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



Gene: dosC Accession Numbers: G6784 (EcoCyc), b1490, ECK1484

Synonyms: yddV

Regulation Summary Diagram: ?

Component of: DosC-DosP complex (summary available)

Summary:
The DosC protein is composed of an N-terminal sensory globin domain that binds heme in an apolar binding pocket, and a C-terminal GGDEF diguanylate cyclase domain. DosC binds oxygen with a Kd of 10-20 µM [Tuckerman09]. Diguanylate cyclase activity of DosC was shown in a coupled assay together with the DosP c-di-GMP phosphodiesterase [Tuckerman09].

The catalytic properties of DosC under various heme loading conditions have been determined; the Fe(III) and Fe(II)-O2 complexes have diguanylate cyclase activity. The enzyme has very low turnover numbers [Kitanishi10]. Tyr43 is required for oxygen recognition [Kitanishi10], and Leu63 is required for stability of the heme Fe(II)-O2 complex [Nakajima12].

Overexpression of DosC leads to increased levels of c-di-GMP in the cell and has a deleterious effect on cell division, increases biofilm formation and decreases motility [MendezOrtiz06, May11]. DosC stimulates expression of csgBAC [Tagliabue10] and pgaABCD [Tagliabue10a]. Deletion of dosC partially restores motility of a yhjH mutant, suggesting that DosC is one of four diguanylate cyclases that adjust c-di-GMP concentration for motility control [Boehm10]. However, DosC does not appear to act as a global regulator of gene expression [Weber06].

Expression of dosC is dependent on σS under a number of stress conditions [Weber06]. dosCP expression is increased at low temperature and in stationary phase [Sommerfeldt09].

DosC: "direct oxygen sensing cyclase" [Tuckerman09]

Review: [Romling05]

Gene Citations: [Jonas08]

Locations: cytosol

Map Position: [1,563,782 <- 1,565,164] (33.7 centisomes)
Length: 1383 bp / 460 aa

Molecular Weight of Polypeptide: 53.178 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004965 , EchoBASE:EB3554 , EcoGene:EG13793 , EcoliWiki:b1490 , OU-Microarray:b1490 , PortEco:dosC , Pride:P0AA89 , Protein Model Portal:P0AA89 , RefSeq:NP_416007 , RegulonDB:G6784 , SMR:P0AA89 , String:511145.b1490 , UniProt:P0AA89

Relationship Links: InterPro:IN-FAMILY:IPR000160 , InterPro:IN-FAMILY:IPR001054 , InterPro:IN-FAMILY:IPR009050 , InterPro:IN-FAMILY:IPR012292 , Pfam:IN-FAMILY:PF00990 , Prosite:IN-FAMILY:PS50887 , Smart:IN-FAMILY:SM00267

In Paralogous Gene Group: 117 (13 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006950 - response to stress Inferred from experiment [Weber06]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0015671 - oxygen transport Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Tuckerman09]
GO:0019825 - oxygen binding Inferred from experiment Inferred by computational analysis [GOA01a, Tuckerman09]
GO:0020037 - heme binding Inferred from experiment Inferred by computational analysis [GOA01a, Tuckerman09]
GO:0052621 - diguanylate cyclase activity Inferred from experiment Inferred by computational analysis [GOA01, Kitanishi10, Boehm10, MendezOrtiz06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA01a]
GO:0005525 - GTP binding Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes adaptations
cell processes motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
regulation

Essentiality data for dosC 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]

Credits:
Created 28-Sep-2009 by Keseler I , SRI International
Last-Curated ? 16-Aug-2012 by Keseler I , SRI International


Enzymatic reaction of: diguanylate cyclase

EC Number: 2.7.7.65

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.


