RegulonDB RegulonDB 10.9: Operon Form
   

csgDEFG operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: csgDEFG
Gene(s): csgG, csgF, csgE, csgD   Genome Browser M3D Gene expression COLOMBOS
Note(s): High concentrations of intracellular GlcNAc-6P signal the cells to downregulate the csgBA and csgDEFG operons 16816193
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Ogasawara H., et al., 2007
Promoter
Name: csgDp
+1: 1103335
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 139
Sequence: tagttacatgtttaacacttgatttaagatttgtaatggctagattgaaatcagatgtaaTccattagttttatattttac
                   -35                   -10                +1                   
Evidence: [TIM]
Reference(s): [1] Ogasawara H., et al., 2007
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FliZ repressor csgDp nd nd nd nd nd [BPP], [GEA], [IGI] [2], [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-Phosphorylated1 repressor csgDp 1103388 1103402 -59.5 atataacgagTTACATTTAGTTACAtgtttaacac nd [APIORCISFBSCS], [BPP], [GEA] [1]
Note(s): 1RstA activates csgDEFG only under acidic conditions at low pH Ogasawara H,2010.1RstA activates csgDEFG only under acidic conditions at low pH Ogasawara H,2010.


Transcription unit          
Name: csgDEFG
Gene(s): csgG, csgF, csgE, csgD   Genome Browser M3D Gene expression COLOMBOS
Note(s): High concentrations of intracellular GlcNAc-6P signal the cells to downregulate the csgBA and csgDEFG operons 16816193
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Ogasawara H., et al., 2007
Promoter
Name: csgDp2
+1: 1103335
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 139
Sequence: tagttacatgtttaacacttgatttaagatttgtaatggctagattgaaatcagatgtaaTccattagttttatattttac
                        -35                     -10         +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[1] Ogasawara H., et al., 2007
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FliZ repressor csgDp2 nd nd nd nd nd [BPP], [GEA], [IGI] [2], [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-Phosphorylated1 repressor csgDp2 1103388 1103402 -59.5 atataacgagTTACATTTAGTTACAtgtttaacac nd [APIORCISFBSCS], [BPP], [GEA] [1]
Note(s): 1RstA activates csgDEFG only under acidic conditions at low pH Ogasawara H,2010.1RstA activates csgDEFG only under acidic conditions at low pH Ogasawara H,2010.


