RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: fdnGHI
Synonym(s): OP00216
Gene(s): fdnG, fdnH, fdnI   Genome Browser M3D Gene expression COLOMBOS
Note(s): Despite Rabin and Stewart Rabin RS,1993 reporting that NarP was a weak activator of the fdnGHI transcription unit, Wang and Gunsalus Wang H,2003 concluded that NarP cannot induce that expression, rather, NarP antagonizes the ability of NarL to activate the operon.
This transcription unit is anaerobically induced in the presence of nitrate Wang H,2003
Based on qRT-PCR, it was found that three selenopolypeptide genes, fdnG, fdoG, and fdhF, were induced more than 2-fold by both 0.01 and 5 mM Na2SeO3 (sodium selenite) Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH,2014
The transcription of the fdnI gene is induced during the first 24 h after the induction of nitrogen starvation Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020.
Reference(s): [1] Berg BL., et al., 1991
[2] Li J., et al., 1994
[3] Li J., et al., 1992
Promoter
Name: fdnGp
+1: 1547372
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: agatgttctttttgatttcgcgcaaaaagattcagaattttactgttagtttcctcgcgcAgtaatacccctgaaaaaaga
                     -35                       -10          +1                   
Evidence: [ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[3] Li J., et al., 1992
[5] Salgado H, et al., 2012
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR activator fdnGp 1547268 1547281 -97.5 tctaccgctaTTGAGGTAGGTCAAtttgcgaagg nd [GEA], [APIORCISFBSCS], [SM] [3]
proximal FNR activator fdnGp 1547323 1547336 -42.5 gatgttctttTTGATTTCGCGCAAaaagattcag nd [GEA], [APIORCISFBSCS], [SM] [3]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR repressor fdnGp 1547268 1547281 -97.5 tctaccgctaTTGAGGTAGGTCAAtttgcgaagg nd [GEA], [APIORCISFBSCS], [SM] [3]
[NarL,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NarL-phosphorylated activator fdnGp 1547245 1547251 -124.0 cctgtcaggcAGTGGTGcgtttttcta nd [GEA], [APIORCISFBSCS], [BCE], [SM] [2], [6], [7], [8], [9]
remote NarL-phosphorylated activator fdnGp 1547260 1547266 -109.0 tgcgtttttcTACCGCTattgaggtag nd [GEA], [BCE], [SM] [3], [9]
remote NarL-phosphorylated activator fdnGp 1547269 1547275 -100.0 ctaccgctatTGAGGTAggtcaatttg nd [GEA], [APIORCISFBSCS], [BPP], [SM] [6], [7], [8], [9]
proximal NarL-phosphorylated activator fdnGp 1547292 1547298 -77.0 tttgcgaaggCGGATTAttttgtggca nd [GEA], [APIORCISFBSCS], [BCE], [SM] [6], [7], [8], [9]
[NarP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NarP-phosphorylated repressor fdnGp 1547255 1547270 -109.0 agtggtgcgtTTTTCTACCGCTATTGaggtaggtca nd [GEA], [SM] [7], [9]
remote NarP-phosphorylated repressor fdnGp 1547264 1547279 -100.0 tttttctaccGCTATTGAGGTAGGTCaatttgcgaa nd [GEA], [SM] [7], [9]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [10] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.6 1547280 1547304 aggtaggtcaATTTGCGAAGGCGGATTATTTTGTggcaaacaga
  anti-terminator -9.2 1547250 1547287 aggcagtggtGCGTTTTTCTACCGCTATTGAGGTAGGTCAATTTGCGaaggcggatt
  anti-anti-terminator -6.6 1547245 1547266 ctgtcaggcaGTGGTGCGTTTTTCTACCGCTattgaggtag
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"
REGULATION, RNA cis-regulatory element:  
Rfam type: Cis-reg
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [11] null null
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  Selenocysteine insertion sequence 3 84.3 1547983 1548041 ccaggcgcgcGUCUGACACGGACCAACGGUAGCAAGUCUUGCUCCAACAUUUGGUCGCGGUGCGAUGACcaaccacugg
Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"


Evidence    

 [ICWHO] Inferred computationally without human oversight

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

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

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

 [SM] Site mutation

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Berg BL., Li J., Heider J., Stewart V., 1991, Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. I. Nucleotide sequence of the fdnGHI operon and evidence that opal (UGA) encodes selenocysteine., J Biol Chem 266(33):22380-5

 [2] Li J., Kustu S., Stewart V., 1994, In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12., J Mol Biol 241(2):150-65

 [3] Li J., Stewart V., 1992, Localization of upstream sequence elements required for nitrate and anaerobic induction of fdn (formate dehydrogenase-N) operon expression in Escherichia coli K-12., J Bacteriol 174(15):4935-42

 [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] Berg BL., Stewart V., 1990, Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12., Genetics 125(4):691-702

 [7] Darwin AJ., Tyson KL., Busby SJ., Stewart V., 1997, Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement., Mol Microbiol 25(3):583-95

 [8] Rabin RS., Stewart V., 1993, Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12., J Bacteriol 175(11):3259-68

 [9] Wang H., Gunsalus RP., 2003, Coordinate regulation of the Escherichia coli formate dehydrogenase fdnGHI and fdhF genes in response to nitrate, nitrite, and formate: roles for NarL and NarP., J Bacteriol 185(17):5076-85

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

 [11] null, null, null, null


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