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CreB DNA-binding transcriptional dual regulator

Synonyms: CreB, CreB-phosphorylated
Summary:
CreB "Carbon source responsive response regulator," is a DNA-binding transcriptional dual regulator [2, 3] and belongs to the CreBC two-component system (TCS) [2, 3, 4], which controls genes involved in acetate [5] and ribose [6] metabolism, in the maltose regulon [7], in the pentose phosphate pathway [8], and genes which repair DNA damage associated with the replication fork [9]. CreBC regulates the expression of cre regulon genes in response to a switch from complex to minimal medium [2].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
CreB Non-Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
CreB-phosphorylated Functional Covalent Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
Evolutionary Family: OmpR
TFBs length: 18
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: creB
  Genome position: 4636007-4636696
  Length: 690 bp / 229 aa
Operon name: creABCD
TU(s) encoding the TF:
Transcription unit        Promoter
creABC
creAp2
creABCD
creAp


Regulon       
Regulated gene(s) creD, malE, malF, malG, malH, talA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (3)
carbon compounds (2)
ABC superfamily, membrane component (2)
ABC superfamily, periplasmic binding component (1)
motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc) (1)
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Regulated operon(s) creABCD, malEFGH, talA-tktB
First gene in the operon(s) creD, malE, talA
Simple and complex regulons CRP,CreB,Fis,H-NS,MalT,StpA
CreB
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[CreB,+](2)
[CreB,-](1)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
 LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  CreB-phosphorylated activator creDp nd -52.5 -70.5 creD
cctcgcttcgACTTCACCGTCACTTCACAtagcttcaaa
 4638099 4638117 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3]
  CreB-phosphorylated repressor malEp Sigma70 18.5 -27.5 malE, malF, malG, malH
ccgtttaggtGTTTTCACGAGCACTTCACcaacaaggac
 4246438 4246456 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  CreB-phosphorylated activator talAp nd -211.5 -269.5 talA
ttggttgttcCTTTCACGTAACGTTCACAaataaagtgt
 2578388 2578406 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  CreB-phosphorylated activator recG Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
  CreB-phosphorylated activator nudF-yqiB-cpdA-yqiA-parE Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
  CreB-phosphorylated activator ackA-pta Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
  CreB-phosphorylated activator cbrB Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]
  CreB-phosphorylated activator cbrA Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

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

 [EXP-IPI] Inferred from physical interaction

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

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

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


Reference(s)    

 [1] Yamamoto K., Hirao K., Oshima T., Aiba H., Utsumi R., Ishihama A., 2005, Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli., J Biol Chem 280(2):1448-56

 [2] 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

 [3] 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

 [4] Amemura M, Makino K, Shinagawa H, Nakata A, 1990, Cross talk to the phosphate regulon of Escherichia coli by PhoM protein: PhoM is a histidine protein kinase and catalyzes phosphorylation of PhoB and PhoM-open reading frame 2., J Bacteriol, 172(11):6300 10.1128/jb.172.11.6300-6307.1990

 [5] Kakuda H., Hosono K., Shiroishi K., Ichihara S., 1994, Identification and characterization of the ackA (acetate kinase A)-pta (phosphotransacetylase) operon and complementation analysis of acetate utilization by an ackA-pta deletion mutant of Escherichia coli., J Biochem 116(4):916-22

 [6] Dunn CA, O'Handley SF, Frick DN, Bessman MJ, 1999, Studies on the ADP-ribose pyrophosphatase subfamily of the nudix hydrolases and tentative identification of trgB, a gene associated with tellurite resistance., J Biol Chem, 274(45):32318 10.1074/jbc.274.45.32318

 [7] Richet E., 1996, On the role of the multiple regulatory elements involved in the activation of the Escherichia coli malEp promoter., J Mol Biol 264(5):852-62

 [8] Sprenger GA, 1995, Genetics of pentose-phosphate pathway enzymes of Escherichia coli K-12., Arch Microbiol, 164(5):324 10.1007/BF02529978

 [9] Saveson CJ., Lovett ST., 1999, Tandem repeat recombination induced by replication fork defects in Escherichia coli requires a novel factor, RadC., Genetics 152(1):5-13

 [10] Wanner BL, Latterell P, 1980, Mutants affected in alkaline phosphatase, expression: evidence for multiple positive regulators of the phosphate regulon in Escherichia coli., Genetics, 96(2):353 10.1093/genetics/96.2.353

 [11] Ho YH, Sung TC, Chen CS, 2012, Lactoferricin B inhibits the phosphorylation of the two-component system response regulators BasR and CreB., Mol Cell Proteomics, 11(4):M111.014720 10.1074/mcp.M111.014720

 [12] Miyake Y., Yamamoto K., 2020, Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli., Sci Rep 10(1):3661


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