RegulonDB RegulonDB 10.6.3: 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 |CITS:[ 30225374]|.
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 |CITS:[ 30225374]|.
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 |CITS:[ 30225374]|.
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
                            -10                     -35     +1                   
Note(s): The basal level of rsd transcription is maintained by using the downstream rsdp2 promoter recognized by Eσ70. On the basis of sequence similarity and unique expression patterns, such as the inverse relationship with the growth rate, the rsdp2 promoter can be classified as a member of the gearbox family of promoters, but it cannot be transcribed by Eσ38 in vivo or in vitro. Under certain circumstances, the upstream sequence including the rsdp1 promoter exerts an inhibitory effect on the rsdp2 function, because the deletion of the rsdp1 region results in an increase in transcription from the downstream rsdp2 promoter. The mechanism of inhibition by the upstream sequence remains unsolved.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Jishage M., et al., 1999
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-Phosphorylated1 repressor rsdp2 nd nd nd nd nd [BPP], [GEA], [2]
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 [BPP], [GEA], [2]
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 [BPP], [GEA], [2]
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 [BPP], [GEA], [2]
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 [BPP], [GEA], [2]
Note(s): 1The ArcA binding site was predicted to be within a narrow sequence near 100 bp upstream from the Rsd coding sequence. The known consensus sequence recognized by ArcA, 5¿¿-(AT)GTTAATTA(AT)-3, exists in the upstream region of the rsd gene Yoshida H,
rsd expression is repressed by ArcA during the exponential growth phase Yoshida H,5The ArcA binding site was predicted to be within a narrow sequence near 100 bp upstream from the Rsd coding sequence. The known consensus sequence recognized by ArcA, 5¿¿-(AT)GTTAATTA(AT)-3, exists in the upstream region of the rsd gene Yoshida H,
rsd expression is repressed by ArcA during the exponential growth phase Yoshida H,


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
                         -10               -35              +1                   
Note(s): Transcription from the upstream rsdp1 promoter by Eσ38 takes place only in the early stationary phase.
Under certain circumstances, the upstream sequence including the rsdp1 promoter exerts an inhibitory effect on the rsdp2 promoter function, because the deletion of the rsdp1 region results in an increase in transcription from the downstream rsdp2 promoter. The mechanism of inhibition by the upstream sequence remains unsolved.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Jishage M., et al., 1999





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