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Name: | ptsG | ||||||||||
Gene(s): | ptsG Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The ptsG gene appears to be regulated by FNR, but Shalel-Levanon et al. Shalel-Levanon S,2005reported a positive effect and Salmon et al. Shalel-Levanon S,2005reported a negative effect of this regulation; none of them reported which of the two promoters (ptsGp1 or ptsGp2) is affected, even is not known if this regulation is direct or indirect. On the other hand, under nitrogen-rich growth conditions, the expression of the ptsG gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011 ptsG expression is under heat shock stress conditions Shin D,2001 Expression of ptsG is increased severalfold during cell growth on glucose or other PTS substrates Shin D, Cho N, Kim YJ, Seok YJ, Ryu S,2008 ptsG is regulated posttranscriptionally by modulation of mRNA stability in response to glycolytic flux Kimata K, Tanaka Y, Inada T, Aiba H,2001and to the availability of oxygen Shin D, Cho N, Kim YJ, Seok YJ, Ryu S,2008 On the other hand, accumulation of glucose-6-phosphate induces expression of the SgrS small RNA and, subsequently, possible base paring with the 5'-UTR of the ptsG mRNA accelerates RNase E-dependent degradation of the ptsG transcript Kimata K, Tanaka Y, Inada T, Aiba H,2001. Vanderpool CK,2004 The expression of the gene ptsG is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 |
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Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified | ||||||||||
Reference(s): | [1] Plumbridge J. 1998 | ||||||||||
Promoter | |||||||||||
Name: | ptsGp2 | ||||||||||
+1: | 1157626 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 243 | ||||||||||
Sequence: |
atccgttgaatgagtttttttaaagctcgtaattaatggctaaaacgagtaaagttcaccGccgaaaattgggcggtgaat -10 +1 |
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Note(s): | A third promoter in the region located between ptsGp1 and ptsGp2 was identified by in vitro transcription and by RNA polymerase footprinting techniques, as well as in vivo by S1 analysis and fusions with a lacZ reporter gene Pennetier C, Oberto J, Plumbridge J,2010 It expresses a transcript antisense to ptsG that has characteristics more like a divergently expressed cryptic unstable transcript (CUT) than a prokaryotic sRNA Pennetier C, Oberto J, Plumbridge J,2010 ptsGp2 was validated experimentally in aerobic conditions Chung D,2013. |
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Evidence: |
[COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): | [1] Plumbridge J. 1998 |
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 | Fis | repressor | ptsGp2 | 1157614 | 1157628 | -5.0 | gctaaaacgaGTAAAGTTCACCGCCgaaaattggg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
proximal | Fis | repressor | ptsGp2 | 1157640 | 1157654 | 22.0 | aaaattgggcGGTGAATAACCACGTttgaaatatt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
remote | Fis | repressor | ptsGp2 | 1157679 | 1157693 | 61.0 | catatgttttGTCAAAATGTGCAACttctccaatg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
remote | Fis | repressor | ptsGp2 | 1157740 | 1157754 | 122.0 | caaacaaattGGCACTGAATTATTTtactctgtgt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
remote | Fis | repressor | ptsGp2 | 1157761 | 1157775 | 143.0 | attttactctGTGTAATAAATAAAGggcgcttaga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
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 | ptsGp2 | 1157580 | 1157602 | -35.0 | gttgaatgagTTTTTTTAAAGCTCGTAATTAATggctaaaacg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] |
sRNA | TU Regulated | Function | Binding Sites | Regulatory Mechanism | Evidence (Confirmed, Strong, Weak) | Reference(s) | ||
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PosLeft | PosRight | Target sequence (mRNA) | ||||||
small regulatory RNA SgrS | ptsG | repressor | 1157841 | 1157872 | GCACCCAUACUCAGGAGCACUCUCAAUUAUGU | TRANSLATION-BLOCKING, MRNA-DEGRADATION | [EXP-IDA], [EXP-IMP-SITE-MUTATION] | [2] |
Name: | ptsG | ||||||||||
Gene(s): | ptsG Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The ptsG gene appears to be regulated by FNR, but Shalel-Levanon et al. Shalel-Levanon S,2005reported a positive effect and Salmon et al. Shalel-Levanon S,2005reported a negative effect of this regulation; none of them reported which of the two promoters (ptsGp1 or ptsGp2) is affected, even is not known if this regulation is direct or indirect. On the other hand, under nitrogen-rich growth conditions, the expression of the ptsG gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011 ptsG expression is under heat shock stress conditions Shin D,2001 Expression of ptsG is increased severalfold during cell growth on glucose or other PTS substrates Shin D, Cho N, Kim YJ, Seok YJ, Ryu S,2008 ptsG is regulated posttranscriptionally by modulation of mRNA stability in response to glycolytic flux Kimata K, Tanaka Y, Inada T, Aiba H,2001and to the availability of oxygen Shin D, Cho N, Kim YJ, Seok YJ, Ryu S,2008 On the other hand, accumulation of glucose-6-phosphate induces expression of the SgrS small RNA and, subsequently, possible base paring with the 5'-UTR of the ptsG mRNA accelerates RNase E-dependent