KEGG   PATHWAY: eco02026
Entry
eco02026                    Pathway                                
Name
Biofilm formation - Escherichia coli - Escherichia coli K-12 MG1655
Description
Bacteria inhabiting a biofilm are protected from physical stress, antimicrobials, and the host immune system, and thereby cause severe medical, environmental, and technical problems. Biofilm formation in Escherichia coli is regulated by two inversely controlled transcriptional feedforward cascades, the FlhDC/FliA cascade and the sigmaS/MlrA/CsgD cascade, which are active in post-exponentially growing and in stationary phase cells, respectively. Their final outputs, flagella production or the synthesis of the biofilm matrix components curli and cellulose, are mutually exclusive due to complementary sigma factor requirements, the abundant DNA-binding regulator FliZ, and opposite regulation by c-di-GMP. The RNA-binding protein CsrA, a central component of the global regulatory system, inhibits synthesis of the poly-N-acetyl-glucosamine (PGA) exopolysaccharide and glycogen and stimulates the expression of the flagellar master regulator FlhDC. CsrA activity is counteracted by two sRNAs, CsrB and CsrC. The lower figure shows that FlhDC, sigmaS, and CsgD, the transcription factors that control large regulons involved in flagellar and biofilm formation, serve as regulatory hubs for multiple environmental signal integration with a series of sRNAs providing distinct inputs.
Class
Cellular Processes; Cellular community - prokaryotes
Pathway map
eco02026  Biofilm formation - Escherichia coli
eco02026

Organism
Escherichia coli K-12 MG1655 [GN:eco]
Gene
b0145  dksA; RNA polymerase-binding transcription factor DksA [KO:K06204]
b0254  perR; CP4-6 prophage; putative transcriptional regulator PerR [KO:K03566]
b0385  dgcC; diguanylate cyclase DgcC [KO:K18968] [EC:2.7.7.65]
b0983  gfcE; putative exopolysaccharide export lipoprotein GfcE [KO:K01991]
b1021  pgaD; poly-N-acetyl-D-glucosamine synthase subunit PgaD [KO:K11937]
b1022  pgaC; poly-N-acetyl-D-glucosamine synthase subunit PgaC [KO:K11936] [EC:2.4.1.-]
b1023  pgaB; poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase and beta-1,6 glycoside hydrolase [KO:K11931] [EC:3.5.1.-]
b1024  pgaA; partially deacetylated poly-beta-1,6-N-acetyl-D-glucosamine outer membrane porin [KO:K11935]
b1040  csgD; DNA-binding transcriptional dual regulator CsgD [KO:K04333]
b1041  csgB; curlin, minor subunit [KO:K04335]
b1042  csgA; curlin, major subunit [KO:K04334]
b1043  csgC; curlin chaperone [KO:K04336]
b1071  flgM; anti-sigma factor for FliA (sigma(28)) [KO:K02398]
b1194  ycgR; flagellar brake protein YcgR [KO:K21087]
b1285  pdeR; cyclic di-GMP phosphodiesterase PdeR [KO:K14051] [EC:3.1.4.52]
b1341  dgcM; diguanylate cyclase DgcM [KO:K21088] [EC:2.7.7.65]
b1512  lsrR; DNA-binding transcriptional repressor LsrR [KO:K11531]
b1815  pdeD; putative c-di-GMP phosphodiesterase PdeD [KO:K21090] [EC:3.1.4.52]
b1891  flhC; DNA-binding transcriptional dual regulator FlhC [KO:K02402]
b1892  flhD; DNA-binding transcriptional dual regulator FlhD [KO:K02403]
b1914  uvrY; DNA-binding transcriptional activator UvrY [KO:K07689]
b1916  sdiA; DNA-binding transcriptional dual regulator SdiA [KO:K07782]
b1921  fliZ; DNA-binding transcriptional regulator FliZ [KO:K02425]
b1922  fliA; RNA polymerase, sigma 28 (sigma F) factor [KO:K02405]
b1951  rcsA; DNA-binding transcriptional activator RcsA [KO:K07781]
b1954  dsrA; small regulatory RNA DsrA [KO:K18502]
b1956  dgcQ; putative diguanylate cyclase DgcQ [KO:K21085] [EC:2.7.7.65]
b2000  flu; CP4-44 prophage; self recognizing antigen 43 (Ag43) autotransporter [KO:K12687]
b2062  wza; outer membrane polysaccharide export protein Wza [KO:K01991]
b2067  dgcE; putative diguanylate cyclase DgcE [KO:K21084] [EC:2.7.7.65]
b2127  mlrA; DNA-binding transcriptional activator MlrA [KO:K21089]
b2216  rcsD; RcsD phosphotransferase [KO:K07676] [EC:2.7.13.3]
b2217  rcsB; DNA-binding transcriptional activator RcsB [KO:K07687]
b2218  rcsC; histidine kinase RcsC [KO:K07677] [EC:2.7.13.3]
b2417  crr; Enzyme IIA(Glc) [KO:K02777] [EC:2.7.1.-]
