RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: creABC
Gene(s): creA, creB, creC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The function of the creC gene could only be detected in the phoR mutants.
The expression of the gene phoM (creC) is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression appears to be caused by the transcription factor PhoB Marzan LW,2013 This gene is the third in the operon in which it is transcribed, but an effect of these growth conditions and PhoB on the other genes in the operon has not been observed.
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Nonaka G., et al., 2006
Promoter
Name: creAp2
+1: 4635243
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 278
Sequence: ttaaacattctctgtaagtgccacttggaataacctgctttcgccgctacattgtcgagcGacaggggctgatccagatga
                         -35                 -10            +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Nonaka G., et al., 2006


Transcription unit          
Name: creABCD
Synonym(s): orf1-orf2-phoM-orf4, phoM
Gene(s): creA, creB, creC, creD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The function of the creC gene could only be detected in the phoR mutants.
J. Oberto in 2010 predicted this binding site for NagC Oberto J.,2010 which overlaps with the divergent promoter creAp, but it is unknown whether this protein could regulate the rob gene. In this case it is not known if NagC regulates transcription in both directions.
The expression of the gene phoM (creC) is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression appears to be caused by the transcription factor PhoB Marzan LW,2013 This gene is the third in the operon in which it is transcribed, but an effect of these growth conditions and PhoB on the other genes in the operon has not been observed.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [3] Amemura M., et al., 1986
Promoter
Name: creAp
+1: 4635477
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 44
Sequence: ttagggcttgacggaaataaaagtattgagattttgttcttaatcaatatgttatttaccGtgacgaactaattgctcgtg
                          -35                   -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [3] Amemura M., et al., 1986
[2] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: taaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta
Reference(s): [3] Amemura M., et al., 1986
TF binding sites (TFBSs)
[NagC,-] 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 NagC repressor creAp 4635467 4635489 2.0 taatcaatatGTTATTTACCGTGACGAACTAATtgctcgtgta nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd nd


Transcription unit          
Name: creD
Gene(s): creD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene creD is increased when colicin (at 30 ng/ml) is added to the medium Kamen?ek S, ?gur-Bertok D,2013.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [4] Cariss SJ., et al., 2008
Promoter
Name: creDp
+1: 4638160
Distance from start of the gene: 18
Sequence: cttcaccgtcacttcacatagcttcaaattcttcccacatagtcttcgtatcctgctgccAttgcaaaggagaagactatg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Cariss SJ., et al., 2008
Terminator(s)
Type: rho-independent
Sequence: taaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta
Reference(s): [3] Amemura M., et al., 1986
TF binding sites (TFBSs)
[CreB,+] 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 CreB-phosphorylated activator creDp 4638099 4638117 -52.5 cctcgcttcgACTTCACCGTCACTTCACAtagcttcaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -19.3 4638137 4638180 ttcttcccacATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGttgaaatccc
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

 [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-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

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

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


Reference(s)    

 [1] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [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] Amemura M., Makino K., Shinagawa H., Nakata A., 1986, Nucleotide sequence of the phoM region of Escherichia coli: four open reading frames may constitute an operon., J Bacteriol 168(1):294-302

 [4] Cariss SJ., Tayler AE., Avison MB., 2008, Defining the growth conditions and promoter-proximal DNA sequences required for activation of gene expression by CreBC in Escherichia coli., J Bacteriol 190(11):3930-9

 [5] Avison MB., Horton RE., Walsh TR., Bennett PM., 2001, Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media., J Biol Chem 276(29):26955-61

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