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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. Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE 20470880 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system 20470880 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 |
Evidence: | [ITC] Inferred through co-regulation [LTED] Length of transcript experimentally determined |
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: | Sigma38, Sigma70, Sigma70, Sigma38 |
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: |
[CV(RS-EPT-CBR/TA)] [CV(TA/TIM)] [HIPP] [RS-EPT-CBR] [TIM] |
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 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | FliZ1 | repressor | hdeAp | 3656757 | 3656812 | 8.0 | catatacagaAAACCAGGTTATAACCTCAGTGTCGAAATTGATTCGTGACGGCTCTTTCACTTTATagttgaggat | nd | [BPP], [GEA] | [16] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadE | activator | hdeAp | 3656773 | 3656792 | 9.5 | ataacctcagTGTCGAAATTGATTCGTGACggctctttca | nd | , [IHBCE], | [11] |
remote | GadE2 | activator | hdeAp | 3656899 | 3656918 | -117.5 | aatgcagtcgATTTAATAAAAATTTCCTAAttgcagtatc | nd | [AIBSCS], [APIORCISFBSCS], [BPP], , [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IHBCE], | [2], [5], [7], [10], [11] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadW | activator | hdeAp | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [AIBSCS], [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [7], [12] |
proximal | GadW | activator | hdeAp | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [7], [12] |
remote | GadW | activator | hdeAp | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadW | repressor | hdeAp | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [AIBSCS], [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [7], [12] |
proximal | GadW | repressor | hdeAp | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [7], [12] |
remote | GadW | repressor | hdeAp | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadX1 | activator | hdeAp | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [7], [10], [12] |
proximal | GadX2 | activator | hdeAp | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [AIBSCS], [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [7], [10], [12] |
remote | GadX | activator | hdeAp | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadX1 | repressor | hdeAp | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [7], [10], [12] |
proximal | GadX2 | repressor | hdeAp | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [AIBSCS], [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [7], [10], [12] |
remote | GadX | repressor | hdeAp | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | H-NS1 | repressor | hdeAp | 3656902 | 3656916 | -118.0 | tgcagtcgatTTAATAAAAATTTCCtaattgcagt | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [3], [8], [9] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | Lrp-leucine | repressor | hdeAp | 3656802 | 3656817 | -18.0 | catgacatatACAGAAAACCAGGTTAtaacctcagt | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [7] |
proximal | Lrp-leucine | repressor | hdeAp | 3656839 | 3656854 | -55.0 | tgaaataaaaATATCTGATTTTGATAttttccatca | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [7] |
proximal | Lrp-leucine | repressor | hdeAp | 3656848 | 3656863 | -64.0 | tcattgtattGAAATAAAAATATCTGattttgatat | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [7] |
remote | Lrp-leucine | repressor | hdeAp | 3656881 | 3656896 | -97.0 | tttcctaattGCAGTATCTGATGCATctgtaactca | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [7] |
remote | Lrp-leucine | repressor | hdeAp | 3656900 | 3656915 | -116.0 | gcagtcgattTAATAAAAATTTCCTAattgcagtat | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [7] |
remote | Lrp-leucine | repressor | hdeAp | 3656943 | 3656958 | -159.0 | aaatcccctgCTATCAATCTATGCCAaaaacgcgtc | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | MarA1 | repressor | hdeAp | 3656820 | 3656839 | -39.0 | tgattttgatATTTTCCATCAACATGACATatacagaaaa | nd | [APIORCISFBSCS], [APPH], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] | [13] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | PhoP-Phosphorylated | activator | hdeAp | 3656815 | 3656831 | -32.0 | atattttccaTCAACATGACATATACAgaaaaccagg | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [14] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | TorR-Pasp1 | activator | hdeAp | 3656814 | 3656823 | -27.5 | catcaacatgACATATACAGaaaaccaggt | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [7], [15] |
