RegulonDB RegulonDB 11.1: Operon Form
   

bdm-sra operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: sra
Gene(s): sra   Genome Browser M3D Gene expression COLOMBOS
Note(s): Global transcriptional regulators FIS, IHF, cAMP-CRP, and ppGpp directly or indirectly regulate positively the transcription of sra during the stationary phase, and the region between bp -455 and -325 from its ATG codon appears to be responsible for the action of these regulators, which do not interfere with sra expression in the exponential phase Izutsu K,2001.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Izutsu K., et al., 2001
Promoter
Name: srap
+1: 1556046
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 83
Sequence: acgatcaattatgtggtcagtggccagcaccctacgctttaaggtgctatgcttgatcggCaacctaatttaggggtttag
                             -35                     -10    +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Izutsu K., et al., 2001
[3] Lacour S., et al., 2004
TF binding sites (TFBSs)
[Fis,+] 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 Fis activator srap nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
[IHF,+] 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 IHF activator srap nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
[OmpR,-] 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 OmpR-phosphorylated repressor srap nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation srap nd   [EXP-IEP]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] 		[1]
[4]
Evidence: [EXP-IEP] Inferred from expression pattern
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [1] Izutsu K., et al., 2001
[4] Traxler MF., et al., 2008


Transcription unit          
Name: bdm-sra
Gene(s): sra, bdm   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene bdm is increased when colicin (at 30 ng/ml) is added to the medium Kamen?ek S, ?gur-Bertok D,2013.
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [5] Francez-Charlot A., et al., 2005
Promoter
Name: bdmp
+1: 1556340
Distance from start of the gene: 60
Sequence: aaaatcatcaaccaggactaatcttaacaacgaagcggcaaatatttgccatgctgaatgTgctttataaatctgcgatcc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Francez-Charlot A., et al., 2005
TF binding sites (TFBSs)
[RcsB,+] 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
proximal RcsB-phosphorylated activator bdmp 1556375 1556388 -41.5 aatcatcaacCAGGACTAATCTTAacaacgaagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -7.4 1555970 1555997 ggcgatgttgTCCTTAAAACTAGCTACAGGATTGAGGagttaaaatg
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    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IEP] Inferred from expression pattern

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

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


Reference(s)    

 [1] Izutsu K., Wada C., Komine Y., Sako T., Ueguchi C., Nakura S., Wada A., 2001, Escherichia coli ribosome-associated protein SRA, whose copy number increases during stationary phase., J Bacteriol 183(9):2765-73

 [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] Lacour S., Landini P., 2004, SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences., J Bacteriol 186(21):7186-95

 [4] Traxler MF., Summers SM., Nguyen HT., Zacharia VM., Hightower GA., Smith JT., Conway T., 2008, The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli., Mol Microbiol 68(5):1128-48

 [5] Francez-Charlot A., Castanie-Cornet MP., Gutierrez C., Cam K., 2005, Osmotic regulation of the Escherichia coli bdm (biofilm-dependent modulation) gene by the RcsCDB His-Asp phosphorelay., J Bacteriol 187(11):3873-7

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