Transcription unit          
Name: csgDEFG
Gene(s): csgG, csgF, csgE, csgD   Genome Browser M3D Gene expression COLOMBOS
Note(s): This operon encodes several proteins involved in the control of expression of the curli subunits encoded by csgBA.
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.
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.
in vitro experiments demonstrated that OmpR and CpxR bind simultaneously at the csgD promoter; for this reason, a competition between both could exist, allowing for a gradual curli gene expression. OmpR can bind only to a one site at the csgD promoter region, whereas CpxR binds cooperatively to multiple sites at the csg intergenic region, affecting to both csgBA and csgDEFG operons. The Cpx metabolic pathway is activated by high osmolarity, and this way CpxR represses the transcription of csgD in response to this condition Jubelin G,2005.
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
High concentrations of intracellular GlcNAc-6P signal the cells to downregulate the csgBA and csgDEFG operons 16816193
IHF and CpxR have high affinity for the csgDp1 promoter, followed in declining affinity by
OmpR, H-NS, and RstA Ogasawara H,2010.
Two regions have been designated as hot spot I and hot spot II. In the hot spot I region,
IHF, CpxR, and H-NS bind to the same upstream region between -188 and -159, while in the hot spot
II region, IHF, CpxR, H-NS, OmpR, and RstA bind at the downstream region between -61 and -43
Ogasawara H,2010.
IHF and H-NS compete with each other for binding to the respective target sequences in the
presence of high concentrations of both proteins Ogasawara H,2010.
In studies using DNase I footprinting, it was shown that H-NS binds a long sequence of 229 bp upstream of the csgDp1 promoter, from -201 to +28, including AT-rich sequences and the site where H-NS
is silencing to this promoter, and the sequence probably includes four binding sites, covering almost the entirety of this region Ogasawara H,2010. However, specific sequences where H-NS binds were not shown.
csgD expression is controlled through two diguanylate cyclases (DGCs), YegE and YdaM, and two phosphodiesterases (PDEs), YhjH and Gmr, and by the transcriptional regulator MlrA through a signaling cascade that controls curli biosynthesis by reducing transcription of the regulator CsgD 23708798.
Based on gene expression analysis, it was determined that Fis activates csgD expression Amores GR,2017
Epigallocatechin gallate (EGCG) activates the σE pathway, blocking the transcription of csgD through CpxR 29497416
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Ogasawara H., et al., 2007
Promoter
Name: csgDp3
+1: 1103344
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 148
Sequence: agttacatttagttacatgtttaacacttgatttaagatttgtaatggctagattgaaatCagatgtaatccattagtttt
                            -35              -10            +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [5] Hammar M., et al., 1995
[4] Huerta AM., et al., 2003
[1] Ogasawara H., et al., 2007
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal BasR-Phosphorylated activator csgDp3 1103425 1103444 -90.5 ctatcatttcTAAACTTAATAAAACCTTAAGgttaacattt nd [APIORCISFBSCS], [BPP], [GEA] [19]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd BolA-phosphate1 activator csgDp3 nd nd nd nd nd [BPP], [GEA], [IGI] [23]
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 csgDp3 1103303 1103314 37.0 tatattttacCCATTTAGGGCTgatttattac nd [AIBSPD], [GEA], [GS] [22]
proximal BtsR-Phosphorylated repressor csgDp3 1103364 1103375 -25.0 tttaacacttGATTTAAGATTTgtaatggcta nd [AIBSPD], [GEA], [GS] [22]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator csgDp3 1103376 1103397 -42.5 aacgagttacATTTAGTTACATGTTTAACACTTgatttaagat nd [AIBSCS], [GEA] [15]
remote CRP-cAMP activator csgDp3 1103504 1103525 -170.5 ttttatatgcATTATTAGTAAGTTATCACCATTtgtatgattt nd [AIBSCS], [GEA] [15]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-Phosphorylated repressor csgDp3 1103335 1103349 3.0 atggctagatTGAAATCAGATGTAATccattagttt nd [APIORCISFBSCS], [BPP], [GEA] [18]
