RegulonDB RegulonDB 10.8: Gene Form

hns gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

galU tdk hns Fis Fis H-NS Fis Fis H-NS Fis H-NS Fis Fis DsrA terminator tdkp1 tdkp1 tdkp8 tdkp8 hnsp hnsp TSS_1575 TSS_1575 TSS_1574 TSS_1574 TSS_1573 TSS_1573 TSS_1572 (cluster) TSS_1572 (cluster) TSS_1571 TSS_1571 TSS_1570 TSS_1570 TSS_1569 TSS_1569 TSS_1568 TSS_1568 TSS_1567 TSS_1567

Name: hns    Texpresso search in the literature
Synonym(s): B1, ECK1232, EG10457, H1, b1237, bglY, cur, drc, drdX, drs, fimG, hnsA, irk, msyA, osmZ, pilG, topS, topX, virR
Genome position(nucleotides): 1292509 <-- 1292922 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
External database links:  

Name: DNA-binding transcriptional dual regulator H-NS
Synonym(s): BglY, Cur, DNA-binding protein HLP-II (HU, BH2, HD, NS), Drc, DrdX, Drs, FimG, H-NS, Hns, HnsA, Irk, MsyA, OsmZ, PilG, TopS, TopX, VirR
Sequence: Get amino acid sequence Fasta Format
Regulator Family: HNS
Cellular location: bacterial nucleoid,cytosol
Molecular weight: 15.54
Isoelectric point: 5.13
Type Positions Sequence
12 -> 12 R
32 -> 32 K
112 -> 117 QGRTPA
15 -> 15 R
111 -> 111 G


Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  2 - information transfer --> 2.3 - protein related --> 2.3.7 - nucleoproteins, basic proteins
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0009295 - nucleoid
GO:0032993 - protein-DNA complex
molecular_function GO:0003680 - AT DNA binding
GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003723 - RNA binding
GO:0003681 - bent DNA binding
GO:0042802 - identical protein binding
GO:0046983 - protein dimerization activity
GO:0000976 - transcription regulatory region sequence-specific DNA binding
GO:0001217 - DNA-binding transcription repressor activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006417 - regulation of translation
GO:0016458 - gene silencing
GO:0045892 - negative regulation of transcription, DNA-templated
GO:1900232 - negative regulation of single-species biofilm formation on inanimate substrate
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
[IMP] Inferred from mutant phenotype
[IPI] Inferred from physical interaction
Reference(s): [1] Becker NA., et al., 2007
[2] Bertin P., et al., 1999
[3] Bertin P., et al., 2001
[4] Corbett D., et al., 2007
[5] Dame RT. 2005
[6] Dorman CJ. 2004
[7] Falconi M., et al., 1988
[8] Falconi M., et al., 1993
[9] Giangrossi M., et al., 2005
[10] Goransson M., et al., 1990
[11] Kajitani M., et al., 1991
[12] Laine B., et al., 1984
[13] Lang B., et al., 2007
[14] Luijsterburg MS., et al., 2006
[15] Madrid C., et al., 2007
[16] May G., et al., 1990
[17] Pon CL., et al., 1988
[18] Sonden B., et al., 1996
[19] Ueguchi C., et al., 1992
[20] Ueguchi C., et al., 1993
[21] Ussery DW., et al., 1994
[22] Williams RM., et al., 1997
[23] Wolf T., et al., 2006
[24] Yamada H., et al., 1990
[25] Zimmerman SB. 2006
External database links:  

Name: hns         
Operon arrangement:
Transcription unit        Promoter

Transcriptional Regulation      
Display Regulation             
Activated by: GadX, CspA, Fis
Repressed by: H-NS

Regulation by small RNA    
  Display Regulation
small RNA dsrA

Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1567 1291580 forward nd [RS-EPT-CBR] [26]
  promoter TSS_1568 1291585 forward nd [RS-EPT-CBR] [26]
  promoter TSS_1569 1292735 reverse nd [RS-EPT-CBR] [26]
  promoter TSS_1570 1292806 reverse nd [RS-EPT-CBR] [26]
  promoter TSS_1571 1292820 reverse nd [RS-EPT-CBR] [26]
  promoter TSS_1572 (cluster) 1292827 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [26]
  promoter TSS_1573 1292931 reverse nd [RS-EPT-CBR] [26]
  promoter TSS_1574 1292937 reverse nd [RS-EPT-CBR] [26]
  promoter TSS_1575 1292942 reverse nd [RS-EPT-CBR] [26]
  promoter tdkp8 1293493 forward Similarity to the consensus
Read more >
[ICWHO] [27]
  promoter tdkp1 1293516 forward Similarity to the consensus
Read more >
[ICWHO] [27]


 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight


 [1] Becker NA., Kahn JD., Maher LJ., 2007, Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli., Nucleic Acids Res 35(12):3988-4000

 [2] Bertin P., Benhabiles N., Krin E., Laurent-Winter C., Tendeng C., Turlin E., Thomas A., Danchin A., Brasseur R., 1999, The structural and functional organization of H-NS-like proteins is evolutionarily conserved in gram-negative bacteria., Mol Microbiol 31(1):319-29

