RegulonDB

Gene
Name:	rpoH
Synonym(s):	ECK3445, EG10897, b3461, fam, hin, htpR
Genome position(nucleotides):	3599929 <-- 3600783 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.15
External database links:

ASAP:	ABE-0011303
CGSC:	618
ECHOBASE:	EB0890
ECOLIHUB:	rpoH
OU-MICROARRAY:	b3461
STRING:	511145.b3461
COLOMBOS:	rpoH

Gene

Name:

rpoH

Synonym(s):

ECK3445, EG10897, b3461, fam, hin, htpR

Genome position(nucleotides):

3599929 <-- 3600783 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

54.15

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

228 -> 280

AMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRA

77 -> 80

DLIQ

118 -> 125

LRNWRIVK

193 -> 194

232 -> 284

LDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA

Type

Positions

Sequence

228 -> 280

AMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRA

77 -> 80

DLIQ

118 -> 125

LRNWRIVK

193 -> 194

232 -> 284

LDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA

133 -> 140

RKLFFNLR

149 -> 195

FNQDEVEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPM

53 -> 122

LILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR

54 -> 54

80 -> 80

58 -> 90

LRFVVHIARNYAGYGLPQADLIQEGNIGLMKAV

253 -> 272

LQELADRYGVSAERVRQLEK

185 -> 185

Multifun Terms (GenProtEC)

2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related

3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.1 - sigma factors, anti-sigmafactors

3 - regulation --> 3.3 - genetic unit regulated --> 3.3.3 - stimulon

5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes

Gene Ontology Terms (GO)

cellular_component

GO:0031421 - invertasome
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0005886 - plasma membrane

molecular_function

GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0016987 - sigma factor activity
GO:0003700 - DNA-binding transcription factor activity
GO:0009009 - site-specific recombinase activity
GO:0001000 - bacterial-type RNA polymerase core enzyme binding
GO:0000985 - bacterial-type RNA polymerase core promoter sequence-specific DNA binding
GO:0001216 - DNA-binding transcription activator activity

biological_process

GO:0006310 - DNA recombination
GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0009408 - response to heat
GO:0006352 - DNA-templated transcription, initiation
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0010468 - regulation of gene expression
GO:0001121 - bacterial transcription
GO:2000142 - regulation of DNA-templated transcription, initiation
GO:0001123 - transcription initiation from bacterial-type RNA polymerase promoter

Transcriptional Regulation
	Display Regulation
Activated by:	CRP, CpxR, IHF
Repressed by:	CRP, DnaA, CytR

Transcriptional Regulation

Display Regulation

Activated by:

CRP, CpxR, IHF

Repressed by:

CRP, DnaA, CytR

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_4062	3599692	reverse	nd	[RS-EPT-CBR]	[12]
promoter	TSS_4063 (cluster)	3599761	reverse	nd	[RS-EPT-CBR]	[12]
promoter	TSS_4066	3600865	reverse	nd	[RS-EPT-CBR]	[12]
promoter	TSS_4067	3600867	reverse	nd	[RS-EPT-CBR]	[12]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_4062

3599692

reverse

[RS-EPT-CBR]

[12]

promoter

TSS_4063 (cluster)

3599761

reverse

[RS-EPT-CBR]

[12]

promoter

TSS_4066

3600865

reverse

[RS-EPT-CBR]

[12]

promoter

TSS_4067

3600867

reverse

[RS-EPT-CBR]

[12]

