RegulonDB RegulonDB 11.2: Operon Form
   

pstSCAB-phoU operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: phoU
Gene(s): phoU   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene phoU is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression appears to be caused by the transcription factor PhoB Marzan LW,2013
The phoU gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Reference(s): [1] Spira B., et al., 2010
Promoter
Name: phoUp
+1: 3907665
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 87
Sequence: ggctgcgcgttgttccgaccacacggcgtttatgtacctgggcgaattgattgagttcagCaacacggacgatctgttcac
                             -35                      -10   +1                   
Note(s): The phoUp promoter makes a modest contribution in the transcription of the gene phoU. The main contributor in transcription of this gene is the pstSp promoter, which is located upstream of the gene pstS Spira B,2010
The phoUp promoter appears to be modulated negatively by RpoS Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Spira B., et al., 2010
TF binding sites (TFBSs)
[PhoB,+] 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
nd PhoB-phosphorylated activator phoUp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [3]


Transcription unit       
Name: pstB-phoU
Gene(s): phoU, pstB   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [4] Amemura M., et al., 1985
Promoter
Name: pstBp3
+1: 3908447
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 81
Sequence: agaggggcgaggggaccgaccgagcgcctttttgactctgtacacggttaacactttgccGgatgcggcgtgaacgcctga
                                  -35                  -10  +1                   
Note(s): We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, present a distance of 6 nucleotides between the transcriptional start site and the -10 box Harley CB, Reynolds RP,1987.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [4] Amemura M., et al., 1985
[2] Huerta AM., et al., 2003


Transcription unit       
Name: pstB-phoU
Gene(s): phoU, pstB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Spira B., et al., 2010
Promoter
Name: pstBp1
+1: 3908556
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 190
Sequence: ttaccctgtgcgtactgctgctgaacattctggcgcgcgttgtttttgcgaagaataaacAcggttgatattgctgacacg
                                 -35                    -10 +1                   
Note(s): The pstBp1 promoter makes a modest contribution in the transcription of the genes pstB and phoU. The main contributor in transcription of these genes is the pstSp promoter, which is located upstream of the gene pstS Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Spira B., et al., 2010


Transcription unit       
Name: pstB-phoU
Gene(s): phoU, pstB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Spira B., et al., 2010
Promoter
Name: pstBp2
+1: 3908556
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 190
Sequence: ttaccctgtgcgtactgctgctgaacattctggcgcgcgttgtttttgcgaagaataaacAcggttgatattgctgacacg
                                   -35                  -10 +1                   
Note(s): The pstBp1 promoter makes a modest contribution in the transcription of the genes pstB and phoU. The main contributor in transcription of these genes is the pstSp promoter, which is located upstream of the gene pstS Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Spira B., et al., 2010


Transcription unit       
Name: pstCAB-phoU
Gene(s): phoU, pstB, pstA, pstC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Spira B., et al., 2010
Promoter
Name: pstCp2
+1: 3910542
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 144
Sequence: cggggctaaacaggcgaacgacctggattacgccagcctgccggatagtgtagttgaacaGgttcgcgctgcgtggaagac
                            -35                  -10        +1                   
Note(s): The pstCp promoter makes a modest contribution in the transcription of the genes pstC, pstA, pstB, and phoU. The main contributor in transcription of these genes is the pstSp promoter, which is located upstream of the gene pstS Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Spira B., et al., 2010


Transcription unit       
Name: pstCAB-phoU
Gene(s): phoU, pstB, pstA, pstC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Spira B., et al., 2010
Promoter
Name: pstCp
+1: 3910542
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 144
Sequence: cggggctaaacaggcgaacgacctggattacgccagcctgccggatagtgtagttgaacaGgttcgcgctgcgtggaagac
                            -35                    -10      +1                   
Note(s): The pstCp promoter makes a modest contribution in the transcription of the genes pstC, pstA, pstB, and phoU. The main contributor in transcription of these genes is the pstSp promoter, which is located upstream of the gene pstS Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Spira B., et al., 2010