degradation of the ptsG transcript Kimata K, Tanaka Y, Inada T, Aiba H,2001. Vanderpool CK,2004 The expression of the ptsG gene is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The plasticity of the promoter regions was demonstrated for two CRP target genes, ptsG and manX . Four genetically different strains with the crp gene deleted were propagated in a glucose minimal medium. This deletion led to deleterious effects on growth in the four strains, but most of the populations quickly evolved compensatory changes that restored fast growth and were specific to the glucose environment in which they evolved. The adaptation involved plasticity of the promoter regions of two CRP target genes involved in glucose transport, ptsG and manX Lamrabet O, Plumbridge J, Martin M, Lenski RE, Schneider D, Hindré T,2019 |
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Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified | ||||||||||
Reference(s): | [1] Plumbridge J. 1998 | ||||||||||
Promoter | |||||||||||
Name: | ptsGp1 | ||||||||||
+1: | 1157766 | ||||||||||
Distance from start of the gene: | 103 | ||||||||||
Sequence: |
ctgaagttgaaacgtgatagccgtcaaacaaattggcactgaattattttactctgtgtaAtaaataaagggcgcttagat |
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Note(s): | ~90% of the ptsG mRNA is transcribed from a major promoter, P1 (ptsGp1) Plumbridge J.,1998 A third promoter in the region located between ptsGp1 and ptsGp2 was identified by in vitro transcription and by RNA polymerase footprinting techniques, as well as in vivo by S1 analysis and fusions with a lacZ reporter gene Pennetier C, Oberto J, Plumbridge J,2010 It expresses a transcript antisense to ptsG that has characteristics more like a divergently expressed cryptic unstable transcript (CUT) than a prokaryotic sRNA Pennetier C, Oberto J, Plumbridge J,2010 ptsGp1 was validated experimentally in aerobic conditions Chung D,2013. |
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Evidence: |
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
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Reference(s): |
[1] Plumbridge J. 1998 [4] Rungrassamee W., et al., 2008 [5] Salgado H, et al., 2012 |
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 | ArcA-phosphorylated | repressor | ptsGp1 | 1157674 | 1157688 | -85.0 | tgtgacatatGTTTTGTCAAAATGTgcaacttctc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7] |
proximal | ArcA-phosphorylated | repressor | ptsGp1 | 1157711 | 1157725 | -48.0 | atgatctgaaGTTGAAACGTGATAGccgtcaaaca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7] |
proximal | ArcA-phosphorylated | repressor | ptsGp1 | 1157760 | 1157774 | 2.0 | tattttactcTGTGTAATAAATAAAgggcgcttag | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7] |
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 | ||||||||
remote | CRP-cyclic-AMP | activator | ptsGp1 | 1157661 | 1157682 | -94.5 | acgtttgaaaTATTGTGACATATGTTTTGTCAaaatgtgcaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
proximal | CRP-cyclic-AMP | activator | ptsGp1 | 1157715 | 1157736 | -40.5 | tctgaagttgAAACGTGATAGCCGTCAAACAAattggcactg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [8] |
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 | Fis | activator | ptsGp1 | 1157740 | 1157754 | -19.0 | caaacaaattGGCACTGAATTATTTtactctgtgt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
proximal | Fis | activator | ptsGp1 | 1157761 | 1157775 | 3.0 | attttactctGTGTAATAAATAAAGggcgcttaga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
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 | ||||||||
remote | Fis | repressor | ptsGp1 | 1157614 | 1157628 | -145.0 | gctaaaacgaGTAAAGTTCACCGCCgaaaattggg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
remote | Fis | repressor | ptsGp1 | 1157640 | 1157654 | -119.0 | aaaattgggcGGTGAATAACCACGTttgaaatatt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
proximal | Fis | repressor | ptsGp1 | 1157679 | 1157693 | -80.0 | catatgttttGTCAAAATGTGCAACttctccaatg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
proximal | Fis | repressor | ptsGp1 | 1157740 | 1157754 | -19.0 | caaacaaattGGCACTGAATTATTTtactctgtgt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
proximal | Fis | repressor | ptsGp1 | 1157761 | 1157775 | 3.0 | attttactctGTGTAATAAATAAAGggcgcttaga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [3] |
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 | ptsGp1 | 1157749 | 1157771 | -6.0 | tggcactgaaTTATTTTACTCTGTGTAATAAATaaagggcgct | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [3] |
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 | SoxS | activator | ptsGp1 | 1157673 | 1157693 | -83.5 | ttgtgacataTGTTTTGTCAAAATGTGCAACttctccaatg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [4] |
sRNA | TU Regulated | Function | Binding Sites | Regulatory Mechanism | Evidence (Confirmed, Strong, Weak) | Reference(s) | ||
---|---|---|---|---|---|---|---|---|
PosLeft | PosRight | Target sequence (mRNA) | ||||||
small regulatory RNA SgrS | ptsG | repressor | 1157841 | 1157872 | GCACCCAUACUCAGGAGCACUCUCAAUUAUGU | TRANSLATION-BLOCKING, MRNA-DEGRADATION | [EXP-IDA], [EXP-IMP-SITE-MUTATION] | [2], [6] |
Reference(s) |
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