|
|
| Operon |  |
|---|---|
| Name: | ptsHI-crr |
| This page displays every known transcription unit of this operon and their known regulation. | |
| 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: | [BTEI] Boundaries of transcription experimentally identified [LTED] 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 18402772 The ptsHp5 (ptsOb) promoter is activated during growth in the presence of glucose Ryu S.,1998 |
| Evidence: | [TIM] |
| Reference(s): |
[1] De Reuse H., et al., 1988 [2] Ryu S., et al., 1995 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | cagtgaaaaaTGGCGCCCATCGGCGCCAtttttttatg |
| Reference(s): | [1] De Reuse H., et al., 1988 |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | CRP-cAMP1 | activator | ptsHp5 | 2533427 | 2533448 | -60.5 | ttaggtgcttTTTTGTGGCCTGCTTCAAACTTtcgcccctcc | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [4] |
| Note(s): |
1When the template is linear, transcriptional initiation is switched from POa to POb, 3 bp farther upstream from POa, and transcription becomes more CRP dependent. There is no PO expression in the absence of CRP or cAMP in the cell, unless glucose is present.1This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.1When the template is linear, transcriptional initiation is switched from POa to POb, 3 bp farther upstream from POa, and transcription becomes more CRP dependent. There is no PO expression in the absence of CRP or cAMP in the cell, unless glucose is present. 2This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor. |
| 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: | [BTEI] Boundaries of transcription experimentally identified [LTED] 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: | Sigma32, Sigma70 |
| 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: |
[CV(RS-EPT-CBR/TA)] [CV(TA/TIM)] [HIPP] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[6] Plumbridge J. 1999 [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 |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | CRP-cAMP1 | activator | ptsHp4 | 2533427 | 2533448 | -63.5 | ttaggtgcttTTTTGTGGCCTGCTTCAAACTTtcgcccctcc | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [4], [9] |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | Mlc | repressor | ptsHp4 | 2533502 | 2533524 | 13.0 | aaccagactaATTATTTTGATGCGCGAAATTAAtcgttacagg | nd | [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [4], [9], [10] |
| Note(s): |
1Marginally stimulated by CRP-cAMP. When the template is linear, transcriptional initiation is switched from POa to POb, 3 bp farther upstream from POa, and transcription becomes more CRP dependent.1This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.1Marginally stimulated by CRP-cAMP. When the template is linear, transcriptional initiation is switched from POa to POb, 3 bp farther upstream from POa, and transcription becomes more CRP dependent. 2This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor. |
| 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: | [BTEI] Boundaries of transcription experimentally identified [LTED] 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: |
[CV(RS-EPT-CBR/TA)] [CV(TA/TIM)] [RS-EPT-CBR] [TIM] |
| 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 |
| Note(s): | 1This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor.1This binding site was determined from a computational prediction based on different statistical methods Oberto J.,2010 The function of the binding site was assigned according to the distance from the transcription start, with NagC as the transcriptional repressor. |
| 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: | [BTEI] Boundaries of transcription experimentally identified [LTED] 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: | [TIM] |
| Reference(s): |
[1] De Reuse H., et al., 1988 [11] De Reuse H., et al., 1992 [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 |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | CRP-cAMP1 | repressor | ptsHp2 | 2533555 | 2533576 | -35.5 | gctgaatcgaTTTTATGATTTGGTTCAATTCTtcctttagcg | nd | [AIBSCS], [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] | [1], [2], [13] |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | Cra1 | activator | ptsHp2 | 2533544 | 2533561 | -48.5 | gaaaagccaaAGCTGAATCGATTTTATGatttggttca | nd | [AIBSCS], [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [12] |
| Note(s): |
1CRP binds to the ptsHP2 promoter when there is a superhelicoidal template in vitro.1FruR could repress ptsHP1b transcription by displacing CRP-cAMP from its binding site, thus restoring ptsHp2 activity from CRP-cAMP inhibition Ryu S,1995.1FruR could repress ptsHP1b transcription by displacing CRP-cAMP from its binding site, thus restoring ptsHp2 activity from CRP-cAMP inhibition Ryu S,1995. 2CRP binds to the ptsHP2 promoter when there is a superhelicoidal template in vitro. |
| 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: | [BTEI] Boundaries of transcription experimentally identified [LTED] 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: |
[CV(RS-EPT-CBR/TA)] [CV(TA/TIM)] [RS-EPT-CBR] [TIM] |
| 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 |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | CRP-cAMP1 | activator | ptsHp1 | 2533555 | 2533576 | -42.5 | gctgaatcgaTTTTATGATTTGGTTCAATTCTtcctttagcg | nd | [AIBSCS], [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] | [1], [2], [13] |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | Cra1 | repressor | ptsHp1 | 2533544 | 2533561 | -55.5 | gaaaagccaaAGCTGAATCGATTTTATGatttggttca | nd | [AIBSCS], [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] | [2], [12] |
| Note(s): |
1CRP binds to the ptsHP1 promoter when there is a superhelicoidal template in vitro.1A high concentration of FruR was needed for ptsHP1b repression in vitro. FruR could repress pstHP1b transcription by displacing CRP-cAMP from its binding site, thus restoring P1a activity from CRP-cAMP inhibition Ryu S,1995.1A high concentration of FruR was needed for ptsHP1b repression in vitro. FruR could repress pstHP1b transcription by displacing CRP-cAMP from its binding site, thus restoring P1a activity from CRP-cAMP inhibition Ryu S,1995. 2CRP binds to the ptsHP1 promoter when there is a superhelicoidal template in vitro. |
| 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: | [BTEI] Boundaries of transcription experimentally identified [LTED] 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: | [TIM] |
| 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 |
| 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: | [BTEI] Boundaries of transcription experimentally identified [LTED] 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: | [TIM] |
| 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 |
| Reference(s) |
|
|---|---|
[TIM] Transcription initiation mapping