RegulonDB RegulonDB 11.1: 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: [EXP-IDA-BOUNDARIES-DEFINED] 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
                              -35                 -10       +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-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: casABCDE12
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 Dyszel JL,2010 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 Westra ER,2010. LeuO counteracts H-NS-dependent repression of casAp by reorganizing the DNA-protein contacts within the transcription initiation region Westra ER,2010.
Repression of the CRP in the casABCDE-cas1-cas2 operon is H-NS independent Yang CD,2014 In fact, both compete for binding to the casAp promoter Yang CD,2014
The casABCDE-cas12 operon is repressed by the StpA protein when H-NS is absent Miti? D, Radov?i? M, Markulin D, Ivan?i?-Ba?e I,2020
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [3] Pul U., et al., 2010
Promoter
Name: casAp
+1: 2884319
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 181
Sequence: tttctttaataataaaacgaataacttgcagatttgaaatgcatgcattattgtctttaaAcaattcaacacatcttaata
                               -35                    -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IPI]
Reference(s): [2] Huerta AM., et al., 2003
[3] Pul U., et al., 2010
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 repressor casAp 2884399 2884419 -89.5 gtatgaatatTTTATGTAATAAAATTCATGGtaattattat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]
[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
proximal H-NS repressor casAp 2884358 2884372 -46.0 aagtttctttAATAATAAAACGAATaacttgcaga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [4], [6], [8], [9]
[LeuO,+] 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 LeuO activator casAp 2884263 2884283 47.0 ataggttaatTGTATTAAACCAATGAATATAtttttgcagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4], [6]
proximal LeuO activator casAp 2884289 2884309 21.0 acaattcaacACATCTTAATATATGTATAGGttaattgtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4], [6]
proximal LeuO activator casAp 2884389 2884409 -80.0 tttatgtaatAAAATTCATGGTAATTATTATaactaaaagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [6]
remote LeuO activator casAp 2884419 2884439 -110.0 tatgagatttTATATTCACAGTATGAATATTttatgtaata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [IC], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [4], [5], [6]
[SlyA,+] 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 SlyA activator casAp 2884233 2884244 81.5 gtgaatgtgaTTATTGAATTAAttacgccgta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
[StpA,+] 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 StpA activator casAp 2884358 2884372 -46.0 aagtttctttAATAATAAAACGAATaacttgcaga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [8]


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 Wade JT,2006. 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: [EXP-IDA]
[EXP-IEP]
Reference(s): [11] Wade JT., et al., 2006


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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

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

 [EXP-IPI] Inferred from physical interaction

 [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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [IC] Inferred by curator

 [EXP-IEP-MICROARRAY] Expression microarray evidence

 [EXP-GSELEX] genomic SELEX

 [EXP-IDA] Inferred from direct assay

 [EXP-IEP] Inferred from expression pattern


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] 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

 [4] 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):708-15

 [5] Stratmann T., Pul U., Wurm R., Wagner R., Schnetz K., 2012, RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants., Mol Microbiol 83(6):1109-23

 [6] 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

 [7] 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

 [8] Sun D., Mao X., Fei M., Chen Z., Zhu T., Qiu J., 2020, Histone-like Nucleoid-Structuring Protein (H-NS) Paralogue StpA Activates the Type I-E CRISPR-Cas System against Natural Transformation in Escherichia coli., Appl Environ Microbiol 86(14)

 [9] Yang D., Wang Z., Ma J., Fu Q., Wu L., Wang H., Wang S., Yan Y., Sun J., 2020, Glycine Cleavage System and cAMP Receptor Protein Co-Regulate CRISPR/ cas3 Expression to Resist Bacteriophage., Viruses 12(1)

 [10] Curran TD., Abacha F., Hibberd SP., Rolfe MD., Lacey MM., Green J., 2017, Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon., Microbiology 163(3):400-409

 [11] 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

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