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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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
CsgD Functional   nd nd nd
Evolutionary Family: LuxR/UhpA
TFBs length: 11
TFBs symmetry: asymmetric
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
csgDp
csgDEFG
csgDp1
csgDEFG
csgDp2
csgDEFG
csgDp3


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, ubiT, wrbA, yccJ, yccT, yhbS
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) (8)
flagellum (5)
fimbri, pili (3)
Transcription related (3)
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Regulated operon(s) csgBAC, csgDEFG, dgcC, flgAMN, fliAZ-tcyJ, fliE, fliFGHIJK, iraP, nlpA, pepD, ubiT-yhbS, wrbA-yccJ, yccT
First gene in the operon(s) dgcC, csgB, csgD, flgM, fliA, fliE, fliF, iraP, nlpA, pepD, ubiT, wrbA, yccT
Simple and complex regulons BasR,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp
BasR,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
BtsR,CpxR,CsgD,FliZ
CsgD
CsgD,DksA-ppGpp,ppGpp
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[CsgD,-](7)
[CsgD,+](9)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
 LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  CsgD activator adrAp Sigma38 -65.5 -81.5 dgcC
ctgatagtgcTAACGGGTGAGCTACgaaaatggct
 403615 403629 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2]
  CsgD activator adrAp Sigma38 -47.0 -63.0 dgcC
gctacgaaaaTGGCTCACCCGaaatatcata
 403635 403645 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1]
  CsgD activator csgBp Sigma70 -80.5 -172.5 csgB, csgA, csgC
atttacgtggGTTTTAATACTTTGGtatgaactaa
 1103772 1103786 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgBp Sigma70 -57.5 -149.5 csgB, csgA, csgC
ggtatgaactAAAAAAGAAAAATACaacgcgcggg
 1103795 1103809 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgBp Sigma70 -38.0 -130.0 csgB, csgA, csgC
atacaacgcgCGGGTGAGTTAttaaaaatat
 1103816 1103826 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1]
  CsgD activator csgBp Sigma70 -27.5 -119.5 csgB, csgA, csgC
gcgggtgagtTATTAAAAATATTTCcgcagacata
 1103825 1103839 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgBp2 Sigma38 -80.5 -172.5 csgB, csgA, csgC
atttacgtggGTTTTAATACTTTGGtatgaactaa
 1103772 1103786 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgBp2 Sigma38 -57.5 -149.5 csgB, csgA, csgC
ggtatgaactAAAAAAGAAAAATACaacgcgcggg
 1103795 1103809 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgBp2 Sigma38 -38.0 -130.0 csgB, csgA, csgC
atacaacgcgCGGGTGAGTTAttaaaaatat
 1103816 1103826 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1]
  CsgD activator csgBp2 Sigma38 -27.5 -119.5 csgB, csgA, csgC
gcgggtgagtTATTAAAAATATTTCcgcagacata
 1103825 1103839 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgDp1 Sigma70 -166.5 -314.5 csgD, csgE, csgF, csgG
gcattattagTAAGTTATCACCATTtgtatgattt
 1103504 1103518 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgDp1 Sigma70 -118.5 -266.5 csgD, csgE, csgF, csgG
aataaaaaccAAATGTACAACTTTTctatcatttc
 1103456 1103470 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgDp1 Sigma70 9.5 -139.5 csgD, csgE, csgF, csgG
gattgaaatcAGATGTAATCCATTAgttttatatt
 1103329 1103343 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgDp1 Sigma70 29.5 -119.5 csgD, csgE, csgF, csgG
cattagttttATATTTTACCCATTTagggctgatt
 1103309 1103323 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgDp3 Sigma38 -166.5 -314.5 csgD, csgE, csgF, csgG
gcattattagTAAGTTATCACCATTtgtatgattt
 1103504 1103518 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgDp3 Sigma38 -118.5 -266.5 csgD, csgE, csgF, csgG
aataaaaaccAAATGTACAACTTTTctatcatttc
 1103456 1103470 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgDp3 Sigma38 9.5 -139.5 csgD, csgE, csgF, csgG
gattgaaatcAGATGTAATCCATTAgttttatatt
 1103329 1103343 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator csgDp3 Sigma38 29.5 -119.5 csgD, csgE, csgF, csgG
cattagttttATATTTTACCCATTTagggctgatt
 1103309 1103323 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD repressor flgMp Sigma28 1.5 -36.5 flgM, flgN
cttgccgataAATAAGCAACACATGataaaagcgc
 1130158 1130172 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
  CsgD repressor flgMp Sigma28 17.5 -20.5 flgM, flgN
caacacatgaTAAAAGCGCCCTCAAtgaggaataa
 1130142 1130156 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
  CsgD repressor fliAp1 Sigma70 -10.5 -40.5 fliA, fliZ, tcyJ
aaaccctgcaGAAACGGATAATCATgccgataact
 2001823 2001837 [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
  CsgD repressor fliEp1 Sigma70 -39.5 -61.5 fliE
ttttttgttgCTATTTAGCGCCTTTgtcttattga
 2013069 2013083 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2]
  CsgD repressor fliEp1 Sigma70 -24.5 -46.5 fliE
tagcgcctttGTCTTATTGACTTACtggtaggctt
 2013054 2013068 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2]
  CsgD repressor fliEp2 Sigma28 18.5 -61.5 fliE
ttttttgttgCTATTTAGCGCCTTTgtcttattga
 2013069 2013083 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2]
  CsgD repressor fliEp2 Sigma28 33.5 -46.5 fliE
tagcgcctttGTCTTATTGACTTACtggtaggctt
 2013054 2013068 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2]
  CsgD repressor fliFp1 Sigma70 -85.5 -168.5 fliF, fliG, fliH, fliI, fliJ, fliK
aagcctaccaGTAAGTCAATAAGACaaaggcgcta
 2013054 2013068 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD repressor fliFp1 Sigma70 -70.5 -153.5 fliF, fliG, fliH, fliI, fliJ, fliK
tcaataagacAAAGGCGCTAAATAGcaacaaaaaa
 2013069 2013083 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator iraPp1 Sigma70 nd nd iraP
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4], [5]
  CsgD activator nlpAp nd -91.5 -115.5 nlpA
cgtggtcagtAAGAAGTGCCAGACTttatattcca
 3840102 3840116 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator nlpAp nd -76.5 -100.5 nlpA
gtgccagactTTATATTCCACTTTTattccttttt
 3840087 3840101 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD repressor pepDp3 Sigma70 2.0 -20.0 pepD
tactgttttgCGGGTGATCGAcaaggagact
 255731 255741 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1]
  CsgD repressor ubiTp2 nd -12.5 -37.5 ubiT, yhbS
gttatttttcTGATATGGCAAAATAggatgattgt
 3301307 3301321 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD repressor ubiTp2 nd 15.5 -10.5 ubiT, yhbS
atgattgttgAAACAGGGAGTAAAActcgtgttgg
 3301280 3301294 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  CsgD activator wrbAp Sigma38 -166.5 -216.5 wrbA, yccJ
gcttcttagcGAGAATAGATATCATctccaataat
 1067918 1067932 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
  CsgD activator wrbAp Sigma38 -136.5 -186.5 wrbA, yccJ
ataattatccATAAGCCGCTCTTATgattaaaaaa
 1067888 1067902 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
  CsgD activator wrbAp Sigma38 -114.5 -164.5 wrbA, yccJ
tatgattaaaAAAACGCGATGAGATaaaaatgtgt
 1067866 1067880 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
  CsgD activator yccTp nd -42.5 -106.5 yccT
aaccatgcagCTAATACGAATGAATgagagcaaaa
 1027873 1027887 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]


