RegulonDB RegulonDB 10.9: 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

Gene      
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 %:  
46.62
External database links:  
ASAP:
ABE-0004152
CGSC:
960
ECHOBASE:
EB0452
ECOLIHUB:
hns
OU-MICROARRAY:
b1237
STRING:
511145.b1237
COLOMBOS: hns


Product      
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
Motif(s):
 
Type Positions Sequence
12 -> 12 R
112 -> 117 QGRTPA
15 -> 15 R
32 -> 127 KLEVVVNERREEESAAAAEVEERTRKLQQYREMLIADGIDPNELLNSLAAVKSGTKAKRAQRPAKYSYVDENGETKTWTGQGRTPAVIKKAMDEQG
111 -> 111 G

 

Classification:
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 --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - 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 - minor groove of adenine-thymine-rich 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:  
DIP:
DIP-35853N
DISPROT:
DP00776
ECOCYC:
PD00288
ECOLIWIKI:
b1237
INTERPRO:
IPR027444
INTERPRO:
IPR001801
INTERPRO:
IPR037150
INTERPRO:
IPR027454
MINT:
P0ACF8
PDB:
2MW2
PDB:
1NI8
PDB:
1LR1
PDB:
1HNS
PDB:
1HNR
PFAM:
PF00816
PRIDE:
P0ACF8
PRODB:
PRO_000022909
REFSEQ:
NP_415753
SMART:
SM00528
SMR:
P0ACF8
UNIPROT:
P0ACF8


Operon      
Name: hns         
Operon arrangement:
Transcription unit        Promoter
hns


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


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]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [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


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