RegulonDB RegulonDB 11.1: Operon Form
   

ptsHI-crr operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ptsHI-crr
Gene(s): ptsH, ptsI, crr   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analyses, it was concluded that FNR represses crr gene expression under anaerobiosis, although it is still not known which promoter is affected by FNR. Two putative FNR-binding sites were found: one of them is located upstream of the crr gene and the other one is located upstream of the ptsH gene, which is the first gene of the operon Salmon K,2003.
Jeong et al. (2004) demonstrated experimentally that ArcA as well CRP regulate ptsH expression Jeong JY,2004 However, the authors did not mention the promoter that these regulators regulate (ptsH has five promoters). In addition, they did not mention the position or the effect exerted by these regulators.
Under nitrogen-rich growth conditions, the expression of the ptsH gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the five promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene ptsH is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Reuse H., et al., 1988
[2] Ryu S., et al., 1995
[3] Saffen DW., et al., 1987
Promoter
Name: ptsHp5
+1: 2533498
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 266
Sequence: gcttcaaactttcgcccctcctggcattgattcagcctgtcggaactggtatttaaccagActaattattttgatgcgcga
Note(s): The half-life of mRNA produced by ptsHp5 (P0) is 4.4 and 11 min in the presence and absence of oxygen, respectively Shin D, Cho N, Kim YJ, Seok YJ, Ryu S,2008
The ptsHp5 (ptsOb) promoter is activated during growth in the presence of glucose Ryu S.,1998
Evidence: [EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] De Reuse H., et al., 1988
[4] Ryu S. 1998
[2] Ryu S., et al., 1995
Terminator(s)
Type: rho-independent
Sequence: cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg
Reference(s): [1] De Reuse H., et al., 1988
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator ptsHp5 2533427 2533448 -60.5 ttaggtgcttTTTTGTGGCCTGCTTCAAACTTtcgcccctcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
[NagC,-] 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 NagC repressor ptsHp5 2533502 2533524 16.0 aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd nd


Transcription unit          
Name: ptsHI-crr
Gene(s): ptsH, ptsI, crr   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analyses, it was concluded that FNR represses crr gene expression under anaerobiosis, although it is still not known which promoter is affected by FNR. Two putative FNR-binding sites were found: one of them is located upstream of the crr gene and the other one is located upstream of the ptsH gene, which is the first gene of the operon Salmon K,2003.
Jeong et al. (2004) demonstrated experimentally that ArcA as well CRP regulate ptsH expression Jeong JY,2004 However, the authors did not mention the promoter that these regulators regulate (ptsH has five promoters). In addition, they did not mention the position or the effect exerted by these regulators.
Under nitrogen-rich growth conditions, the expression of the ptsH gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the five promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene ptsH is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Reuse H., et al., 1988
[2] Ryu S., et al., 1995
[3] Saffen DW., et al., 1987
Promoter
Name: ptsHp
+1: 2533501
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 263
Sequence: tcaaactttcgcccctcctggcattgattcagcctgtcggaactggtatttaaccagactAattattttgatgcgcgaaat
                -35                         -10             +1                   
Note(s): The ptsHp4 (ptsOa) promoter is activated during growth in the presence of glucose Ryu S.,1998
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [6] Plumbridge J. 1999
[4] Ryu S. 1998
[7] Ryu S., et al., 1994
[2] Ryu S., et al., 1995
[8] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg
Reference(s): [1] De Reuse H., et al., 1988
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator ptsHp 2533427 2533448 -63.5 ttaggtgcttTTTTGTGGCCTGCTTCAAACTTtcgcccctcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [5], [9]
[Mlc,-] 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 Mlc repressor ptsHp 2533502 2533524 13.0 aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5], [9]
[NagC,-] 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 NagC repressor ptsHp 2533502 2533524 13.0 aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [10]


Transcription unit          
Name: ptsHI-crr
Gene(s): ptsH, ptsI, crr   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analyses, it was concluded that FNR represses crr gene expression under anaerobiosis, although it is still not known which promoter is affected by FNR. Two putative FNR-binding sites were found: one of them is located upstream of the crr gene and the other one is located upstream of the ptsH gene, which is the first gene of the operon Salmon K,2003.
Jeong et al. (2004) demonstrated experimentally that ArcA as well CRP regulate ptsH expression Jeong JY,2004 However, the authors did not mention the promoter that these regulators regulate (ptsH has five promoters). In addition, they did not mention the position or the effect exerted by these regulators.
Under nitrogen-rich growth conditions, the expression of the ptsH gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the five promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene ptsH is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Reuse H., et al., 1988
[2] Ryu S., et al., 1995
[3] Saffen DW., et al., 1987
Promoter
Name: ptsHp4
+1: 2533501
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 263
Sequence: tcaaactttcgcccctcctggcattgattcagcctgtcggaactggtatttaaccagactAattattttgatgcgcgaaat
                        -35                    -10          +1                   
Note(s): The ptsHp4 (ptsOa) promoter is activated during growth in the presence of glucose Ryu S.,1998
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [11] Huerta AM., et al., 2003
[6] Plumbridge J. 1999
[4] Ryu S. 1998
[7] Ryu S., et al., 1994
[2] Ryu S., et al., 1995
[8] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg
Reference(s): [1] De Reuse H., et al., 1988
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator ptsHp4 2533427 2533448 -63.5 ttaggtgcttTTTTGTGGCCTGCTTCAAACTTtcgcccctcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [5], [9]
[Mlc,-] 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 Mlc repressor ptsHp4 2533502 2533524 13.0 aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5], [9]
[NagC,-] 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 NagC repressor ptsHp4 2533502 2533524 13.0 aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [10]