b2479  gcvR; putative transcriptional regulator GcvR [KO:K03567]
b2687  luxS; S-ribosylhomocysteine lyase [KO:K07173] [EC:4.4.1.21]
b2696  csrA; carbon storage regulator [KO:K03563]
b2741  rpoS; RNA polymerase, sigma S (sigma 38) factor [KO:K03087]
b2786  barA; sensor histidine kinase BarA [KO:K07678] [EC:2.7.13.3]
b2808  gcvA; DNA-binding transcriptional dual regulator GcvA [KO:K03566]
b3210  arcB; sensor histidine kinase ArcB [KO:K07648] [EC:2.7.13.3]
b3357  crp; DNA-binding transcriptional dual regulator CRP [KO:K10914]
b3404  envZ; sensor histidine kinase EnvZ [KO:K07638] [EC:2.7.13.3]
b3405  ompR; DNA-binding transcriptional dual regulator OmpR [KO:K07659]
b3417  malP; maltodextrin phosphorylase [KO:K00688] [EC:2.4.1.1]
b3428  glgP; glycogen phosphorylase [KO:K00688] [EC:2.4.1.1]
b3429  glgA; glycogen synthase [KO:K00703] [EC:2.4.1.21]
b3430  glgC; glucose-1-phosphate adenylyltransferase [KO:K00975] [EC:2.7.7.27]
b3525  pdeH; c-di-GMP phosphodiesterase PdeH [KO:K21086] [EC:3.1.4.52]
b3533  bcsA; cellulose synthase catalytic subunit [KO:K00694] [EC:2.4.1.12]
b3806  cyaA; adenylate cyclase [KO:K05851] [EC:4.6.1.1]
b3961  oxyR; DNA-binding transcriptional dual regulator OxyR [KO:K04761]
b4401  arcA; DNA-binding transcriptional dual regulator ArcA [KO:K07773]
b4408  csrB; small regulatory RNA CsrB [KO:K18515]
b4426  mcaS; small regulatory RNA McaS [KO:K21091]
b4431  rprA; small regulatory RNA RprA [KO:K18518]
b4443  gcvB; small regulatory RNA GcvB [KO:K18521]
b4444  omrA; small regulatory RNA OmrA [KO:K18522]
b4445  omrB; small regulatory RNA OmrB [KO:K18523]
b4450  arcZ; small regulatory RNA ArcZ [KO:K18504]
b4457  csrC; small regulatory RNA CsrC [KO:K18516]
b4458  oxyS; small regulatory RNA OxyS [KO:K18528]
b4597  rydC; small regulatory RNA RydC [KO:K18509]
Compound
C00037  Glycine
C00575  3',5'-Cyclic AMP
C01228  Guanosine 3',5'-bis(diphosphate)
C04494  Guanosine 3'-diphosphate 5'-triphosphate
C16463  3',5'-Cyclic diGMP
C21382  R-THMF
Reference
  Authors
Mika F, Hengge R
  Title
Small RNAs in the control of RpoS, CsgD, and biofilm architecture of Escherichia coli.
  Journal
RNA Biol 11:494-507 (2014)
DOI:10.4161/rna.28867
Reference
  Authors
Mika F, Hengge R
  Title
Small Regulatory RNAs in the Control of Motility and Biofilm Formation in E. coli and Salmonella.
  Journal
Int J Mol Sci 14:4560-79 (2013)
DOI:10.3390/ijms14034560
Reference
  Authors
Hengge R
  Title
Principles of c-di-GMP signalling in bacteria.
  Journal
Nat Rev Microbiol 7:263-73 (2009)
DOI:10.1038/nrmicro2109
Reference
  Authors
Chambers JR, Sauer K
  Title
Small RNAs and their role in biofilm formation.
  Journal
Trends Microbiol 21:39-49 (2013)
DOI:10.1016/j.tim.2012.10.008
Reference
  Authors
Martinez LC, Vadyvaloo V
  Title
Mechanisms of post-transcriptional gene regulation in bacterial biofilms.
  Journal
Front Cell Infect Microbiol 4:38 (2014)
DOI:10.3389/fcimb.2014.00038
Reference
  Authors
Kalia D, Merey G, Nakayama S, Zheng Y, Zhou J, Luo Y, Guo M, Roembke BT, Sintim HO
  Title
Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis.
  Journal
Chem Soc Rev 42:305-41 (2013)
DOI:10.1039/c2cs35206k
Reference
  Authors
Seyll E, Van Melderen L
  Title
The ribonucleoprotein Csr network.
  Journal
Int J Mol Sci 14:22117-31 (2013)
DOI:10.3390/ijms141122117
Reference
  Authors
Pesavento C, Becker G, Sommerfeldt N, Possling A, Tschowri N, Mehlis A, Hengge R
  Title
Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli.
  Journal
Genes Dev 22:2434-46 (2008)
DOI:10.1101/gad.475808
Reference
  Authors
Huang YH, Ferrieres L, Clarke DJ
  Title
The role of the Rcs phosphorelay in Enterobacteriaceae.
  Journal
Res Microbiol 157:206-12 (2006)
DOI:10.1016/j.resmic.2005.11.005
Reference
  Authors
Li J, Attila C, Wang L, Wood TK, Valdes JJ, Bentley WE
  Title
Quorum sensing in Escherichia coli is signaled by AI-2/LsrR: effects on small RNA and biofilm architecture.
  Journal
J Bacteriol 189:6011-20 (2007)
DOI:10.1128/JB.00014-07
Related
pathway
eco02024  Quorum sensing
eco02040  Flagellar assembly
KO pathway
ko02026   

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