RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: ytfK
Gene(s): ytfK   Genome Browser M3D Gene expression COLOMBOS
Note(s): Analysis of gene expression has proved that under NlpE lipoprotein overexpression, the presence of the protein CpxR causes increased transcription of the ytfK gene; however, no DNA sequence related to the consensus DNA-binding site of CpxR has been identified in the regulatory region of the gene. Therefore, the effect of CpxR on ytfK is probably indirect Raivio TL,2013
Promoter
Name: ytfKp
+1: 4439511
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 76
Sequence: ctttaggtaaaaaaagttatacgcggtggaaacattgcccggatagtctatagtcactaaGcattaaaatttgcgcctcat
                          -35               -10             +1                   
Evidence: [CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Lacour S., et al., 2004
[2] Salgado H, et al., 2012
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 PhoB-Phosphorylated1 activator ytfKp 4439444 4439462 -58.0 ttctgaataaTTGTAACCTTTAGGTAAAAaaagttatac nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [3], [4]
proximal PhoB-Phosphorylated2 activator ytfKp 4439466 4439484 -36.0 ggtaaaaaaaGTTATACGCGGTGGAAACAttgcccggat nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [3], [4]
Note(s): 1Baek and Lee demonstrated that the protein PhoB positively regulates transcription initiation of the gene ytfK in strain W3110, a strain derived from the K-12 strain Baek JH,2006 They also proposed a putative Pho box to be recognized by PhoB, but it overlaps with the identified transcriptional start site. On the other hand, based on DNase I footprinting analysis, Yoshida et al. demostrated that in E. coli strain O157:H7, the protein PhoB recognizes and binds to two transcription factor-binding sites (TFBSs) located upstream of the transcriptional start site of ytfK Yoshida Y,2011The E. coli strains W3110 and MG1655 contain a sequence, upstream of ytfK, that is identical to the one mentioned above for O157:H7; therefore, taking into account the results above, we have added the regulation reported by Baek and Lee (Baek JH,2006using the TFBS identified by Yoshida et al. Yoshida Y,2011
2Baek and Lee demonstrated that the protein PhoB positively regulates transcription initiation of the gene ytfK in strain W3110, a strain derived from the K-12 strain Baek JH,2006 They also proposed a putative Pho box to be recognized by PhoB, but it overlaps with the identified transcriptional start site. On the other hand, based on DNase I footprinting analysis, Yoshida et al. demostrated that in E. coli strain O157:H7, the protein PhoB recognizes and binds to two transcription factor-binding sites (TFBSs) located upstream of the transcriptional start site of ytfK Yoshida Y,2011The E. coli strains W3110 and MG1655 contain a sequence, upstream of ytfK, that is identical to the one mentioned above for O157:H7; therefore, taking into account the results above, we have added the regulation reported by Baek and Lee (Baek JH,2006using the TFBS identified by Yoshida et al. Yoshida Y,20111Baek and Lee demonstrated that the protein PhoB positively regulates transcription initiation of the gene ytfK in strain W3110, a strain derived from the K-12 strain Baek JH,2006 They also proposed a putative Pho box to be recognized by PhoB, but it overlaps with the identified transcriptional start site. On the other hand, based on DNase I footprinting analysis, Yoshida et al. demostrated that in E. coli strain O157:H7, the protein PhoB recognizes and binds to two transcription factor-binding sites (TFBSs) located upstream of the transcriptional start site of ytfK Yoshida Y,2011The E. coli strains W3110 and MG1655 contain a sequence, upstream of ytfK, that is identical to the one mentioned above for O157:H7; therefore, taking into account the results above, we have added the regulation reported by Baek and Lee (Baek JH,2006using the TFBS identified by Yoshida et al. Yoshida Y,2011
2Baek and Lee demonstrated that the protein PhoB positively regulates transcription initiation of the gene ytfK in strain W3110, a strain derived from the K-12 strain Baek JH,2006 They also proposed a putative Pho box to be recognized by PhoB, but it overlaps with the identified transcriptional start site. On the other hand, based on DNase I footprinting analysis, Yoshida et al. demostrated that in E. coli strain O157:H7, the protein PhoB recognizes and binds to two transcription factor-binding sites (TFBSs) located upstream of the transcriptional start site of ytfK Yoshida Y,2011The E. coli strains W3110 and MG1655 contain a sequence, upstream of ytfK, that is identical to the one mentioned above for O157:H7; therefore, taking into account the results above, we have added the regulation reported by Baek and Lee (Baek JH,2006using the TFBS identified by Yoshida et al. Yoshida Y,2011





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