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Name: | rpoS |
Gene(s): | rpoS Genome Browser M3D Gene expression COLOMBOS |
Note(s): | At the transcriptional level, (p)ppGpp positively affects rpoS transcript elongation and/or stability 1849609 The expression of the gene rpoS is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of seven transcribing rpoS, is affected by PhoB. |
Evidence: | [IC] Inferred by curator |
Promoter | |
Name: | rpoSp1 |
+1: | 2867567 |
Distance from start of the gene: | 16 |
Sequence: |
tgccgcagcgataaatcggcggaaccaggcttttgcttgaatgttccgtcaagggatcacGggtaggagccaccttatgag |
Evidence: | [HTIM] |
Reference(s): | [1] Mendoza-Vargas A., et al., 2009 |
Evidence: | [GEA] Gene expression analysis |
Reference(s): | [2] Gopalkrishnan S., et al., 2014 |
Name: | rpoS |
Gene(s): | rpoS Genome Browser M3D Gene expression COLOMBOS |
Note(s): | At the transcriptional level, (p)ppGpp positively affects rpoS transcript elongation and/or stability 1849609 The expression of the gene rpoS is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of seven transcribing rpoS, is affected by PhoB. |
Evidence: | [IC] Inferred by curator |
Promoter | |
Name: | rpoSp2 |
+1: | 2867607 |
Distance from start of the gene: | 56 |
Sequence: |
attcgttacaaggggaaatccgtaaacccgctgcgttatttgccgcagcgataaatcggcGgaaccaggcttttgcttgaa |
Evidence: | [HTIM] |
Reference(s): | [1] Mendoza-Vargas A., et al., 2009 |
Name: | rpoS |
Gene(s): | rpoS Genome Browser M3D Gene expression COLOMBOS |
Note(s): | At the transcriptional level, (p)ppGpp positively affects rpoS transcript elongation and/or stability 1849609 The expression of the gene rpoS is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of seven transcribing rpoS, is affected by PhoB. |
Evidence: | [IC] Inferred by curator |
Promoter | |
Name: | rpoSp3 |
+1: | 2867654 |
Distance from start of the gene: | 103 |
Sequence: |
cgaccatgggtagcaccggaaccagttcaacacgcttgcattttgaaattcgttacaaggGgaaatccgtaaacccgctgc |
Evidence: | [HTIM] |
Reference(s): | [1] Mendoza-Vargas A., et al., 2009 |
Name: | rpoS |
Gene(s): | rpoS Genome Browser M3D Gene expression COLOMBOS |
Note(s): | At the transcriptional level, (p)ppGpp positively affects rpoS transcript elongation and/or stability 1849609 The expression of the gene rpoS is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of seven transcribing rpoS, is affected by PhoB. |
Evidence: | [IC] Inferred by curator |
Promoter | |
Name: | rpoSp4 |
+1: | 2867724 |
Distance from start of the gene: | 173 |
Sequence: |
agtgcctacgcccataacgacacaatgctggtccgggaacaacaagaagttaaggcggggCaaaaaatagcgaccatgggt |
Evidence: | [HTIM] |
Reference(s): | [1] Mendoza-Vargas A., et al., 2009 |
Name: | rpoS |
Gene(s): | rpoS Genome Browser M3D Gene expression COLOMBOS |
Note(s): | Jung IL,2003demonstrated that both rpoS and katE gene expression, which codify a transcriptional regulator and a product essential for the detoxification against H2O2-induced stress, respectively, were absolutely dependent on polyamines during entry into the stationary phase. These data suggest that polyamines could be directly participating in the defense mechanism against oxidative stress. The expression of the rpoS gene is induced in cells that overexpress the fluoroquinolone transport system AcrAB, but the induction is delayed in AcrAB mutant cells 16467145 Under nitrogen-rich growth conditions, the expression of the rpoS 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. However, it is unknown if the effects of the transcriptional regulators act directly on gene expression Kumar R,2011 The expression of the gene rpoS is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 but it is not known which promoter, of seven transcribing rpoS, is affected by PhoB. Originally, Lange and colleagues found that rpoS was induced during the transition from exponential to stationary phase and was negatively regulated by cAMP 1849609 Based on gene