RegulonDB RegulonDB 10.8: Operon Form
   

ptrA-recBD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ptrA
Gene(s): ptrA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcript of ptrA is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Reference(s): [1] Claverie-Martin F., et al., 1987
Promoter
Name: ptrAp
+1: 2959011
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 127
Sequence: aatcagtcatgagtgctgtataaaaattgcgcaatctatccgcttactttatgatgcgcaCcagtcacggactgatggtta
                           -35                    -10       +1                   
Note(s): A potential σ54 or putative nitrogen-regulated (CTGGCAGATGATTTGCG) promoter is located downstream from the -35 and -10 regions of ptrAp Claverie-Martin F,1987. However, whether this promoter is functional in vivo has not been determined Claverie-Martin F,1987.
Evidence: [TIM]
Reference(s): [1] Claverie-Martin F., et al., 1987
TF binding sites (TFBSs)
[LexA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal LexA1 repressor ptrAp 2958982 2959001 20.5 ccagtcacggACTGATGGTTATATAAACATaggctgactc nd [BPP], [CV(CHIP-SV/SM)], [SM] [2]
Note(s): 1Although the ptrAp promoter lacks a canonical LexA sequence, it is recognized by LexA based on ChIP-chip analysis and mutation site experiments Wade JT,2005. This aberrant version of the LexA motif suggests that another transcription factor could be involved in the regulation of the ptrAp promoter in vivo Wade JT,2005.1Although the ptrAp promoter lacks a canonical LexA sequence, it is recognized by LexA based on ChIP-chip analysis and mutation site experiments Wade JT,2005. This aberrant version of the LexA motif suggests that another transcription factor could be involved in the regulation of the ptrAp promoter in vivo Wade JT,2005.


Transcription unit          
Name: ptrA-recBD
Gene(s): recD, recB, ptrA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcript of ptrA is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: ptrAp
+1: 2959011
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 127
Sequence: aatcagtcatgagtgctgtataaaaattgcgcaatctatccgcttactttatgatgcgcaCcagtcacggactgatggtta
                           -35                    -10       +1                   
Note(s): A potential σ54 or putative nitrogen-regulated (CTGGCAGATGATTTGCG) promoter is located downstream from the -35 and -10 regions of ptrAp Claverie-Martin F,1987. However, whether this promoter is functional in vivo has not been determined Claverie-Martin F,1987.
Evidence: [TIM]
Reference(s): [1] Claverie-Martin F., et al., 1987
TF binding sites (TFBSs)
[LexA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal LexA1 repressor ptrAp 2958982 2959001 20.5 ccagtcacggACTGATGGTTATATAAACATaggctgactc nd [BPP], [CV(CHIP-SV/SM)], [SM] [2]
Note(s): 1Although the ptrAp promoter lacks a canonical LexA sequence, it is recognized by LexA based on ChIP-chip analysis and mutation site experiments Wade JT,2005. This aberrant version of the LexA motif suggests that another transcription factor could be involved in the regulation of the ptrAp promoter in vivo Wade JT,2005.1Although the ptrAp promoter lacks a canonical LexA sequence, it is recognized by LexA based on ChIP-chip analysis and mutation site experiments Wade JT,2005. This aberrant version of the LexA motif suggests that another transcription factor could be involved in the regulation of the ptrAp promoter in vivo Wade JT,2005.


Evidence    

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)

 [SM] Site mutation


Reference(s)    

 [1] Claverie-Martin F., Diaz-Torres MR., Kushner SR., 1987, Analysis of the regulatory region of the protease III (ptr) gene of Escherichia coli K-12., Gene 54(2-3):185-95

 [2] Wade JT., Reppas NB., Church GM., Struhl K., 2005, Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites., Genes Dev 19(21):2619-30

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