RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: katE
Gene(s): katE   Genome Browser M3D Gene expression COLOMBOS
Note(s): The first characterization for this transcription unit was done by von Ossowski I,1991 in 1991; its transcriptional start site was determined to be -123 bp upstream the ATG codon, and the investigators proposed a promoter sequence for σ38. This promoter sequence does not agree with the later-determined consensus for σ38 (based on several more promoters known to be σ38 affected), so in 1997 at Tanaka K,1997 the transcriptional start site for the katE transcription unit was restudied, and it was found to be a unique transcript that begins at -53/-54 bp upstream of the start codon, together with a really strong -10 box for the σ38 factor, very close to the consensus. In accordance with these new data, the +1 position and promoter sequence for katE transcription unit have been actualized here.
Jung IL,2003demonstrated that both rpoS and katE genes, which codify a transcriptional regulator and a product essential for the detoxification against H2O2-induced stress, respectively, were absolutely dependent on polyamines during entry into the stationary phase. These data suggest that polyamines could be directly participating in the defense mechanism against oxidative stress.
The katE gene is downregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Schellhorn HE., et al., 1988
[2] Tanaka K., et al., 1997
[3] von Ossowski I., et al., 1991
Promoter
Name: katEp
+1: 1813814
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 53
Sequence: aacaccgtttccagaatagtctccgaagcgggatctggctggtggtctatagttagagagTtttttgaccaaaacagcggc
                       -35                 -10              +1                   
Note(s): The promoter sequence and start transcription site for the katE gene were originally reported by von Ossowski I,1991 but faced with a strange σ38 sequence that was not similar to its consensus, the promoter sequence was recharacterized. Tanaka K,1997found a unique +1 start transcription site, closer to the start codon of the gene (at bp -53) and a -10 promoter sequence (cTATAGT) very similar to the consensus for σ38 (TATAAT, described by Tanaka K, Takayanagi Y, Fujita N, Ishihama A, Takahashi H,1993.
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IMP]
Reference(s): [4] Huerta AM., et al., 2003
[5] Maciag A., et al., 2011
[2] Tanaka K., et al., 1997
[3] von Ossowski I., et al., 1991
Terminator(s)
Type: rho-independent
Sequence: aaacacgtagGCCTGATAAGCGAAGCGCATCAGGCagttttgcgt
Reference(s): [3] von Ossowski I., et al., 1991
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor katEp 1813809 1813823 3.0 tctatagttaGAGAGTTTTTTGACCaaaacagcgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
[Fur,+] 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 Fur-Fe2+ activator katEp nd nd nd nd nd [EXP-IEP] W [7]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.4 1813787 1813820 gaagcgggatCTGGCTGGTGGTCTATAGTTAGAGAGTTTTTTGaccaaaacag
  anti-terminator -12.8 1813756 1813797 atttcataacACCGTTTCCAGAATAGTCTCCGAAGCGGGATCTGGCTGGTGgtctatagtt
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

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

 [EXP-IEP] Inferred from expression pattern

 [EXP-IMP] Inferred from mutant phenotype

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

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


Reference(s)    

 [1] Schellhorn HE., Hassan HM., 1988, Transcriptional regulation of katE in Escherichia coli K-12., J Bacteriol 170(9):4286-92

 [2] Tanaka K., Handel K., Loewen PC., Takahashi H., 1997, Identification and analysis of the rpoS-dependent promoter of katE, encoding catalase HPII in Escherichia coli., Biochim Biophys Acta 1352(2):161-6

 [3] von Ossowski I., Mulvey MR., Leco PA., Borys A., Loewen PC., 1991, Nucleotide sequence of Escherichia coli katE, which encodes catalase HPII., J Bacteriol 173(2):514-20

 [4] 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

 [5] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [6] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [7] Hoerter JD., Arnold AA., Ward CS., Sauer M., Johnson S., Fleming T., Eisenstark A., 2005, Reduced hydroperoxidase (HPI and HPII) activity in the Deltafur mutant contributes to increased sensitivity to UVA radiation in Escherichia coli., J Photochem Photobiol B 79(2):151-7

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