RegulonDB RegulonDB 11.2: Operon Form
   

hdeAB-yhiD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: hdeAB-yhiD
Gene(s): yhiD, hdeB, hdeA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The hdeAB-yhiD operon is induced under stationary phase Shin M,2005. Weber H,2005 and at acid pH Hayes ET,2006. Tucker DL,2003. Marzan LW,2013 in a RcsB-dependent manner Johnson MD,2011
Lrp represses the hdeAB-yhiD operon only in the exponential phase at pH 7.0, and MarA reduces this repression Ruiz C,2008.
The hdeAB genes are upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010
The mdtEF-tolC, malEFG, gadBC, treBC, entCEBA-ybdB, hdeAB-yhiD, and alaE operons were differentially regulated after induction of the nonnative organic acid citramalate Webb J,2019
The expression of hdeB appears to be slightly repressed by Rob under butanol stress Wang Z,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Arnqvist A., et al., 1994
[2] Tucker DL., et al., 2003
[3] Yoshida T., et al., 1993
Promoter
Name: hdeAp2
+1: 3656791
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 51
Sequence: tctgattttgatattttccatcaacatgacatatacagaaaaccaggttataacctcagtGtcgaaattgattcgtgacgg
                               -35                      -10 +1                   
Note(s): The same transcriptional start site for this promoter is used in hns rpoS mutant strains as well as strains wild type for H-NS and σ38. This indicates that the same promoter can be utilized by both σ38 and σ70 in vivo. This promoter has significant homology to the consensus of a σ70 promoter even though it is dependent upon σ38 Arnqvist A,1994.
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [1] Arnqvist A., et al., 1994
[4] Dudin O., et al., 2013
[5] Itou J., et al., 2009
[6] Salgado H, et al., 2012
TF binding sites (TFBSs)
[FliZ,-] 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 FliZ repressor hdeAp2 3656757 3656812 8.0 catatacagaAAACCAGGTTATAACCTCAGTGTCGAAATTGATTCGTGACGGCTCTTTCACTTTATagttgaggat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [16]
[GadE,+] 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 GadE activator hdeAp2 3656773 3656792 9.5 ataacctcagTGTCGAAATTGATTCGTGACggctctttca nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [11]
remote GadE activator hdeAp2 3656899 3656918 -117.5 aatgcagtcgATTTAATAAAAATTTCCTAAttgcagtatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [7], [10], [11]
[GadW,+] 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 GadW activator hdeAp2 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12]
proximal GadW activator hdeAp2 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12]
remote GadW activator hdeAp2 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [7]
[GadW,-] 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 GadW repressor hdeAp2 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12]
proximal GadW repressor hdeAp2 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12]
remote GadW repressor hdeAp2 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [7]
[GadX,+] 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 GadX activator hdeAp2 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [10], [12]
proximal GadX activator hdeAp2 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [10], [12]
remote GadX activator hdeAp2 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [7]
[GadX,-] 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 GadX repressor hdeAp2 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [10], [12]
proximal GadX repressor hdeAp2 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [10], [12]
remote GadX repressor hdeAp2 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [7]
[H-NS,-] 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 H-NS repressor hdeAp2 3656902 3656916 -118.0 tgcagtcgatTTAATAAAAATTTCCtaattgcagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [3], [8], [9]
[Lrp,-] 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 Lrp-L-leucine repressor hdeAp2 3656802 3656817 -18.0 catgacatatACAGAAAACCAGGTTAtaacctcagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal Lrp-L-leucine repressor hdeAp2 3656839 3656854 -55.0 tgaaataaaaATATCTGATTTTGATAttttccatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal Lrp-L-leucine repressor hdeAp2 3656848 3656863 -64.0 tcattgtattGAAATAAAAATATCTGattttgatat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
remote Lrp-L-leucine repressor hdeAp2 3656881 3656896 -97.0 tttcctaattGCAGTATCTGATGCATctgtaactca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
remote Lrp-L-leucine repressor hdeAp2 3656900 3656915 -116.0 gcagtcgattTAATAAAAATTTCCTAattgcagtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
remote Lrp-L-leucine repressor hdeAp2 3656943 3656958 -159.0 aaatcccctgCTATCAATCTATGCCAaaaacgcgtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[MarA,-] 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 MarA repressor hdeAp2 3656820 3656839 -39.0 tgattttgatATTTTCCATCAACATGACATatacagaaaa nd [EXP-IDA-PURIFIED-PROTEIN], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-PURIFIED-PROTEIN], [EXP-IMP-SITE-MUTATION] W [13]
[PhoP,+] 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 PhoP-phosphorylated activator hdeAp2 3656815 3656831 -32.0 atattttccaTCAACATGACATATACAgaaaaccagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14]
[RcsB,+] 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 RcsB-phosphorylated activator hdeAp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [17]
[TorR,+] 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 TorR-phosphorylated activator hdeAp2 3656814 3656823 -27.5 catcaacatgACATATACAGaaaaccaggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [15]
proximal TorR-phosphorylated activator hdeAp2 3656838 3656847 -51.5 aaaatatctgATTTTGATATtttccatcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]


