RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: pepD
Gene(s): pepD   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for pepD . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Henrich B., et al., 1990
Promoter
Name: pepDp3
+1: 255737
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 21
Sequence: cctgtcttgtgttgacaacattttctgctaaccctgtgacctgcaatactgttttgcgggTgatcgacaaggagacttaac
                     -35                     -10            +1                   
Note(s): Although Henrich B,1990 identified two promoters upstream of the pepD gene, he did not identify the pepDp3 promoter, which was found in the stationary phase of growth by Brombacher E,2003.
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Brombacher E., et al., 2003
[3] Huerta AM., et al., 2003
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CsgD1 repressor pepDp3 255731 255741 2.0 atactgttttGCGGGTGATCGAcaaggagact nd [AIBSCS], [GEA] [2]
Note(s): 1Since the CsgD-binding site overlaps the pepDp3 promoter and the transcription factor has a negative effect on the transcription of the pepD gene Brombacher E,2003, the regulatory effect of CsgD has been linked to the pepDp3 promoter, although an effect of the protein on the other promoters has not been discarded.1Since the CsgD-binding site overlaps the pepDp3 promoter and the transcription factor has a negative effect on the transcription of the pepD gene Brombacher E,2003, the regulatory effect of CsgD has been linked to the pepDp3 promoter, although an effect of the protein on the other promoters has not been discarded.


Transcription unit       
Name: pepD
Gene(s): pepD   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for pepD . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Henrich B., et al., 1990
Promoter
Name: pepDp2
+1: 255776
Distance from start of the gene: 60
Sequence: acgcgggataaagtggtattctcaaacatatctcgcaagcctgtcttgtgttgacaacatTttctgctaaccctgtgacct
Note(s): Brombacher E,2003 could not identify the transcriptional start site of the pepDp2 promoter in the stationary phase of growth, but 39 bp downstream of this promoter, he found another promoter (pepDp3) that was not identified by Henrich B,1990.
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [1] Henrich B., et al., 1990
[4] Salgado H, et al., 2012


Transcription unit       
Name: pepD
Gene(s): pepD   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for pepD . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Henrich B., et al., 1990
Promoter
Name: pepDp1
+1: 255809
Distance from start of the gene: 93
Sequence: agtccgcgtctttttacgcactgcctctccctgacgcgggataaagtggtattctcaaacAtatctcgcaagcctgtcttg
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [2] Brombacher E., et al., 2003
[1] Henrich B., et al., 1990
[4] Salgado H, et al., 2012





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