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CsgD DNA-binding transcriptional dual regulator

Synonyms: CsgD
Summary:
The protein CsgD, for Curlin subunit gene D, is a transcriptional regulator [6]that regulates a number of genes involved in the Curli assembly, transport, and structural components [6, 7] which are important for biofilm formation [1] In addition, it also regulates genes related to cell surface-associated structures [1, 4, 8] It may also have the capability to respond to starvation and high cell density [1]and positively controls σS expression [5, 9] In general the environmental conditions, such as low osmolarity, low growth temperature (<32°C), and low growth, affect the expression of csgD and the production of the biofilm and cellulose [8, 10, 11]
Since csgD is induced during the mid-exponential phase of growth and the CsgD-dependent activation of csg genes is detected in the stationary phase, it has been suggested that CsgD is posttranscriptionally activated in the stationary phase [1]
CsgD might activate transcription through two different mechanisms, as suggested by the different locations of its binding sites in the regulatory regions of the genes it activates.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
CsgD     nd nd
Evolutionary Family: LuxR/UhpA
Connectivity class: Local Regulator
Gene name: csgD
  Genome position: 1102546-1103196
  Length: 651 bp / 216 aa
Operon name: csgDEFG
TU(s) encoding the TF:
Transcription unit        Promoter
csgDEFG
csgDp1
csgDEFG
csgDp2


Regulon       
Regulated gene(s) csgA, csgB, csgC, csgD, csgE, csgF, csgG, dgcC, flgM, flgN, fliA, fliE, fliF, fliG, fliH, fliI, fliJ, fliK, fliZ, iraP, nlpA, pepD, tcyJ, wrbA, yccJ, yccT, yhbS, yhbT
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
flagella (10)
motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc) (9)
flagellum (7)
Transcription related (3)
fimbri, pili (2)
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Regulated operon(s) csgBAC, csgDEFG, dgcC, flgAMN, fliAZ-tcyJ, fliE, fliFGHIJK, iraP, nlpA, pepD, wrbA-yccJ, yccT, yhbTS
First gene in the operon(s) csgB, csgD, dgcC, flgM, fliA, fliE, fliE, fliF, iraP, nlpA, pepD, wrbA, yccT, yhbT
Simple and complex regulons BasR,CRP,CpxR,Cra,CsgD,FliZ,IHF,MlrA,MqsA,OmpR,RcdA,RcsB,RstA
CpxR,CsgD,FliZ
CsgD
CsgD,FlhDC
CsgD,FlhDC,H-NS,MatA,NsrR,SutR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[CsgD,-](7)
[CsgD,+](6)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  CsgD activator adrAp Sigma38 -65.5 -81.5 dgcC
ctgatagtgcTAACGGGTGAGCTAcgaaaatggc
403615 403628 [AIBSCS], [BPP], [GEA], [HIBSCS], [SM] [1], [2]
  CsgD activator adrAp Sigma38 -47.0 -63.0 dgcC
gctacgaaaaTGGCTCACCCGaaatatcata
403635 403645 [AIBSCS], [GEA], [SM] [1]
  CsgD activator csgBp Sigma38 -80.5 -172.5 csgB, csgA, csgC
atttacgtggGTTTTAATACTTTGgtatgaacta
1103772 1103785 [BPP], [GEA], [HIBSCS] [2]
  CsgD activator csgBp Sigma38 -57.5 -149.5 csgB, csgA, csgC
ggtatgaactAAAAAAGAAAAATAcaacgcgcgg
1103795 1103808 [BPP], [GEA], [HIBSCS] [2]
  CsgD activator csgBp Sigma38 -38.0 -130.0 csgB, csgA, csgC
atacaacgcgCGGGTGAGTTAttaaaaatat
1103816 1103826 [AIBSCS], [GEA], [SM] [1]
  CsgD activator csgBp Sigma38 -27.5 -119.5 csgB, csgA, csgC
gcgggtgagtTATTAAAAATATTTccgcagacat
1103825 1103838 [BPP], [GEA], [HIBSCS] [2]
  CsgD activator csgDp1 Sigma38 -166.5 -314.5 csgD, csgE, csgF, csgG
cattattagtAAGTTATCACCATTtgtatgattt
1103504 1103517 [BPP], [GEA], [HIBSCS] [2]
  CsgD activator csgDp1 Sigma38 -118.5 -266.5 csgD, csgE, csgF, csgG
ataaaaaccaAATGTACAACTTTTctatcatttc
1103456 1103469 [BPP], [GEA], [HIBSCS] [2]
  CsgD activator csgDp1 Sigma38 9.5 -139.5 csgD, csgE, csgF, csgG
attgaaatcaGATGTAATCCATTAgttttatatt
1103329 1103342 [BPP], [GEA], [HIBSCS] [2]
  CsgD activator csgDp1 Sigma38 29.5 -119.5 csgD, csgE, csgF, csgG
attagttttaTATTTTACCCATTTagggctgatt
1103309 1103322 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor flgMp Sigma28 1.5 -36.5 flgM, flgN
ttgccgataaATAAGCAACACATGataaaagcgc
1130158 1130171 [BPP], [HIBSCS] [3]
  CsgD repressor flgMp Sigma28 17.5 -20.5 flgM, flgN
aacacatgatAAAAGCGCCCTCAAtgaggaataa
1130142 1130155 [BPP], [HIBSCS] [3]
  CsgD repressor fliAp1 Sigma70 -10.5 -40.5 fliA, fliZ, tcyJ
aaccctgcagAAACGGATAATCATgccgataact
2001823 2001836 [AIBSCS], [BPP] [3]
  CsgD repressor fliEp Sigma28 18.5 -61.5 fliE
tttttgttgcTATTTAGCGCCTTTgtcttattga
2013069 2013082 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor fliEp Sigma28 33.5 -46.5 fliE
agcgcctttgTCTTATTGACTTACtggtaggctt
2013054 2013067 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor fliEp1 Sigma70 -39.5 -61.5 fliE
tttttgttgcTATTTAGCGCCTTTgtcttattga
2013069 2013082 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor fliEp1 Sigma70 -24.5 -46.5 fliE
agcgcctttgTCTTATTGACTTACtggtaggctt
2013054 2013067 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor fliFp1 Sigma70 -85.5 -168.5 fliF, fliG, fliH, fliI, fliJ, fliK
aagcctaccaGTAAGTCAATAAGAcaaaggcgct
2013054 2013067 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor fliFp1 Sigma70 -70.5 -153.5 fliF, fliG, fliH, fliI, fliJ, fliK
tcaataagacAAAGGCGCTAAATAgcaacaaaaa
2013069 2013082 [BPP], [GEA], [HIBSCS] [2]
  CsgD activator iraPp1 Sigma70 nd nd iraP nd nd [GEA] [4], [5]
  CsgD activator nlpAp nd -91.5 -115.5 nlpA
gtggtcagtaAGAAGTGCCAGACTttatattcca
3840102 3840115 [BPP], [GEA] [2]
  CsgD activator nlpAp nd -76.5 -100.5 nlpA
tgccagacttTATATTCCACTTTTattccttttt
3840087 3840100 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor pepDp3 Sigma70 2.0 -20.0 pepD
tactgttttgCGGGTGATCGAcaaggagact
255731 255741 [AIBSCS], [GEA] [1]
  CsgD activator wrbAp Sigma38 -166.5 -216.5 wrbA, yccJ
cttcttagcgAGAATAGATATCATctccaataat
1067918 1067931 [BPP], [HIBSCS] [2]
  CsgD activator wrbAp Sigma38 -136.5 -186.5 wrbA, yccJ
taattatccaTAAGCCGCTCTTATgattaaaaaa
1067888 1067901 [BPP], [HIBSCS] [2]
  CsgD activator wrbAp Sigma38 -114.5 -164.5 wrbA, yccJ
atgattaaaaAAACGCGATGAGATaaaaatgtgt
1067866 1067879 [BPP], [HIBSCS] [2]
  CsgD activator yccTp nd -42.5 -106.5 yccT
accatgcagcTAATACGAATGAATgagagcaaaa
1027873 1027886 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor yhbTp2 nd -12.5 -37.5 yhbT, yhbS
ttatttttctGATATGGCAAAATAggatgattgt
3301307 3301320 [BPP], [GEA], [HIBSCS] [2]
  CsgD repressor yhbTp2 nd 15.5 -10.5 yhbT, yhbS
tgattgttgaAACAGGGAGTAAAActcgtgttgg
3301280 3301293 [BPP], [GEA], [HIBSCS] [2]


