RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: hycABCDEFGHI
Synonym(s): OP00208
Gene(s): hycI, hycH, hycG, hycF, hycE, hycD, hycC, hycB, hycA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Regulation of the hyc operon by ZraR (HydG) was suggested. However, this protein is not a physiological regulator of the operon Leonhartsberger S,2001
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Bohm R., et al., 1990
[2] Hopper S., et al., 1994
[3] Rossmann R., et al., 1995
Promoter
Name: hycAp
+1: 2850461
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 26
Sequence: ttaaaaatctctttaataacaataaattaaaagttggcacaaaaaatgcttaaagctggcAtctctgttaaacgggtaacc
                                   -24         -12          +1                   
Evidence: [ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Lutz S., et al., 1990
[6] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: aaccatgaagGCCCGATAAGCGCAGCGCATCGGGCaatttagcat
Reference(s): [3] Rossmann R., et al., 1995
TF binding sites (TFBSs)
[FhlA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FhlA-formate activator hycAp 2850539 2850552 -84.5 cgaaatgacaCGTCGACACGGCGAcgaaattcat nd [GEA], [APIORCISFBSCS], [BPP] [2], [8], [9]
remote FhlA-formate activator hycAp 2850553 2850566 -98.0 aatgtcgatgATGTCGAAATGACAcgtcgacacg nd [GEA], [APIORCISFBSCS], [BPP] [2], [8], [9], [10]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator hycAp 2850493 2850505 -38.5 atctctttaaTAACAATAAATTAaaagttggca nd [GEA], [APIORCISFBSCS], [BPP] [2]
[ModE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ModE-molybdate activator hycAp 2850641 2850664 -192.0 cccgttggcaGAGGGTTATTTCGTGCATATCGCCtcccattaac nd [GEA], [BPP] [7]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NsrR repressor hycAp 2850526 2850537 -70.0 acacggcgacGAAATTCATCTTtagcttaaaa nd [GEA], [APIORCISFBSCS] [11]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.6 2849883 2849923 gggatgggcgTGTCGATGAGTGTCGAAAATGACATTTCATCGGCATGTTTtcgtcaaaaa
  anti-terminator -14.8 2849911 2849953 tgcccgttttGCAGGCGTTACGCCTGTTTGGGGATGGGCGTGTCGATGAGTGtcgaaaatga
  anti-anti-terminator -14.8 2849932 2849961 tgaggctttgCCCGTTTTGCAGGCGTTACGCCTGTTTGGggatgggcgt
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

 [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.

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Bohm R., Sauter M., Bock A., 1990, Nucleotide sequence and expression of an operon in Escherichia coli coding for formate hydrogenlyase components., Mol Microbiol 4(2):231-43

 [2] Hopper S., Babst M., Schlensog V., Fischer HM., Hennecke H., Bock A., 1994, Regulated expression in vitro of genes coding for formate hydrogenlyase components of Escherichia coli., J Biol Chem 269(30):19597-604

 [3] Rossmann R., Maier T., Lottspeich F., Bock A., 1995, Characterisation of a protease from Escherichia coli involved in hydrogenase maturation., Eur J Biochem 227(1-2):545-50

 [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] Lutz S., Bohm R., Beier A., Bock A., 1990, Characterization of divergent NtrA-dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli., Mol Microbiol 4(1):13-20

 [6] 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.

 [7] Self WT., Grunden AM., Hasona A., Shanmugam KT., 1999, Transcriptional regulation of molybdoenzyme synthesis in Escherichia coli in response to molybdenum: ModE-molybdate, a repressor of the modABCD (molybdate transport) operon is a secondary transcriptional activator for the hyc and nar operons., Microbiology 145 ( Pt 1):41-55

 [8] Leonhartsberger S., Ehrenreich A., Bock A., 2000, Analysis of the domain structure and the DNA binding site of the transcriptional activator FhlA., Eur J Biochem 267(12):3672-84

 [9] Schlensog V., Lutz S., Bock A., 1994, Purification and DNA-binding properties of FHLA, the transcriptional activator of the formate hydrogenlyase system from Escherichia coli., J Biol Chem 269(30):19590-6

 [10] Self WT., Shanmugam KT., 2000, Isolation and characterization of mutated Fh1A proteins which activate transcription of the hyc operon (formate hydrogenlyase) of Escherichia coli in the absence of molybdate(1)., FEMS Microbiol Lett 184(1):47-52

 [11] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

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