proximal CpxR-Phosphorylated repressor csgDp3 1103359 1103373 -21.5 taacacttgaTTTAAGATTTGTAATggctagattg nd [APIORCISFBSCS], [BPP], [GEA] [14], [18]
proximal CpxR-Phosphorylated repressor csgDp3 1103380 1103394 -43.0 gagttacattTAGTTACATGTTTAACacttgattta nd [APIORCISFBSCS], [BPP], [GEA] [14]
proximal CpxR-Phosphorylated repressor csgDp3 1103385 1103399 -48.0 ataacgagttACATTTAGTTACATGTttaacacttg nd [APIORCISFBSCS], [BPP], [GEA] [18]
proximal CpxR-Phosphorylated repressor csgDp3 1103389 1103403 -52.0 taatataacgAGTTACATTTAGTTACatgtttaaca nd [APIORCISFBSCS], [BPP], [GEA] [18], [21]
proximal CpxR-Phosphorylated repressor csgDp3 1103411 1103425 -73.5 aaaaccttaaGGTTAACATTTTAATataacgagtt nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp3 1103433 1103447 -95.5 ttctatcattTCTAAACTTAATAAAaccttaaggt nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp3 1103437 1103451 -100.0 aacttttctaTCATTTCTAAACTTAAtaaaacctta nd [APIORCISFBSCS], [BPP], [GEA] [14], [18]
remote CpxR-Phosphorylated repressor csgDp3 1103446 1103460 -108.5 aaatgtacaaCTTTTCTATCATTTCtaaacttaat nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp3 1103466 1103482 -129.5 ttaaaattgtGCAATAAAAACCAAATGtacaactttt nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp3 1103478 1103492 -141.0 tgtatgatttTTTAAAATTGTGCAATaaaaaccaaa nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp3 1103503 1103517 -166.0 gcattattagTAAGTTATCACCATTTgtatgatttt nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp3 1103516 1103529 -178.0 attttttataTGCATTATTAGTAAgttatcacca nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp3 1103523 1103537 -186.0 caccgaaataTTTTTTATATGCATTAttagtaagtt nd [APIORCISFBSCS], [BPP], [GEA] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra activator csgDp3 1103290 1103307 46.5 ttacccatttAGGGCTGATTTATTACTACacacagcagt nd [AIBSCS], [BPP], [GEA], [SM] [12]
remote Cra activator csgDp3 1103532 1103549 -196.5 acgaaaggacTACACCGAAATATTTTTTAtatgcattat nd [AIBSCS], [BPP], [GEA], [SM] [12]
remote Cra activator csgDp3 1103563 1103580 -227.5 gtgtggagaaAAAACAAGAACGTTTTACAtgacgaaagg nd [AIBSCS], [BPP], [GEA], [SM] [12]
remote Cra activator csgDp3 1103899 1103916 -563.5 acatttaagaAATTAAATCATTTCAACTTggttgttaac nd [AIBSCS], [BPP], [GEA] [12]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CsgD activator csgDp3 1103309 1103323 29.5 cattagttttATATTTTACCCATTTagggctgatt nd [APIORCISFBSCS], [BPP], [GEA] [16]
proximal CsgD activator csgDp3 1103329 1103343 9.5 gattgaaatcAGATGTAATCCATTAgttttatatt nd [APIORCISFBSCS], [BPP], [GEA] [16]
remote CsgD activator csgDp3 1103456 1103470 -118.5 aataaaaaccAAATGTACAACTTTTctatcatttc nd [APIORCISFBSCS], [BPP], [GEA] [16]
remote CsgD activator csgDp3 1103504 1103518 -166.5 gcattattagTAAGTTATCACCATTtgtatgattt nd [APIORCISFBSCS], [BPP], [GEA] [16]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FliZ repressor csgDp3 nd nd nd nd nd [BPP], [GEA], [IGI] [2], [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor csgDp3 nd nd nd nd nd [BPP], [GEA], [IGI] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator csgDp3 1103381 1103441 -66.5 catttctaaaCTTAATAAAACCTTAAGGTTAACATTTTAATATAACGAGTTACATTTAGTTACATGTTTAAcacttgattt nd [BPP], [GEA] [14]
remote IHF2 activator csgDp3 1103503 1103533 -173.5 aaatatttttTATATGCATTATTAGTAAGTTATCACCATTTgtatgatttt nd [BPP], [GEA] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote MlrA1 activator csgDp3 1103457 1103491 -129.5 tatgatttttTAAAATTGTGCAATAAAAACCAAATGTACAACTTTtctatcattt nd [BPP], [GEA] [17]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MqsA1 repressor csgDp3 1103421 1103434 -83.5 aaacttaataAAACCTTAAGGTTAacattttaat nd [APIORCISFBSCS], [BPP], [GEA] [20]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OmpR-P activator csgDp3 1103384 1103403 -49.5 taatataacgAGTTACATTTAGTTACATGTTtaacacttga nd [APIORCISFBSCS], [BPP], [GEA] [14], [18], [21]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RcdA1 activator csgDp3 1103638 1103648 -298.5 tgcgatatgtCTTGCGCACAAgccgtgacaa nd [BPP], [GEA], [IC] [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcsAB repressor csgDp3 nd nd nd nd nd [BPP], [GEA], [IGI] [24]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-Phosphorylated repressor csgDp3 1103388 1103402 -50.5 atataacgagTTACATTTAGTTACAtgtttaacac nd [APIORCISFBSCS], [BPP], [GEA] [1], [14]