Alignment and PSSM for CsgD TFBSs    

Aligned TFBS of CsgD   
  Sequence
 

Position weight matrix (PWM).   
A	0	2	15	2	12	4	5	7	5	9	4	6	4	8	1	4	4
C	3	10	2	0	4	0	3	0	3	8	14	11	13	3	3	0	6
G	5	4	6	8	5	3	7	1	4	4	3	4	3	3	0	3	0
T	16	8	1	14	3	17	9	16	12	3	3	3	4	10	20	17	14

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation



Reference(s)    

 [1] 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

 [2] 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

 [3] Dudin O., Geiselmann J., Ogasawara H., Ishihama A., Lacour S., 2014, Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation., J Bacteriol. 196(3):707-15

 [4] Brombacher E., Baratto A., Dorel C., Landini P., 2006, Gene expression regulation by the Curli activator CsgD protein: modulation of cellulose biosynthesis and control of negative determinants for microbial adhesion., J Bacteriol. 188(6):2027-37

 [5] Gualdi L., Tagliabue L., Landini P., 2007, Biofilm formation-gene expression relay system in Escherichia coli: modulation of sigmaS-dependent gene expression by the CsgD regulatory protein via sigmaS protein stabilization., J Bacteriol. 189(22):8034-43

 [6] 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

 [7] Loferer H., Hammar M., Normark S., 1997, Availability of the fibre subunit CsgA and the nucleator protein CsgB during assembly of fibronectin-binding curli is limited by the intracellular concentration of the novel lipoprotein CsgG., Mol Microbiol. 26(1):11-23

 [8] Gualdi L., Tagliabue L., Bertagnoli S., Ierano T., De Castro C., Landini P., 2008, Cellulose modulates biofilm formation by counteracting curli-mediated colonization of solid surfaces in Escherichia coli., Microbiology. 154(Pt 7):2017-24

 [9] Bougdour A., Wickner S., Gottesman S., 2006, Modulating RssB activity: IraP, a novel regulator of sigma(S) stability in Escherichia coli., Genes Dev. 20(7):884-97

 [10] 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

 [11] Olsen A., Arnqvist A., Hammar M., Normark S., 1993, Environmental regulation of curli production in Escherichia coli., Infect Agents Dis. 2(4):272-4

 [12] Volz K., 1993, Structural conservation in the CheY superfamily., Biochemistry. 32(44):11741-53

 [13] Boehm A., Vogel J., 2012, The csgD mRNA as a hub for signal integration via multiple small RNAs., Mol Microbiol. 84(1):1-5

 [14] 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

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

 [16] Perni S., Preedy EC., Landini P., Prokopovich P., 2016, Influence of csgD and ompR on Nanomechanics, Adhesion Forces, and Curli Properties of E. coli., Langmuir. 32(31):7965-74



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