RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: hyaABCDEF
Gene(s): hyaA, hyaB, hyaC, hyaD, hyaE, hyaF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The hyaABCDEF operon is induced under anaerobiosis and repressed by nitrate Richard DJ,1999 ArcA and Appy antagonize the IscR repression effect under anaerobic conditions Nesbit AD,2012
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Maciag A., et al., 2011
[2] Menon NK., et al., 1990
[3] Menon NK., et al., 1991
Promoter
Name: hyaAp
+1: 1031984
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 155
Sequence: aaaagataaatccacacagtttgtattgttttgtgcaaaagtttcactacgctttattaaCaatactttctggcgacgtgc
                     -35                        -10         +1                   
Note(s): The hyaA promoter does not have much similarity to the consensus -10 and -35 promoter sequences for σ70, as shown by Richard DJ,1999. But, as reported in Atlung T,1997, a correlation with σ38 and hya operon expression has been proved under different conditions, so the promoter seems to be σ38.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IMP]
Reference(s): [4] Atlung T., et al., 1997
[5] Huerta AM., et al., 2003
[1] Maciag A., et al., 2011
[6] Richard DJ., et al., 1999
Terminator(s)
Type: rho-independent
Sequence: ccgacgtaaaAAGACGGTAAGTATCGCTTTCAGTCTTatgaatatcg
Reference(s): [2] Menon NK., et al., 1990
TF binding sites (TFBSs)
[AppY,+] 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
nd AppY activator hyaAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [11]
[ArcA,+] 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
proximal ArcA-phosphorylated activator hyaAp 1031910 1031924 -67.0 aaaaataggtCCATTTTTATCGCTAaaagataaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
proximal ArcA-phosphorylated activator hyaAp 1031966 1031988 -7.5 gtgcaaaagtTTCACTACGCTTTATTAACAATActttctggcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
[Fis,-] 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
proximal Fis repressor hyaAp 1031956 1031970 -21.0 gtattgttttGTGCAAAAGTTTCACtacgctttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [10]
[IscR,-] 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
proximal IscR repressor hyaAp 1031930 1031954 -42.0 cgctaaaagaTAAATCCACACAGTTTGTATTGTTTtgtgcaaaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8]
proximal IscR repressor hyaAp 1031933 1031957 -39.0 taaaagataaATCCACACAGTTTGTATTGTTTTGTgcaaaagttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [9]
[NarL,-] 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
proximal NarL-phosphorylated repressor hyaAp 1031971 1031977 -10.0 aaagtttcacTACGCTTtattaacaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W nd
proximal NarL-phosphorylated repressor hyaAp 1031987 1031993 7.0 ttattaacaaTACTTTCtggcgacgtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W nd
[NarP,-] 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
proximal NarP-phosphorylated repressor hyaAp 1031966 1031981 -10.0 gtgcaaaagtTTCACTACGCTTTATTaacaatactt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W nd
proximal NarP-phosphorylated repressor hyaAp 1031982 1031997 7.0 acgctttattAACAATACTTTCTGGCgacgtgcgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W nd
[YdeO,+] 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
proximal YdeO activator hyaAp 1031912 1031935 -61.0 aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]