proximal | TorR-Pasp2 | activator | hdeAp | 3656838 | 3656847 | -51.5 | aaaatatctgATTTTGATATtttccatcaa | nd | [AIBSCS], [CV(GEA/ROMA)], [GEA] | [7] |
Note(s): |
1No DNA consensus sequence that is recognized by FliZ has been established. Therefore, for this DNA-binding site we added the complete region, determined by footprinting analysis Pesavento C,2012 to which FliZ binds.2GadE is the main activator of the hdeAB-yhiD operon. Both H-NS and GadE are involved in increasing the hdeAB-yhiD repression levels by MarA that occur as the cell enters the stationary phase Ruiz C,2008.1GadX has a positive direct or indirect effect on the hdeAB-yhiD operon only in stationary-phase cells at pH 5.5, but it is a repressor in exponential growth phase at pH 7.0 Ruiz C,2008. 2GadX has a positive direct or indirect effect on the hdeAB-yhiD operon only in stationary-phase cells at pH 5.5, but it is a repressor in exponential growth phase at pH 7.0 Ruiz C,2008. 1GadX has a positive direct or indirect effect on the hdeAB-yhiD operon only in stationary-phase cells at pH 5.5, but it is a repressor in exponential growth phase at pH 7.0 Ruiz C,2008. 2GadX has a positive direct or indirect effect on the hdeAB-yhiD operon only in stationary-phase cells at pH 5.5, but it is a repressor in exponential growth phase at pH 7.0 Ruiz C,2008. 1H-NS represses transcription through the binding to supercoiled DNA Yoshida T,1993. H-NS represses the transcription initiation at hdeAp by σ70, but not by σ38. This repression is not through a direct interaction with σ70; instead, it acts as a cofactor for DNA looping. H-NS bound at 118 laterally extends to the promoter downstream sequence and wraps the DNA around σ70 through the cooperative recruitment of other H-NS molecules Shin M,2005. H-NS is the main repressor of the hdeAB-yhiD operon. Both H-NS and GadE are involved in increasing the hdeAB-yhiD repression levels by MarA that occur as the cell enters the stationary phase Ruiz C,2008. 1MarA plays a very important role in the complex negative regulation of the hdeAB-yhiD operon during the stationary phase and acid resistance that depends on the growth conditions, on other regulators of hdeAB-yhiD expression, and on the degree of induction of marA expression. MarA also controls it, by modifying the effects of the other regulators. This transcriptional regulator binds to a marbox partially overlapping the -35 box of the hdeAp promoter, competing with the RNA polymerase for DNA binding and/or direct interactions between MarA and σ70, σ38, or other subunits of RNA polymerase. In addition, several putative binding sites are located near the marbox . MarA reduces the repression caused by GadX and Lrp during exponential phase and it helps H-NS repression, although it is not clear how. On the other hand, MarA reduces the ability of GadE to activate the hdeAB-yhiD operon during the stationary phase, since they compete for DNA binding or for interacting. This regulator also reduces the repression caused by GadW during stationary phase. Finally, MarA seems to compete functionally with GadX, GadW, RpoS, and Lrp under some conditions, which might ensure that hdeAB-yhiD expression is not repressed more than necessary Ruiz C,2008.1TorR shows no significant effect in the expression of hdeAB-yhiD, which suggests that TorR only regulates the hdeAB-yhiD operon after induction of the TorRS system by trimethylamine, N-oxide, and anaerobiosis Bordi C,2003. Ruiz C,2008. Two predicted sites have been reported Ruiz C,2008. 