Note(s): 1Galego et al. demonstrated that the phosphorylation of BolA is essential for its activity as a transcriptional regulator; they demonstrated this using a promoter of the mreB gene, which is regulated by this protein Galego L,2020.2The site for IHF (-173.5), determined experimentally by DNase I footprinting, covers a region of 30 bp upstream of csgDp1 Ogasawara H,2010]. It is likely that there are several sites for IHF, so the consensus sequence for this regulator is 13 bp.1BluF can interact with MlrA, antagonizing its effects in vitro, and when BluF is overexpressed in vivo it interferes with csgD expression Tschowri N,2012.1Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the csgD 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.1DNase I digestion patterns showed that RcdA binds within the sequence between -192 and -308 of the transcription start site of csgD Shimada T,2012. According to this evidence and electrophoretic mobility shift assay results Shimada T,2012, the curator assigned one possible binding site of 10 bp for RcdA, located at -298.5 relative to the transcription start site of csgD. The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,20122DNase I digestion patterns showed that RcdA binds within the sequence between -192 and -308 of the transcription start site of csgD Shimada T,2012. According to this evidence and electrophoretic mobility shift assay results Shimada T,2012, the curator assigned one possible binding site of 10 bp for RcdA, located at -298.5 relative to the transcription start site of csgD. The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,2012
7The site for IHF (-173.5), determined experimentally by DNase I footprinting, covers a region of 30 bp upstream of csgDp1 Ogasawara H,2010]. It is likely that there are several sites for IHF, so the consensus sequence for this regulator is 13 bp.
12BluF can interact with MlrA, antagonizing its effects in vitro, and when BluF is overexpressed in vivo it interferes with csgD expression Tschowri N,2012.
19Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the csgD 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.
35Galego et al. demonstrated that the phosphorylation of BolA is essential for its activity as a transcriptional regulator; they demonstrated this using a promoter of the mreB gene, which is regulated by this protein Galego L,2020.
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA McaS csgDEFG repressor 1103277 1103291 UGCACUGCUGUGUGU MRNA-DEGRADATION [GEA], [IDA], [IPI], [SM] [6], [7]
small regulatory RNA GcvB csgDEFG repressor 1103272 1103289 GAUGUUGCACUGCUGUGU MRNA-DEGRADATION [IDA], [IEP] [6], [7]
small regulatory RNA RydC csgDEFG repressor 1103194 1103215 CAUGAUGAAACCCCGCUUUUUU TRANSLATION-BLOCKING [IEP], [IMP] [8]
small regulatory RNA OmrA csgDEFG repressor 1103257 1103275 CCAGAAGUACUGACAGAUG TRANSLATION-BLOCKING [IDA], [SM] [9]
small regulatory RNA RprA csgDEFG repressor 1103190 1103210 UAAACAUGAUGAAACCCCGCU TRANSLATION-BLOCKING, MRNA-DEGRADATION [SM] [6], [10]
small regulatory RNA RprA csgDEFG repressor 1103280 1103315 ACUGCUGUGUGUAGUAAUAAAUCAGCCCUAAAUGGG TRANSLATION-BLOCKING, MRNA-DEGRADATION [IDA], [IMP], [SM] [6], [7], [10]
small regulatory RNA RybB csgDEFG repressor 1103278 1103285 GCACUGCU nd [IEP], [SM] [11]
small regulatory RNA OmrB csgDEFG repressor 1103257 1103275 CCAGAAGUACUGACAGAUG TRANSLATION-BLOCKING [IDA], [SM] [9]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation csgDp3 nd   [GEA] [25]
Evidence: [GEA] Gene expression analysis
Reference(s): [25] Yamanaka K., et al., 1997