Transcription unit          
Name: hyaABCDEF
Gene(s): hyaA, hyaB, hyaC, hyaD, hyaE, hyaF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The hyaABCDEF operon is induced under anaerobiosis and repressed by nitrate Richard DJ,1999 ArcA and Appy antagonize the IscR repression effect under anaerobic conditions Nesbit AD,2012
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Maciag A., et al., 2011
[2] Menon NK., et al., 1990
[3] Menon NK., et al., 1991
Promoter
Name: hyaAp2
+1: 1031984
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 155
Sequence: aaaagataaatccacacagtttgtattgttttgtgcaaaagtttcactacgctttattaaCaatactttctggcgacgtgc
                          -35              -10              +1                   
Note(s): The hyaA promoter does not have much similarity to the consensus -10 and -35 promoter sequences for σ70, as shown by Richard DJ,1999. But, as reported in Atlung T,1997, a correlation with σ38 and hya operon expression has been proved under different conditions, so the promoter seems to be σ38.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IMP]
Reference(s): [4] Atlung T., et al., 1997
[5] Huerta AM., et al., 2003
[1] Maciag A., et al., 2011
[6] Richard DJ., et al., 1999
Terminator(s)
Type: rho-independent
Sequence: ccgacgtaaaAAGACGGTAAGTATCGCTTTCAGTCTTatgaatatcg
Reference(s): [2] Menon NK., et al., 1990
TF binding sites (TFBSs)
[AppY,+] 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
nd AppY activator hyaAp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [11]
[ArcA,+] 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
proximal ArcA-phosphorylated activator hyaAp2 1031910 1031924 -67.0 aaaaataggtCCATTTTTATCGCTAaaagataaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
proximal ArcA-phosphorylated activator hyaAp2 1031966 1031988 -7.5 gtgcaaaagtTTCACTACGCTTTATTAACAATActttctggcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]
[Fis,-] 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
proximal Fis repressor hyaAp2 1031956 1031970 -21.0 gtattgttttGTGCAAAAGTTTCACtacgctttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [10]
[IscR,-] 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
proximal IscR repressor hyaAp2 1031930 1031954 -42.0 cgctaaaagaTAAATCCACACAGTTTGTATTGTTTtgtgcaaaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8]
proximal IscR repressor hyaAp2 1031933 1031957 -39.0 taaaagataaATCCACACAGTTTGTATTGTTTTGTgcaaaagttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [9]
[NarL,-] 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
proximal NarL-phosphorylated repressor hyaAp2 1031971 1031977 -10.0 aaagtttcacTACGCTTtattaacaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W nd
proximal NarL-phosphorylated repressor hyaAp2 1031987 1031993 7.0 ttattaacaaTACTTTCtggcgacgtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W nd
[NarP,-] 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
proximal NarP-phosphorylated repressor hyaAp2 1031966 1031981 -10.0 gtgcaaaagtTTCACTACGCTTTATTaacaatactt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W nd
proximal NarP-phosphorylated repressor hyaAp2 1031982 1031997 7.0 acgctttattAACAATACTTTCTGGCgacgtgcgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W nd
[YdeO,+] 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
proximal YdeO activator hyaAp2 1031912 1031935 -61.0 aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

 [EXP-IEP] Inferred from expression pattern

 [EXP-IMP] Inferred from mutant phenotype

 [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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing


Reference(s)    

 [1] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [2] Menon NK., Robbins J., Peck HD., Chatelus CY., Choi ES., Przybyla AE., 1990, Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames., J Bacteriol 172(4):1969-77

 [3] Menon NK., Robbins J., Wendt JC., Shanmugam KT., Przybyla AE., 1991, Mutational analysis and characterization of the Escherichia coli hya operon, which encodes [NiFe] hydrogenase 1., J Bacteriol 173(15):4851-61

 [4] Atlung T., Knudsen K., Heerfordt L., Brondsted L., 1997, Effects of sigmaS and the transcriptional activator AppY on induction of the Escherichia coli hya and cbdAB-appA operons in response to carbon and phosphate starvation., J Bacteriol 179(7):2141-6

 [5] 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

 [6] Richard DJ., Sawers G., Sargent F., McWalter L., Boxer DH., 1999, Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli., Microbiology 145 ( Pt 10):2903-12

 [7] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962

 [8] Giel JL., Rodionov D., Liu M., Blattner FR., Kiley PJ., 2006, IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli., Mol Microbiol 60(4):1058-75

 [9] Nesbit AD., Fleischhacker AS., Teter SJ., Kiley PJ., 2012, ArcA and AppY antagonize IscR repression of hydrogenase-1 expression under anaerobic conditions, revealing a novel mode of O2 regulation of gene expression in Escherichia coli., J Bacteriol 194(24):6892-9

 [10] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [11] King PW., Przybyla AE., 1999, Response of hya expression to external pH in Escherichia coli., J Bacteriol 181(17):5250-6

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