RegulonDB RegulonDB 11.0: Operon Form
   

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




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


Transcription unit          
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
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
TF binding sites (TFBSs)
[CRP,+] Phrase
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]
[RhaR,+] Phrase
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], [BPP] [11]
[RhaS,+] Phrase
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], [BPP] [1], [10]
[RhaS,?] Phrase
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]


Transcription unit          
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
Promoter
Name: rhaSp
+1: 4097711
Sigma Factor: Sigma70 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
TF binding sites (TFBSs)
[CRP,+] Phrase
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]
[RhaR,+] Phrase
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], [BPP] [11]
[RhaS,+] Phrase
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], [BPP] [1], [10]
[RhaS,?] Phrase
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]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [IEP] Inferred from expression pattern

 [IHBCE] Inferred by a human based on computational evidence

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [SM] Site mutation

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


Reference(s)    

 [1] Egan SM., Schleif RF., 1993, A regulatory cascade in the induction of rhaBAD., J Mol Biol 234(1):87-98

 [2] 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

 [3] Tobin JF., Schleif RF., 1987, Positive regulation of the Escherichia coli L-rhamnose operon is mediated by the products of tandemly repeated regulatory genes., J Mol Biol 196(4):789-99

 [4] Via P., Badia J., Baldoma L., Obradors N., Aguilar J., 1996, Transcriptional regulation of the Escherichia coli rhaT gene., Microbiology 142 ( Pt 7):1833-40

 [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] Tobin JF., Schleif RF., 1990, Transcription from the rha operon psr promoter., J Mol Biol 211(1):1-4

 [7] Tobin JF., Schleif RF., 1990, Purification and properties of RhaR, the positive regulator of the L-rhamnose operons of Escherichia coli., J Mol Biol 211(1):75-89

 [8] Holcroft CC., Egan SM., 2000, Interdependence of activation at rhaSR by cyclic AMP receptor protein, the RNA polymerase alpha subunit C-terminal domain, and rhaR., J Bacteriol 182(23):6774-82

 [9] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [10] Wickstrum JR., Skredenske JM., Balasubramaniam V., Jones K., Egan SM., 2010, The AraC/XylS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation., J Bacteriol 192(1):225-32

 [11] Wickstrum JR., Skredenske JM., Kolin A., Jin DJ., Fang J., Egan SM., 2007, Transcription activation by the DNA-binding domain of the AraC family protein RhaS in the absence of its effector-binding domain., J Bacteriol 189(14):4984-93

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