RegulonDB RegulonDB 11.1: 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 Raivio TL,2013
An rmf mutant had reduced viability during stationary phase and did not contain ribosome dimers Yamagishi M,1993, whereas the essential role of RMF is for the storage of unused ribosomes under starvation conditions Shimada T,2013.
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 Yoshida H,2018
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 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: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-BOUNDARIES-DEFINED] 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: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
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)
[ArcA,-] 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
nd ArcA-phosphorylated repressor rmfp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[CRP,+] 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
remote CRP-cyclic-AMP activator rmfp 1015536 1015552 -113.5 tgcggaaaaaTTTGTTCCTCTTCACATtttttgtaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
[McbR,+] 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
nd McbR activator rmfp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[RcdA,+] 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
nd RcdA activator rmfp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[SdiA,+] 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
nd SdiA activator rmfp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[SlyA,+] 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
nd SlyA activator rmfp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation rmfp nd   [EXP-IEP] [4]
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [4] Izutsu K., et al., 2001


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  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"


Evidence    

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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


Reference(s)    

 [1] Aiso T., Yoshida H., Wada A., Ohki R., 2005, Modulation of mRNA stability participates in stationary-phase-specific expression of ribosome modulation factor., J Bacteriol 187(6):1951-8

 [2] Shimada T., Yoshida H., Ishihama A., 2013, Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli., J Bacteriol 195(10):2212-9

 [3] Yoshida H., Shimada T., Ishihama A., 2018, Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase., mSystems 3(5)

 [4] Izutsu K., Wada A., Wada C., 2001, Expression of ribosome modulation factor (RMF) in Escherichia coli requires ppGpp., Genes Cells 6(8):665-76

RegulonDB