RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: fkpA
Gene(s): fkpA   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for fkpA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IEP] Inferred from expression pattern
Reference(s): [1] Rhodius VA., et al., 2005
Promoter
Name: fkpAp2
+1: 3477499
Distance from start of the gene: 80
Sequence: gaaactaatttaaacaaaaagagtctgaaaatagatgataatagggcgtgtctgtatgtaGatttgttcgacaacgcttta
Note(s): When σE is overproduced, this promoter is not active Danese PN,1997.
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Danese PN., et al., 1997


Transcription unit       
Name: fkpA
Gene(s): fkpA   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for fkpA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [1] Rhodius VA., et al., 2005
Promoter
Name: fkpAp1
+1: 3477525
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 106
Sequence: gagacagcactcatttcgcggtcatcgaaactaatttaaacaaaaagagtctgaaaatagAtgataatagggcgtgtctgt
                                 -35                  -10   +1                   
Note(s): The fkpAp1 promoter was induced by zinc in a microarray analysis Yamamoto K,2005
The transcriptional start site of the fkpAp1 promoter was also determined by Rhodius VA,2005, although they identified two transcription initiation sites for this promoter with the following absolute positions: 3475548 and 3475547.
It was suggested, from high-throughput screening of maps of transcriptional start sites (TSSs), that the TSS (3477525 ) assigned for this promoter is an RNA processing site Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [2] Danese PN., et al., 1997
[3] Dartigalongue C., et al., 2001
[4] Huerta AM., et al., 2003
[1] Rhodius VA., et al., 2005
[5] Salgado H, et al., 2012
[6] Yamamoto K., et al., 2005
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation fkpAp1 nd   [EXP-IEP] [7]
[8]
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [7] Costanzo A., et al., 2006
[8] Costanzo A., et al., 2008


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IEP] Inferred from expression pattern

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


Reference(s)    

 [1] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [2] Danese PN., Silhavy TJ., 1997, The sigma(E) and the Cpx signal transduction systems control the synthesis of periplasmic protein-folding enzymes in Escherichia coli., Genes Dev 11(9):1183-93

 [3] Dartigalongue C., Missiakas D., Raina S., 2001, Characterization of the Escherichia coli sigma E regulon., J Biol Chem 276(24):20866-75

 [4] 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

 [5] 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.

 [6] Yamamoto K., Ishihama A., 2005, Transcriptional response of Escherichia coli to external zinc., J Bacteriol 187(18):6333-40

 [7] Costanzo A., Ades SE., 2006, Growth phase-dependent regulation of the extracytoplasmic stress factor, sigmaE, by guanosine 3',5'-bispyrophosphate (ppGpp)., J Bacteriol 188(13):4627-34

 [8] Costanzo A., Nicoloff H., Barchinger SE., Banta AB., Gourse RL., Ades SE., 2008, ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms., Mol Microbiol 67(3):619-32

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