RegulonDB RegulonDB 10.8: Operon Form
   

ytiCD-idlP-iraD operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ytiCD-idlP-iraD
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: iraD
Gene(s): ytiC, ytiD, idlP, iraD   Genome Browser M3D Gene expression COLOMBOS
Note(s): iraD is involved in posttranslational regulation of RpoS Bougdour A,2008.
iraD promotes accumulation of RpoS, which binds to the adaptor RssB protein that targets RpoS for degradation 19124769 for proteolysis by ClpXP in vitro Bougdour A,2008. These results established the importance of RpoS stabilization in proliferating bacterial cells in which replication has been directly blocked, confirming a role for the RpoS regulon in DNA damage repair or tolerance.
iraD transcription is induced by DNA damage via a mechanism independent of the SOS response, and both iraD and the SOS regulatory pathway could be acting synergistically to ensure survival of cells faced with oxidative or DNA damaging stress during cellular growth 19124769.
The expression of iraD is growth phase and ppGpp dependent Merrikh H,2009. ppGpp modulates iraD expression not only during the transition to stationary phase but also very sensitively in the mid-exponential phase Merrikh H,2009. Both RelA and SpoT are required for maximal iraD expression during exponential phase Merrikh H,2009. The effects of ppGpp and DksA on iraD regulatory expression are opposing, because DksA inhibits IraD expression, although this effect could be direct or indirect Merrikh H,2009.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Merrikh H., et al., 2009
Promoter
Name: iraDp1
+1: 4556576
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: -2
Sequence: aagcatatcttattactaattggaatttgatgttgctatattgaggtctatattaataatGcctgtgaatggtatttttga
                           -35                   -10        +1                   
Note(s): iraDp1 is present during entry into stationary phase but not in exponential phase Merrikh H,2009. RelA or SpoT is required during the transition to stationary phase of iraDp1. ppGpp production is primarily RelA dependent in growing cells but switches to more balanced production by both RelA and SpoT in the late exponential phase Merrikh H,2009. This promoter has an AT-rich discriminator region downstream of the -10 sequence which could be involved with direct positive regulation by ppGpp Merrikh H,2009.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Merrikh H., et al., 2009
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition iraDp1   [GEA]
[IMP]
[1]
  ppGpp activation iraDp1   [GEA]
[IMP]
[1]
Evidence: [GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
Reference(s): [1] Merrikh H., et al., 2009


Transcription unit          
Name: iraD
Synonym(s): yjiD
Gene(s): idlP, iraD   Genome Browser M3D Gene expression COLOMBOS
Note(s): iraD is involved in posttranslational regulation of RpoS Bougdour A,2008
iraD promotes accumulation of RpoS, which binds to the adaptor RssB protein that targets RpoS for degradation 19124769for proteolysis by ClpXP in vitro Bougdour A,2008 These results established the importance of RpoS stabilization in proliferating bacterial cells in which replication has been directly blocked, confirming a role for the RpoS regulon in DNA damage repair or tolerance.
iraD transcription is induced by DNA damage via a mechanism independent of the SOS response, and both iraD and the SOS regulatory pathway could be acting synergistically to ensure survival of cells faced with oxidative or DNA damaging stress during cellular growth 19124769
The expression of iraD is growth phase and ppGpp dependent Merrikh H,2009 ppGpp modulates iraD expression not only during the transition to stationary phase but also very sensitively in the mid-exponential phase Merrikh H,2009 Both RelA and SpoT are required for maximal iraD expression during exponential phase Merrikh H,2009 The effects of ppGpp and DksA on iraD regulatory expression are opposing, because DksA inhibits IraD expression, although this effect could be direct or indirect Merrikh H,2009
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Merrikh H., et al., 2009
Promoter
Name: iraDp2
+1: 4556856
Sigma Factor: Sigma38, Sigma70
Distance from start of the gene: 57
Sequence: gacttttttcctgaaaagtcagtagatattcataggcaagtaaggttttatactttgctgAcaggattcaggcctgtctca
                         -35                -10             +1                   
Note(s): iraDp2 is present under both entry into stationary phase and during exponential phase Merrikh H,2009 This promoter becomes (p)ppGpp independent during the stationary phase, but it requires RelA predominantly during exponential growth Merrikh H,2009
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Mendoza-Vargas A., et al., 2009
[1] Merrikh H., et al., 2009
[3] Salgado H, et al., 2012
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 FNR1 activator iraDp2 nd nd nd nd nd [AIBSCS], [CV(GEA)], [GEA] [4]
Note(s): 1By making use of microarray analyses, Constantinidou et al. Constantinidou C,2006 concluded that FNR activates yjiD gene expression. They also identified a putative FNR-binding site upstream of the gene, but the sequence was not shown.1By making use of microarray analyses, Constantinidou et al. Constantinidou C,2006 concluded that FNR activates yjiD gene expression. They also identified a putative FNR-binding site upstream of the gene, but the sequence was not shown.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition iraDp2   [GEA]
[IMP]
[1]
  ppGpp activation iraDp2   [GEA]
[IMP]
[1]
Evidence: [GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
Reference(s): [1] Merrikh H., et al., 2009





RegulonDB