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Name: | rhaSR | |||||||||
Synonym(s): | OP00087, rha | |||||||||
Gene(s): | rhaS, rhaR Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | This is an unusual transcription unit that codes for two genes encoding two transcriptional regulators, RhaS and RhaR, both members of the AraC family of regulators. It is interesting that the rhaSR transcription unit is located close to a divergently transcribed transcription unit encoding the rhaBAD genes. This organization is similar to that of the divergent araC-araBAD genes. RhaR is a transcriptional regulator that positively regulates the rhaSR operon. Its effect has been experimentally demonstrated to be enhanced by CRP. In vivo and in vitro experiments demonstrated that the centered position of CRP at -111.5 relative to the rhaSp is required for the majority of the CRP-dependent activation of the rhaSR operon. In vitro transcription assays indicated that the α-CTD of the RNA polymerase is both partially dispensable for RhaR activation and required for CRP activation of the rhaSR operon Wickstrum JR,2005. Besides the RhaS and RhaR regulators, there are four sites for a CRP transcriptional regulator that are localized at the rhaSR-rhaBAD intergenic region. It seems that all of the proteins that control the rhaSR operon are on the same face of the DNA and on the opposite face of the DNA relative to the proteins that control the rhaBAD operon Wickstrum JR,2005. Wickstrum et al. (2009) proposed a model for RhaS negative autoregulation where RhaS competes with RhaR for binding at the rhaSR promoter. In addition, this model proposes that differential DNA bending by RhaS and RhaR may be the basis for the differences in CRP coactivation. At relatively low RhaS concentrations, RhaR and CRP both contribute to rhaSR activation; at that time, expression is at its maximum level and CRP contacts the α-C-terminal domain (CTD). On the other hand, at relatively high RhaS concentrations, RhaS binds to the RhaR-binding site, thus replacing RhaR. RhaS activates the rhaSR operon but CRP is not effectively coactivated, and in this way, rhaSR expression is reduced by three- to fourfold. Here, CRP does not contact the α-CTD Wickstrum JR,2010 This mechanism is unusual in that a transcriptional activator functions to decrease expression of an operon by activating transcription Wickstrum JR,2010 |
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Evidence: | [ITCR] Inferred through co-regulation | |||||||||
Reference(s): |
[1] Egan SM., et al., 1993 [2] Maciag A., et al., 2011 [3] Tobin JF., et al., 1987 [4] Via P., et al., 1996 |
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Promoter | ||||||||||
Name: | rhaSp | |||||||||
+1: | 4097711 | |||||||||
Sigma Factor: | Sigma70 Sigmulon | |||||||||
Distance from start of the gene: | 25 | |||||||||
Sequence: |
tacgtggttttccgtcgaaaatttaaggtaagaacctgacctcgtgattactatttcgccGtgttgacgacatcaggaggc -35 -10 +1 |
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Evidence: |
[ICWHO] [IEP] [IHBCE] [TIM] |
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Reference(s): |
[1] Egan SM., et al., 1993 [5] Huerta AM., et al., 2003 [2] Maciag A., et al., 2011 [6] Tobin JF., et al., 1990 [7] Tobin JF., et al., 1990 [3] Tobin JF., et al., 1987 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | CRP-cyclic-AMP | activator | rhaSp | 4097589 | 4097610 | -111.5 | tgaattgtggTGATGTGATGCTCACCGCATTTcctgaaaatt | nd | [GEA], [AIBSCS], [BPP], [SM] | [8], [9] |
proximal | CRP-cyclic-AMP | activator | rhaSp | 4097608 | 4097629 | -92.5 | gctcaccgcaTTTCCTGAAAATTCACGCTGTAtcttgaaaaa | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | RhaR-L-rhamnose | activator | rhaSp | 4097629 | 4097645 | -74.0 | ttcacgctgtATCTTGAAAAATCGACGttttttacgt | nd | [GEA], [BPP] | [1], [11] |
proximal | RhaR-L-rhamnose | activator | rhaSp | 4097663 | 4097679 | -40.0 | cgtggttttcCGTCGAAAATTTAAGGTaagaacctga | nd | [GEA], [APIORCISFBSCS], [BPP] | [11] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | RhaS-L-rhamnose | activator | rhaSp | 4097629 | 4097645 | -74.0 | ttcacgctgtATCTTGAAAAATCGACGttttttacgt | nd | [GEA], [BPP] | [1], [10] |
proximal | RhaS-L-rhamnose | activator | rhaSp | 4097663 | 4097679 | -40.0 | cgtggttttcCGTCGAAAATTTAAGGTaagaacctga | nd | [GEA], [APIORCISFBSCS], [BPP] | [1], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | RhaS | unknown | rhaSp | 4098617 | 4098634 | 915.0 | gcgaataatcAACTTCGTTCTCTGGCCGaggtagccac | nd | [APIORCISFBSCS], [BPP] | [11] |