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

Evidence

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

Reference(s)
[1] Barros SA., Yoon I., Chenoweth DM., 2016, Modulation of the E. coli rpoH Temperature Sensor with Triptycene-Based Small Molecules., Angew Chem Int Ed Engl 55(29):8258-61
[2] Grossman AD., Erickson JW., Gross CA., 1984, The htpR gene product of E. coli is a sigma factor for heat-shock promoters., Cell 38(2):383-90
[3] Liberek K., Galitski TP., Zylicz M., Georgopoulos C., 1992, The DnaK chaperone modulates the heat shock response of Escherichia coli by binding to the sigma 32 transcription factor., Proc Natl Acad Sci U S A 89(8):3516-20
[4] Meyer AS., Baker TA., 2011, Proteolysis in the Escherichia coli heat shock response: a player at many levels., Curr Opin Microbiol 14(2):194-9
[5] Neidhardt FC., VanBogelen RA., Lau ET., 1983, Molecular cloning and expression of a gene that controls the high-temperature regulon of Escherichia coli., J Bacteriol 153(2):597-603
[6] Straus DB., Walter WA., Gross CA., 1989, The activity of sigma 32 is reduced under conditions of excess heat shock protein production in Escherichia coli., Genes Dev 3(12A):2003-10
[7] Suzuki H., Ikeda A., Tsuchimoto S., Adachi K., Noguchi A., Fukumori Y., Kanemori M., 2012, Synergistic binding of DnaJ and DnaK chaperones to heat shock transcription factor σ32 ensures its characteristic high metabolic instability: implications for heat shock protein 70 (Hsp70)-Hsp40 mode of function., J Biol Chem 287(23):19275-83
[8] Tobe T., Ito K., Yura T., 1984, Isolation and physical mapping of temperature-sensitive mutants defective in heat-shock induction of proteins in Escherichia coli., Mol Gen Genet 195(1-2):10-6
[9] Urech C., Koby S., Oppenheim AB., Munchbach M., Hennecke H., Narberhaus F., 2000, Differential degradation of Escherichia coli sigma32 and Bradyrhizobium japonicum RpoH factors by the FtsH protease., Eur J Biochem 267(15):4831-9
[10] Yamamori T., Yura T., 1982, Genetic control of heat-shock protein synthesis and its bearing on growth and thermal resistance in Escherichia coli K-12., Proc Natl Acad Sci U S A 79(3):860-4
[11] Yura T., Tobe T., Ito K., Osawa T., 1984, Heat shock regulatory gene (htpR) of Escherichia coli is required for growth at high temperature but is dispensable at low temperature., Proc Natl Acad Sci U S A 81(21):6803-7
[12] 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.

Reference(s)

[1] Barros SA., Yoon I., Chenoweth DM., 2016, Modulation of the E. coli rpoH Temperature Sensor with Triptycene-Based Small Molecules., Angew Chem Int Ed Engl 55(29):8258-61

[2] Grossman AD., Erickson JW., Gross CA., 1984, The htpR gene product of E. coli is a sigma factor for heat-shock promoters., Cell 38(2):383-90

[3] Liberek K., Galitski TP., Zylicz M., Georgopoulos C., 1992, The DnaK chaperone modulates the heat shock response of Escherichia coli by binding to the sigma 32 transcription factor., Proc Natl Acad Sci U S A 89(8):3516-20

[4] Meyer AS., Baker TA., 2011, Proteolysis in the Escherichia coli heat shock response: a player at many levels., Curr Opin Microbiol 14(2):194-9

[5] Neidhardt FC., VanBogelen RA., Lau ET., 1983, Molecular cloning and expression of a gene that controls the high-temperature regulon of Escherichia coli., J Bacteriol 153(2):597-603

[6] Straus DB., Walter WA., Gross CA., 1989, The activity of sigma 32 is reduced under conditions of excess heat shock protein production in Escherichia coli., Genes Dev 3(12A):2003-10

[7] Suzuki H., Ikeda A., Tsuchimoto S., Adachi K., Noguchi A., Fukumori Y., Kanemori M., 2012, Synergistic binding of DnaJ and DnaK chaperones to heat shock transcription factor σ32 ensures its characteristic high metabolic instability: implications for heat shock protein 70 (Hsp70)-Hsp40 mode of function., J Biol Chem 287(23):19275-83

[8] Tobe T., Ito K., Yura T., 1984, Isolation and physical mapping of temperature-sensitive mutants defective in heat-shock induction of proteins in Escherichia coli., Mol Gen Genet 195(1-2):10-6

[9] Urech C., Koby S., Oppenheim AB., Munchbach M., Hennecke H., Narberhaus F., 2000, Differential degradation of Escherichia coli sigma32 and Bradyrhizobium japonicum RpoH factors by the FtsH protease., Eur J Biochem 267(15):4831-9

[10] Yamamori T., Yura T., 1982, Genetic control of heat-shock protein synthesis and its bearing on growth and thermal resistance in Escherichia coli K-12., Proc Natl Acad Sci U S A 79(3):860-4

[11] Yura T., Tobe T., Ito K., Osawa T., 1984, Heat shock regulatory gene (htpR) of Escherichia coli is required for growth at high temperature but is dispensable at low temperature., Proc Natl Acad Sci U S A 81(21):6803-7

[12] 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.