RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
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
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                   
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]
Reference(s): [1] Arnqvist A., et al., 1994
[2] Bougdour A., et al., 2004
[3] Dudin O., et al., 2013
TF binding sites (TFBSs)
[BtsR,-] Phrase
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]
[CpxR,-] Phrase
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]
[CsgD,+] Phrase
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]
[FliZ,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FliZ repressor csgBp2 nd nd nd nd nd [GEA], [BPP] [9]


Transcription unit          
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
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]
Reference(s): [1] Arnqvist A., et al., 1994
[2] Bougdour A., et al., 2004
[10] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[BtsR,-] Phrase
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]
[CpxR,-] Phrase
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]
[CsgD,+] Phrase
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]
[FliZ,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FliZ repressor csgBp nd nd nd nd nd [GEA], [BPP] [9]


Transcription unit          
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
TF binding sites (TFBSs)
[BolA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd BolA-phosphorylated activator csgAp nd nd nd nd nd [GEA], [BPP] [12]


Transcription unit       
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    
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"


Evidence    

 [CV(RPF/TIM)] cross validation(RPF/TIM)

 [IHBCE] Inferred by a human based on computational evidence

 [RPF] RNA polymerase footprinting

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSPD] Automated inference based on sequence pattern discovery

 [GS] genomic SELEX

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [SM] Site mutation

 [ICWHO] Inferred computationally without human oversight

 [IEP] Inferred from expression pattern


Reference(s)    

 [1] Arnqvist A., Olsen A., Normark S., 1994, Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS., Mol Microbiol 13(6):1021-32

 [2] Bougdour A., Lelong C., Geiselmann J., 2004, Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase., J Biol Chem 279(19):19540-50

 [3] Dudin O., Lacour S., Geiselmann J., 2013, Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli., Res Microbiol 164(8):838-47

 [4] 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

 [5] De Wulf P., McGuire AM., Liu X., Lin EC., 2002, Genome-wide profiling of promoter recognition by the two-component response regulator CpxR-P in Escherichia coli., J Biol Chem 277(29):26652-61

 [6] 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

 [7] Brombacher E., Dorel C., Zehnder AJ., Landini P., 2003, The curli biosynthesis regulator CsgD co-ordinates the expression of both positive and negative determinants for biofilm formation in Escherichia coli., Microbiology 149(Pt 10):2847-57

 [8] 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)

 [9] 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

 [10] 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

 [11] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376

 [12] 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

 [13] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

 [14] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

RegulonDB