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Name: | csgBAC | |||||||||
Gene(s): | csgB, csgA, csgC Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | This TU is transcribed only at low osmolarity, probably as a result of activation by the nonphosphorylated form of OmpR. There are nine elements involved in the regulation of curli expression through a complex network of interactions between transcription factors and the csg regulatory region Jubelin G,2005. csgBA mRNA levels are increased when csgD is overexpressed Perni S, Preedy EC, Landini P, Prokopovich P,2016 High concentrations of intracellular GlcNAc-6P signal the cells to downregulate the csgBA and csgDEFG operons Barnhart MM, Lynem J, Chapman MR,2006 FruR (Cra) binds to four target sites in the csgDEFG-csgBAC intergenic region and has the ability to bend the DNA to activate the transcription of these operons, but there is a possibility that FruR may indirectly regulate the expression of the operon csgBAC via the regulator CsgD Reshamwala SM,2011. Based on a microarray assay to identify genes relevant to the interaction between the bacterium and lettuce plant, the csgBA genes, which are involved in curli production, were found to be significantly upregulated Fink RC, Black EP, Hou Z, Sugawara M, Sadowsky MJ, Diez-Gonzalez F,2012 DnaK increases the expression of the csgBAC and csgDEFG operons, which are responsible for curli production, via quantity and quality control of RpoS and CsgD Sugimoto S,2018 |
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Evidence: | [LTED] Length of transcript experimentally determined | |||||||||
Reference(s): | [1] Arnqvist A., et al., 1994 | |||||||||
Promoter | ||||||||||
Name: | csgBp2 | |||||||||
+1: | 1103859 | |||||||||
Sigma Factor: | Sigma38 Sigmulon | |||||||||
Distance from start of the gene: | 92 | |||||||||
Sequence: |
aagaaaaatacaacgcgcgggtgagttattaaaaatatttccgcagacatactttccatcGtaacgcagcgttaacaaaat -35 -10 +1 |
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Note(s): | Of the transcriptional start site of this promoter, an AT-rich upstream activation sequence was determined that is required for transcriptional activation during entry into stationary phase; it is positioned between -98 and -54 with respect to the transcriptional start point. There are two transcripts in the csgBA operon; one primary transcript is initiated from the csgB promoter, which is differentially degraded to give a shorter transcript corresponding to the csgA gene. Crl is a new thermosensor identified in the Escherichia coli RpoS regulon which interacts directly with σS, promoting the binding of EσS to the csgBp promoter Bougdour A,2004 | |||||||||
Evidence: |
[CV(RPF/TIM)] [IHBCE] [RPF] [TIM] |
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Reference(s): |
[1] Arnqvist A., et al., 1994 [2] Bougdour A., et al., 2004 [3] Dudin O., et al., 2013 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | BtsR-Phosphorylated | repressor | csgBp2 | 1103915 | 1103926 | 62.0 | aaatgatttaATTTCTTAAATGtacgaccagg | nd | [GEA], [AIBSPD], [GS] | [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | CpxR-phosphorylated | repressor | csgBp2 | 1103388 | 1103402 | -464.0 | gtgttaaacaTGTAACTAAATGTAActcgttatat | nd | [GEA], [APIORCISFBSCS], [BPP] | [4] |
remote | CpxR-phosphorylated | repressor | csgBp2 | 1103597 | 1103611 | -255.0 | cacacctccgTGGACAATTTTTTACtgcaaaaaga | nd | [APIORCISFBSCS] | [5] |
proximal | CpxR-phosphorylated | repressor | csgBp2 | 1103859 | 1103873 | 8.0 | actttccatcGTAACGCAGCGTTAAcaaaatacag | nd | [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] | [4], [5] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | CsgD | activator | csgBp2 | 1103772 | 1103786 | -80.5 | atttacgtggGTTTTAATACTTTGGtatgaactaa | nd | [GEA], [APIORCISFBSCS], [BPP] | [6] |
proximal | CsgD | activator | csgBp2 | 1103795 | 1103809 | -57.5 | ggtatgaactAAAAAAGAAAAATACaacgcgcggg | nd | [GEA], [APIORCISFBSCS], [BPP] | [6] |
proximal | CsgD | activator | csgBp2 | 1103816 | 1103826 | -38.0 | atacaacgcgCGGGTGAGTTAttaaaaatat | nd | [GEA], [AIBSCS], [SM] | [7] |
proximal | CsgD | activator | csgBp2 | 1103825 | 1103839 | -27.5 | gcgggtgagtTATTAAAAATATTTCcgcagacata | nd | [GEA], [APIORCISFBSCS], [BPP] | [6] |
Name: | csgBAC | |||||||||
