Escherichia coli K-12 substr. MG1655 Enzyme: diguanylate cyclase

Gene: ydaM Accession Numbers: G6673 (EcoCyc), b1341, ECK1338

Regulation Summary Diagram: ?

Regulation summary diagram for ydaM

Subunit composition of diguanylate cyclase = [YdaM]4
         diguanylate cyclase = YdaM

YdaM is part of a signaling cascade that controls curli biosynthesis by inducing transcription of the regulator CsgD. The YciR phosphodiesterase inhibits YdaM; this inhibition is relieved when YciR binds and hydrolyzes c-di-GMP, allowing YdaM to activate the transcription factor MlrA. Production of c-di-GMP by YdaM contributes to, but is not essential for MlrA activation by YdaM [Lindenberg13].

YdaM does not play a global regulatory role; csgD transcription may be its only target. YciR/Gmr acts antagonistically to YdaM [Weber06a]. Genetic analysis using epistasis experiments elucidated the presence of a signaling cascade, with the YegE/YhjH diguanylate cyclase (DGC)/phosphodiesterase (PDE) pair acting upstream of YciR, which itself is upstream of the DGC YdaM, and all acting upstream of the MlrA transcription factor. The direct interaction between YciR and YdaM appears to inhibit the DGC activity of YdaM [Lindenberg13].

YdaM contains an N-terminal PAS domain and a C-terminal GGDEF domain, which is often associated with diguanylate cyclase activity. YdaM displays weak diguanylate cyclase activity in vitro, and a strain containing mutations in the acidic residues essential for diguanylate cyclase activity no longer complements a ydaM null mutant [Weber06a]. YdaM interacts directly with YciR and MlrA, primarily via its N-terminal domain. However, when isolated, YdaM's GGDEF domain interacts with the predicted ligand-binding C-terminal domain of MlrA [Lindenberg13].

Expression of ydaM is increased during the transition to stationary phase and is dependent on σS [Weber06a, Sommerfeldt09]. H-NS plays a role in regulating ydaM expression [Weber06a]. ydaM expression is higher at 28°C than at 37°C [Sommerfeldt09] and is under post-transcriptional control by the small RNA RprA [Mika12].

A ydaM mutant is deficient in Congo red binding, indicating a change in various outer membrane and surface properties. Curli-shaped fibers are absent. Transcription of csgD, which controls production of curli, is strongly reduced in a ydaM mutant [Weber06a]. Overexpression of YdaM from a plasmid results in a more than 150-fold increase in intracellular c-di-GMP levels [Tagliabue10].

Review: [Romling05], Comment: [Jenal13]

Citations: [Steiner13, Pesavento08]

Map Position: [1,404,587 <- 1,405,819] (30.27 centisomes, 109°)
Length: 1233 bp / 410 aa

Molecular Weight of Polypeptide: 46.452 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004504 , DIP:DIP-28053N , EchoBASE:EB3138 , EcoGene:EG13355 , EcoliWiki:b1341 , ModBase:P77302 , OU-Microarray:b1341 , PortEco:ydaM , Protein Model Portal:P77302 , RefSeq:NP_415857 , RegulonDB:G6673 , SMR:P77302 , String:511145.b1341 , UniProt:P77302

Relationship Links: InterPro:IN-FAMILY:IPR000014 , InterPro:IN-FAMILY:IPR000160 , InterPro:IN-FAMILY:IPR000700 , InterPro:IN-FAMILY:IPR001610 , InterPro:IN-FAMILY:IPR013656 , InterPro:IN-FAMILY:IPR029787 , Pfam:IN-FAMILY:PF00990 , Pfam:IN-FAMILY:PF08448 , Prosite:IN-FAMILY:PS50113 , Prosite:IN-FAMILY:PS50887 , Smart:IN-FAMILY:SM00086 , Smart:IN-FAMILY:SM00091 , Smart:IN-FAMILY:SM00267

