RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit          
Name: rmf
Gene(s): rmf   Genome Browser M3D Gene expression COLOMBOS
Note(s): Analysis of gene expression has proved that under NlpE lipoprotein overexpression, the presence of the protein CpxR causes increased transcription of the rmf gene; however, no DNA sequence related to the consensus DNA-binding site of CpxR has been identified in the regulatory region of the gene. Therefore, the effect of CpxR on rmf is probably indirect |CITS:[ 23564175]|.
An rmf mutant had reduced viability during stationary phase and did not contain ribosome dimers |CITS: [8440252]|, whereas the essential role of RMF is for the storage of unused ribosomes under starvation conditions |CITS: [23475967]|.
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 2 TFs (DsdC and PaaX) were estimated to bind to the rmf promoter |CITS:[ 30225374]|.
The binding regions for TFs regulating rmf expression were predicted on the basis of the gel pattern. The order of the size increase of TF-binding sequences is as follows: ArcA < SlyA < McbR < RcdA < SdiA. The sizes of these TFs were basically the same as those observed with the rsd promoter |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: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Aiso T., et al., 2005
Promoter
Name: rmfp
+1: 1015657
Distance from start of the gene: 58
Sequence: tggcgtgaattttgcgcattgacggcagttatgattcgcggtattgcttaactgtgattgCacatttagtaatcactgttt
Evidence: [TIM] ; Method: Primer Extension
[TIM]
Reference(s): [1] Aiso T., et al., 2005
Terminator(s)
Type: rho-independent
Sequence: tctttaaaaaGAAACCTCCGCATTGCGGAGGTTTCgccttttgat
Reference(s): [1] Aiso T., et al., 2005
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 rmfp nd nd nd nd nd [BPP], [GEA], [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP1 activator rmfp 1015536 1015552 -113.5 tgcggaaaaaTTTGTTCCTCTTCACATtttttgtaca nd [AIBSCS], [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 rmfp nd nd nd nd nd [BPP], [GEA], [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 rmfp nd nd nd nd nd [BPP], [GEA], [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 rmfp nd nd nd nd nd [BPP], [GEA], [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 rmfp nd nd nd nd nd [BPP], [GEA], [3]
Note(s): 1CRP regulates positively the activation of the rmf gene for formation of 100S ribosome dimers Shimada T,2013. rmfp expression is increased during the transition from exponential- to stationary-phase growth Wada A, Yamazaki Y, Fujita N, Ishihama A,1990. Maki Y, Yoshida H, Wada A,2000. Shimada T,2013.1CRP regulates positively the activation of the rmf gene for formation of 100S ribosome dimers Shimada T,2013. rmfp expression is increased during the transition from exponential- to stationary-phase growth Wada A, Yamazaki Y, Fujita N, Ishihama A,1990. Maki Y, Yoshida H, Wada A,2000. Shimada T,2013.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation rmfp rmf transcription is induced positively and directly by cellular ppGpp concentrations rather than by the decreased growth rate |CITS:[11532026]|. [IEP] [4]
Evidence: [IEP] Inferred from expression pattern
Reference(s): [4] Izutsu K., et al., 2001


Transcription unit       
Gene(s): rmf   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the rmf gene is induced during the transition from exponential phase to stationary phase |CITS:[ 20964794]|. Single-cell assays have shown that the transcription of this gene is heterogeneously activated in cells within the same culture. In some cells the transcription is activated to a greater extent than in others; in approximately 20% of the cells in a given culture, the transcription of rmf is not activated |CITS:[ 20964794]|.
Based on DNA microarray analysis and Fourier transform-infrared spectroscopy, an Escherichia coli strain was exposed to 10 adverse conditions. Expression of three genes, ygaW, rmf, and ghrA, was significantly changed under each of these conditions (except in the presence of the disinfectant benzalkonium chloride) |CITS:[19767843]|.
Evidence: [ICWHO] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [5] null null
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.1 1015480 1015517 tgtaaatataACCGTCTCCGGTATGTTGCCTGAGGCGGTTTTTTTGTctctaacgtg
  anti-terminator -3.8 1015476 1015496 gatttgtaaaTATAACCGTCTCCGGTATGTtgcctgaggc
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"





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