integration host factor and homologies with other site-specific recombinases. J Bacteriol. 1987;169:3840-3 pubmed..Mutations in either the himA-or the himD (hip) gene, which encode the alpha and beta subunits of IHF, respectively, prevented phase variation and locked ..
- Rice P, Yang S, Mizuuchi K, Nash H. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell. 1996;87:1295-306 pubmed..One such readout involves a six-base A tract, providing evidence for the importance of a narrow minor groove. ..
- 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
- Aviv M, Giladi H, Schreiber G, Oppenheim A, Glaser G. Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation. Mol Microbiol. 1994;14:1021-31 pubmedTranscriptional control of the himA and the himD/hip genes coding for the two subunits of the integration host factor (IHF) was investigated. The promoters for the two genes were identified by the use of primer extension and S1 analysis...
- Mengeritsky G, Goldenberg D, Mendelson I, Giladi H, Oppenheim A. Genetic and biochemical analysis of the integration host factor of Escherichia coli. J Mol Biol. 1993;231:646-57 pubmed..DNA-binding protein of Escherichia coli composed of two subunits, alpha and beta, encoded by the himA and hip genes, respectively. IHF binds to the minor groove at a consensus sequence and bends DNA...
- Vitko J, Rujan I, Androga L, Mukerji I, Bolton P. Molecular beacon-equilibrium cyclization detection of DNA-protein complexes. Biophys J. 2007;93:3210-7 pubmed..These MBEC results have been compared with those from other approaches. ..
- Hoover T, Santero E, Porter S, Kustu S. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell. 1990;63:11-22 pubmed..IHF binds to nif promoter regulatory regions from a variety of organisms within the phylum "purple bacteria," suggesting a general ability to stimulate NIFA-mediated activation of nif transcription. ..
- Pagel J, Hatfield G. Integration host factor-mediated expression of the ilvGMEDA operon of Escherichia coli. J Biol Chem. 1991;266:1985-96 pubmed
- Nuñez J, Bai L, Harrington L, Hinder T, Doudna J. CRISPR Immunological Memory Requires a Host Factor for Specificity. Mol Cell. 2016;62:824-833 pubmed publisher..Together, these results reveal that Cas1-Cas2-mediated spacer integration requires IHF-induced target DNA bending and explain the elusive role of CRISPR leader sequences during spacer acquisition. ..
- Presutti D, Hassan H. Binding of integration host factor (IHF) to the Escherichia coli sodA gene and its role in the regulation of a sodA-lacZ fusion gene. Mol Gen Genet. 1995;246:228-35 pubmed..The same deletion in himA did not cause derepression of sodA-lacZ during anaerobic growth, but resulted in an increased response (about twofold) to the presence of 2,2'-dipyridyl compared to the isogenic wild-type strain. ..
- Boccard F, Prentki P. Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3' end of transcription units. EMBO J. 1993;12:5019-27 pubmed..RIB elements are at the end of transcription units, and thus define a new class of ihf sites. Possible implications for genome structure and DNA topology are discussed. ..
- Kikuchi A, Flamm E, Weisberg R. An Escherichia coli mutant unable to support site-specific recombination of bacteriophage lambda. J Mol Biol. 1985;183:129-40 pubmedWe report the isolation of mutations in, and the characterization of, an Escherichia coli gene, hip, that is required for site-specific recombination of phage lambda...
- Miller H, Kirk M, Echols H. SOS induction and autoregulation of the himA gene for site-specific recombination in Escherichia coli. Proc Natl Acad Sci U S A. 1981;78:6754-8 pubmed
- Ryan V, Grimwade J, Camara J, Crooke E, Leonard A. Escherichia coli prereplication complex assembly is regulated by dynamic interplay among Fis, IHF and DnaA. Mol Microbiol. 2004;51:1347-59 pubmed
- Dhavan G, Crothers D, Chance M, Brenowitz M. Concerted binding and bending of DNA by Escherichia coli integration host factor. J Mol Biol. 2002;315:1027-37 pubmed
- Friedman D. Integration host factor: a protein for all reasons. Cell. 1988;55:545-54 pubmed
- Giladi H, Koby S, Gottesman M, Oppenheim A. Supercoiling, integration host factor, and a dual promoter system, participate in the control of the bacteriophage lambda pL promoter. J Mol Biol. 1992;224:937-48 pubmed..In addition, IHF enhances RNA polymerase binding to pL. These data suggest that stimulation of pL by IHF involves the interaction of IHF and RNA polymerase to form a loop or otherwise distort the DNA between their binding sites. ..
- 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. ..