Transcription unit          
Name: ptsHI-crr
Gene(s): ptsH, ptsI, crr   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analyses, it was concluded that FNR represses crr gene expression under anaerobiosis, although it is still not known which promoter is affected by FNR. Two putative FNR-binding sites were found: one of them is located upstream of the crr gene and the other one is located upstream of the ptsH gene, which is the first gene of the operon Salmon K,2003.
Jeong et al. (2004) demonstrated experimentally that ArcA as well CRP regulate ptsH expression Jeong JY,2004 However, the authors did not mention the promoter that these regulators regulate (ptsH has five promoters). In addition, they did not mention the position or the effect exerted by these regulators.
Under nitrogen-rich growth conditions, the expression of the ptsH gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the five promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene ptsH is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Reuse H., et al., 1988
[2] Ryu S., et al., 1995
[3] Saffen DW., et al., 1987
Promoter
Name: ptsHp3
+1: 2533507
Distance from start of the gene: 257
Sequence: tttcgcccctcctggcattgattcagcctgtcggaactggtatttaaccagactaattatTttgatgcgcgaaattaatcg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [7] Ryu S., et al., 1994
[8] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg
Reference(s): [1] De Reuse H., et al., 1988
TF binding sites (TFBSs)
[NagC,-] 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 NagC repressor ptsHp3 2533502 2533524 7.0 aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [10]


Transcription unit          
Name: ptsHI-crr
Gene(s): ptsH, ptsI, crr   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analyses, it was concluded that FNR represses crr gene expression under anaerobiosis, although it is still not known which promoter is affected by FNR. Two putative FNR-binding sites were found: one of them is located upstream of the crr gene and the other one is located upstream of the ptsH gene, which is the first gene of the operon Salmon K,2003.
Jeong et al. (2004) demonstrated experimentally that ArcA as well CRP regulate ptsH expression Jeong JY,2004 However, the authors did not mention the promoter that these regulators regulate (ptsH has five promoters). In addition, they did not mention the position or the effect exerted by these regulators.
Under nitrogen-rich growth conditions, the expression of the ptsH gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the five promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene ptsH is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Reuse H., et al., 1988
[2] Ryu S., et al., 1995
[3] Saffen DW., et al., 1987
Promoter
Name: ptsHp2
+1: 2533601
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 163
Sequence: caaagctgaatcgattttatgatttggttcaattcttcctttagcggcataatgtttaatGacgtacgaaacgtcagcggt
                            -35                   -10       +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] De Reuse H., et al., 1988
[12] De Reuse H., et al., 1992
[11] Huerta AM., et al., 2003
[6] Plumbridge J. 1999
[7] Ryu S., et al., 1994
[2] Ryu S., et al., 1995
Terminator(s)
Type: rho-independent
Sequence: cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg
Reference(s): [1] De Reuse H., et al., 1988
TF binding sites (TFBSs)
[CRP,-] 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 CRP-cyclic-AMP repressor ptsHp2 2533555 2533576 -35.5 gctgaatcgaTTTTATGATTTGGTTCAATTCTtcctttagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [14]
[Cra,+] 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 Cra activator ptsHp2 2533544 2533561 -48.5 gaaaagccaaAGCTGAATCGATTTTATGatttggttca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [13]


Transcription unit          
Name: ptsHI-crr
Gene(s): ptsH, ptsI, crr   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analyses, it was concluded that FNR represses crr gene expression under anaerobiosis, although it is still not known which promoter is affected by FNR. Two putative FNR-binding sites were found: one of them is located upstream of the crr gene and the other one is located upstream of the ptsH gene, which is the first gene of the operon Salmon K,2003.
Jeong et al. (2004) demonstrated experimentally that ArcA as well CRP regulate ptsH expression Jeong JY,2004 However, the authors did not mention the promoter that these regulators regulate (ptsH has five promoters). In addition, they did not mention the position or the effect exerted by these regulators.
Under nitrogen-rich growth conditions, the expression of the ptsH gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the five promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene ptsH is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Reuse H., et al., 1988
[2] Ryu S., et al., 1995
[3] Saffen DW., et al., 1987
Promoter
Name: ptsHp1
+1: 2533608
Distance from start of the gene: 156
Sequence: gaatcgattttatgatttggttcaattcttcctttagcggcataatgtttaatgacgtacGaaacgtcagcggtcaacacc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [7] Ryu S., et al., 1994
[2] Ryu S., et al., 1995
[8] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg
Reference(s): [1] De Reuse H., et al., 1988
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator ptsHp1 2533555 2533576 -42.5 gctgaatcgaTTTTATGATTTGGTTCAATTCTtcctttagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [14]
[Cra,-] 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 Cra repressor ptsHp1 2533544 2533561 -55.5 gaaaagccaaAGCTGAATCGATTTTATGatttggttca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [13]