Alignment and PSSM for CsgD TFBSs    

Aligned TFBS of CsgD   
  Sequence
  AAAATGGCTCACCC
  TAAATGGGTAAAAT
  TAAGTCAATAAGAC
  CTAATGGATTACAT
  AAAGGCGCTAAATA
  TAAATAAGCAACAC
  TTAATAACTCACCC
  AGAATAGATATCAT
  CAAATGGTGATAAC
  CTTGTCGATCACCC
  ACAGGGAGTAAAAC
  AAAAGCGCCCTCAA
  GAAACGGATAATCA
  CAAAGTATTAAAAC
  AAAGTGGAATATAA
  CAAATGTACAACTT
  TTCGTAGCTCACCC
  TAAGCCGCTCTTAT
  CGATGAGATAAAAA
  TGAGTTATTAAAAA
  AAAAAGAAAAATAC
  GATATGGCAAAATA
  AAAGTCTGGCACTT
  CGAATGAATGAGAG

Position weight matrix (PWM). CsgD matrix-quality result    
A	8	15	21	14	1	5	8	10	3	14	20	8	15	7
C	7	1	1	0	2	6	0	7	3	7	0	10	5	10
G	2	4	0	9	5	11	14	4	2	1	0	2	0	1
T	7	4	2	1	16	2	2	3	16	2	4	4	4	6

Consensus    
;	consensus.strict             	caAatgGataAcac
;	consensus.strict.rc          	GTGTTATCCATTTG
;	consensus.IUPAC              	maArksRmtmAmmm
;	consensus.IUPAC.rc           	KKKTKAKYSMYTTK
;	consensus.regexp             	[ac]aA[ag][gt][cg][AG][ac]t[ac]A[ac][ac][ac]
;	consensus.regexp.rc          	[GT][GT][GT]T[GT]A[GT][CT][CG][AC][CT]TT[GT]

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    

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

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

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

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

 [EXP-IMP-SITE-MUTATION] 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] Olsén A, Arnqvist A, Hammar M, Normark S, 1993, Environmental regulation of curli production in Escherichia coli., Infect Agents Dis, 2(4):272 None

 [12] Volz K, 1993, Structural conservation in the CheY superfamily., Biochemistry, 32(44):11741 10.1021/bi00095a001

 [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 10.1021/acs.langmuir.6b02342

 [17] Sugimoto S., Arita-Morioka KI., Terao A., Yamanaka K., Ogura T., Mizunoe Y., 2018, Multitasking of Hsp70 chaperone in the biogenesis of bacterial functional amyloids., Commun Biol 1:52


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