RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: kdpFABC
Synonym(s): OP00044, kdpABC
Gene(s): kdpC, kdpB, kdpA, kdpF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The kdpABC operon should now be referred to as kdpFABC Gassel M,1999.
The mRNA that contains the kdpB gene has been observed mainly in the cellular membrane 31540875.
Evidence: [ITCR] Inferred through co-regulation
[PAGTSBP] Products of adjacent genes in the same biological process
[PM] Polar mutation
Reference(s): [1] Asha H., et al., 1993
[2] Gassel M., et al., 1999
[3] Hesse JE., et al., 1984
[4] Nakashima K., et al., 1993
[5] Rhoads DB., et al., 1978
Promoter
Name: kdpFp
+1: 728849
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: tttacaccccgcccgcagatttttgcgaaatctttgcagccagaattctacccttccggtAtcacttttaggccactggag
                       -35                       -10        +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [6] Huerta AM., et al., 2003
[7] Sugiura A., et al., 1992
TF binding sites (TFBSs)
[KdpE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal KdpE-Pasp activator kdpFp 728904 728921 -63.0 cttttgccatTTTTATACTTTTTTTACAccccgcccgc nd [APIORCISFBSCS], [BPP], [GEA], [GS], [SM] [7], [8], [9]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [10] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -7.4 728778 728803 aggcgtgataACCGGCGTATTGCTGGTGTTTTTATtactgggtta
  terminator -11.4 728821 728853 tctacccttcCGGTATCACTTTTAGGCCACTGGAGGTGCACTgtgagtgcag
  anti-terminator -10.89 728795 728841 gtatcactttTAGGCCACTGGAGGTGCACTGTGAGTGCAGGCGTGATAACCGGCGTattgctggtg
  anti-anti-terminator -14.4 728817 728857 gaattctaccCTTCCGGTATCACTTTTAGGCCACTGGAGGTGCACTGTGAgtgcaggcgt
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    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [GS] genomic SELEX

 [SM] Site mutation


Reference(s)    

 [1] Asha H., Gowrishankar J., 1993, Regulation of kdp operon expression in Escherichia coli: evidence against turgor as signal for transcriptional control., J Bacteriol 175(14):4528-37

 [2] Gassel M., Mollenkamp T., Puppe W., Altendorf K., 1999, The KdpF subunit is part of the K(+)-translocating Kdp complex of Escherichia coli and is responsible for stabilization of the complex in vitro., J Biol Chem 274(53):37901-7

 [3] Hesse JE., Wieczorek L., Altendorf K., Reicin AS., Dorus E., Epstein W., 1984, Sequence homology between two membrane transport ATPases, the Kdp-ATPase of Escherichia coli and the Ca2+-ATPase of sarcoplasmic reticulum., Proc Natl Acad Sci U S A 81(15):4746-50

 [4] Nakashima K., Sugiura A., Kanamaru K., Mizuno T., 1993, Signal transduction between the two regulatory components involved in the regulation of the kdpABC operon in Escherichia coli: phosphorylation-dependent functioning of the positive regulator, KdpE., Mol Microbiol 7(1):109-16

 [5] Rhoads DB., Laimins L., Epstein W., 1978, Functional organization of the kdp genes of Escherichia coli K-12., J Bacteriol 135(2):445-52

 [6] 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

 [7] Sugiura A., Nakashima K., Tanaka K., Mizuno T., 1992, Clarification of the structural and functional features of the osmoregulated kdp operon of Escherichia coli., Mol Microbiol 6(13):1769-76

 [8] Narayanan A., Paul LN., Tomar S., Patil DN., Kumar P., Yernool DA., 2012, Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites., PLoS One 7(1):e30102

 [9] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [10] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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