RegulonDB RegulonDB 10.6.3: Operon Form
   

casABCDE12 operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: casABCDE12
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: ygbF
Gene(s): cas2   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Nonaka G., et al., 2006
Promoter
Name: ygbFp
+1: 2878915
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 62
Sequence: gcttatagaggacgtgcttgccgctggagaaatacaaccgccggccccacctgaagatgcAcagcctgttgccattccgct
                         -10                 -35            +1                   
Evidence: [AIPP]
[TIM]
Reference(s): [1] Nonaka G., et al., 2006


Transcription unit          
Gene(s): cas2, cas1, casE, casD, casC, casB, casA   Genome Browser M3D Gene expression COLOMBOS
Note(s): HNS binds in tandem at the casA-cas3 intergenic region, and it represses the transcription of the casA gene by inhibiting the RNA polymerase interaction with the casAp promoter. Analyses for footprinting show that HNS protects two long regions without defining the central positions of the binding sites of the protein HNS; for this reason, we only show the sequence of the hypersensitive site, TCGTTTTATT |CITS:[20126629]|. HNS also represses the expression of the anti-Pcas divergent promoter, which is reported to produce an RNA with a length between 150 and 200 bp. There exists the possibility that this divergent promoter affects the transcription or translation of the ygcB gene.
H-NS and LeuO are antagonistic regulators of casABCDE-cas12 |CITS: [20659289]|. LeuO counteracts H-NS-dependent repression of casAp by reorganizing the DNA-protein contacts within the transcription initiation region |CITS: [20659289]|.
Repression of the CRP in the casABCDE-cas1-cas2 operon is H-NS independent |CITS:[24720807]|. In fact, both compete for binding to the casAp promoter |CITS:[24720807]|.
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
[LTED] Length of transcript experimentally determined
Reference(s): [2] Pul U., et al., 2010
Promoter
Name: casAp
+1: 2884319
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 181
Sequence: tttctttaataataaaacgaataacttgcagatttgaaatgcatgcattattgtctttaaAcaattcaacacatcttaata
                          -10                    -35        +1                   
Evidence: [TIM] ; Method: Primer Extension
[TIM]
Reference(s): [2] Pul U., et al., 2010
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP repressor casAp 2884399 2884419 -89.5 gtatgaatatTTTATGTAATAAAATTCATGGtaattattat nd [BPP], [GEA], [HIBSCS] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal H-NS repressor casAp 2884358 2884372 -46.0 aagtttctttAATAATAAAACGAATaacttgcaga nd [BPP], [GEA] [2], [3], [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote LeuO activator casAp 2884263 2884283 47.0 ataggttaatTGTATTAAACCAATGAATATAtttttgcagt nd [BPP], [GEA], [IC] [3], [4]
proximal LeuO activator casAp 2884289 2884309 21.0 acaattcaacACATCTTAATATATGTATAGGttaattgtat nd [BPP], [GEA], [IC] [3], [4]
proximal LeuO activator casAp 2884389 2884409 -80.0 tttatgtaatAAAATTCATGGTAATTATTATaactaaaagt nd [BPP], [GEA], [IC] [3], [4]
remote LeuO activator casAp 2884419 2884439 -110.0 tatgagatttTATATTCACAGTATGAATATTttatgtaata nd [BPP], [GEA], [IC] [3], [4]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote SlyA activator casAp 2884233 2884244 81.5 gtgaatgtgaTTATTGAATTAAttacgccgta nd [AIBSCS], [BPP], [GEA] [6]


Transcription unit       
Name: casDE-ygbTF
Synonym(s): ygcIH-ygbTF
Gene(s): cas2, cas1, casE, casD   Genome Browser M3D Gene expression COLOMBOS
Note(s): ygcH, ygbT, and ygbF genes are transcribed together with three other genes located upstream of them. On the other hand, a σ32-dependent promoter was suggested to be located upstream of ygcI |CITS: [16892065]|. Therefore, we inferred that the four genes (ygcIH-ygbTF) form a transcription unit transcribed from the σ32 promoter.
Evidence: [IC] Inferred by curator
Promoter
Name: casDp
+1: Unknown
Sigma Factor: Sigma32 Sigmulon
Evidence: [IDA]
[IEP]
Reference(s): [7] Wade JT., et al., 2006


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown repressor       [IMP] [8]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"




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] Pul U., Wurm R., Arslan Z., Geissen R., Hofmann N., Wagner R., 2010, Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS., Mol Microbiol 75(6):1495-512

 [3] Arslan Z., Stratmann T., Wurm R., Wagner R., Schnetz K., Pul U., 2013, RcsB-BglJ-mediated activation of Cascade operon does not induce the maturation of CRISPR RNAs in E. coli K12., RNA Biol 10(5)

 [4] Westra ER., Pul U., Heidrich N., Jore MM., Lundgren M., Stratmann T., Wurm R., Raine A., Mescher M., Van Heereveld L., Mastop M., Wagner EG., Schnetz K., Van Der Oost J., Wagner R., Brouns SJ., 2010, H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO., Mol Microbiol 77(6):1380-93

 [5] Yang CD., Chen YH., Huang HY., Huang HD., Tseng CP., 2014, CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication., Mol Microbiol 92(5):1072-91

 [6] Curran T., Abacha F., Hibberd S., Rolfe M., Lacey M., Green J., 2017, Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon., Microbiology

 [7] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [8] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14


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