RegulonDB RegulonDB 11.1: Operon Form
   

hypABCDE-fhlA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: hypABCDE
Synonym(s): OP00209, hydBEF
Gene(s): hypA, hypB, hypC, hypD, hypE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Hopper S., et al., 1994
[2] Lutz S., et al., 1991
Promoter
Name: hypAp
+1: 2850627
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 20
Sequence: catcgacattattcaccgcagggataatcaacactggcacaattattgcttgtagctggcAatagttaatgggaggcgata
                                   -24         -12          +1                   
Note(s): Based on primer extension hypA and hypB promoters have similar activities Hopper S,1994.
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[2] Lutz S., et al., 1991
Terminator(s)
Type: rho-independent
Sequence: atgaccttttGCACCGCTTTGCGGTGCTttcctggaag
Reference(s): [2] Lutz S., et al., 1991
TF binding sites (TFBSs)
[FhlA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FhlA-formate activator hypAp 2849869 2849882 -751.5 ctcaggtgatTGTCATTTTTGACGaaaacatgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [5]
remote FhlA-formate activator hypAp 2849900 2849913 -720.5 gccgatgaaaTGTCATTTTCGACActcatcgaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [5]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator hypAp 2850493 2850505 -127.5 tgccaactttTAATTTATTGTTAttaaagagat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NsrR repressor hypAp 2850526 2850537 -96.0 ttttaagctaAAGATGAATTTCgtcgccgtgt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]


Transcription unit          
Name: hypABCDE-fhlA
Gene(s): hypA, hypB, hypC, hypD, hypE, fhlA   Genome Browser M3D Gene expression COLOMBOS
Note(s): It has been suggested that sometimes the downstream gene fhlA is transcribed along with the hypABCDE operon genes; however, fhlA has its own promoter (unpublished data Lutz S,1991).
Evidence: [AS-NAS] Non-traceable author statement
[EXP-IEP] Inferred from expression pattern
Reference(s): [2] Lutz S., et al., 1991
[7] Schlensog V., et al., 1990
Promoter
Name: hypAp
+1: 2850627
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 20
Sequence: catcgacattattcaccgcagggataatcaacactggcacaattattgcttgtagctggcAatagttaatgggaggcgata
                                   -24         -12          +1                   
Note(s): Based on primer extension hypA and hypB promoters have similar activities Hopper S,1994.
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[2] Lutz S., et al., 1991
TF binding sites (TFBSs)
[FhlA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FhlA-formate activator hypAp 2849869 2849882 -751.5 ctcaggtgatTGTCATTTTTGACGaaaacatgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [5]
remote FhlA-formate activator hypAp 2849900 2849913 -720.5 gccgatgaaaTGTCATTTTCGACActcatcgaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [5]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator hypAp 2850493 2850505 -127.5 tgccaactttTAATTTATTGTTAttaaagagat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NsrR repressor hypAp 2850526 2850537 -96.0 ttttaagctaAAGATGAATTTCgtcgccgtgt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]


Transcription unit          
Name: hypBCDE-fhlA
Gene(s): hypB, hypC, hypD, hypE, fhlA   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was suggested that sometimes fhlA is transcribed with the hyp operon. However, this gene is also transcribed from its own promoter (unpublished data of S. Lutz and A. Bock, cited by Lutz, 1991 Lutz S,1991).
Evidence: [AS-NAS] Non-traceable author statement
[EXP-IEP] Inferred from expression pattern
Reference(s): [2] Lutz S., et al., 1991
[7] Schlensog V., et al., 1990
Promoter
Name: hypBp
+1: 2850839
Distance from start of the gene: 162
Sequence: gccttttgttttgatctggtttgccgcggcagcgtggcggaaggttgtaaactgcacctcGaagaacaagaggccgaatgc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Lutz S., et al., 1991
[8] Salgado H, et al., 2012
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR activator hypBp 2850683 2850696 -149.5 ggcactggaaTTGATCGAACAGCAggccgcaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
proximal FNR activator hypBp 2850789 2850802 -43.5 gccttttgttTTGATCTGGTTTGCcgcggcagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]


Transcription unit          
Name: hypBCDE
Synonym(s): hydBEF
Gene(s): hypB, hypC, hypD, hypE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [2] Lutz S., et al., 1991
Promoter
Name: hypBp
+1: 2850839
Distance from start of the gene: 162
Sequence: gccttttgttttgatctggtttgccgcggcagcgtggcggaaggttgtaaactgcacctcGaagaacaagaggccgaatgc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Lutz S., et al., 1991
[8] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: atgaccttttGCACCGCTTTGCGGTGCTttcctggaag
Reference(s): [2] Lutz S., et al., 1991
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR activator hypBp 2850683 2850696 -149.5 ggcactggaaTTGATCGAACAGCAggccgcaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
proximal FNR activator hypBp 2850789 2850802 -43.5 gccttttgttTTGATCTGGTTTGCcgcggcagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.3 2854298 2854328 agtcaatgacCTTTTGCACCGCTTTGCGGTGCTTTCCTGGaagaacaaaa
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-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] 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

 [2] Lutz S., Jacobi A., Schlensog V., Bohm R., Sawers G., Bock A., 1991, Molecular characterization of an operon (hyp) necessary for the activity of the three hydrogenase isoenzymes in Escherichia coli., Mol Microbiol 5(1):123-35

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] Schlensog V., Bock A., 1990, Identification and sequence analysis of the gene encoding the transcriptional activator of the formate hydrogenlyase system of Escherichia coli., Mol Microbiol 4(8):1319-27

 [8] 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.

 [9] Messenger SL., Green J., 2003, FNR-mediated regulation of hyp expression in Escherichia coli., FEMS Microbiol Lett 228(1):81-6

 [10] Argaman L., Altuvia S., 2000, fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex., J Mol Biol 300(5):1101-12

 [11] Salim NN., Feig AL., 2010, An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction., PLoS One 5(9)

 [12] Zhang A., Wassarman KM., Ortega J., Steven AC., Storz G., 2002, The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs., Mol Cell 9(1):11-22

 [13] Altuvia S., Zhang A., Argaman L., Tiwari A., Storz G., 1998, The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding., EMBO J 17(20):6069-75

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