2TorR shows no significant effect in the expression of hdeAB-yhiD, which suggests that TorR only regulates the hdeAB-yhiD operon after induction of the TorRS system by trimethylamine, N-oxide, and anaerobiosis Bordi C,2003. Ruiz C,2008. Two predicted sites have been reported Ruiz C,2008.6H-NS represses transcription through the binding to supercoiled DNA Yoshida T,1993. H-NS represses the transcription initiation at hdeAp by σ70, but not by σ38. This repression is not through a direct interaction with σ70; instead, it acts as a cofactor for DNA looping. H-NS bound at 118 laterally extends to the promoter downstream sequence and wraps the DNA around σ70 through the cooperative recruitment of other H-NS molecules Shin M,2005. H-NS is the main repressor of the hdeAB-yhiD operon. Both H-NS and GadE are involved in increasing the hdeAB-yhiD repression levels by MarA that occur as the cell enters the stationary phase Ruiz C,2008. 7GadE is the main activator of the hdeAB-yhiD operon. Both H-NS and GadE are involved in increasing the hdeAB-yhiD repression levels by MarA that occur as the cell enters the stationary phase Ruiz C,2008. 10GadX has a positive direct or indirect effect on the hdeAB-yhiD operon only in stationary-phase cells at pH 5.5, but it is a repressor in exponential growth phase at pH 7.0 Ruiz C,2008. 12GadX has a positive direct or indirect effect on the hdeAB-yhiD operon only in stationary-phase cells at pH 5.5, but it is a repressor in exponential growth phase at pH 7.0 Ruiz C,2008. 17GadX has a positive direct or indirect effect on the hdeAB-yhiD operon only in stationary-phase cells at pH 5.5, but it is a repressor in exponential growth phase at pH 7.0 Ruiz C,2008. 19GadX has a positive direct or indirect effect on the hdeAB-yhiD operon only in stationary-phase cells at pH 5.5, but it is a repressor in exponential growth phase at pH 7.0 Ruiz C,2008. 20TorR shows no significant effect in the expression of hdeAB-yhiD, which suggests that TorR only regulates the hdeAB-yhiD operon after induction of the TorRS system by trimethylamine, N-oxide, and anaerobiosis Bordi C,2003. Ruiz C,2008. Two predicted sites have been reported Ruiz C,2008. 21MarA plays a very important role in the complex negative regulation of the hdeAB-yhiD operon during the stationary phase and acid resistance that depends on the growth conditions, on other regulators of hdeAB-yhiD expression, and on the degree of induction of marA expression. MarA also controls it, by modifying the effects of the other regulators. This transcriptional regulator binds to a marbox partially overlapping the -35 box of the hdeAp promoter, competing with the RNA polymerase for DNA binding and/or direct interactions between MarA and σ70, σ38, or other subunits of RNA polymerase. In addition, several putative binding sites are located near the marbox . MarA reduces the repression caused by GadX and Lrp during exponential phase and it helps H-NS repression, although it is not clear how. On the other hand, MarA reduces the ability of GadE to activate the hdeAB-yhiD operon during the stationary phase, since they compete for DNA binding or for interacting. This regulator also reduces the repression caused by GadW during stationary phase. Finally, MarA seems to compete functionally with GadX, GadW, RpoS, and Lrp under some conditions, which might ensure that hdeAB-yhiD expression is not repressed more than necessary Ruiz C,2008. 23TorR shows no significant effect in the expression of hdeAB-yhiD, which suggests that TorR only regulates the hdeAB-yhiD operon after induction of the TorRS system by trimethylamine, N-oxide, and anaerobiosis Bordi C,2003. Ruiz C,2008. Two predicted sites have been reported Ruiz C,2008. 25No DNA consensus sequence that is recognized by FliZ has been established. Therefore, for this DNA-binding site we added the complete region, determined by footprinting analysis Pesavento C,2012 to which FliZ binds. |
Gene(s): | yhiD Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [ICWHO] Inferred computationally without human oversight |
Regulation by sRNA | ![]() |
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Small RNA name (Regulator) | Regulation type | Mechanism | Function | Binding Sites | Evidence | Reference | |||
---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Sequence (RNA-strand) | |||||||
gcvB | unknown | unknown | repressor | [IMP] | [18] | ||||
oxyS | antisense | post-transcriptional regulation | repressor |
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'" |
RNA cis-regulatory element | ![]() |
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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" |
Reference(s) |
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