Transcription unit          
Name: pstSCAB-phoU
Synonym(s): OP00284, phoT, pstSCABphoU
Gene(s): phoU, pstB, pstA, pstC, pstS   Genome Browser M3D Gene expression COLOMBOS
Note(s): pst operon transcription is activated under conditions of phosphate shortage Aguena M, Ferreira GM, Spira B,2009
The pstSCAB-phoU mRNA is processed by RNase E , but the smaller ptsS and pstSCA transcripts are still observed in a RNase E mutant Aguena M, Spira B,2009
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [5] Aguena M., et al., 2002
[4] Amemura M., et al., 1985
[6] Magota K., et al., 1984
[7] Steed PM., et al., 1993
[8] Surin BP., et al., 1985
Promoter
Name: pstSp
+1: 3911568
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: tcataaaactgtcatattccttacatataactgtcacctgtttgtcctattttgcttctcGtagccaacaaacaatgcttt
                          -35                        -10    +1                   
Note(s): Although the operon pstSCAB-phoU has several internal promoters, the promoter pstSp is the most important promoter for transcription of all genes in the operon Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Aguena M., et al., 2002
[2] Huerta AM., et al., 2003
[6] Magota K., et al., 1984
[9] Makino K., et al., 1988
[10] Surin BP., et al., 1984
[11] Taschner NP., et al., 2004
TF binding sites (TFBSs)
[FNR,+] 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
nd FNR activator pstSp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [15]
[IHF,+] 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 IHF activator pstSp 3911546 3911558 16.5 gtagccaacaAACAATGCTTTATgaatcctccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11], [13], [14]
[PhoB,+] 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 PhoB-phosphorylated activator pstSp 3911591 3911609 -32.0 tgtcatattcCTTACATATAACTGTCACCtgtttgtcct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]
proximal PhoB-phosphorylated activator pstSp 3911613 3911631 -54.0 ctttatctctCTGTCATAAAACTGTCATAttccttacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]


Transcription unit          
Name: pstS
Gene(s): pstS   Genome Browser M3D Gene expression COLOMBOS
Note(s): Repetitive extragenic palindrome (REP) displays a low transcription termination activity of the pstS gene. It also stabilizes to pstS mRNA and increases the level of PstS proteins Aguena M, Ferreira GM, Spira B,2009
The expression of the gene pstS is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression appears to be caused by the transcription factor PhoB Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [6] Magota K., et al., 1984
Promoter
Name: pstSp
+1: 3911568
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: tcataaaactgtcatattccttacatataactgtcacctgtttgtcctattttgcttctcGtagccaacaaacaatgcttt
                          -35                        -10    +1                   
Note(s): Although the operon pstSCAB-phoU has several internal promoters, the promoter pstSp is the most important promoter for transcription of all genes in the operon Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Aguena M., et al., 2002
[2] Huerta AM., et al., 2003
[6] Magota K., et al., 1984
[9] Makino K., et al., 1988
[10] Surin BP., et al., 1984
[11] Taschner NP., et al., 2004
Terminator(s)
Type: rho-independent
Sequence: attttgtaatGCCGGATGCGGCGTAAAACACCGTACCCGGCctggagtttt
Reference(s): [6] Magota K., et al., 1984
TF binding sites (TFBSs)
[FNR,+] 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
nd FNR activator pstSp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [15]
[IHF,+] 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 IHF activator pstSp 3911546 3911558 16.5 gtagccaacaAACAATGCTTTATgaatcctccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11], [13], [14]
[PhoB,+] 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 PhoB-phosphorylated activator pstSp 3911591 3911609 -32.0 tgtcatattcCTTACATATAACTGTCACCtgtttgtcct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]
proximal PhoB-phosphorylated activator pstSp 3911613 3911631 -54.0 ctttatctctCTGTCATAAAACTGTCATAttccttacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]


Transcription unit          
Name: pstSCA
Gene(s): pstA, pstC, pstS   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [4] Amemura M., et al., 1985
[6] Magota K., et al., 1984
Promoter
Name: pstSp2
+1: 3911568
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 43
Sequence: tcataaaactgtcatattccttacatataactgtcacctgtttgtcctattttgcttctcGtagccaacaaacaatgcttt
                             -35                     -10    +1                   
Note(s): Although the operon pstSCAB-phoU has several internal promoters, the promoter pstSp is the most important promoter for transcription of all genes in the operon Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Aguena M., et al., 2002
[2] Huerta AM., et al., 2003
[6] Magota K., et al., 1984
[9] Makino K., et al., 1988
[10] Surin BP., et al., 1984
[11] Taschner NP., et al., 2004
Terminator(s)
Type: rho-independent
Sequence: tcggtcggtcCCCTCGCCCCTCTGGGGAGAGGGttagggtgag
Reference(s): [4] Amemura M., et al., 1985
TF binding sites (TFBSs)
[FNR,+] 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
nd FNR activator pstSp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [15]
[IHF,+] 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 IHF activator pstSp2 3911546 3911558 16.5 gtagccaacaAACAATGCTTTATgaatcctccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11], [13], [14]
[PhoB,+] 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 PhoB-phosphorylated activator pstSp2 3911591 3911609 -32.0 tgtcatattcCTTACATATAACTGTCACCtgtttgtcct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]
proximal PhoB-phosphorylated activator pstSp2 3911613 3911631 -54.0 ctttatctctCTGTCATAAAACTGTCATAttccttacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]