Transcription unit          
Name: hdeAB-yhiD
Gene(s): yhiD, hdeB, hdeA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The hdeAB-yhiD operon is induced under stationary phase Shin M,2005. Weber H,2005 and at acid pH Hayes ET,2006. Tucker DL,2003. Marzan LW,2013 in a RcsB-dependent manner Johnson MD,2011
Lrp represses the hdeAB-yhiD operon only in the exponential phase at pH 7.0, and MarA reduces this repression Ruiz C,2008.
The hdeAB genes are upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010
The mdtEF-tolC, malEFG, gadBC, treBC, entCEBA-ybdB, hdeAB-yhiD, and alaE operons were differentially regulated after induction of the nonnative organic acid citramalate Webb J,2019
The expression of hdeB appears to be slightly repressed by Rob under butanol stress Wang Z,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Arnqvist A., et al., 1994
[2] Tucker DL., et al., 2003
[3] Yoshida T., et al., 1993
Promoter
Name: hdeAp
+1: 3656791
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 51
Sequence: tctgattttgatattttccatcaacatgacatatacagaaaaccaggttataacctcagtGtcgaaattgattcgtgacgg
                               -35                    -10   +1                   
Note(s): The same transcriptional start site for this promoter is used in hns rpoS mutant strains as well as strains wild type for H-NS and σ38. This indicates that the same promoter can be utilized by both σ38 and σ70 in vivo. This promoter has significant homology to the consensus of a σ70 promoter even though it is dependent upon σ38 Arnqvist A,1994.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Arnqvist A., et al., 1994
[4] Dudin O., et al., 2013
[18] Huerta AM., et al., 2003
[5] Itou J., et al., 2009
[6] Salgado H, et al., 2012
TF binding sites (TFBSs)
[FliZ,-] 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 FliZ repressor hdeAp 3656757 3656812 8.0 catatacagaAAACCAGGTTATAACCTCAGTGTCGAAATTGATTCGTGACGGCTCTTTCACTTTATagttgaggat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [16]
[GadE,+] 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 GadE activator hdeAp 3656773 3656792 9.5 ataacctcagTGTCGAAATTGATTCGTGACggctctttca nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [11]
remote GadE activator hdeAp 3656899 3656918 -117.5 aatgcagtcgATTTAATAAAAATTTCCTAAttgcagtatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [7], [10], [11]
[GadW,+] 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 GadW activator hdeAp 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12]
proximal GadW activator hdeAp 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12]
remote GadW activator hdeAp 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [7]
[GadW,-] 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 GadW repressor hdeAp 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12]
proximal GadW repressor hdeAp 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12]
remote GadW repressor hdeAp 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [7]
[GadX,+] 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 GadX activator hdeAp 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [10], [12]
proximal GadX activator hdeAp 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [10], [12]
remote GadX activator hdeAp 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [7]
[GadX,-] 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 GadX repressor hdeAp 3656835 3656854 -53.5 tgaaataaaaATATCTGATTTTGATATTTTccatcaacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [10], [12]
proximal GadX repressor hdeAp 3656856 3656875 -74.5 tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [10], [12]
remote GadX repressor hdeAp 3656908 3656927 -126.5 gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [7]
[H-NS,-] 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 H-NS repressor hdeAp 3656902 3656916 -118.0 tgcagtcgatTTAATAAAAATTTCCtaattgcagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [3], [8], [9]
[Lrp,-] 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 Lrp-L-leucine repressor hdeAp 3656802 3656817 -18.0 catgacatatACAGAAAACCAGGTTAtaacctcagt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal Lrp-L-leucine repressor hdeAp 3656839 3656854 -55.0 tgaaataaaaATATCTGATTTTGATAttttccatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal Lrp-L-leucine repressor hdeAp 3656848 3656863 -64.0 tcattgtattGAAATAAAAATATCTGattttgatat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
remote Lrp-L-leucine repressor hdeAp 3656881 3656896 -97.0 tttcctaattGCAGTATCTGATGCATctgtaactca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
remote Lrp-L-leucine repressor hdeAp 3656900 3656915 -116.0 gcagtcgattTAATAAAAATTTCCTAattgcagtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
remote Lrp-L-leucine repressor hdeAp 3656943 3656958 -159.0 aaatcccctgCTATCAATCTATGCCAaaaacgcgtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[MarA,-] 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 MarA repressor hdeAp 3656820 3656839 -39.0 tgattttgatATTTTCCATCAACATGACATatacagaaaa nd [EXP-IDA-PURIFIED-PROTEIN], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-PURIFIED-PROTEIN], [EXP-IMP-SITE-MUTATION] W [13]
[PhoP,+] 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 PhoP-phosphorylated activator hdeAp 3656815 3656831 -32.0 atattttccaTCAACATGACATATACAgaaaaccagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14]
[RcsB,+] 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 RcsB-phosphorylated activator hdeAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [17]
[TorR,+] 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 TorR-phosphorylated activator hdeAp 3656814 3656823 -27.5 catcaacatgACATATACAGaaaaccaggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [15]
proximal TorR-phosphorylated activator hdeAp 3656838 3656847 -51.5 aaaatatctgATTTTGATATtttccatcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]