Subunit of: DosC-DosP complex

Subunit composition of DosC-DosP complex = [DosP][DosC]
         c-di-GMP phosphodiesterase, heme-regulated = DosP (extended summary available)
         diguanylate cyclase = DosC (extended summary available)

Summary:
Slightly overexpressed DosC and DosP proteins copurify in a complex [Tuckerman09]. In addition, a ribonucleoprotein complex containing DosC, DosP and other proteins, including PNPase, enolase, and RNase E, can be purified [Tuckerman11]. PNPase within the complex is active under anaerobic, but not aerobic conditions [Tuckerman11].

GO Terms:

Molecular Function: GO:0052621 - diguanylate cyclase activity Inferred from experiment [Tuckerman11, Tuckerman09]
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity Inferred from experiment [Tuckerman11]

Credits:
Created 28-Sep-2009 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 43
[Tagliabue10a, Kitanishi10, UniProt12]
Alternate sequence: Y → W; UniProt: Same biofilm formation activity as wild-type. Markedly enhanced O(2) dissociation but not association rate constants. Highly enhanced autoxidation rate constant.
Alternate sequence: Y → F; UniProt: Same biofilm formation activity as wild-type. Markedly enhanced O(2) dissociation but not association rate constants. Highly enhanced autoxidation rate constant.
Alternate sequence: Y → L; UniProt: Same biofilm formation activity as wild-type. Large decrease in O(2) affinity.
Alternate sequence: Y → A; UniProt: Same biofilm formation activity as wild-type. Large decrease in O(2) affinity.
Amino-Acid-Site 43
[UniProt12]
UniProt: Involved in oxygen binding and important for the stability of the Fe(II)-O(2) complex; Sequence Annotation Type: site.
Mutagenesis-Variant 60
[Tagliabue10a, Kitanishi10, UniProt12]
Alternate sequence: Q → L; UniProt: Same biofilm formation activity as wild-type. 5-fold reduction in O(2) dissociation rate constant. Significant decrease in the autoxidation rate constant.
Alternate sequence: Q → E; UniProt: Same biofilm formation activity as wild-type. Enhanced O(2) dissociation but not association rate constants. Enhanced autoxidation rate constant.
Alternate sequence: Q → A; UniProt: Same biofilm formation activity as wild-type. Enhanced O(2) dissociation but not association rate constants. Enhanced autoxidation rate constant.
Amino-Acid-Site 60
[UniProt12]
UniProt: Important for oxygen binding and stability of the Fe(II)-O(2) complex; Sequence Annotation Type: site.
Mutagenesis-Variant 65
[Nakajima12, Tagliabue10a, UniProt12]
Alternate sequence: L → Q; UniProt: Enhanced autoxidation rate constant. Decrease in O(2) association rate constant.
Alternate sequence: L → M; UniProt: Enhanced autoxidation rate constant. Decrease in O(2) association rate constant.
Alternate sequence: L → T; UniProt: Enhanced autoxidation rate constant. Markedly enhanced O(2) association rate constant.
Alternate sequence: L → G; UniProt: Enhanced autoxidation rate constant. Markedly enhanced O(2) association rate constant.
Amino-Acid-Site 65
[UniProt12]
UniProt: Critical for restricting water access to the heme distal side to avoid rapid autoxidation; Sequence Annotation Type: site.
Mutagenesis-Variant 98
[Tagliabue10a, Kitanishi10, UniProt12]
Alternate sequence: H → A; UniProt: Same biofilm formation activity as wild-type. Loss of heme-binding ability.
Metal-Binding-Site 98
[UniProt12]
UniProt: Iron (heme proximal ligand).
Mutagenesis-Variant 223
[Tagliabue10a, Kitanishi10, UniProt12]
Alternate sequence: H → A; UniProt: Same biofilm formation activity as wild-type.
Conserved-Region 325 -> 458
[UniProt09]
UniProt: GGDEF;
Metal-Binding-Site 333
[UniProt10a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 338
[UniProt10a]
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 341
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 350
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 365
[Tagliabue10a, Kitanishi10, UniProt12]
Alternate sequence: R → A; UniProt: Same biofilm formation activity as wild-type.
Mutagenesis-Variant 368
[Tagliabue10a, Kitanishi10, UniProt12]
Alternate sequence: D → A; UniProt: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity.
Mutagenesis-Variant 376
[Tagliabue10a, Kitanishi10, UniProt12]
Alternate sequence: D → A; UniProt: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity.
Alternate sequence: DE → AA; UniProt: Loss of DGC activity. Stimulation of PNAG production and activation of pgaABCD expression are abolished.
Metal-Binding-Site 376
[UniProt10a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Active-Site 376
[UniProt10a]
UniProt: Proton acceptor; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 377
[Tagliabue10a, Kitanishi10, UniProt12]
Alternate sequence: E → A; UniProt: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Ingrid Keseler on Tue May 6, 2008:
ORF start site changed according to annotation in EcoGene.
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.