Transcription unit          
Name: csgDEFG
Gene(s): csgG, csgF, csgE, csgD   Genome Browser M3D Gene expression COLOMBOS
Note(s): This operon encodes several proteins involved in the control of expression of the curli subunits encoded by csgBA.
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.
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.
in vitro experiments demonstrated that OmpR and CpxR bind simultaneously at the csgD promoter; for this reason, a competition between both could exist, allowing for a gradual curli gene expression. OmpR can bind only to a one site at the csgD promoter region, whereas CpxR binds cooperatively to multiple sites at the csg intergenic region, affecting to both csgBA and csgDEFG operons. The Cpx metabolic pathway is activated by high osmolarity, and this way CpxR represses the transcription of csgD in response to this condition Jubelin G,2005.
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
High concentrations of intracellular GlcNAc-6P signal the cells to downregulate the csgBA and csgDEFG operons 16816193
IHF and CpxR have high affinity for the csgDp1 promoter, followed in declining affinity by
OmpR, H-NS, and RstA Ogasawara H,2010.
Two regions have been designated as hot spot I and hot spot II. In the hot spot I region,
IHF, CpxR, and H-NS bind to the same upstream region between -188 and -159, while in the hot spot
II region, IHF, CpxR, H-NS, OmpR, and RstA bind at the downstream region between -61 and -43
Ogasawara H,2010.
IHF and H-NS compete with each other for binding to the respective target sequences in the
presence of high concentrations of both proteins Ogasawara H,2010.
In studies using DNase I footprinting, it was shown that H-NS binds a long sequence of 229 bp upstream of the csgDp1 promoter, from -201 to +28, including AT-rich sequences and the site where H-NS
is silencing to this promoter, and the sequence probably includes four binding sites, covering almost the entirety of this region Ogasawara H,2010. However, specific sequences where H-NS binds were not shown.
csgD expression is controlled through two diguanylate cyclases (DGCs), YegE and YdaM, and two phosphodiesterases (PDEs), YhjH and Gmr, and by the transcriptional regulator MlrA through a signaling cascade that controls curli biosynthesis by reducing transcription of the regulator CsgD 23708798.
Based on gene expression analysis, it was determined that Fis activates csgD expression Amores GR,2017
Epigallocatechin gallate (EGCG) activates the σE pathway, blocking the transcription of csgD through CpxR 29497416
The csgD gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides 32385082.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Ogasawara H., et al., 2007
Promoter
Name: csgDp1
+1: 1103344
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 148
Sequence: agttacatttagttacatgtttaacacttgatttaagatttgtaatggctagattgaaatCagatgtaatccattagtttt
                            -35                   -10       +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [5] Hammar M., et al., 1995
[4] Huerta AM., et al., 2003
[1] Ogasawara H., et al., 2007
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal BasR-Phosphorylated activator csgDp1 1103425 1103444 -90.5 ctatcatttcTAAACTTAATAAAACCTTAAGgttaacattt nd [APIORCISFBSCS], [BPP], [GEA] [19]
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 csgDp1 1103303 1103314 37.0 tatattttacCCATTTAGGGCTgatttattac nd [AIBSPD], [GEA], [GS] [22]
proximal BtsR-Phosphorylated repressor csgDp1 1103364 1103375 -25.0 tttaacacttGATTTAAGATTTgtaatggcta nd [AIBSPD], [GEA], [GS] [22]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator csgDp1 1103376 1103397 -42.5 aacgagttacATTTAGTTACATGTTTAACACTTgatttaagat nd [AIBSCS], [GEA] [15]
