RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: stpA
Gene(s): stpA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Repression of the stpA gene by H-NS is significantly more effective when a downstream sequence encompassing the stpA coding region is present. It is possible that StpA acts on a transcriptional level or that the RNA chaperone StpA binds to its mRNA Gueune H,2008.
Lrp may partly act to overcome the negative effect of HNS. Lrp activates the transcription of stpA in minimal medium; in rich medium the lower level and more transient expression of stpA is independent of Lrp.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Free A., et al., 1997
[2] Sonden B., et al., 1996
Promoter
Name: stpAp1
+1: 2798536
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 41
Sequence: gactgtaaatagattaaattttgtggaaatataataagtgatcgcttacactacgcgacgAaatactttttttgttttggc
                          -35                       -10     +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Free A., et al., 1997
[3] Huerta AM., et al., 2003
[2] Sonden B., et al., 1996
TF binding sites (TFBSs)
[H-NS,-] 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
nd H-NS repressor stpAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [2]
[Lrp,+] 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 Lrp activator stpAp1 2798636 2798650 -107.0 aatatataatCTTGAAATTATTCTGagagtttcag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [5]
remote Lrp activator stpAp1 2799019 2799034 -490.0 aaatttttatTTAGTCAGTTTTTGTAgataaaatat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [4], [5]
remote Lrp activator stpAp1 2799068 2799083 -539.0 gcattttcgcATAGCGTATATCGCTGgctatgacta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2], [4], [5]
[StpA,-] 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
nd StpA repressor stpAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]


Transcription unit       
Name: stpA
Gene(s): stpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Free A., et al., 1997
[2] Sonden B., et al., 1996
Promoter
Name: stpAp2
+1: 2798556
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 61
Sequence: gctgaaataatctcgcgcaggactgtaaatagattaaattttgtggaaatataataagtgAtcgcttacactacgcgacga
                                                       -10  +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Free A., et al., 1997
[2] Sonden B., et al., 1996


Transcription unit       
Name: stpA
Gene(s): stpA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Free A., et al., 1997
[2] Sonden B., et al., 1996
Promoter
Name: stpAp3
+1: 2798578
Distance from start of the gene: 83
Sequence: ctgagagtttcagaaaataacagctgaaataatctcgcgcaggactgtaaatagattaaaTtttgtggaaatataataagt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Sonden B., et al., 1996


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

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

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

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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

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

 [EXP-IEP-RNA-SEQ] RNA-seq evidence

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-SEQ] ChIP-seq evidence


Reference(s)    

 [1] Free A., Dorman CJ., 1997, The Escherichia coli stpA gene is transiently expressed during growth in rich medium and is induced in minimal medium and by stress conditions., J Bacteriol 179(3):909-18

 [2] 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

 [3] 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

 [4] Ihara K., Sato K., Hori H., Makino Y., Shigenobu S., Ando T., Isogai E., Yoneyama H., 2017, Expression of the alaE gene is positively regulated by the global regulator Lrp in response to intracellular accumulation of l-alanine in Escherichia coli., J Biosci Bioeng 123(4):444-450

 [5] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [6] Gueune H., Durand MJ., Thouand G., DuBow MS., 2008, The ygaVP genes of Escherichia coli form a tributyltin-inducible operon., Appl Environ Microbiol 74(6):1954-8

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