Transcription unit       
Name: yhiD
Gene(s): yhiD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.3 3655903 3655948 caagtaaaaaGGAGTAGCAAGTTGAGCCATCTTGCTGCTCCTTTTTGCATTTTTAtatgacagca
  terminator -8.7 3656300 3656331 agctattcctCCTGTTCATATATAATCTCTATATTGAATGGgttacaaaat
  anti-terminator -9.06 3655933 3656001 tttgtataccTTCAAAAATCAAGCATCTAATGACTTGCCGAATTAATGAGGTGCAAGTAAAAAGGAGTAGCAAGTTGAgccatcttgc
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-HINF] Inferred by a human based on computational evidence

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

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IEP] Inferred from expression pattern

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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Arnqvist A., Olsen A., Normark S., 1994, Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS., Mol Microbiol 13(6):1021-32

 [2] Tucker DL., Tucker N., Ma Z., Foster JW., Miranda RL., Cohen PS., Conway T., 2003, Genes of the GadX-GadW regulon in Escherichia coli., J Bacteriol 185(10):3190-201

 [3] Yoshida T., Ueguchi C., Yamada H., Mizuno T., 1993, Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant., Mol Gen Genet 237(1-2):113-22

 [4] Dudin O., Lacour S., Geiselmann J., 2013, Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli., Res Microbiol 164(8):838-47

 [5] Itou J., Eguchi Y., Utsumi R., 2009, Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12., Biosci Biotechnol Biochem 73(4):870-8

 [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] Ruiz C., McMurry LM., Levy SB., 2008, Role of the multidrug resistance regulator MarA in global regulation of the hdeAB acid resistance operon in Escherichia coli., J Bacteriol 190(4):1290-7

 [8] De Biase D., Tramonti A., Bossa F., Visca P., 1999, The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system., Mol Microbiol 32(6):1198-211

 [9] Shin M., Song M., Rhee JH., Hong Y., Kim YJ., Seok YJ., Ha KS., Jung SH., Choy HE., 2005, DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping., Genes Dev 19(19):2388-98

 [10] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [11] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

 [12] Tramonti A., De Canio M., De Biase D., 2008, GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites., Mol Microbiol 70(4):965-82

 [13] Schneiders T., Barbosa TM., McMurry LM., Levy SB., 2004, The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA., J Biol Chem 279(10):9037-42

 [14] Zwir I., Shin D., Kato A., Nishino K., Latifi T., Solomon F., Hare JM., Huang H., Groisman EA., 2005, Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica., Proc Natl Acad Sci U S A 102(8):2862-7

 [15] Bordi C., Theraulaz L., Mejean V., Jourlin-Castelli C., 2003, Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli., Mol Microbiol 48(1):211-23

 [16] Pesavento C., Hengge R., 2012, The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity., Nucleic Acids Res 40(11):4783-93

 [17] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [18] 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

RegulonDB