remote CRP-cAMP activator csgDp1 1103504 1103525 -170.5 ttttatatgcATTATTAGTAAGTTATCACCATTtgtatgattt nd [AIBSCS], [GEA] [15]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-Phosphorylated repressor csgDp1 1103335 1103349 3.0 atggctagatTGAAATCAGATGTAATccattagttt nd [APIORCISFBSCS], [BPP], [GEA] [18]
proximal CpxR-Phosphorylated repressor csgDp1 1103359 1103373 -21.5 taacacttgaTTTAAGATTTGTAATggctagattg nd [APIORCISFBSCS], [BPP], [GEA] [14], [18]
proximal CpxR-Phosphorylated repressor csgDp1 1103380 1103394 -43.0 gagttacattTAGTTACATGTTTAACacttgattta nd [APIORCISFBSCS], [BPP], [GEA] [14]
proximal CpxR-Phosphorylated repressor csgDp1 1103385 1103399 -48.0 ataacgagttACATTTAGTTACATGTttaacacttg nd [APIORCISFBSCS], [BPP], [GEA] [18]
proximal CpxR-Phosphorylated repressor csgDp1 1103389 1103403 -52.0 taatataacgAGTTACATTTAGTTACatgtttaaca nd [APIORCISFBSCS], [BPP], [GEA] [18], [21]
proximal CpxR-Phosphorylated repressor csgDp1 1103411 1103425 -73.5 aaaaccttaaGGTTAACATTTTAATataacgagtt nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp1 1103433 1103447 -95.5 ttctatcattTCTAAACTTAATAAAaccttaaggt nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp1 1103437 1103451 -100.0 aacttttctaTCATTTCTAAACTTAAtaaaacctta nd [APIORCISFBSCS], [BPP], [GEA] [14], [18]
remote CpxR-Phosphorylated repressor csgDp1 1103446 1103460 -108.5 aaatgtacaaCTTTTCTATCATTTCtaaacttaat nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp1 1103466 1103482 -129.5 ttaaaattgtGCAATAAAAACCAAATGtacaactttt nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp1 1103478 1103492 -141.0 tgtatgatttTTTAAAATTGTGCAATaaaaaccaaa nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp1 1103503 1103517 -166.0 gcattattagTAAGTTATCACCATTTgtatgatttt nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp1 1103516 1103529 -178.0 attttttataTGCATTATTAGTAAgttatcacca nd [APIORCISFBSCS], [BPP], [GEA] [14]
remote CpxR-Phosphorylated repressor csgDp1 1103523 1103537 -186.0 caccgaaataTTTTTTATATGCATTAttagtaagtt nd [APIORCISFBSCS], [BPP], [GEA] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra activator csgDp1 1103290 1103307 46.5 ttacccatttAGGGCTGATTTATTACTACacacagcagt nd [AIBSCS], [BPP], [GEA], [SM] [12]
remote Cra activator csgDp1 1103532 1103549 -196.5 acgaaaggacTACACCGAAATATTTTTTAtatgcattat nd [AIBSCS], [BPP], [GEA], [SM] [12]
remote Cra activator csgDp1 1103563 1103580 -227.5 gtgtggagaaAAAACAAGAACGTTTTACAtgacgaaagg nd [AIBSCS], [BPP], [GEA], [SM] [12]
remote Cra activator csgDp1 1103899 1103916 -563.5 acatttaagaAATTAAATCATTTCAACTTggttgttaac nd [AIBSCS], [BPP], [GEA] [12]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CsgD activator csgDp1 1103309 1103323 29.5 cattagttttATATTTTACCCATTTagggctgatt nd [APIORCISFBSCS], [BPP], [GEA] [16]
proximal CsgD activator csgDp1 1103329 1103343 9.5 gattgaaatcAGATGTAATCCATTAgttttatatt nd [APIORCISFBSCS], [BPP], [GEA] [16]
remote CsgD activator csgDp1 1103456 1103470 -118.5 aataaaaaccAAATGTACAACTTTTctatcatttc nd [APIORCISFBSCS], [BPP], [GEA] [16]
remote CsgD activator csgDp1 1103504 1103518 -166.5 gcattattagTAAGTTATCACCATTtgtatgattt nd [APIORCISFBSCS], [BPP], [GEA] [16]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FliZ repressor csgDp1 nd nd nd nd nd [BPP], [GEA], [IGI] [2], [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor csgDp1 nd nd nd nd nd [BPP], [GEA], [IGI] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator csgDp1 1103381 1103441 -66.5 catttctaaaCTTAATAAAACCTTAAGGTTAACATTTTAATATAACGAGTTACATTTAGTTACATGTTTAAcacttgattt nd [BPP], [GEA] [14]
