RegulonDB RegulonDB 11.1: 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 Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST,2009 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 Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST,2009.
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: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[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 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[1]
  ppGpp activation iraDp1 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[1]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-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 Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST,2009for 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 Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST,2009
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: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Merrikh H., et al., 2009
Promoter
Name: idlPp
+1: 4556856
Sigma Factor: Sigma38 Sigmulon
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Mendoza-Vargas A., et al., 2009
[1] Merrikh H., et al., 2009
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator idlPp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [5]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition idlPp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[1]
  ppGpp activation idlPp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[1]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-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 Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST,2009for 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 Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST,2009
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: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Merrikh H., et al., 2009
Promoter
Name: iraDp2
+1: 4556856
Sigma Factor: Sigma70 Sigmulon
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Mendoza-Vargas A., et al., 2009
[1] Merrikh H., et al., 2009
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator iraDp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

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


Reference(s)    

 [1] Merrikh H., Ferrazzoli AE., Lovett ST., 2009, Growth phase and (p)ppGpp control of IraD, a regulator of RpoS stability, in Escherichia coli., J Bacteriol 191(24):7436-46

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

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