RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: sbcDC
Gene(s): sbcC, sbcD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the sbcDC operon is indirectly induced by the action of RpoS; this in some way suggests the presence of another regulatory system Darmon E,2007
Evidence: [COMP-AINF] Inferred computationally without human oversight
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Darmon E., et al., 2007
Promoter
Name: sbcDp
+1: 416977
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: tattgatttccgtggcgcagaaaaaagcaaatggcacatctgtttgggtataatcgcgccCatgctttttcgccagggaac
                               -35                    -10   +1                   
Note(s): We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, present a distance of 6 nucleotides between the transcriptional start site and the -10 box Harley CB, Reynolds RP,1987.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [2] Huerta AM., et al., 2003
[3] Naom IS., et al., 1989
TF binding sites (TFBSs)
[PhoB,-] 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 PhoB-phosphorylated repressor sbcDp 417061 417079 -93.0 gcgtcagattTATGACAGATTTATGAAAAgctcgtcgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.7 416967 416996 tggcacatctGTTTGGGTATAATCGCGCCCATGCTTTTTcgccagggaa
  anti-terminator -6.0 416990 417029 gttattgattTCCGTGGCGCAGAAAAAAGCAAATGGCACATCTGTTTGGgtataatcgc
  anti-anti-terminator -7.6 417018 417059 ttatgaaaagCTCGTCGCACATATCTTCAGGTTATTGATTTCCGTGGCGCAgaaaaaagca
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

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

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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


Reference(s)    

 [1] Darmon E., Lopez-Vernaza MA., Helness AC., Borking A., Wilson E., Thacker Z., Wardrope L., Leach DR., 2007, SbcCD regulation and localization in Escherichia coli., J Bacteriol 189(18):6686-94

 [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] Naom IS., Morton SJ., Leach DR., Lloyd RG., 1989, Molecular organization of sbcC, a gene that affects genetic recombination and the viability of DNA palindromes in Escherichia coli K-12., Nucleic Acids Res 17(20):8033-45

 [4] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [5] Yang C., Huang TW., Wen SY., Chang CY., Tsai SF., Wu WF., Chang CH., 2012, Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli., PLoS One 7(10):e47314

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