remote IHF2 activator csgDp1 1103503 1103533 -173.5 aaatatttttTATATGCATTATTAGTAAGTTATCACCATTTgtatgatttt nd [BPP], [GEA] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote MlrA1 activator csgDp1 1103457 1103491 -129.5 tatgatttttTAAAATTGTGCAATAAAAACCAAATGTACAACTTTtctatcattt nd [BPP], [GEA] [17]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MqsA1 repressor csgDp1 1103421 1103434 -83.5 aaacttaataAAACCTTAAGGTTAacattttaat nd [APIORCISFBSCS], [BPP], [GEA] [20]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OmpR-P activator csgDp1 1103384 1103403 -49.5 taatataacgAGTTACATTTAGTTACATGTTtaacacttga nd [APIORCISFBSCS], [BPP], [GEA] [14], [18], [21]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RcdA1 activator csgDp1 1103638 1103648 -298.5 tgcgatatgtCTTGCGCACAAgccgtgacaa nd [BPP], [GEA], [IC] [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd RcsAB repressor csgDp1 nd nd nd nd nd [BPP], [GEA], [IGI] [24]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-Phosphorylated repressor csgDp1 1103388 1103402 -50.5 atataacgagTTACATTTAGTTACAtgtttaacac nd [APIORCISFBSCS], [BPP], [GEA] [1], [14]
Note(s): 2The site for IHF (-173.5), determined experimentally by DNase I footprinting, covers a region of 30 bp upstream of csgDp1 Ogasawara H,2010]. It is likely that there are several sites for IHF, so the consensus sequence for this regulator is 13 bp.1BluF can interact with MlrA, antagonizing its effects in vitro, and when BluF is overexpressed in vivo it interferes with csgD expression Tschowri N,2012.1Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the csgD 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.1DNase I digestion patterns showed that RcdA binds within the sequence between -192 and -308 of the transcription start site of csgD Shimada T,2012. According to this evidence and electrophoretic mobility shift assay results Shimada T,2012, the curator assigned one possible binding site of 10 bp for RcdA, located at -298.5 relative to the transcription start site of csgD. The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,20122DNase I digestion patterns showed that RcdA binds within the sequence between -192 and -308 of the transcription start site of csgD Shimada T,2012. According to this evidence and electrophoretic mobility shift assay results Shimada T,2012, the curator assigned one possible binding site of 10 bp for RcdA, located at -298.5 relative to the transcription start site of csgD. The curator assigned the possible central position of this binding site based on similarity to a consensus sequence (TTGTGTACA) identified by Shimada et al. in 2012 Shimada T,2012
7The site for IHF (-173.5), determined experimentally by DNase I footprinting, covers a region of 30 bp upstream of csgDp1 Ogasawara H,2010]. It is likely that there are several sites for IHF, so the consensus sequence for this regulator is 13 bp.
12BluF can interact with MlrA, antagonizing its effects in vitro, and when BluF is overexpressed in vivo it interferes with csgD expression Tschowri N,2012.
19Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the csgD 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.
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA GcvB csgDEFG repressor 1103272 1103289 GAUGUUGCACUGCUGUGU MRNA-DEGRADATION [IDA], [IEP] [6], [7]
small regulatory RNA OmrA csgDEFG repressor 1103257 1103275 CCAGAAGUACUGACAGAUG TRANSLATION-BLOCKING [IDA], [SM] [9]
small regulatory RNA RprA csgDEFG repressor 1103280 1103315 ACUGCUGUGUGUAGUAAUAAAUCAGCCCUAAAUGGG TRANSLATION-BLOCKING, MRNA-DEGRADATION [IDA], [IMP], [SM] [6], [7], [10]
small regulatory RNA RydC csgDEFG repressor 1103194 1103215 CAUGAUGAAACCCCGCUUUUUU TRANSLATION-BLOCKING [IEP], [IMP] [8]
small regulatory RNA McaS csgDEFG repressor 1103277 1103291 UGCACUGCUGUGUGU MRNA-DEGRADATION [GEA], [IDA], [IPI], [SM] [6], [7]
small regulatory RNA OmrB csgDEFG repressor 1103257 1103275 CCAGAAGUACUGACAGAUG TRANSLATION-BLOCKING [IDA], [SM] [9]
small regulatory RNA RprA csgDEFG repressor 1103190 1103210 UAAACAUGAUGAAACCCCGCU TRANSLATION-BLOCKING, MRNA-DEGRADATION [SM] [6], [10]
small regulatory RNA RybB csgDEFG repressor 1103278 1103285 GCACUGCU nd [IEP], [SM] [11]




