RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit       
Name: eptB
Gene(s): eptB   Genome Browser M3D Gene expression COLOMBOS
Note(s): MgrR, a small RNA (sRNA), strongly negatively regulates eptB Moon K,2013 PhoQP also negatively regulates eptB expression, indirectly via the mgrR sRNA Moon K,2013
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: eptBp
+1: 3710581
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 106
Sequence: tttgtgcttcatgcacactctttccccacactttttccctttgctgtggtctacttattcGcgcgtgtagattttacttat
                               -35                  -10     +1                   
Note(s): The expression of the eptB gene is induced primarily by σ70, and it is totally repressed by MgrR Moon K,2013 However, when σE is induced, expression of eptB is significant even in the presence of MgrR Moon K,2013
This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence: [ICWHO]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[2] Moon K., et al., 2009
[3] Moon K., et al., 2013
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA MgrR eptB repressor 3710468 3710482 UAUCUCAUGCAAACA nd [IDA], [IHBCE], [IMP] [2], [3], [4]
small regulatory RNA ArcZ eptB repressor 3710482 3710498 AAACCCUGGACAAACAG nd [SM] [3]


Transcription unit       
Name: eptB
Gene(s): eptB   Genome Browser M3D Gene expression COLOMBOS
Note(s): MgrR, a small RNA (sRNA), strongly negatively regulates eptB Moon K,2013 PhoQP also negatively regulates eptB expression, indirectly via the mgrR sRNA Moon K,2013
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: eptBp2
+1: 3710581
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 106
Sequence: tttgtgcttcatgcacactctttccccacactttttccctttgctgtggtctacttattcGcgcgtgtagattttacttat
                                               -10          +1                   
Note(s): The expression of the eptB gene is induced primarily by σ70, and it is totally repressed by MgrR Moon K,2013 However, when σE is induced, expression of eptB is significant even in the presence of MgrR Moon K,2013
This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence: [IHBCE]
[TIM]
Reference(s): [2] Moon K., et al., 2009
[3] Moon K., et al., 2013
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA ArcZ eptB repressor 3710482 3710498 AAACCCUGGACAAACAG nd [SM] [3]
small regulatory RNA MgrR eptB repressor 3710468 3710482 UAUCUCAUGCAAACA nd [IDA], [IHBCE], [IMP] [2], [3], [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.5 3710483 3710522 gggcctgaaaAGCCACTAAGCAGGGTGTTATCACCTGTTTGTCCAGGGTttgtttgcat
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"


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [IDA] Inferred from direct assay

 [IHBCE] Inferred by a human based on computational evidence

 [IMP] Inferred from mutant phenotype

 [SM] Site mutation


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] Moon K., Gottesman S., 2009, A PhoQ/P-regulated small RNA regulates sensitivity of Escherichia coli to antimicrobial peptides., Mol Microbiol 74(6):1314-30

 [3] Moon K., Six DA., Lee HJ., Raetz CR., Gottesman S., 2013, Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification., Mol Microbiol 89(1):52-64

 [4] Kwiatkowska J., Wroblewska Z., Johnson KA., Olejniczak M., 2018, The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs., RNA 24(12):1761-1784

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