- Engelhorn M, Boccard F, Murtin C, Prentki P, Geiselmann J. In vivo interaction of the Escherichia coli integration host factor with its specific binding sites. Nucleic Acids Res. 1995;23:2959-65 pubmed..The occupancy of binding sites varies with the concentration of IHF in the cell and allows to estimate the concentration of free IHF protein in the cell. ..
- Yang C, Nash H. The interaction of E. coli IHF protein with its specific binding sites. Cell. 1989;57:869-80 pubmed
- Granston A, Nash H. Characterization of a set of integration host factor mutants deficient for DNA binding. J Mol Biol. 1993;234:45-59 pubmed..We discuss the positions of the mutant amino acid residues as they relate to a proposed molecular model of an IHF:DNA complex. ..
- Rowbury R, Hussain N. Exposure of Escherichia coli to acid habituation conditions sensitizes it to alkaline stress. Lett Appl Microbiol. 1996;22:57-61 pubmed..Alkali sensitivity failed to appear at pHo 5.5 plus DNA gyrase inhibitors and was markedly reduced by himA, himD, hns, ompC and nhaA lesions. A tonB deletion mutant showed alkali sensitivity at pHo 7.0...
- Ellenberger T, Landy A. A good turn for DNA: the structure of integration host factor bound to DNA. Structure. 1997;5:153-7 pubmed..IHF exerts leverage in the minor groove and wraps DNA around the body of the protein, providing another example of sequence-specific recognition of the minor groove. ..
- dos Santos M, Rodrigues P. A genomic-scale search for regulatory binding sites in the integration host factor regulon of Escherichia coli K12. Genet Mol Res. 2005;4:783-9 pubmed..We concluded that IHF may regulate two genes encoding ATP-dependent RNA helicases. This interaction is not described in RegulonDB, even as a computational prediction. IHF may also regulate RNA modification processes. ..
- Lee S, Lim C, DrÃ¶ge P, Yan J. Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF. Sci Rep. 2015;5:18146 pubmed publisher..The environment dependent selection between IHF and Dps results in different physical organizations of DNA. Overall, our findings provide important insights into E. coli nucleoid architecture. ..
- 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...
- Sarkar T, Petrov A, Vitko J, Santai C, Harvey S, Mukerji I, et al. Integration host factor (IHF) dictates the structure of polyamine-DNA condensates: implications for the role of IHF in the compaction of bacterial chromatin. Biochemistry. 2009;48:667-75 pubmed publisher..We propose that a common function of IHF and HU in bacterial cells is to facilitate DNA organization in the nucleoid by the introduction of sharp bends in chromosomal DNA. ..
- Zurla C, Samuely T, Bertoni G, Valle F, Dietler G, Finzi L, et al. Integration host factor alters LacI-induced DNA looping. Biophys Chem. 2007;128:245-52 pubmed
- Kuznetsov S, Sugimura S, Vivas P, Crothers D, Ansari A. Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF. Proc Natl Acad Sci U S A. 2006;103:18515-20 pubmed..Thus, our results suggest that spontaneous thermal disruption in base-paring, nucleated at an A:T site, may be sufficient to overcome the free energy barrier needed to partially bend/kink DNA before forming a tight complex with IHF. ..
- Sun X, Mierke D, Biswas T, Lee S, Landy A, Radman Livaja M. Architecture of the 99 bp DNA-six-protein regulatory complex of the lambda att site. Mol Cell. 2006;24:569-80 pubmed
- Kur J, Hasan N, Szybalski W. Integration host factor (IHF) binds to many sites in the A + T-rich b2 region of phage lambda DNA. Gene. 1992;111:1-9 pubmed..We discuss the possibility that some of the IHF-binding sites could be instrumental in repressing in vivo transcription from the A + T-rich b2 region during the lambda prophage state [Rosenvold et al., Virology 107 (1980) 476-487]. ..
- Nash H, Robertson C, Flamm E, Weisberg R, Miller H. Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits. J Bacteriol. 1987;169:4124-7 pubmed..We have constructed strains in which the two subunits of IHF, encoded by the himA and hip genes of Escherichia coli, are expressed under the control of the lambda rho L promoter...
- Pagel J, Winkelman J, Adams C, Hatfield G. DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli. J Mol Biol. 1992;224:919-35 pubmed
- Nash H, Granston A. Similarity between the DNA-binding domains of IHF protein and TFIID protein. Cell. 1991;67:1037-8 pubmed
- von Freiesleben U, Rasmussen K, Atlung T, Hansen F. Rifampicin-resistant initiation of chromosome replication from oriC in ihf mutants. Mol Microbiol. 2000;37:1087-93 pubmed..This indicates that cells lacking IHF replicate their chromosome(s) very fast. ..
