|Gene:||ihfB||Accession Numbers: EG10441 (EcoCyc), b0912, ECK0903|
Synonyms: hip, himD, integration host factor (IHF), β subunit; site-specific recombination
Component of: IHF DNA-binding transcriptional dual regulator (extended summary available)
The protein family is HI-HN-S
|Map Position: [963,051 -> 963,335] (20.76 centisomes, 75°)||Length: 285 bp / 94 aa|
Molecular Weight of Polypeptide: 10.651 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0003107, CGSC:637, DIP:DIP-41099N, EchoBASE:EB0436, EcoGene:EG10441, EcoliWiki:b0912, Mint:MINT-365163, ModBase:P0A6Y1, OU-Microarray:b0912, PortEco:ihfB, PR:PRO_000022999, Pride:P0A6Y1, Protein Model Portal:P0A6Y1, RefSeq:NP_415432, RegulonDB:EG10441, SMR:P0A6Y1, String:511145.b0912, UniProt:P0A6Y1
Relationship Links: InterPro:IN-FAMILY:IPR000119, InterPro:IN-FAMILY:IPR005685, InterPro:IN-FAMILY:IPR010992, InterPro:IN-FAMILY:IPR020816, PDB:Structure:1IHF, PDB:Structure:1OUZ, PDB:Structure:1OWF, PDB:Structure:1OWG, PDB:Structure:2HT0, PDB:Structure:2IIE, PDB:Structure:2IIF, Pfam:IN-FAMILY:PF00216, Prints:IN-FAMILY:PR01727, Prosite:IN-FAMILY:PS00045, Smart:IN-FAMILY:SM00411
|MultiFun Terms:||information transfer → DNA related → DNA recombination|
|information transfer → protein related → nucleoproteins, basic proteins|
|information transfer → RNA related → Transcription related|
|regulation → type of regulation → transcriptional level → activator|
|regulation → type of regulation → transcriptional level → repressor|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB enriched||Yes||37||Aerobic||6.95||Yes [Gerdes03, Comment 1]|
|LB Lennox||Yes||37||Aerobic||7||Yes [Baba06, Comment 2]|
|M9 medium with 1% glycerol||Yes||37||Aerobic||7.2||0.35||Yes [Joyce06, Comment 3]|
|MOPS medium with 0.4% glucose||Yes||37||Aerobic||7.2||0.22||Yes [Baba06, Comment 2]|
Subunit of: IHF DNA-binding transcriptional dual regulator
Subunit composition of
IHF DNA-binding transcriptional dual regulator = [IhfA][IhfB]
integration host factor (IHF), α subunit = IhfA (summary available)
integration host factor (IHF), β subunit = IhfB (summary available)
IHF, "Integration host factor," is a global regulatory protein that helps to maintain DNA architecture. It binds and bends DNA at specific sites. IHF plays a role in DNA supercoiling and DNA duplex destabilization and affects processes such as DNA replication, recombination, and the expression of many genes [Swinger04, Freundlich92, Dhavan02].
IHF is highly abundant in the cell. Its total intracellular concentration varies with growth rate and is higher in exponential phase, with 6,000 dimers per cell, than in stationary phase (3,000 dimers per cell) [Ali99].
IHF acts mostly as an accessory factor, stabilizing a correct nucleoprotein complex. For example, IHF was originally found to be required for the site-specific recombination of phage λ with the chromosome [Miller80]. For this, IHF stabilizes the bending of the DNA to facilitate binding of the bivalent integrase molecules [Moitoso89]. As another example, IHF stimulates transcription at σ54-dependent promoters. Here, IHF acts to facilitate the formation of the loop between the upstream bound activator and the σ54 holoenzyme [Hoover90, Santero92].
Like HU, IHF plays a role in polyamine-dependent DNA condensation. The binding to low-affinity sites and introduction of sharp bends in chromosomal DNA promote the formation of rod-like condensed structures in chromosomal DNA [Sarkar09].
IHF is a heterodimer consisting of the two subunits, IhfA (HimA) and IhfB (HimD, Hip), that share about 25% amino acid identity [Nash87]. The structure of IHF bound to DNA has been solved [Rice96, Ellenberger97]. It binds tightly to DNA regions of about 40 bp carrying the 13-bp consensus sequence with A/T-rich elements upstream of the core consensus sequence. [Goodrich90, Friedman88, Hales96]. IHF makes no contact with the major groove and only a few contacts with the minor groove [Yang89a]. Therefore, specificity is believed to be due to the sequence-dependent structural parameters of the DNA, where A/T-rich regions play an important role. The bend angle induced by IHF is approximately 160° [Rice96].