Transcription unit          
Name: pstSCA
Gene(s): pstA, pstC, pstS   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [4] Amemura M., et al., 1985
[6] Magota K., et al., 1984
Promoter
Name: pstSp
+1: 3911568
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: tcataaaactgtcatattccttacatataactgtcacctgtttgtcctattttgcttctcGtagccaacaaacaatgcttt
                          -35                        -10    +1                   
Note(s): Although the operon pstSCAB-phoU has several internal promoters, the promoter pstSp is the most important promoter for transcription of all genes in the operon Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Aguena M., et al., 2002
[2] Huerta AM., et al., 2003
[6] Magota K., et al., 1984
[9] Makino K., et al., 1988
[10] Surin BP., et al., 1984
[11] Taschner NP., et al., 2004
Terminator(s)
Type: rho-independent
Sequence: tcggtcggtcCCCTCGCCCCTCTGGGGAGAGGGttagggtgag
Reference(s): [4] Amemura M., et al., 1985
TF binding sites (TFBSs)
[FNR,+] 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
nd FNR activator pstSp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [15]
[IHF,+] 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 IHF activator pstSp 3911546 3911558 16.5 gtagccaacaAACAATGCTTTATgaatcctccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11], [13], [14]
[PhoB,+] 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 PhoB-phosphorylated activator pstSp 3911591 3911609 -32.0 tgtcatattcCTTACATATAACTGTCACCtgtttgtcct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]
proximal PhoB-phosphorylated activator pstSp 3911613 3911631 -54.0 ctttatctctCTGTCATAAAACTGTCATAttccttacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]


Transcription unit          
Name: pstSCAB-phoU
Synonym(s): OP00284, phoT, pstSCABphoU
Gene(s): phoU, pstB, pstA, pstC, pstS   Genome Browser M3D Gene expression COLOMBOS
Note(s): pst operon transcription is activated under conditions of phosphate shortage Aguena M, Ferreira GM, Spira B,2009
The pstSCAB-phoU mRNA is processed by RNase E , but the smaller ptsS and pstSCA transcripts are still observed in a RNase E mutant Aguena M, Spira B,2009
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [5] Aguena M., et al., 2002
[4] Amemura M., et al., 1985
[6] Magota K., et al., 1984
[7] Steed PM., et al., 1993
[8] Surin BP., et al., 1985
Promoter
Name: pstSp2
+1: 3911568
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 43
Sequence: tcataaaactgtcatattccttacatataactgtcacctgtttgtcctattttgcttctcGtagccaacaaacaatgcttt
                             -35                     -10    +1                   
Note(s): Although the operon pstSCAB-phoU has several internal promoters, the promoter pstSp is the most important promoter for transcription of all genes in the operon Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Aguena M., et al., 2002
[2] Huerta AM., et al., 2003
[6] Magota K., et al., 1984
[9] Makino K., et al., 1988
[10] Surin BP., et al., 1984
[11] Taschner NP., et al., 2004
TF binding sites (TFBSs)
[FNR,+] 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
nd FNR activator pstSp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [15]
[IHF,+] 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 IHF activator pstSp2 3911546 3911558 16.5 gtagccaacaAACAATGCTTTATgaatcctccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11], [13], [14]
[PhoB,+] 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 PhoB-phosphorylated activator pstSp2 3911591 3911609 -32.0 tgtcatattcCTTACATATAACTGTCACCtgtttgtcct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]
proximal PhoB-phosphorylated activator pstSp2 3911613 3911631 -54.0 ctttatctctCTGTCATAAAACTGTCATAttccttacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]


