RegulonDB

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 Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence:	[EXP-IEP-COREGULATION] Inferred through co-regulation [EXP-IMP-POLAR-MUTATION] Polar mutation [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
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:	[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
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	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
proximal	KdpE-phosphorylated	activator	kdpFp	728904	728921	-63.0	cttttgccatTTTTATACTTTTTTTACAccccgcccgc	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[7], [8], [9]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
KdpE-phosphorylated	activator	kdpFp	728904	728921	-63.0	cttttgccatTTTTATACTTTTTTTACAccccgcccgc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[7], [8], [9]

RNA cis-regulatory element

Regulation, transcriptional elongation
Attenuator type:	Transcriptional
Strand:	reverse

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
[COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[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-GSELEX] genomic SELEX
[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IMP-SITE-MUTATION] 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

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