RegulonDB RegulonDB 10.9: Operon Form
   

dnaK-tpke11-dnaJ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: dnaK-tpke11-dnaJ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: dnaKJ
Gene(s): dnaK, tpke11, dnaJ   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the dnaKJ operon is increased under the stress condition caused by the introduction of the R1-16 plasmid, which encodes the type IV secretion system (T4S machinery) in the cell. dnaKJ operon expression is σ32 dependent, and it was observed that the expression of the σ32 gene is enhanced with the R1-16 plasmid in the cell in a CpxR-dependent way Zahrl D,2006
The dnaKJ operon is upregulated by short-term (30 min) exposure of E. coli to some biocides 32385082.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dnaK . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [PM] Polar mutation
Reference(s): [1] Thomas JG., et al., 1996
[2] Zhou YN., et al., 1988
Promoter
Name: dnaKp1
+1: 12048
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 115
Sequence: gcacaaaaaatttttgcatctcccccttgatgacgtggtttacgaccccatttagtagtcAaccgcagtgagtgagtctgc
                           -35                -10           +1                   
Note(s): Transcripts from dnaKp1 and dnaKp2 are the major products of in vitro transcription of the dnaKJ operon by σ32. This sigma holoenzyme transcribes dnaKp3 poorly.
Evidence: [HIPP]
[ICWHO]
[IDA]
[IEP]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Cowing DW., et al., 1985
[4] Huerta AM., et al., 2003
[5] Nonaka G., et al., 2006
[6] Salgado H, et al., 2012
[7] Wade JT., et al., 2006
[8] Wagner MA., et al., 2009
[2] Zhou YN., et al., 1988


Transcription unit       
Name: dnaKJ
Gene(s): dnaK, tpke11, dnaJ   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the dnaKJ operon is increased under the stress condition caused by the introduction of the R1-16 plasmid, which encodes the type IV secretion system (T4S machinery) in the cell. dnaKJ operon expression is σ32 dependent, and it was observed that the expression of the σ32 gene is enhanced with the R1-16 plasmid in the cell in a CpxR-dependent way Zahrl D,2006
The dnaKJ operon is upregulated by short-term (30 min) exposure of E. coli to some biocides 32385082
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dnaK . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [PM] Polar mutation
Reference(s): [9] Bardwell JC., et al., 1986
Promoter
Name: dnaKp2
+1: 12123
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 40
Sequence: gtctgcaaaaaaatgaaattgggcagttgaaaccagacgtttcgcccctattacagactcAcaaccacatgatgaccgaat
                           -35                -10           +1                   
Note(s): Transcripts from dnaKp1 and dnaKp2 are the major products of in vitro transcription of the dnaKJ operon by σ32. This sigma holoenzyme transcribes dnaKp3 poorly.
Evidence: [HIPP]
[ICWHO]
[IDA]
[IEP]
[TIM]
Reference(s): [3] Cowing DW., et al., 1985
[4] Huerta AM., et al., 2003
[5] Nonaka G., et al., 2006
[7] Wade JT., et al., 2006
[8] Wagner MA., et al., 2009
[2] Zhou YN., et al., 1988


Transcription unit       
Name: dnaKJ
Gene(s): dnaK, tpke11, dnaJ   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the dnaKJ operon is increased under the stress condition caused by the introduction of the R1-16 plasmid, which encodes the type IV secretion system (T4S machinery) in the cell. dnaKJ operon expression is σ32 dependent, and it was observed that the expression of the σ32 gene is enhanced with the R1-16 plasmid in the cell in a CpxR-dependent way Zahrl D,2006
The dnaKJ operon is upregulated by short-term (30 min) exposure of E. coli to some biocides 32385082.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dnaK . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [PM] Polar mutation
Reference(s): [9] Bardwell JC., et al., 1986
Promoter
Name: dnaKp3
+1: 12144
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 19
Sequence: ggcagttgaaaccagacgtttcgcccctattacagactcacaaccacatgatgaccgaatAtatagtggagacgtttagat
                          -35               -10             +1                   
Note(s): Transcripts from dnaKp1 and dnaKp2 are the major products of in vitro transcription of the dnaKJ operon by σ32, but this sigma factor polymerase transcribes dnaKp3 poorly.
Evidence: [HIPP]
[ICWHO]
[IDA]
[IEP]
[TIM]
Reference(s): [3] Cowing DW., et al., 1985
[4] Huerta AM., et al., 2003
[7] Wade JT., et al., 2006
[8] Wagner MA., et al., 2009
[2] Zhou YN., et al., 1988


Transcription unit       
Name: tpke11
Gene(s): tpke11   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IHBCE] Inferred by a human based on computational evidence


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [10] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.6 14134 14155 ttcctctccgCCCGTGCATTCATCTAGGGGCaatttaaaaa
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"




Reference(s)    

 [1] Thomas JG., Baneyx F., 1996, Protein folding in the cytoplasm of Escherichia coli: requirements for the DnaK-DnaJ-GrpE and GroEL-GroES molecular chaperone machines., Mol Microbiol 21(6):1185-96

 [2] Zhou YN., Kusukawa N., Erickson JW., Gross CA., Yura T., 1988, Isolation and characterization of Escherichia coli mutants that lack the heat shock sigma factor sigma 32., J Bacteriol 170(8):3640-9

 [3] Cowing DW., Bardwell JC., Craig EA., Woolford C., Hendrix RW., Gross CA., 1985, Consensus sequence for Escherichia coli heat shock gene promoters., Proc Natl Acad Sci U S A 82(9):2679-83

 [4] 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

 [5] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [6] 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.

 [7] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [8] Wagner MA., Zahrl D., Rieser G., Koraimann G., 2009, Growth phase- and cell division-dependent activation and inactivation of the {sigma}32 regulon in Escherichia coli., J Bacteriol 191(5):1695-702

 [9] Bardwell JC., Tilly K., Craig E., King J., Zylicz M., Georgopoulos C., 1986, The nucleotide sequence of the Escherichia coli K12 dnaJ+ gene. A gene that encodes a heat shock protein., J Biol Chem 261(4):1782-5

 [10] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


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