IHF is necessary for the induction of arginine- and lysine-dependent acid resistance (AR) via both transcriptional and translational controls of gene expression, as IHF activates expression of a specific set of genes involved in survival at extremely acidic pH [Bi14a].
DNA binding site length: 13 base-pairs
Symmetry: Inverted Repeat
|Pfam PF00216||1 -> 91|
10/20/97 Gene b0912 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10441; confirmed by SwissProt match.
Ali99: Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A (1999). "Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid." J Bacteriol 181(20);6361-70. PMID: 10515926
Aviv94: Aviv M, Giladi H, Schreiber G, Oppenheim AB, Glaser G (1994). "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(5);1021-31. PMID: 7715442
Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554
DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371
Friedman84a: Friedman DI, Olson EJ, Carver D, Gellert M (1984). "Synergistic effect of himA and gyrB mutations: evidence that him functions control expression of ilv and xyl genes." J Bacteriol 157(2);484-9. PMID: 6229530
Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938
Goodrich90: Goodrich JA, Schwartz ML, McClure WR (1990). "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 18(17);4993-5000. PMID: 2205834
Hales96: Hales LM, Gumport RI, Gardner JF (1996). "Examining the contribution of a dA+dT element to the conformation of Escherichia coli integration host factor-DNA complexes." Nucleic Acids Res 24(9);1780-6. PMID: 8650000
Hoover90: Hoover TR, Santero E, Porter S, Kustu S (1990). "The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons." Cell 63(1);11-22. PMID: 2208275
Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394
Lee92c: Lee EC, Hales LM, Gumport RI, Gardner JF (1992). "The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities." EMBO J 11(1);305-13. PMID: 1531459
Mengeritsky93: Mengeritsky G, Goldenberg D, Mendelson I, Giladi H, Oppenheim AB (1993). "Genetic and biochemical analysis of the integration host factor of Escherichia coli." J Mol Biol 231(3);646-57. PMID: 8515442
Nash87: Nash HA, Robertson CA, Flamm E, Weisberg RA, Miller HI (1987). "Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits." J Bacteriol 169(9);4124-7. PMID: 3305480
Presutti95: Presutti DG, Hassan HM (1995). "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(2);228-35. PMID: 7862094
Santero92: Santero E, Hoover TR, North AK, Berger DK, Porter SC, Kustu S (1992). "Role of integration host factor in stimulating transcription from the sigma 54-dependent nifH promoter." J Mol Biol 227(3);602-20. PMID: 1404379
Sarkar09: Sarkar T, Petrov AS, Vitko JR, Santai CT, Harvey SC, Mukerji I, Hud NV (2009). "Integration host factor (IHF) dictates the structure of polyamine-DNA condensates: implications for the role of IHF in the compaction of bacterial chromatin." Biochemistry 48(4);667-75. PMID: 19132923
Stenzel87: Stenzel TT, Patel P, Bastia D (1987). "The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101." Cell 49(5);709-17. PMID: 3555843
Zulianello94: Zulianello L, de la Gorgue de Rosny E, van Ulsen P, van de Putte P, Goosen N (1994). "The HimA and HimD subunits of integration host factor can specifically bind to DNA as homodimers." EMBO J 13(7);1534-40. PMID: 8156991
Zulianello95: Zulianello L, van Ulsen P, van de Putte P, Goosen N (1995). "Participation of the flank regions of the integration host factor protein in the specificity and stability of DNA binding." J Biol Chem 270(30);17902-7. PMID: 7629095
Christiansen81: Christiansen L, Pedersen S (1981). "Cloning, restriction endonuclease mapping and post-transcriptional regulation of rpsA, the structural gene for ribosomal protein S1." Mol Gen Genet 181(4);548-51. PMID: 6267426
Lemke11: Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL (2011). "Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA." Proc Natl Acad Sci U S A 108(14);5712-7. PMID: 21402902
Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220
Skouv90: Skouv J, Schnier J, Rasmussen MD, Subramanian AR, Pedersen S (1990). "Ribosomal protein S1 of Escherichia coli is the effector for the regulation of its own synthesis." J Biol Chem 265(28);17044-9. PMID: 2120211
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