References

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

Boehm10: Boehm A, Kaiser M, Li H, Spangler C, Kasper CA, Ackermann M, Kaever V, Sourjik V, Roth V, Jenal U (2010). "Second messenger-mediated adjustment of bacterial swimming velocity." Cell 141(1);107-16. PMID: 20303158

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Jonas08: Jonas K, Edwards AN, Simm R, Romeo T, Romling U, Melefors O (2008). "The RNA binding protein CsrA controls cyclic di-GMP metabolism by directly regulating the expression of GGDEF proteins." Mol Microbiol 70(1);236-57. PMID: 18713317

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

Kitanishi10: Kitanishi K, Kobayashi K, Kawamura Y, Ishigami I, Ogura T, Nakajima K, Igarashi J, Tanaka A, Shimizu T (2010). "Important roles of Tyr43 at the putative heme distal side in the oxygen recognition and stability of the Fe(II)-O2 complex of YddV, a globin-coupled heme-based oxygen sensor diguanylate cyclase." Biochemistry 49(49);10381-93. PMID: 21067162

May11: May T, Okabe S (2011). "Enterobactin is required for biofilm development in reduced-genome Escherichia coli." Environ Microbiol 13(12);3149-62. PMID: 21980953

MendezOrtiz06: Mendez-Ortiz MM, Hyodo M, Hayakawa Y, Membrillo-Hernandez J (2006). "Genome-wide transcriptional profile of Escherichia coli in response to high levels of the second messenger 3',5'-cyclic diguanylic acid." J Biol Chem 281(12);8090-9. PMID: 16418169

Nakajima12: Nakajima K, Kitanishi K, Kobayashi K, Kobayashi N, Igarashi J, Shimizu T (2012). "Leu65 in the heme distal side is critical for the stability of the Fe(II)-O2 complex of YddV, a globin-coupled oxygen sensor diguanylate cyclase." J Inorg Biochem 108;163-70. PMID: 22005448

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

Tagliabue10: Tagliabue L, Maciag A, Antoniani D, Landini P (2010). "The yddV-dos operon controls biofilm formation through the regulation of genes encoding curli fibers' subunits in aerobically growing Escherichia coli." FEMS Immunol Med Microbiol 59(3);477-84. PMID: 20553324

Tagliabue10a: 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

Tuckerman09: Tuckerman JR, Gonzalez G, Sousa EH, Wan X, Saito JA, Alam M, Gilles-Gonzalez MA (2009). "An Oxygen-Sensing Diguanylate Cyclase and Phosphodiesterase Couple for c-di-GMP Control." Biochemistry 48(41):9764-74. PMID: 19764732

Tuckerman11: Tuckerman JR, Gonzalez G, Gilles-Gonzalez MA (2011). "Cyclic di-GMP activation of polynucleotide phosphorylase signal-dependent RNA processing." J Mol Biol 407(5);633-9. PMID: 21320509

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Weber06: 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

Other References Related to Gene Regulation

Lessard98: Lessard IA, Pratt SD, McCafferty DG, Bussiere DE, Hutchins C, Wanner BL, Katz L, Walsh CT (1998). "Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function." Chem Biol 5(9);489-504. PMID: 9751644


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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 18.5 on Sat Dec 20, 2014, BIOCYC14B.