RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: cspD
Gene(s): cspD   Genome Browser M3D Gene expression COLOMBOS
Note(s): cspD expression is induced during stationary phase and it is independent of σS Uppal S,2014 In addition, cspD is associated with biofilms and persister cell formation Uppal S,2014
CRP is activated via a class I-type mechanism that involves cspD expression Uppal S,2014 Based on mutant alleles, it was determined that the AR1 domain in CRP is critical for cspD activation, whereas the AR2 domain of CRP is not necessary Uppal S,2014
The mRNA produced by the cspD gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Yamanaka K., et al., 1997
Promoter
Name: cspDp
+1: 922676
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 86
Sequence: tgccccttgtcccctgtcaaatgcttgacggctcgccctaattctctaaattgtatttctAgagttggcgaggttttgaac
                              -35                   -10     +1                   
Note(s): The activity of this promoter appears to be decreased in the presence of σE. It is repressed during the first 5 minutes following σE induction and decreased from 5 to 10 minutes and from 10 to 20 minutes after induction of the σ factor Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Yamanaka K., et al., 1997
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator cspDp 922749 922770 -83.5 ttcctgtcaaTAGCGTTAACTGCTTCAAATTTttgattcata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
remote CRP-cyclic-AMP activator cspDp 922778 922799 -112.5 tatcgttggcATCAGCGACATCTGTCACATTCctgtcaatag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
[H-NS,+] 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 H-NS activator cspDp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W nd
[MqsA,-] 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 MqsA repressor cspDp 922567 922585 101.5 gaagcatggaAAAGGGTACTGTTAAGTGGttcaacaatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
remote MqsA repressor cspDp 922800 922818 -132.5 atgatagataACTATCATCTATCGTTGGCatcagcgaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation cspDp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [1] Yamanaka K., et al., 1997


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [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] Yamanaka K., Inouye M., 1997, Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli., J Bacteriol 179(16):5126-30

 [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] Kim Y., Wang X., Zhang XS., Grigoriu S., Page R., Peti W., Wood TK., 2010, Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD., Environ Microbiol 12(5):1105-21

 [4] Uppal S., Shetty DM., Jawali N., 2014, Cyclic AMP receptor protein regulates cspD, a bacterial toxin gene, in Escherichia coli., J Bacteriol 196(8):1569-77

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