Gene(s): | csgB, csgA, csgC Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | This TU is transcribed only at low osmolarity, probably as a result of activation by the nonphosphorylated form of OmpR. There are nine elements involved in the regulation of curli expression through a complex network of interactions between transcription factors and the csg regulatory region Jubelin G,2005. csgBA mRNA levels are increased when csgD is overexpressed Perni S, Preedy EC, Landini P, Prokopovich P,2016 High concentrations of intracellular GlcNAc-6P signal the cells to downregulate the csgBA and csgDEFG operons Barnhart MM, Lynem J, Chapman MR,2006 FruR (Cra) binds to four target sites in the csgDEFG-csgBAC intergenic region and has the ability to bend the DNA to activate the transcription of these operons, but there is a possibility that FruR may indirectly regulate the expression of the operon csgBAC via the regulator CsgD Reshamwala SM,2011. Based on a microarray assay to identify genes relevant to the interaction between the bacterium and lettuce plant, the csgBA genes, which are involved in curli production, were found to be significantly upregulated Fink RC, Black EP, Hou Z, Sugawara M, Sadowsky MJ, Diez-Gonzalez F,2012 DnaK increases the expression of the csgBAC and csgDEFG operons, which are responsible for curli production, via quantity and quality control of RpoS and CsgD Sugimoto S,2018 |
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Evidence: | [LTED] Length of transcript experimentally determined | |||||||||
Reference(s): | [1] Arnqvist A., et al., 1994 | |||||||||
Promoter | ||||||||||
Name: | csgBp | |||||||||
+1: | 1103859 | |||||||||
Sigma Factor: | Sigma70 Sigmulon | |||||||||
Distance from start of the gene: | 92 | |||||||||
Sequence: |
aagaaaaatacaacgcgcgggtgagttattaaaaatatttccgcagacatactttccatcGtaacgcagcgttaacaaaat -35 -10 +1 |
|||||||||
Note(s): | Of the transcriptional start site of this promoter, an AT-rich upstream activation sequence was determined that is required for transcriptional activation during entry into stationary phase; it is positioned between -98 and -54 with respect to the transcriptional start point. There are two transcripts in the csgBA operon; one primary transcript is initiated from the csgB promoter, which is differentially degraded to give a shorter transcript corresponding to the csgA gene. Crl is a new thermosensor identified in the Escherichia coli RpoS regulon which interacts directly with σS, promoting the binding of EσS to the csgBp promoter Bougdour A,2004 | |||||||||
Evidence: |
[CV(RPF/TIM)] [ICWHO] [RPF] [TIM] |
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Reference(s): |
[1] Arnqvist A., et al., 1994 [2] Bougdour A., et al., 2004 [10] Huerta AM., et al., 2003 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | BtsR-Phosphorylated | repressor | csgBp | 1103915 | 1103926 | 62.0 | aaatgatttaATTTCTTAAATGtacgaccagg | nd | [GEA], [AIBSPD], [GS] | [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | CpxR-phosphorylated | repressor | csgBp | 1103388 | 1103402 | -464.0 | gtgttaaacaTGTAACTAAATGTAActcgttatat | nd | [GEA], [APIORCISFBSCS], [BPP] | [4] |
remote | CpxR-phosphorylated | repressor | csgBp | 1103597 | 1103611 | -255.0 | cacacctccgTGGACAATTTTTTACtgcaaaaaga | nd | [APIORCISFBSCS] | [5] |
proximal | CpxR-phosphorylated | repressor | csgBp | 1103859 | 1103873 | 8.0 | actttccatcGTAACGCAGCGTTAAcaaaatacag | nd | [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] | [4], [5] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | CsgD | activator | csgBp | 1103772 | 1103786 | -80.5 | atttacgtggGTTTTAATACTTTGGtatgaactaa | nd | [GEA], [APIORCISFBSCS], [BPP] | [6] |
proximal | CsgD | activator | csgBp | 1103795 | 1103809 | -57.5 | ggtatgaactAAAAAAGAAAAATACaacgcgcggg | nd | [GEA], [APIORCISFBSCS], [BPP] | [6] |
proximal | CsgD | activator | csgBp | 1103816 | 1103826 | -38.0 | atacaacgcgCGGGTGAGTTAttaaaaatat | nd | [GEA], [AIBSCS], [SM] | [7] |
proximal | CsgD | activator | csgBp | 1103825 | 1103839 | -27.5 | gcgggtgagtTATTAAAAATATTTCcgcagacata | nd | [GEA], [APIORCISFBSCS], [BPP] | [6] |
Name: | csgA |
Gene(s): | csgA Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [IEP] Inferred from expression pattern |
Reference(s): | [11] Li Z., et al., 2019 |
Promoter | |
Name: | csgAp |
+1: | 1104236 |
Sigma Factor: | Sigma70 Sigmulon |
Distance from start of the gene: | 211 |
Sequence: |
agtagcaaccgggcaaagattgaccagacaggagattataaccttgcatatattgatcagGcgggcagtgccaacgatgcc -10 +1 |
Evidence: |
[ICWHO] [TIM] |
Reference(s): | [11] Li Z., et al., 2019 |
Name: | csgC |
Gene(s): | csgC Genome Browser M3D Gene expression COLOMBOS |
Promoter | |
Name: | csgCp |
+1: | Unknown |
Evidence: | [IEP] |
Reference(s): | [13] Zaslaver A., et al., 2006 |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Transcriptional |
Strand: | forward |
Evidence: | [ICA] Inferred by computational analysis |
Reference(s): | [14] Merino E, et al., 2005 |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
terminator | -17.3 | 1104922 | 1104949 | gtattacagaAACAGGGCGCAAGCCCTGTTTTTTTTCgggagaagaa | |
anti-terminator | -10.09 | 1104887 | 1104931 | caacgcgaccGCTCATCAGTACTAATACATCATTTGTATTACAGAAACAGGGCGcaagccctgt | |
anti-anti-terminator | -9.3 | 1104855 | 1104893 | tccgtcaacgTGACTCAGGTTGGCTTTGGTAACAACGCGACCGCTCATcagtactaat |
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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