RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: appY
Gene(s): appY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: appYp
+1: 583567
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 114
Sequence: aataaaaaacaacatacatataataatttaatcttaaatgaaatttattaaaatttgcaaActataattttgtgtataaaa
                           -35                   -10        +1                   
Evidence: [AIPP]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[DpiA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd DpiA-Pasp1 repressor appYp nd nd nd nd nd [APIORCISFBSCS], [CV(GEA)], [GEA] [2]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor appYp nd nd nd nd nd [BPP], [GEA] [3]
Note(s): 1A putative DpiA-binding site, which is an A+T-rich sequence, is located upstream of the appY gene Ingmer H,1998.1The appY promoter region contains a curved DNA which could be specific for the recognition of H-NS. However, it is possible that there might be more than one H-NS-binding site in the appY promoter region. H-NS plays a role in the thermoregulation of the appY gene Atlung T,1996.1A putative DpiA-binding site, which is an A+T-rich sequence, is located upstream of the appY gene Ingmer H,1998.
2The appY promoter region contains a curved DNA which could be specific for the recognition of H-NS. However, it is possible that there might be more than one H-NS-binding site in the appY promoter region. H-NS plays a role in the thermoregulation of the appY gene Atlung T,1996.


Transcription unit       
Name: appY
Gene(s): appY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
Reference(s): [4] Maciag A., et al., 2011
Promoter
Name: appYp3
+1: 583580
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 101
Sequence: atacatataataatttaatcttaaatgaaatttattaaaatttgcaaactataattttgtGtataaaaatataaatgcaca
                                                  -10       +1                   
Evidence: [TIM]
Reference(s): [5] Rangarajan AA., et al., 2018


Transcription unit          
Name: appY
Gene(s): appY   Genome Browser M3D Gene expression COLOMBOS
Note(s): appY is positively regulated by RpoS and ArcA in anaerobiosis and also is induced by phosphate starvation and during entry into stationary phase Atlung T,1997. Brondsted L,1996
Evidence: [IEP] Inferred from expression pattern
Reference(s): [4] Maciag A., et al., 2011
Promoter
Name: appYp2
+1: 583656
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 25
Sequence: gcacatcatcctgattatgattgtgtatttaattggttgttatttgactactatcaacttGttttaattttatgataggtg
                                             -10            +1                   
Note(s): Based on ChIP-microarray analysis, it was shown that StpA binds to the promoter region in appYp2 Atlung T,1996. 19151137 qRT-PCR revealed a strong 75-fold repression of appY by H-NS and more than 1,000-fold repression by H-NS/StpA Rangarajan AA,2018
Transcription directed across H-NS binding regions relieves H-NS-mediated (and H-NS/StpA-mediated) repression of promoters such as proVp3, pdeLp3, and appYp2, and there is a correlation between transcription across the H-NS-bound region and derepression where RNA polymerase is able to remodel the H-NS complex and/or dislodge H-NS from the DNA and thus relieve repression Rangarajan AA,2018
Evidence: [HTIM]
Reference(s): [4] Maciag A., et al., 2011
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-Phosphorylated activator appYp2 583454 583464 -197.0 agtgagtttaTGTTAATAAAAagcatagtaa nd [AIBSCS] [6]


Evidence    

 [AIPP] Automated inference of promoter position

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [TIM] Transcription initiation mapping

 [HTIM] High-throughput transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] 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

 [2] Ingmer H., Miller CA., Cohen SN., 1998, Destabilized inheritance of pSC101 and other Escherichia coli plasmids by DpiA, a novel two-component system regulator., Mol Microbiol 29(1):49-59

 [3] Atlung T., Sund S., Olesen K., Brondsted L., 1996, The histone-like protein H-NS acts as a transcriptional repressor for expression of the anaerobic and growth phase activator AppY of Escherichia coli., J Bacteriol 178(12):3418-25

 [4] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [5] Rangarajan AA., Schnetz K., 2018, Interference of transcription across H-NS binding sites and repression by H-NS., Mol Microbiol 108(3):226-239

 [6] Lynch AS., Lin EC., 1996, Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters., J Bacteriol 178(21):6238-49

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