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Escherichia coli K-12 substr. MG1655 Polypeptide: integration host factor (IHF), β subunit

Gene: ihfB Accession Numbers: EG10441 (EcoCyc), b0912, ECK0903

Synonyms: hip, himD, integration host factor (IHF), β subunit; site-specific recombination

Regulation Summary Diagram: ?

Component of: IHF DNA-binding transcriptional dual regulator (extended summary available)

The protein family is HI-HN-S

Citations: [Aviv94, Goosen95]

Gene Citations: [Weglenska96, Aviv94]

Locations: cytosol

Map Position: [963,051 -> 963,335] (20.76 centisomes)
Length: 285 bp / 94 aa

Molecular Weight of Polypeptide: 10.651 kD (from nucleotide sequence)

pI: 9.38

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 , InterPro:IN-FAMILY:IPR023630 , 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

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, Granston93, Zulianello95, Mengeritsky93, Zulianello94, Presutti95]
GO:0000746 - conjugation Inferred by computational analysis [UniProtGOA11]
GO:0006310 - DNA recombination Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0006417 - regulation of translation Inferred by computational analysis [UniProtGOA11, GOA06]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005694 - chromosome Inferred by computational analysis [GOA01]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

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

Essentiality data for ihfB knockouts: ?

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

Synonyms: IHF

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].

Citations: [Aviv94, Goosen95]

GO Terms:

Biological Process: GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment [Friedman84]
GO:0042150 - plasmid recombination Inferred from experiment [Miller80]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment [Dhavan02]
GO:0044374 - sequence-specific DNA binding, bending Inferred from experiment [Stenzel87]

DNA binding site length: 13 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (89 total): ?


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 9
[Wasinger98, UniProt10]
Alternate sequence: R → S; UniProt: (in Ref. 6; AA sequence);
Mutagenesis-Variant 44
Alternate sequence: E → V; UniProt: Altered DNA-binding specificity;
Alternate sequence: E → K; UniProt: Altered DNA-binding specificity;
Alternate sequence: E → G; UniProt: Altered DNA-binding specificity;

Gene Local Context (not to scale): ?

Transcription Units:


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

Bi14a: Bi H, Zhang C (2014). "Integration host factor is required for the induction of acid resistance in Escherichia coli." Curr Microbiol 69(2);218-24. PMID: 24816374

Dhavan02: Dhavan GM, Crothers DM, Chance MR, Brenowitz M (2002). "Concerted binding and bending of DNA by Escherichia coli integration host factor." J Mol Biol 315(5);1027-37. PMID: 11827473

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

Ellenberger97: Ellenberger T, Landy A (1997). "A good turn for DNA: the structure of integration host factor bound to DNA." Structure 5(2);153-7. PMID: 9032076

Freundlich92: Freundlich M, Ramani N, Mathew E, Sirko A, Tsui P (1992). "The role of integration host factor in gene expression in Escherichia coli." Mol Microbiol 6(18);2557-63. PMID: 1447969

Friedman84: 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

Friedman88: Friedman DI (1988). "Integration host factor: a protein for all reasons." Cell 55(4);545-54. PMID: 2972385

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Goosen95: Goosen N, van de Putte P (1995). "The regulation of transcription initiation by integration host factor." Mol Microbiol 1995;16(1);1-7. PMID: 7651128

Granston93: Granston AE, Nash HA (1993). "Characterization of a set of integration host factor mutants deficient for DNA binding." J Mol Biol 234(1);45-59. PMID: 8230206

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

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

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

Miller80: Miller HI, Friedman DI (1980). "An E. coli gene product required for lambda site-specific recombination." Cell 20(3);711-9. PMID: 6251971

Moitoso89: Moitoso de Vargas L, Kim S, Landy A (1989). "DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase." Science 244(4911);1457-61. PMID: 2544029

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

Rice96: Rice PA, Yang S, Mizuuchi K, Nash HA (1996). "Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn." Cell 87(7);1295-306. PMID: 8980235

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

Swinger04: Swinger KK, Rice PA (2004). "IHF and HU: flexible architects of bent DNA." Curr Opin Struct Biol 14(1);28-35. PMID: 15102446

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Wasinger98: Wasinger VC, Humphery-Smith I (1998). "Small genes/gene-products in Escherichia coli K-12." FEMS Microbiol Lett 169(2);375-82. PMID: 9868784

Weglenska96: Weglenska A, Jacob B, Sirko A (1996). "Transcriptional pattern of Escherichia coli ihfB (himD) gene expression." Gene 1996;181(1-2);85-8. PMID: 8973312

Yang89a: Yang CC, Nash HA (1989). "The interaction of E. coli IHF protein with its specific binding sites." Cell 57(5);869-80. PMID: 2541927

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

Other References Related to Gene Regulation

Boni01: Boni IV, Artamonova VS, Tzareva NV, Dreyfus M (2001). "Non-canonical mechanism for translational control in bacteria: synthesis of ribosomal protein S1." EMBO J 20(15);4222-32. PMID: 11483525

Bykowski98: Bykowski T, Sirko A (1998). "Selected phenotypes of ihf mutants of Escherichia coli." Biochimie 1998;80(12);987-1001. PMID: 9924977

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

Pedersen84: Pedersen S, Skouv J, Kajitani M, Ishihama A (1984). "Transcriptional organization of the rpsA operon of Escherichia coli." Mol Gen Genet 196(1);135-40. PMID: 6384724

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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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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