RegulonDB RegulonDB 10.9: 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: [BTEI] Boundaries of transcription experimentally identified
[ITCR] 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: [HIPP]
[ICWHO]
[IMP]
[TIM]
Reference(s): [4] Atlung T., et al., 1997
[5] Huerta AM., et al., 2003
[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 (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd AppY1 activator hyaAp nd nd nd nd nd [BPP], [GEA], [IGI] [11]
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArcA-phosphorylated1 activator hyaAp 1031910 1031924 -67.0 aaaaataggtCCATTTTTATCGCTAAaagataaatc nd [APIORCISFBSCS], [GEA] [6]
proximal ArcA-phosphorylated activator hyaAp 1031966 1031988 -7.5 gtgcaaaagtTTCACTACGCTTTATTAACAATActttctggcg nd [APIORCISFBSCS], [BPP], [GEA] [9]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor hyaAp 1031956 1031970 -21.0 gtattgttttGTGCAAAAGTTTCACTacgctttatt nd [AIBSCS], [GEA] [10]
[IscR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IscR repressor hyaAp 1031930 1031954 -42.0 cgctaaaagaTAAATCCACACAGTTTGTATTGTTTTgtgcaaaagt nd [BPP], [GEA] [8]
proximal IscR repressor hyaAp 1031933 1031957 -39.0 taaaagataaATCCACACAGTTTGTATTGTTTTGTGcaaaagtttc nd [APIORCISFBSCS], [BPP], [GEA] [9]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-phosphorylated repressor hyaAp 1031971 1031977 -10.0 aaagtttcacTACGCTTTattaacaata nd [APIORCISFBSCS], [GEA] nd
proximal NarL-phosphorylated repressor hyaAp 1031987 1031993 7.0 ttattaacaaTACTTTCTggcgacgtgc nd [APIORCISFBSCS], [GEA] nd
[NarP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarP-phosphorylated repressor hyaAp 1031966 1031981 -10.0 gtgcaaaagtTTCACTACGCTTTATTAacaatacttt nd [APIORCISFBSCS], [GEA] nd
proximal NarP-phosphorylated repressor hyaAp 1031982 1031997 7.0 acgctttattAACAATACTTTCTGGCGacgtgcgcca nd [APIORCISFBSCS], [GEA] nd
[YdeO,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal YdeO activator hyaAp 1031912 1031935 -61.0 aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt nd [BPP], [GEA], [IHBCE] [7]
Note(s): 1AppY actives the transcription of the hyaABCDEF operon during anaerobic growth.1ArcA actives the transcription of the hyaABCDEF operon during anaerobic growth.
1ArcA actives the transcription of the hyaABCDEF operon during anaerobic growth.
11AppY actives the transcription of the hyaABCDEF operon during anaerobic growth.


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: [BTEI] Boundaries of transcription experimentally identified
[ITCR] 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: [HIPP]
[ICWHO]
[IMP]
[TIM]
Reference(s): [4] Atlung T., et al., 1997
[5] Huerta AM., et al., 2003
[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 (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd AppY1 activator hyaAp2 nd nd nd nd nd [BPP], [GEA], [IGI] [11]
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArcA-phosphorylated1 activator hyaAp2 1031910 1031924 -67.0 aaaaataggtCCATTTTTATCGCTAAaagataaatc nd [APIORCISFBSCS], [GEA] [6]
proximal ArcA-phosphorylated activator hyaAp2 1031966 1031988 -7.5 gtgcaaaagtTTCACTACGCTTTATTAACAATActttctggcg nd [APIORCISFBSCS], [BPP], [GEA] [9]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor hyaAp2 1031956 1031970 -21.0 gtattgttttGTGCAAAAGTTTCACTacgctttatt nd [AIBSCS], [GEA] [10]
[IscR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IscR repressor hyaAp2 1031930 1031954 -42.0 cgctaaaagaTAAATCCACACAGTTTGTATTGTTTTgtgcaaaagt nd [BPP], [GEA] [8]
proximal IscR repressor hyaAp2 1031933 1031957 -39.0 taaaagataaATCCACACAGTTTGTATTGTTTTGTGcaaaagtttc nd [APIORCISFBSCS], [BPP], [GEA] [9]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-phosphorylated repressor hyaAp2 1031971 1031977 -10.0 aaagtttcacTACGCTTTattaacaata nd [APIORCISFBSCS], [GEA] nd
proximal NarL-phosphorylated repressor hyaAp2 1031987 1031993 7.0 ttattaacaaTACTTTCTggcgacgtgc nd [APIORCISFBSCS], [GEA] nd
[NarP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarP-phosphorylated repressor hyaAp2 1031966 1031981 -10.0 gtgcaaaagtTTCACTACGCTTTATTAacaatacttt nd [APIORCISFBSCS], [GEA] nd
proximal NarP-phosphorylated repressor hyaAp2 1031982 1031997 7.0 acgctttattAACAATACTTTCTGGCGacgtgcgcca nd [APIORCISFBSCS], [GEA] nd
[YdeO,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal YdeO activator hyaAp2 1031912 1031935 -61.0 aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt nd [BPP], [GEA], [IHBCE] [7]
Note(s): 1AppY actives the transcription of the hyaABCDEF operon during anaerobic growth.1ArcA actives the transcription of the hyaABCDEF operon during anaerobic growth.
1ArcA actives the transcription of the hyaABCDEF operon during anaerobic growth.
11AppY actives the transcription of the hyaABCDEF operon during anaerobic growth.


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IMP] Inferred from mutant phenotype

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IGI] Inferred from genetic interaction

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

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [IHBCE] Inferred by a human based on computational evidence


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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