In Paralogous Gene Group: 117 (13 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for ydaM

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01a, Weber06a]
GO:0019935 - cyclic-nucleotide-mediated signaling Inferred from experiment [Lindenberg13]
GO:0051091 - positive regulation of sequence-specific DNA binding transcription factor activity Inferred from experiment [Lindenberg13]
GO:1900233 - positive regulation of single-species biofilm formation on inanimate substrate Inferred from experiment [Sommerfeldt09]
GO:0000160 - phosphorelay signal transduction system Inferred by computational analysis [GOA01]
GO:0007165 - signal transduction Inferred by computational analysis [GOA01]
GO:0023014 - signal transduction by protein phosphorylation Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Lindenberg13]
GO:0042802 - identical protein binding Inferred from experiment [Lindenberg13]
GO:0052621 - diguanylate cyclase activity Inferred from experiment Inferred by computational analysis [GOA01a, Weber06a]
GO:0000155 - phosphorelay sensor kinase activity Inferred by computational analysis [GOA01]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0004871 - signal transducer activity Inferred by computational analysis [GOA01]
GO:0005525 - GTP binding Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [GOA01]

MultiFun Terms: information transfer RNA related Transcription related

Essentiality data for ydaM knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Created 25-Oct-2013 by Keseler I , SRI International
Last-Curated ? 25-Oct-2013 by Keseler I , SRI International

Enzymatic reaction of: diguanylate cyclase

EC Number:

2 GTP <=> cyclic di-3',5'-guanylate + 2 diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of diguanylate cyclase with features indicated

Feature Class Location Citations Comment
Conserved-Region 3 -> 70
UniProt: PAS 1;
Conserved-Region 129 -> 198
UniProt: PAS 2;
Conserved-Region 199 -> 251
UniProt: PAC;
Conserved-Region 283 -> 410
UniProt: GGDEF;
Metal-Binding-Site 291
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 296
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 299
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 308
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 334 -> 335
[Weber06a, UniProt11]
UniProt: No longer complements a ydaM disruption, loss of csgB induction.
Metal-Binding-Site 334
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Active-Site 334
UniProt: Proton acceptor; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Jenal13: Jenal U (2013). "Think globally, act locally: how bacteria integrate local decisions with their global cellular programme." EMBO J 32(14);1972-4. PMID: 23749210

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lindenberg13: Lindenberg S, Klauck G, Pesavento C, Klauck E, Hengge R (2013). "The EAL domain protein YciR acts as a trigger enzyme in a c-di-GMP signalling cascade in E. coli biofilm control." EMBO J 32(14);2001-14. PMID: 23708798

Mika12: 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. PMID: 22356413

Pesavento08: 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. PMID: 18765794

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Romling05: Romling U, Gomelsky M, Galperin MY (2005). "C-di-GMP: the dawning of a novel bacterial signalling system." Mol Microbiol 57(3);629-39. PMID: 16045609

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Sommerfeldt09: Sommerfeldt N, Possling A, Becker G, Pesavento C, Tschowri N, Hengge R (2009). "Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli." Microbiology 155(Pt 4);1318-31. PMID: 19332833

Steiner13: Steiner S, Lori C, Boehm A, Jenal U (2013). "Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein-protein interaction." EMBO J 32(3);354-68. PMID: 23202856

Tagliabue10: Tagliabue L, Antoniani D, Maciag A, Bocci P, Raffaelli N, Landini P (2010). "The diguanylate cyclase YddV controls production of the exopolysaccharide poly-N-acetylglucosamine (PNAG) through regulation of the PNAG biosynthetic pgaABCD operon." Microbiology 156(Pt 10);2901-11. PMID: 20576684

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Weber06a: Weber H, Pesavento C, Possling A, Tischendorf G, Hengge R (2006). "Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli." Mol Microbiol 62(4);1014-34. PMID: 17010156

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Sat Oct 10, 2015, biocyc13.