RegulonDB

RegulonDB RegulonDB 11.1: Gene Form

hns gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	hns
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
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:

cytosol,bacterial nucleoid,membrane

Molecular weight:

15.54

Isoelectric point:

5.13

Motif(s):

Type	Positions	Sequence	Comment
	2 -> 20	SEALKILNNIRTLRAQARE	UniProt: No longer complements a deletion mutant, has dominant-negative effects on wild-type protein, oligomerizes..
	6 -> 6	K	UniProt: No effect on oligomerization of N-terminal fragment 1-89..
	12 -> 12	R	UniProt: Derepression of proV and bgl expression, normal DNA-binding, normal oligomerization..
	15 -> 15	R	UniProt: Derepression of proV and bgl expression..
	17 -> 17	Q	UniProt: Abolishes oligomerization of N-terminal fragment 1-89..

Type	Positions	Sequence	Comment
	2 -> 20	SEALKILNNIRTLRAQARE	UniProt: No longer complements a deletion mutant, has dominant-negative effects on wild-type protein, oligomerizes..
	6 -> 6	K	UniProt: No effect on oligomerization of N-terminal fragment 1-89..
	12 -> 12	R	UniProt: Derepression of proV and bgl expression, normal DNA-binding, normal oligomerization..
	15 -> 15	R	UniProt: Derepression of proV and bgl expression..
	17 -> 17	Q	UniProt: Abolishes oligomerization of N-terminal fragment 1-89..
	21 -> 63	CTLETLEEMLEKLEVVVNERREEESAAAAEVEERTRKLQQYRE	UniProt: Involved in dimerization; Sequence Annotation Type: region of interest.
	26 -> 26	L	UniProt: Partial loss of repressor function..
	30 -> 30	L	UniProt: Wild-type function..
	32 -> 32	K	UniProt: Loss of Hha binding by fragment 1-64, protein folding is unaffected..
	33 -> 127	LEVVVNERREEESAAAAEVEERTRKLQQYREMLIADGIDPNELLNSLAAVKSGTKAKRAQRPAKYSYVDENGETKTWTGQGRTPAVIKKAMDEQG
	53 -> 55	ERT	UniProt: Partial loss of repressor function..
	54 -> 54	R	UniProt: Derepression of proV and bgl expression..
	64 -> 137	MLIADGIDPNELLNSLAAVKSGTKAKRAQRPAKYSYVDENGETKTWTGQGRTPAVIKKAMDEQGKSLDDFLIKQ	UniProt: No longer complements a deletion mutant, has dominant-negative effects on wild-type protein, oligomerizes..
	90 -> 90	R	UniProt: Derepression of proV expression..
	91 -> 91	A	UniProt: Derepression of proV expression..
	92 -> 137	QRPAKYSYVDENGETKTWTGQGRTPAVIKKAMDEQGKSLDDFLIKQ	UniProt: Required for DNA-binding; Sequence Annotation Type: region of interest.
	93 -> 93	R	UniProt: Derepression of proV expression..
	94 -> 94	P	UniProt: Derepression of proV expression..
	95 -> 95	A	UniProt: Derepression of proV expression..
	97 -> 97	Y	UniProt: Partial loss of repressor function..
	110 -> 110	T	UniProt: Partial loss of repressor function..
	111 -> 111	G	UniProt: Derepression of proV expression..
	112 -> 117	QGRTPA
	113 -> 113	G	UniProt: Partial loss of repressor function..
	114 -> 114	R	UniProt: Derepression of proV expression..
	115 -> 115	T	UniProt: Derepression of proV expression..
	116 -> 116	P	UniProt: Partial loss of repressor function. Protein localizes to nucleoid but forms about 20-fold fewer localization points..
	119 -> 119	I	UniProt: Partial loss of repressor function..
	122 -> 137	AMDEQGKSLDDFLIKQ	UniProt: Partial loss of repressor function..
	133 -> 133	F	UniProt: Partial loss of repressor function..

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:0005667 - transcription regulator complex GO:0036411 - H-NS-Cnu complex GO:0097495 - H-NS-Hha complex GO:1990121 - H-NS complex GO:0005737 - cytoplasm GO:0005829 - cytosol GO:0016020 - membrane 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 cis-regulatory region binding GO:0001217 - DNA-binding transcription repressor activity
	biological_process	GO:0036386 - bacterial nucleoid DNA packaging GO:0006355 - regulation of transcription, DNA-templated GO:0006417 - regulation of translation 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:

[COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP] Inferred from expression pattern
[EXP-IMP] Inferred from mutant phenotype
[EXP-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:

ALPHAFOLD:

DIP:

DISPROT:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MINT:

PDB:

PDB:

PDB:

PDB:

PDB:

PFAM:

PRIDE:

PRODB:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

hns

Operon arrangement:

Transcription unit	Promoter
hns	hnsp

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	nd	[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	nd	[COMP-AINF]	[27]
	promoter	tdkp1	1293516		forward	nd	[COMP-AINF]	[27]

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