Transcription unit       
Name: crr
Gene(s): crr   Genome Browser M3D Gene expression COLOMBOS
Note(s): Using microarray analyses, it was concluded that under anaerobiosis FNR repress crr gene expression, but it is not known which promoter is affected by FNR. Two putative FNR-binding sites were found; one of them is located upstream of the crr gene and the other one is located upstream of the ptsH gene, which is the first gene of the operon Salmon K,2003.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Reuse H., et al., 1988
Promoter
Name: crrp2
+1: 2535480
Distance from start of the gene: 354
Sequence: gcaccaatgatttaacgcagtacactctggcagttgaccgtggtaatgatatgatttcacAcctttaccagccaatgtcac
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] De Reuse H., et al., 1988
Terminator(s)
Type: rho-independent
Sequence: cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg
Reference(s): [1] De Reuse H., et al., 1988


Transcription unit       
Name: crr
Gene(s): crr   Genome Browser M3D Gene expression COLOMBOS
Note(s): Using microarray analyses, it was concluded that under anaerobiosis FNR repress crr gene expression, but it is not known which promoter is affected by FNR. Two putative FNR-binding sites were found; one of them is located upstream of the crr gene and the other one is located upstream of the ptsH gene, which is the first gene of the operon Salmon K,2003.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] De Reuse H., et al., 1988
Promoter
Name: crrpI
+1: 2535610
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 224
Sequence: aggcaaatggactggcatgtgtggtgagcttgctggcgatgaacgtgctacacttctgttGctggggatgggtctggacga
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [1] De Reuse H., et al., 1988
[15] Lelong C., et al., 2007
Terminator(s)
Type: rho-independent
Sequence: cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg
Reference(s): [1] De Reuse H., et al., 1988


Evidence    

 [EXP-IDA] Inferred from direct assay

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

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

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

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

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

 [COMP-HINF] Inferred by a human based on computational evidence

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

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

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] De Reuse H., Danchin A., 1988, The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription., J Bacteriol 170(9):3827-37

 [2] Ryu S., Ramseier TM., Michotey V., Saier MH., Garges S., 1995, Effect of the FruR regulator on transcription of the pts operon in Escherichia coli., J Biol Chem 270(6):2489-96

 [3] Saffen DW., Presper KA., Doering TL., Roseman S., 1987, Sugar transport by the bacterial phosphotransferase system. Molecular cloning and structural analysis of the Escherichia coli ptsH, ptsI, and crr genes., J Biol Chem 262(33):16241-53

 [4] Ryu S., 1998, CRP.cAMP-dependent transcription activation of the Escherichia coli pts Po promoter by the heat shock RNA polymerase (Esigma32) in vitro., Mol Cells 8(5):614-7

 [5] Tanaka Y., Kimata K., Inada T., Tagami H., Aiba H., 1999, Negative regulation of the pts operon by Mlc: mechanism underlying glucose induction in Escherichia coli., Genes Cells 4(7):391-9

 [6] Plumbridge J., 1999, Expression of the phosphotransferase system both mediates and is mediated by Mlc regulation in Escherichia coli., Mol Microbiol 33(2):260-73

 [7] Ryu S., Garges S., 1994, Promoter switch in the Escherichia coli pts operon., J Biol Chem 269(7):4767-72

 [8] 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.

 [9] Kim SY., Nam TW., Shin D., Koo BM., Seok YJ., Ryu S., 1999, Purification of Mlc and analysis of its effects on the pts expression in Escherichia coli., J Biol Chem 274(36):25398-402

 [10] Oberto J., 2010, FITBAR: a web tool for the robust prediction of prokaryotic regulons., BMC Bioinformatics 11:554

 [11] 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

 [12] De Reuse H., Kolb A., Danchin A., 1992, Positive regulation of the expression of the Escherichia coli pts operon. Identification of the regulatory regions., J Mol Biol 226(3):623-35

 [13] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

 [14] 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

 [15] Lelong C., Aguiluz K., Luche S., Kuhn L., Garin J., Rabilloud T., Geiselmann J., 2007, The Crl-RpoS regulon of Escherichia coli., Mol Cell Proteomics 6(4):648-59

RegulonDB