RegulonDB RegulonDB 11.2: Operon Form
   

hupA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: hupA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: hupA
Gene(s): hupA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Kohno K., et al., 1990
Promoter
Name: hupAp
+1: 4200176
Distance from start of the gene: 105
Sequence:
Note(s): The activity of this promoter appears to be decreased in the presence of σE. It is repressed during the first 5 minutes following σE induction and decreased from 5 to 10 minutes and from 10 to 20 minutes after induction of the σ factor Lacoux C,2020.
Single-cell assays have shown that the hupAp promoter is heterogeneously activated in cells within the same culture. In some cells the promoter is activated to a greater extent than in others; in approximately 20% of the cells in a given culture the promoter is not activated Teramoto J, Yamanishi Y, Magdy el-SH, Hasegawa A, Kori A, Nakajima M, Arai F, Fukuda T, Ishihama A,2010
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Claret L., et al., 1996
[1] Kohno K., et al., 1990
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: agttttaacgAAGGGGTGGTTTCACCCCTTttgtctttct
Reference(s): [1] Kohno K., et al., 1990
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator hupAp 4200102 4200123 -63.5 taagaccagaAAACGTGATTTAACGCCTGATTtgtcgtacct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis activator hupAp 4199914 4199928 -255.0 aggctggtcgCGAAATGAGCGATGAagagcttaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
remote Fis activator hupAp 4199949 4199963 -219.5 gaaaacccagCTGTAGAGCAAGAATgggacattca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
remote Fis activator hupAp 4200001 4200015 -167.5 ttttagctgaGTGCGAAGAACGCGAtatcgagctg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
remote Fis activator hupAp 4200075 4200089 -93.5 agcaatattgGTATAATTTTTCAGCaataagacca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]


Evidence    

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence


Reference(s)    

 [1] Kohno K., Wada M., Kano Y., Imamoto F., 1990, Promoters and autogenous control of the Escherichia coli hupA and hupB genes., J Mol Biol 213(1):27-36

 [2] Claret L., Rouviere-Yaniv J., 1996, Regulation of HU alpha and HU beta by CRP and FIS in Escherichia coli., J Mol Biol 263(2):126-39

 [3] 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.

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