RegulonDB RegulonDB 11.1: 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): We inferred that ytfK is expressed as a monocistronic transcription unit, based on the genomic context of the gene. It is isolated in the forward direction, and the surrounding genes are encoded in the reverse direction.
CRP affects the ytfKp2 promoter and it binds to a sequence close to this promoter. In contrast, although ytfKp1 is also affected by CRP, CRP does not bind close to it, and therefore it was suggested that this effect of CRP is indirect for the p1 promoter Meyer L,2021.
Evidence: [IC] Inferred by curator
Promoter
Name: ytfKp2
+1: 4439413
Distance from start of the gene: 174
Sequence: gatgccagtttgcggtcaagcgcacaaatcatatgaaaaatgaatgcttatactgaagacCgcgcttcggtaaaaagataa
Note(s): This promoter was determined based on transcriptional fusion of the region of this promoter and deletion of the ytfKp1 promoter Meyer L,2021. Transcription activity of the promoter region was observed, but the sequence of the promoter was not shown, and just a putative transcriptional start site was suggested Meyer L,2021.
Evidence: [EXP-IEP]
[RS-EPT-CBR]
Reference(s): [1] Meyer L., et al., 2021
[2] Salgado H, et al., 2012
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 activator ytfKp2 4439350 4439366 -55.5 ttcccgcaagTGTGATGCCAGTTTGCGgtcaagcgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1]


Transcription unit          
Name: ytfK
Gene(s): ytfK   Genome Browser M3D Gene expression COLOMBOS
Note(s): We inferred that ytfK is expressed as a monocistronic transcription unit, based on the genomic context of the gene. It is isolated in the forward direction, and the surrounding genes are encoded in the reverse direction.
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
Evidence: [IC] Inferred by curator
Promoter
Name: ytfKp1
+1: 4439511
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 76
Sequence: ctttaggtaaaaaaagttatacgcggtggaaacattgcccggatagtctatagtcactaaGcattaaaatttgcgcctcat
                          -35               -10             +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Huerta AM., et al., 2003
[4] Lacour S., et al., 2004
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[PhoB,+] 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 PhoB-phosphorylated activator ytfKp1 4439444 4439462 -58.0 ttctgaataaTTGTAACCTTTAGGTAAAAaaagttatac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [6]
proximal PhoB-phosphorylated activator ytfKp1 4439466 4439484 -36.0 ggtaaaaaaaGTTATACGCGGTGGAAACAttgcccggat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [6]


Evidence    

 [EXP-IEP] Inferred from expression pattern

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [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

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Meyer L., Germain E., Maisonneuve E., 2021, Regulation of ytfK by cAMP-CRP Contributes to SpoT-Dependent Accumulation of (p)ppGpp in Response to Carbon Starvation YtfK Responds to Glucose Exhaustion., Front Microbiol 12:775164

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [3] 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

 [4] Lacour S., Landini P., 2004, SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences., J Bacteriol 186(21):7186-95

 [5] Baek JH., Lee SY., 2006, Novel gene members in the Pho regulon of Escherichia coli., FEMS Microbiol Lett 264(1):104-9

 [6] Yoshida Y., Sugiyama S., Oyamada T., Yokoyama K., Kim SK., Makino K., 2011, Identification of PhoB binding sites of the yibD and ytfK promoter regions in Escherichia coli., J Microbiol 49(2):285-9

RegulonDB