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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted diguanylate cyclase



Gene: yfiN Accession Numbers: EG12880 (EcoCyc), b2604, ECK2601

Regulation Summary Diagram: ?

Summary:
YfiN is a predicted diguanylate cyclase and an inner membrane protein with two predicted transmembrane domains. The C terminus is located in the cytoplasm [Daley05].

Deletion of yfiN partially restores motility of a yhjH mutant, suggesting that YfiN is one of four diguanylate cyclases that adjust c-di-GMP concentration for motility control [Boehm10]. Deletion of yfiN also suppresses the swarming defect of a yfiR deletion mutant [Girgis07]. A yfiN deletion mutant shows 18-fold increased early biofilm formation and 10-fold increased swimming motility. Deletion of yfiN does not alter the concentration of c-di-GMP inside the cell [SanchezTorres11].

In uropathogenic E. coli UTI89, YfiN encodes a diguanylate cyclase that contributes to a cellulose production pathway. YfiN is is repressed by the periplasmic protein YfiR [Hufnagel14]. yfiR, yfiN and yfiB may form an operon in E. coli K-12. In Pseudomonas aeruginosa this operon is involved in exopolysaccharide synthesis [Malone10]; in uropathogenic E. coli YfiR and YfiN were shown to have a role in cellulose production but no evidence implicating YfiB in this process was obtained [Hufnagel14]. E. coli K-12 does not produce cellulose due to a mutation in the bcs operon (see cellulose biosynthesis protein, pseudogene lacking N-terminal amino acids).

Locations: inner membrane

Map Position: [2,740,405 -> 2,741,631] (59.06 centisomes)
Length: 1227 bp / 408 aa

Molecular Weight of Polypeptide: 45.989 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008570 , EchoBASE:EB2718 , EcoGene:EG12880 , EcoliWiki:b2604 , OU-Microarray:b2604 , PortEco:yfiN , Pride:P46139 , Protein Model Portal:P46139 , RefSeq:NP_417095 , RegulonDB:EG12880 , SMR:P46139 , String:511145.b2604 , UniProt:P46139

Relationship Links: InterPro:IN-FAMILY:IPR000160 , InterPro:IN-FAMILY:IPR001054 , InterPro:IN-FAMILY:IPR003660 , Pfam:IN-FAMILY:PF00990 , Prosite:IN-FAMILY:PS50885 , Prosite:IN-FAMILY:PS50887 , Smart:IN-FAMILY:SM00267

In Paralogous Gene Group: 117 (13 members)

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [Boehm10, UniProtGOA11a, GOA01]
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility Inferred from experiment [SanchezTorres11]
GO:0007165 - signal transduction Inferred by computational analysis [GOA01a]
Molecular Function: GO:0052621 - diguanylate cyclase activity Inferred from experiment Inferred by computational analysis [GOA01, Boehm10]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0004871 - signal transducer activity 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:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

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

Essentiality data for yfiN 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:
Curated 03-Jan-2011 by Keseler I , SRI International
Last-Curated ? 08-Sep-2014 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 25 -> 45
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 53 -> 73
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 113 -> 133
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 155 -> 175
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 183 -> 236
[UniProt09]
UniProt: HAMP;
Conserved-Region 278 -> 408
[UniProt09]
UniProt: GGDEF;
Metal-Binding-Site 286
[UniProt10]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 291
[UniProt10]
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 294
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 303
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 329
[UniProt10]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Active-Site 329
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
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 ].
10/20/97 Gene b2604 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12880; confirmed by SwissProt match.


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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

Girgis07: Girgis HS, Liu Y, Ryu WS, Tavazoie S (2007). "A comprehensive genetic characterization of bacterial motility." PLoS Genet 3(9);1644-60. PMID: 17941710

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."

Hufnagel14: Hufnagel DA, DePas WH, Chapman MR (2014). "The Disulfide Bonding System Suppresses CsgD-independent Cellulose Production in E. coli." J Bacteriol. PMID: 25112475

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

Malone10: Malone JG, Jaeger T, Spangler C, Ritz D, Spang A, Arrieumerlou C, Kaever V, Landmann R, Jenal U (2010). "YfiBNR mediates cyclic di-GMP dependent small colony variant formation and persistence in Pseudomonas aeruginosa." PLoS Pathog 6(3);e1000804. PMID: 20300602

SanchezTorres11: Sanchez-Torres V, Hu H, Wood TK (2011). "GGDEF proteins YeaI, YedQ, and YfiN reduce early biofilm formation and swimming motility in Escherichia coli." Appl Microbiol Biotechnol 90(2);651-8. PMID: 21181144

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

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.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

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


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 18.5 on Wed Dec 17, 2014, biocyc13.