expression analysis, it was determined that both IHF and Fis repress rpoS expression Amores GR,2017 However, McCann and colleagues observed that rpoS transcription was positively regulated by the cyaA gene 8458856 Later, Lange and colleagues showed that the transcription of rpoS is negatively regulated by cAMP-CRP 7525405 Recently, Guo and colleagues, based on site-directed mutagenesis experiments, found that both of the putative CRP-binding sites around the rpoS promoter are actually activation sites. Therefore, it is speculated that the negative effect of cAMP-CRP on rpoS in the early log phase is indirect. However, the binding interaction between CRP protein and the two putative binding sites requires further confirmation Guo M,2015 |
Evidence: | [PM] Polar mutation |
Reference(s): |
[3] Lange R., et al., 1994 [4] Takayanagi Y., et al., 1994 |
Promoter | |
Name: | rpoSp |
+1: | 2868118 |
Sigma Factor: | Sigma70 Sigmulon |
Distance from start of the gene: | 567 |
Sequence: |
gcctgcacaaaattccaccgttgctgttgcgtcgcaaccgacaattacgtattctgagtcTtcgggtgaacagagtgctaa -35 -10 +1 |
Note(s): | Takayanagi Y,1994 identified two promoters (P1 and P2) upstream from the rpoS gene. However, Lange R,1995tested both promoters and reported that only one of them seemed to be functional (P2). Based on this evidence and the fact that P1 is too far upstream from the rpoS gene (920 bp), we only uploaded P2 as rpoSp to EcoCyc. |
Evidence: |
[CV(RS-EPT-CBR)] [CV(TIM)] [HIPP] [RS-EPT-CBR] [TIM] |
Reference(s): |
[5] Lange R., et al., 1995 [6] Salgado H, et al., 2012 [4] Takayanagi Y., et al., 1994 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | ArcA-Phosphorylated | repressor | rpoSp | 2868088 | 2868102 | 24.0 | tgaacagagtGCTAACAAAATGTTGccgaacaaca | nd | [BPP], [GEA] | [8] |
proximal | ArcA-Phosphorylated | repressor | rpoSp | 2868175 | 2868189 | -64.0 | agagcaaggaGTTGTGATCAAGCCTgcacaaaatt | nd | [BPP], [GEA] | [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | CRP-cAMP1 | repressor | rpoSp | 2868052 | 2868073 | 56.5 | acaacaagccAACTGCGACCACGGTCACAGCGcctgtaacgg | nd | [BCE], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [4], [9], [10] |
proximal | CRP-cAMP2 | repressor | rpoSp | 2868170 | 2868191 | -62.5 | gcagagcaagGAGTTGTGATCAAGCCTGCACAaaattccacc | nd | [BCE], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [4], [9], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | MqsA1 | repressor | rpoSp | 2868258 | 2868273 | -147.0 | gaacgttggtCAGACCTTGCAGGTGGgtaatgcttc | nd | [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [IHBCE], [SM] | [7] |
Note(s): |
1This mechanism of regulation is not yet clearly elucidated. Lange and Hengge-Aronis have shown that the rpoS transcript is negatively regulated by the cya gene1849609. In contrast, McCann et al. reported that rpoS transcription was positively regulated by the cya gene product 8458856. While previous reports have described a contradictory effect of CRP on rpoS at two CRP-binding sites, Ruiz Amores et al. determined, based on glucose system and gene expression analyses, that both sites have a repressive effect Amores GR,2017 2This mechanism of regulation is not yet clearly elucidated. Lange and Hengge-Aronis have shown that the rpoS transcript is negatively regulated by the cya gene1849609. In contrast, McCann et al. reported that rpoS transcription was positively regulated by the cya gene product 8458856. While previous reports have described a contradictory effect of CRP on rpoS at two CRP-binding sites, Ruiz Amores et al. determined, based on glucose system and gene expression analyses, that both sites have a repressive effect Amores GR,20171Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the rpoS promoter. The authors reported that the regulation observed in previous experiments could be nonspecific due to the disproportionate overexpression of the protein used in those earlier experiments.1Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the rpoS promoter. The authors reported that the regulation observed in previous experiments could be nonspecific due to the disproportionate overexpression of the protein used in those earlier experiments. 