Reference(s)    

 [1] Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A., 2007, Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade., J Bacteriol 189(13):4791-9

 [2] Pesavento C., Becker G., Sommerfeldt N., Possling A., Tschowri N., Mehlis A., Hengge R., 2008, Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli., Genes Dev 22(17):2434-46

 [3] Pesavento C., Hengge R., 2012, The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity., Nucleic Acids Res 40(11):4783-93

 [4] 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

 [5] Hammar M., Arnqvist A., Bian Z., Olsen A., Normark S., 1995, Expression of two csg operons is required for production of fibronectin- and congo red-binding curli polymers in Escherichia coli K-12., Mol Microbiol 18(4):661-70

 [6] Andreassen PR., Pettersen JS., Szczerba M., Valentin-Hansen P., Moller-Jensen J., Jorgensen MG., 2018, sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA., Nucleic Acids Res 46(13):6746-6760

 [7] Jorgensen MG., Nielsen JS., Boysen A., Franch T., Moller-Jensen J., Valentin-Hansen P., 2012, Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli., Mol Microbiol 84(1):36-50

 [8] Bordeau V., Felden B., 2014, Curli synthesis and biofilm formation in enteric bacteria are controlled by a dynamic small RNA module made up of a pseudoknot assisted by an RNA chaperone., Nucleic Acids Res 42(7):4682-96

 [9] Holmqvist E., Reimegard J., Sterk M., Grantcharova N., Romling U., Wagner EG., 2010, Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis., EMBO J 29(11):1840-50

 [10] Mika F., Busse S., Possling A., Berkholz J., Tschowri N., Sommerfeldt N., Pruteanu M., Hengge R., 2012, Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli., Mol Microbiol 84(1):51-65

 [11] Serra DO., Mika F., Richter AM., Hengge R., 2016, The green tea polyphenol EGCG inhibits E. coli biofilm formation by impairing amyloid curli fibre assembly and downregulating the biofilm regulator CsgD via the σ(E) -dependent sRNA RybB., Mol Microbiol 101(1):136-51

 [12] Reshamwala SM., Noronha SB., 2011, Biofilm formation in Escherichia coli cra mutants is impaired due to down-regulation of curli biosynthesis., Arch Microbiol 193(10):711-22

 [13] Shimada T., Katayama Y., Kawakita S., Ogasawara H., Nakano M., Yamamoto K., Ishihama A., 2012, A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli., Microbiologyopen 1(4):381-94

 [14] Ogasawara H., Yamada K., Kori A., Yamamoto K., Ishihama A., 2010, Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors., Microbiology 156(Pt 8):2470-83

 [15] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [16] Ogasawara H., Yamamoto K., Ishihama A., 2011, Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis., J Bacteriol 193(10):2587-97

 [17] Ogasawara H., Yamamoto K., Ishihama A., 2010, Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli., FEMS Microbiol Lett 312(2):160-8

 [18] Jubelin G., Vianney A., Beloin C., Ghigo JM., Lazzaroni JC., Lejeune P., Dorel C., 2005, CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli., J Bacteriol 187(6):2038-49

 [19] Ogasawara H., Shinohara S., Yamamoto K., Ishihama A., 2012, Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli., Microbiology 158(Pt 6):1482-92

 [20] Soo VW., Wood TK., 2013, Antitoxin MqsA represses curli formation through the master biofilm regulator CsgD., Sci Rep 3:3186

 [21] Prigent-Combaret C., Brombacher E., Vidal O., Ambert A., Lejeune P., Landini P., Dorel C., 2001, Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene., J Bacteriol 183(24):7213-23

 [22] Ogasawara H., Ishizuka T., Yamaji K., Kato Y., Shimada T., Ishihama A., 2019, Regulatory role of pyruvate-sensing BtsSR in biofilm formation by Escherichia coli K-12., FEMS Microbiol Lett 366(24)

 [23] Azam MW., Zuberi A., Khan AU., 2020, bolA gene involved in curli amyloids and fimbriae production in E. coli: exploring pathways to inhibit biofilm and amyloid formation., J Biol Res (Thessalon) 27:10

 [24] Vianney A., Jubelin G., Renault S., Dorel C., Lejeune P., Lazzaroni JC., 2005, Escherichia coli tol and rcs genes participate in the complex network affecting curli synthesis., Microbiology 151(Pt 7):2487-97

 [25] Yamanaka K., Inouye M., 1997, Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli., J Bacteriol 179(16):5126-30


RegulonDB