- Giladi H, Gottesman M, Oppenheim A. Integration host factor stimulates the phage lambda pL promoter. J Mol Biol. 1990;213:109-21 pubmed..IHF may stimulate recognition of pL by one or more of several mechanisms: (1) by bending DNA; (2) by making protein-protein contacts with RNA polymerase; or (3) by occluding a competing promoter upstream from pL. ..
- Fekete R, Venkova Canova T, Park K, Chattoraj D. IHF-dependent activation of P1 plasmid origin by dnaA. Mol Microbiol. 2006;62:1739-51 pubmed..The role of IHF in activating P1 origin by allowing DnaA binding to a weak site is reminiscent of the role the protein plays in initiating the host chromosomal replication. ..
- Browning D, Grainger D, Beatty C, Wolfe A, Cole J, Busby S. Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression. Mol Microbiol. 2005;57:496-510 pubmed..Hence, Fis protein is a major factor responsible for catabolite repression at the nrf promoter, and Fis can override activation by FNR and NarL or NarP. ..
- Engelhorn M, Geiselmann J. Maximal transcriptional activation by the IHF protein of Escherichia coli depends on optimal DNA bending by the activator. Mol Microbiol. 1998;30:431-41 pubmed..We propose that wild-type IHF induces too strong a DNA bend (180 degrees) for optimal interactions between DNA upstream of the IHF binding site and the back of RNA polymerase. ..
- Dimri G, Rudd K, Morgan M, Bayat H, Ames G. Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria. J Bacteriol. 1992;174:4583-93 pubmed..coli. A search for these sequences in other members of the family Enterobacteriaceae shows a consistent correlation between both the number of occurrences and the hybridization strength and genealogical relationship. ..
- 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. ..
- Griffo G, Oppenheim A, Gottesman M. Repression of the lambda pcin promoter by integrative host factor. J Mol Biol. 1989;209:55-64 pubmed..We propose that IHF binding to the pcin promoter region blocks the binding of RNA polymerase to the promoter, either by covering specific nucleotides or by distorting DNA structure. ..
- Browning D, Beatty C, Sanstad E, Gunn K, Busby S, Wolfe A. Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF. Mol Microbiol. 2004;51:241-54 pubmed..We propose that FIS and IHF each function directly as anti-activators of CRP, each working independently at different times during growth to set the levels of CRP-dependent acs transcription. ..
- Hales L, Gumport R, Gardner J. Examining the contribution of a dA+dT element to the conformation of Escherichia coli integration host factor-DNA complexes. Nucleic Acids Res. 1996;24:1780-6 pubmed..These results indicate the importance of flanking DNA and a dA+dT element in the binding and bending of a site by IHF. ..
- Bao Q, Christ N, Droge P. Single-chain integration host factors as probes for high-precision nucleoprotein complex formation. Gene. 2004;343:99-106 pubmed..coli require different types of high-precision DNA architectural activities. The scIHF variants described here will help to explore further how flexible these requirements are. ..
- 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...
- Taschner N, Yagil E, Spira B. The effect of IHF on sigmaS selectivity of the phoA and pst promoters of Escherichia coli. Arch Microbiol. 2006;185:234-7 pubmed..Introduction of a -13C residue in the promoter region of phoA, another PHO regulon gene that is not directly affected by IHF, did not affect its exclusive transcription initiation by Esigma (D). ..
- Miller H, Friedman D. An E. coli gene product required for lambda site-specific recombination. Cell. 1980;20:711-9 pubmed..Since all of the processes affected by himA mutations ultimately rely on protein-DNA interactions, we suggest that himA protein may act in an auxillary manner to facilitate these interactions. ..
- Wegleńska A, Jacob B, Sirko A. Transcriptional pattern of Escherichia coli ihfB (himD) gene expression. Gene. 1996;181:85-8 pubmedIntegration host factor (IHF) is a small heterodimer containing subunits encoded by the unlinked ihfA (himA) and ihfB (himD, hip) genes...
- Mendelson I, Haluzi H, Koby S, Oppenheim A. Physical map locations of the himA and hip genes of Escherichia coli. J Bacteriol. 1991;173:5249 pubmed
- Wang S, Cosstick R, Gardner J, Gumport R. The specific binding of Escherichia coli integration host factor involves both major and minor grooves of DNA. Biochemistry. 1995;34:13082-90 pubmed..Thus, the specific interaction of IHF with its H' site likely involves interactions with both the minor and major grooves of the DNA. ..
- Resnik E, Pan B, Ramani N, Freundlich M, LaPorte D. Integration host factor amplifies the induction of the aceBAK operon of Escherichia coli by relieving IclR repression. J Bacteriol. 1996;178:2715-7 pubmed..In contrast, IHF has little effect on aceB::lacZ expression under repressing conditions. The ability of IHF to relieve repression under inducing but not repressing conditions allows this protein to amplify the induction of aceBAK. ..