3This mechanism of regulation is not yet clearly elucidated. Lange and Hengge-Aronis have shown that the rpoS transcript is negatively regulated by the cya gene1849609. In contrast, McCann et al. reported that rpoS transcription was positively regulated by the cya gene product 8458856. While previous reports have described a contradictory effect of CRP on rpoS at two CRP-binding sites, Ruiz Amores et al. determined, based on glucose system and gene expression analyses, that both sites have a repressive effect Amores GR,2017 5This mechanism of regulation is not yet clearly elucidated. Lange and Hengge-Aronis have shown that the rpoS transcript is negatively regulated by the cya gene1849609. In contrast, McCann et al. reported that rpoS transcription was positively regulated by the cya gene product 8458856. While previous reports have described a contradictory effect of CRP on rpoS at two CRP-binding sites, Ruiz Amores et al. determined, based on glucose system and gene expression analyses, that both sites have a repressive effect Amores GR,2017 |
Evidence: | [GEA] Gene expression analysis |
Reference(s): | [14] Gentry DR., et al., 1993 |
Name: | nlpD-rpoS |
Gene(s): | rpoS, nlpD Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [PM] Polar mutation |
Reference(s): |
[3] Lange R., et al., 1994 [4] Takayanagi Y., et al., 1994 |
Promoter | |
Name: | nlpDp2 |
+1: | 2868782 |
Sigma Factor: | Sigma70 Sigmulon |
Distance from start of the gene: | 29 |
Sequence: |
gtatcgtgaacatcttttccagtgttcagtagggtgccttgcacggtaattatgtcactgGttattaaccaatttttcctg -35 -10 +1 |
Note(s): | The nlpD promoter region contributes to the low exponential-phase level of rpoS expression but apparently is not involved in growth phase-dependent induction of rpoS Lange R,1994. |
Evidence: | [TIM] |
Reference(s): | [3] Lange R., et al., 1994 |
Name: | nlpD-rpoS |
Gene(s): | rpoS, nlpD Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [PM] Polar mutation |
Reference(s): |
[5] Lange R., et al., 1995 [3] Lange R., et al., 1994 [4] Takayanagi Y., et al., 1994 |
Promoter | |
Name: | nlpDp1 |
+1: | 2868829 |
Sigma Factor: | Sigma70 Sigmulon |
Distance from start of the gene: | 76 |
Sequence: |
gtgaggaaatacctggatttttcctggttattttgccgcaggtcagcgtatcgtgaacatCttttccagtgttcagtaggg -35 -10 +1 |
Note(s): | The nlpD promoter region contributes to the low exponential-phase level of rpoS expression but apparently is not involved in growth-phase-dependent induction of rpoS Lange R,1994. |
Evidence: | [TIM] |
Reference(s): | [3] Lange R., et al., 1994 |
Regulation by sRNA | ![]() |
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Small RNA name (Regulator) | Regulation type | Mechanism | Function | Binding Sites | Evidence | Reference | |||
---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Sequence (RNA-strand) | |||||||
oxyS | antisense | post-transcriptional regulation | repressor | ||||||
rprA | antisense | translational regulation | activator | 2867645 | 2867668 | AATTCGTTACAAGGGGAAATCCG | [IMP] | [15] | |
arcZ | base-pairing | post-transcriptional regulation | activator | 2867642 | 2867673 | TTTGAAATTCGTTACAAGGGGAAATCCGTAA | [GEA] [HIFS] [IMP] [IPI] |
[16] | |
dsrA | antisense | translational regulation | activator | 2867648 | 2867670 | GAAATTCGTTACAAGGGGAAAT |
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'" |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Translational |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
terminator | -13.1 | 2867559 | 2867598 | cggaaccaggCTTTTGCTTGAATGTTCCGTCAAGGGATCACGGGTAGGAgccaccttat |
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
Reference(s) |
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