Transcription unit          
Name: pstS
Gene(s): pstS   Genome Browser M3D Gene expression COLOMBOS
Note(s): Repetitive extragenic palindrome (REP) displays a low transcription termination activity of the pstS gene. It also stabilizes to pstS mRNA and increases the level of PstS proteins Aguena M, Ferreira GM, Spira B,2009
The expression of the gene pstS is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression appears to be caused by the transcription factor PhoB Marzan LW,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [6] Magota K., et al., 1984
Promoter
Name: pstSp2
+1: 3911568
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 43
Sequence: tcataaaactgtcatattccttacatataactgtcacctgtttgtcctattttgcttctcGtagccaacaaacaatgcttt
                             -35                     -10    +1                   
Note(s): Although the operon pstSCAB-phoU has several internal promoters, the promoter pstSp is the most important promoter for transcription of all genes in the operon Spira B,2010
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Aguena M., et al., 2002
[2] Huerta AM., et al., 2003
[6] Magota K., et al., 1984
[9] Makino K., et al., 1988
[10] Surin BP., et al., 1984
[11] Taschner NP., et al., 2004
Terminator(s)
Type: rho-independent
Sequence: attttgtaatGCCGGATGCGGCGTAAAACACCGTACCCGGCctggagtttt
Reference(s): [6] Magota K., et al., 1984
TF binding sites (TFBSs)
[FNR,+] 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
nd FNR activator pstSp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [15]
[IHF,+] 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 IHF activator pstSp2 3911546 3911558 16.5 gtagccaacaAACAATGCTTTATgaatcctccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11], [13], [14]
[PhoB,+] 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 PhoB-phosphorylated activator pstSp2 3911591 3911609 -32.0 tgtcatattcCTTACATATAACTGTCACCtgtttgtcct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]
proximal PhoB-phosphorylated activator pstSp2 3911613 3911631 -54.0 ctttatctctCTGTCATAAAACTGTCATAttccttacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [3], [12]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -10.0 3908387 3908411 cctacggtaaGCCTGATTAGCGAAGTGCATCAGGcacgatgagg
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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IMP] Inferred from mutant phenotype

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

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

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

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Spira B., Aguena M., de Castro Oliveira JV., Yagil E., 2010, Alternative promoters in the pst operon of Escherichia coli., Mol Genet Genomics 284(6):489-98

 [2] 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

 [3] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [4] Amemura M., Makino K., Shinagawa H., Kobayashi A., Nakata A., 1985, Nucleotide sequence of the genes involved in phosphate transport and regulation of the phosphate regulon in Escherichia coli., J Mol Biol 184(2):241-50

 [5] Aguena M., Yagil E., Spira B., 2002, Transcriptional analysis of the pst operon of Escherichia coli., Mol Genet Genomics 268(4):518-24

 [6] Magota K., Otsuji N., Miki T., Horiuchi T., Tsunasawa S., Kondo J., Sakiyama F., Amemura M., Morita T., Shinagawa H., 1984, Nucleotide sequence of the phoS gene, the structural gene for the phosphate-binding protein of Escherichia coli., J Bacteriol 157(3):909-17

 [7] Steed PM., Wanner BL., 1993, Use of the rep technique for allele replacement to construct mutants with deletions of the pstSCAB-phoU operon: evidence of a new role for the PhoU protein in the phosphate regulon., J Bacteriol 175(21):6797-809

 [8] Surin BP., Rosenberg H., Cox GB., 1985, Phosphate-specific transport system of Escherichia coli: nucleotide sequence and gene-polypeptide relationships., J Bacteriol 161(1):189-98

 [9] Makino K., Shinagawa H., Amemura M., Kimura S., Nakata A., Ishihama A., 1988, Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro., J Mol Biol 203(1):85-95

 [10] Surin BP., Jans DA., Fimmel AL., Shaw DC., Cox GB., Rosenberg H., 1984, Structural gene for the phosphate-repressible phosphate-binding protein of Escherichia coli has its own promoter: complete nucleotide sequence of the phoS gene., J Bacteriol 157(3):772-8

 [11] Taschner NP., Yagil E., Spira B., 2004, A differential effect of sigmaS on the expression of the PHO regulon genes of Escherichia coli., Microbiology 150(Pt 9):2985-92

 [12] Miyake Y., Yamamoto K., 2020, Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli., Sci Rep 10(1):3661

 [13] Spira B., Yagil E., 1999, The integration host factor (IHF) affects the expression of the phosphate-binding protein and of alkaline phosphatase in Escherichia coli., Curr Microbiol 38(2):80-5

 [14] Taschner NP., Yagil E., Spira B., 2006, The effect of IHF on sigmaS selectivity of the phoA and pst promoters of Escherichia coli., Arch Microbiol 185(3):234-7

 [15] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

RegulonDB