RegulonDB RegulonDB 11.1: Operon Form
   

tar-tap-cheRBYZ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: tar-tap-cheRBYZ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: tar-tap-cheRBYZ
Gene(s): cheZ, cheY, cheB, cheR, tap, tar   Genome Browser M3D Gene expression COLOMBOS
Note(s): A transcript that contains cheY is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
The mRNA produced by the tar-tap-cheRBYZ operon has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
The cheYZ genes are 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-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Arnosti DN., et al., 1989
[2] Kundu TK., et al., 1997
[3] Parkinson JS. 1978
[4] Parkinson JS., et al., 1982
[5] Slocum MK., et al., 1983
Promoter
Name: tarp
+1: 1972716
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 25
Sequence: caatttcgcggcgggtggcatcagcaataaagtttcccccctccttgccgataacgagatCaacttgttttcaggaaggtg
                                -35                   -10   +1                   
Note(s): Kundu et al. showed in 1997 that transcription of tar is highly dependent on alternative factor σF and can be transcribed by RNA polymerase σ28 in vitro Kundu TK,1997.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Arnosti DN., et al., 1989
[6] Helmann JD., et al., 1987
[7] Huerta AM., et al., 2003
[8] Ide N., et al., 1999
[9] Ko M., et al., 2000
[2] Kundu TK., et al., 1997
[10] Liu X., et al., 1995
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator tarp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [11]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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-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


Reference(s)    

 [1] Arnosti DN., Chamberlin MJ., 1989, Secondary sigma factor controls transcription of flagellar and chemotaxis genes in Escherichia coli., Proc Natl Acad Sci U S A 86(3):830-4

 [2] Kundu TK., Kusano S., Ishihama A., 1997, Promoter selectivity of Escherichia coli RNA polymerase sigmaF holoenzyme involved in transcription of flagellar and chemotaxis genes., J Bacteriol 179(13):4264-9

 [3] Parkinson JS., 1978, Complementation analysis and deletion mapping of Escherichia coli mutants defective in chemotaxis., J Bacteriol 135(1):45-53

 [4] Parkinson JS., Houts SE., 1982, Isolation and behavior of Escherichia coli deletion mutants lacking chemotaxis functions., J Bacteriol 151(1):106-13

 [5] Slocum MK., Parkinson JS., 1983, Genetics of methyl-accepting chemotaxis proteins in Escherichia coli: organization of the tar region., J Bacteriol 155(2):565-77

 [6] Helmann JD., Chamberlin MJ., 1987, DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor., Proc Natl Acad Sci U S A 84(18):6422-4

 [7] 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

 [8] Ide N., Ikebe T., Kutsukake K., 1999, Reevaluation of the promoter structure of the class 3 flagellar operons of Escherichia coli and Salmonella., Genes Genet Syst 74(3):113-6

 [9] Ko M., Park C., 2000, Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli., J Mol Biol 303(3):371-82

 [10] Liu X., Matsumura P., 1995, An alternative sigma factor controls transcription of flagellar class-III operons in Escherichia coli: gene sequence, overproduction, purification and characterization., Gene 164(1):81-4

 [11] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

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