RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: rsd
Gene(s): rsd   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on analysis using a promoter-specific transcription factor screening system (PS-TF), it has been shown that the rsd and rmf promoters are repressed by ArcA and activated by McbR, RcdA, SdiA, and SlyA transcription factors (TFs) during the transition from exponential to stationary growth phase. On the other hand, a total of 11 TFs (CueR, DmlR, GlpR, QseF, OmpR, UxuR, BtsR, YfeR, YhaJ, YiuA, and YijO) were estimated to bind to the rmf promoter Yoshida H,2018
The SlyA-binding site could be overlapping the ArcA-binding site in rsd in the upstream region of the promoter. For the other three TFs (McbR, RcdA, and SdiA), their wide binding sequences are between approximately bp -100 and -200 for McbR, between -120 and -220 for RcdA, and between -50 and -280 for SdiA upstream of the start of the gene Yoshida H,2018
The TFs are controlled by specific effector ligands which decrease in the presence of the corresponding effector, such as AcP for ArcA and AI-1 for SdiA, and increase in its presence, such as AI-2 for McbR, acetate for RcdA, and ppGpp for SlyA Yoshida H,2018
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: rsdp2
+1: 4196859
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 51
Sequence: tcaattatacgatccatagctcttgcactacctttgcatcactggcatgtttaacatggtTtttacatttctcactgagca
                            -35                     -10     +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[IPI]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[2] Jishage M., et al., 1999
[3] Yoshida H., et al., 2018
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
nd ArcA-phosphorylated repressor rsdp2 nd nd nd nd nd [GEA], [BPP] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd McbR activator rsdp2 nd nd nd nd nd [GEA], [BPP] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcdA activator rsdp2 nd nd nd nd nd [GEA], [BPP] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd SdiA activator rsdp2 nd nd nd nd nd [GEA], [BPP] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd SlyA activator rsdp2 nd nd nd nd nd [GEA], [BPP] [3]


Transcription unit       
Name: rsd
Gene(s): rsd   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: rsdp1
+1: 4196954
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 146
Sequence: gatcgaaatttgccgcttcgccatatggcaattctcccttcggcaaccataatttttgttCatggctgacgacccaccagc
                         -35               -10              +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[IMP]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[2] Jishage M., et al., 1999





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