RegulonDB RegulonDB 10.9: Operon Form

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

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

Transcription unit          
Name: tsr
Gene(s): tsr   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
Name: tsrp1
+1: 4591412
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 245
Sequence: aattgaccgctatcctgtagtgatgttgccagagttacgcgcgcgtaaagtaaggtaaatAactgagtggttattttaggg
                       -35                    -10           +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Evidence: [HIPP]
Reference(s): [1] De Wulf P., et al., 1999
[2] Huerta AM., et al., 2003
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 CpxR-Phosphorylated repressor tsrp1 4591396 4591410 -9.0 ttacgcgcgcGTAAAGTAAGGTAAATaactgagtgg nd [BPP] [1]

Transcription unit       
Name: tsr
Gene(s): tsr   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [3] Arnosti DN., et al., 1989
Name: tsrp
+1: 4591633
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 24
Sequence: ctcggcgtaatctccgcgggatattcataaagtttttcctttccaggccgaaaatcttgcAtcggtccacaggaaagagaa
                            -35                -10          +1                   
Note(s): Kundu et al. showed in 1997 that transcription of tsr is highly dependent on alternative factor σF and can be transcribed by RNA polymerase σ28 in vitro Kundu TK,1997.
Evidence: [HIPP]
Reference(s): [3] Arnosti DN., et al., 1989
[4] Chilcott GS., et al., 2000
[5] Helmann JD., et al., 1987
[2] Huerta AM., et al., 2003
[6] Ide N., et al., 1999
[7] Ko M., et al., 2000
[8] Kundu TK., et al., 1997
[9] Park K., et al., 2001

RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.2 4591611 4591649 aagtttttccTTTCCAGGCCGAAAATCTTGCATCGGTCCACAGGAAAGagaaaccatg
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"


 [1] De Wulf P., Kwon O., Lin EC., 1999, The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons., J Bacteriol 181(21):6772-8

 [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] 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

 [4] Chilcott GS., Hughes KT., 2000, Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli., Microbiol Mol Biol Rev 64(4):694-708

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] Park K., Choi S., Ko M., Park C., 2001, Novel sigmaF-dependent genes of Escherichia coli found using a specified promoter consensus., FEMS Microbiol Lett 202(2):243-50