 [3] Bertin P., Hommais F., Krin E., Soutourina O., Tendeng C., Derzelle S., Danchin A., 2001, H-NS and H-NS-like proteins in Gram-negative bacteria and their multiple role in the regulation of bacterial metabolism., Biochimie 83(2):235-41

 [4] Corbett D., Bennett HJ., Askar H., Green J., Roberts IS., 2007, SlyA and H-NS regulate transcription of the Escherichia coli K5 capsule gene cluster, and expression of slyA in Escherichia coli is temperature-dependent, positively autoregulated, and independent of H-NS., J Biol Chem 282(46):33326-35

 [5] Dame RT., 2005, The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin., Mol Microbiol 56(4):858-70

 [6] Dorman CJ., 2004, H-NS: a universal regulator for a dynamic genome., Nat Rev Microbiol 2(5):391-400

 [7] Falconi M., Gualtieri MT., La Teana A., Losso MA., Pon CL., 1988, Proteins from the prokaryotic nucleoid: primary and quaternary structure of the 15-kD Escherichia coli DNA binding protein H-NS., Mol Microbiol 2(3):323-9

 [8] Falconi M., Higgins NP., Spurio R., Pon CL., Gualerzi CO., 1993, Expression of the gene encoding the major bacterial nucleotide protein H-NS is subject to transcriptional auto-repression., Mol Microbiol 10(2):273-82

 [9] Giangrossi M., Zattoni S., Tramonti A., De Biase D., Falconi M., 2005, Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli., J Biol Chem 280(22):21498-505

 [10] Goransson M., Sonden B., Nilsson P., Dagberg B., Forsman K., Emanuelsson K., Uhlin BE., 1990, Transcriptional silencing and thermoregulation of gene expression in Escherichia coli., Nature 344(6267):682-5

 [11] Kajitani M., Ishihama A., 1991, Identification and sequence determination of the host factor gene for bacteriophage Q beta., Nucleic Acids Res 19(5):1063-6

 [12] Laine B., Sautiere P., Spassky A., Rimsky S., 1984, A DNA-binding protein from E. coli isolation, characterization and its relationship with proteins H1 and B1., Biochem Biophys Res Commun 119(3):1147-53

 [13] Lang B., Blot N., Bouffartigues E., Buckle M., Geertz M., Gualerzi CO., Mavathur R., Muskhelishvili G., Pon CL., Rimsky S., Stella S., Babu MM., Travers A., 2007, High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes., Nucleic Acids Res 35(18):6330-7

 [14] Luijsterburg MS., Noom MC., Wuite GJ., Dame RT., 2006, The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective., J Struct Biol 156(2):262-72

 [15] Madrid C., Balsalobre C., Garcia J., Juarez A., 2007, The novel Hha/YmoA family of nucleoid-associated proteins: use of structural mimicry to modulate the activity of the H-NS family of proteins., Mol Microbiol 63(1):7-14

 [16] May G., Dersch P., Haardt M., Middendorf A., Bremer E., 1990, The osmZ (bglY) gene encodes the DNA-binding protein H-NS (H1a), a component of the Escherichia coli K12 nucleoid., Mol Gen Genet 224(1):81-90

 [17] Pon CL., Calogero RA., Gualerzi CO., 1988, Identification, cloning, nucleotide sequence and chromosomal map location of hns, the structural gene for Escherichia coli DNA-binding protein H-NS., Mol Gen Genet 212(2):199-202

 [18] Sonden B., Uhlin BE., 1996, Coordinated and differential expression of histone-like proteins in Escherichia coli: regulation and function of the H-NS analog StpA., EMBO J 15(18):4970-80

 [19] Ueguchi C., Ito K., 1992, Multicopy suppression: an approach to understanding intracellular functioning of the protein export system., J Bacteriol 174(5):1454-61

 [20] Ueguchi C., Kakeda M., Mizuno T., 1993, Autoregulatory expression of the Escherichia coli hns gene encoding a nucleoid protein: H-NS functions as a repressor of its own transcription., Mol Gen Genet 236(2-3):171-8

 [21] Ussery DW., Hinton JC., Jordi BJ., Granum PE., Seirafi A., Stephen RJ., Tupper AE., Berridge G., Sidebotham JM., Higgins CF., 1994, The chromatin-associated protein H-NS., Biochimie 76(10-11):968-80

 [22] Williams RM., Rimsky S., 1997, Molecular aspects of the E. coli nucleoid protein, H-NS: a central controller of gene regulatory networks., FEMS Microbiol Lett 156(2):175-85

 [23] Wolf T., Janzen W., Blum C., Schnetz K., 2006, Differential dependence of StpA on H-NS in autoregulation of stpA and in regulation of bgl., J Bacteriol 188(19):6728-38

 [24] Yamada H., Muramatsu S., Mizuno T., 1990, An Escherichia coli protein that preferentially binds to sharply curved DNA., J Biochem 108(3):420-5

 [25] Zimmerman SB., 2006, Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase., J Struct Biol 153(2):160-75

 [26] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [27] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78