Name: | rhaSR | |||||||||
Synonym(s): | OP00087, rha | |||||||||
Gene(s): | rhaS, rhaR Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | This is an unusual transcription unit that codes for two genes encoding two transcriptional regulators, RhaS and RhaR, both members of the AraC family of regulators. It is interesting that the rhaSR transcription unit is located close to a divergently transcribed transcription unit encoding the rhaBAD genes. This organization is similar to that of the divergent araC-araBAD genes. RhaR is a transcriptional regulator that positively regulates the rhaSR operon. Its effect has been experimentally demonstrated to be enhanced by CRP. In vivo and in vitro experiments demonstrated that the centered position of CRP at -111.5 relative to the rhaSp is required for the majority of the CRP-dependent activation of the rhaSR operon. In vitro transcription assays indicated that the α-CTD of the RNA polymerase is both partially dispensable for RhaR activation and required for CRP activation of the rhaSR operon Wickstrum JR,2005. Besides the RhaS and RhaR regulators, there are four sites for a CRP transcriptional regulator that are localized at the rhaSR-rhaBAD intergenic region. It seems that all of the proteins that control the rhaSR operon are on the same face of the DNA and on the opposite face of the DNA relative to the proteins that control the rhaBAD operon Wickstrum JR,2005. Wickstrum et al. (2009) proposed a model for RhaS negative autoregulation where RhaS competes with RhaR for binding at the rhaSR promoter. In addition, this model proposes that differential DNA bending by RhaS and RhaR may be the basis for the differences in CRP coactivation. At relatively low RhaS concentrations, RhaR and CRP both contribute to rhaSR activation; at that time, expression is at its maximum level and CRP contacts the α-C-terminal domain (CTD). On the other hand, at relatively high RhaS concentrations, RhaS binds to the RhaR-binding site, thus replacing RhaR. RhaS activates the rhaSR operon but CRP is not effectively coactivated, and in this way, rhaSR expression is reduced by three- to fourfold. Here, CRP does not contact the α-CTD Wickstrum JR,2010 This mechanism is unusual in that a transcriptional activator functions to decrease expression of an operon by activating transcription Wickstrum JR,2010 |
|||||||||
Evidence: | [ITCR] Inferred through co-regulation | |||||||||
Reference(s): |
[1] Egan SM., et al., 1993 [2] Maciag A., et al., 2011 [3] Tobin JF., et al., 1987 [4] Via P., et al., 1996 |
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Promoter | ||||||||||
Name: | rhaSp2 | |||||||||
+1: | 4097711 | |||||||||
Sigma Factor: | Sigma38 Sigmulon | |||||||||
Distance from start of the gene: | 25 | |||||||||
Sequence: |
tacgtggttttccgtcgaaaatttaaggtaagaacctgacctcgtgattactatttcgccGtgttgacgacatcaggaggc -35 -10 +1 |
|||||||||
Evidence: |
[ICWHO] [IEP] [IHBCE] [TIM] |
|||||||||
Reference(s): |
[1] Egan SM., et al., 1993 [5] Huerta AM., et al., 2003 [2] Maciag A., et al., 2011 [6] Tobin JF., et al., 1990 [7] Tobin JF., et al., 1990 [3] Tobin JF., et al., 1987 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | CRP-cyclic-AMP | activator | rhaSp2 | 4097589 | 4097610 | -111.5 | tgaattgtggTGATGTGATGCTCACCGCATTTcctgaaaatt | nd | [GEA], [AIBSCS], [BPP], [SM] | [8], [9] |
proximal | CRP-cyclic-AMP | activator | rhaSp2 | 4097608 | 4097629 | -92.5 | gctcaccgcaTTTCCTGAAAATTCACGCTGTAtcttgaaaaa | nd | [GEA], [APIORCISFBSCS], [BPP], [SM] | [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | RhaR-L-rhamnose | activator | rhaSp2 | 4097629 | 4097645 | -74.0 | ttcacgctgtATCTTGAAAAATCGACGttttttacgt | nd | [GEA], [BPP] | [1], [11] |
proximal | RhaR-L-rhamnose | activator | rhaSp2 | 4097663 | 4097679 | -40.0 | cgtggttttcCGTCGAAAATTTAAGGTaagaacctga | nd | [GEA], [APIORCISFBSCS], [BPP] | [11] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | RhaS-L-rhamnose | activator | rhaSp2 | 4097629 | 4097645 | -74.0 | ttcacgctgtATCTTGAAAAATCGACGttttttacgt | nd | [GEA], [BPP] | [1], [10] |
proximal | RhaS-L-rhamnose | activator | rhaSp2 | 4097663 | 4097679 | -40.0 | cgtggttttcCGTCGAAAATTTAAGGTaagaacctga | nd | [GEA], [APIORCISFBSCS], [BPP] | [1], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | RhaS | unknown | rhaSp2 | 4098617 | 4098634 | 915.0 | gcgaataatcAACTTCGTTCTCTGGCCGaggtagccac | nd | [APIORCISFBSCS], [BPP] | [11] |
Reference(s) |
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