- Freundlich M, Ramani N, Mathew E, Sirko A, Tsui P. The role of integration host factor in gene expression in Escherichia coli. Mol Microbiol. 1992;6:2557-63 pubmed
- Bi H, Zhang C. Integration host factor is required for the induction of acid resistance in Escherichia coli. Curr Microbiol. 2014;69:218-24 pubmed publisher..These results indicate that in E. coli, by combined transcriptional and translational controls of gene expression, IHF activates expression of a specific set of genes required for survival at extremely acidic pH. ..
- Haluzi H, Goitein D, Koby S, Mendelson I, Teff D, Mengeritsky G, et al. Genes coding for integration host factor are conserved in gram-negative bacteria. J Bacteriol. 1991;173:6297-9 pubmed..We demonstrate that the himA and hip genes of Serratia marcescens and Aeromonas proteolytica can substitute for the Escherichia coli genes in a variety ..
- 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
- Zulianello L, van Ulsen P, van de Putte P, Goosen N. Participation of the flank regions of the integration host factor protein in the specificity and stability of DNA binding. J Biol Chem. 1995;270:17902-7 pubmed..We observed that the C-terminal alpha 3 helix of HimD is involved in the stability of DNA binding, but not in the specificity...
- Sugimura S, Crothers D. Stepwise binding and bending of DNA by Escherichia coli integration host factor. Proc Natl Acad Sci U S A. 2006;103:18510-4 pubmed..Our observations on the bending step kinetics are in agreement with results using the temperature-jump kinetic method. ..
- Flamm E, Weisberg R. Primary structure of the hip gene of Escherichia coli and of its product, the beta subunit of integration host factor. J Mol Biol. 1985;183:117-28 pubmedWe describe the isolation and sequencing of the hip gene of Escherichia coli and show that it encodes the beta subunit of integration host factor (IHF beta)...
- Paul L, Mishra P, Blumenthal R, Matthews R. Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR. BMC Microbiol. 2007;7:2 pubmed
- Vander Meulen K, Saecker R, Record M. Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA. J Mol Biol. 2008;377:9-27 pubmed publisher..7+/-0.4 at constant KCl activity, indicating the net release of ca. 150 H(2)O molecules from anionic surface. ..
- Browning D, Lee D, Wolfe A, Cole J, Busby S. The Escherichia coli K-12 NarL and NarP proteins insulate the nrf promoter from the effects of integration host factor. J Bacteriol. 2006;188:7449-56 pubmed..The acs-nrf regulatory region is conserved in other pathogenic E. coli strains and related enteric bacteria but differs in Salmonella enterica serovar Typhimurium. ..
- Blomfield I, Kulasekara D, Eisenstein B. Integration host factor stimulates both FimB- and FimE-mediated site-specific DNA inversion that controls phase variation of type 1 fimbriae expression in Escherichia coli. Mol Microbiol. 1997;23:705-17 pubmed..IHF stimulates FimE recombination; In strain MG1655, mutants containing lesions in either the alpha (ihfA) or beta (ihfB) subunits of IHF show a marked decrease in both FimB- (100-fold) and FimE (15,000-fold)-promoted switching...
- Goodrich J, Schwartz M, McClure W. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 1990;18:4993-5000 pubmed..The MacTargsearch program and its potential usefulness in searching for other sites and predicting their relative activities is discussed. ..
- Weisberg R, Freundlich M, Friedman D, Gardner J, Goosen N, Nash H, et al. Nomenclature of the genes encoding IHF. Mol Microbiol. 1996;19:642 pubmed
- Ramani N, Huang L, Freundlich M. In vitro interactions of integration host factor with the ompF promoter-regulatory region of Escherichia coli. Mol Gen Genet. 1992;231:248-55 pubmed..This inhibition was reversed by increasing the concentration of OmpR, a positive activator required for ompF expression, suggesting that IHF may inhibit ompF transcription by altering how OmpR interacts with the ompF promoter. ..
- Hoyt M, Knight D, Das A, Miller H, Echols H. Control of phage lambda development by stability and synthesis of cII protein: role of the viral cIII and host hflA, himA and himD genes. Cell. 1982;31:565-73 pubmed..The synthesis of cII appears to be under the positive control of the host himA and himD genes...
- Frumerie C, Sylwan L, Ahlgren Berg A, Haggård Ljungquist E. Cooperative interactions between bacteriophage P2 integrase and its accessory factors IHF and Cox. Virology. 2005;332:284-94 pubmed..The Int and Cox proteins also bind cooperatively to attP...