RegulonDB RegulonDB 11.1: 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 Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Brombacher E., et al., 2003
[3] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[CsgD,-] 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 CsgD repressor pepDp3 255731 255741 2.0 tactgttttgCGGGTGATCGAcaaggagact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]


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 Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
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 Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Brombacher E., et al., 2003
[1] Henrich B., et al., 1990
[4] Salgado H, et al., 2012


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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


Reference(s)    

 [1] Henrich B., Monnerjahn U., Plapp R., 1990, Peptidase D gene (pepD) of Escherichia coli K-12: nucleotide sequence, transcript mapping, and comparison with other peptidase genes., J Bacteriol 172(8):4641-51

 [2] Brombacher E., Dorel C., Zehnder AJ., Landini P., 2003, The curli biosynthesis regulator CsgD co-ordinates the expression of both positive and negative determinants for biofilm formation in Escherichia coli., Microbiology 149(Pt 10):2847-57

 [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] 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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