Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Protein: methyl accepting chemotaxis protein - dipeptide sensing



Gene: tap Accession Numbers: EG10987 (EcoCyc), b1885, ECK1886

Synonyms: Tap dimer, MCP-IV, dipeptide chemoreceptor protein, chemotaxis signaling protein IV

Regulation Summary Diagram: ?

Component of: chemotaxis signaling complex - dipeptide sensing (extended summary available)

Subunit composition of methyl accepting chemotaxis protein - dipeptide sensing = [Tap]2

Alternative forms of chemotaxis signaling complex - dipeptide sensing:
Tapglu-Me
Tapglu
Tapgln

Summary:
The tap gene product is one of four methyl-accepting chemotaxis proteins (MCPs) in E. coli K-12. MCP-IV interacts with the the periplasmic dipeptide-binding protein DppA to mediate taxis toward dipeptides. Dipeptides are good attractants, tripeptides are poor attractants. Peptides containing D-amino acids are poor attractants [Manson86, Abouhamad91].

E. coli Tap is predicted to be a homodimeric inner membrane protein; the Tap monomer consists of a periplasmic, ligand-sensing domain, two trans-membrane segments (TM1 and TM2) and a cytoplasmic signaling domain containing putative methylation sites [Krikos83, Le96]. Methylation and demethylation of MCPs in E. coli K-12 is catalysed by the CheR methyltransferase and the CheB methylesterase.

The cytoplasmic domains of the four E. coli MCPs have a high degree of sequence similarity [Krikos83, Le96, Alexander07]. Tap contains a HAMP domain (present in histidine kinases, adenylate cyclases, methyl accepting chemotaxis proteins, phosphatases) which is located between the transmembrane region of the molecule and the cytoplasmic signalling region. HAMP domains are thought to mediate input/ouptut signaling (reviewed in [Parkinson10]. E. coli Tap is predicted to form a ternary complexe with the histidine autokinase CheA and the coupling protein CheW.

Tap and Trg are considered to be low-abundance receptors while Tsr and Tar are considered to be high-abundance [Hazelbauer81, Hazelbauer81a, Harayama82]

tap: taxis associated protein

Reviews: [Stock00, Hazelbauer08]

Citations: [Slocum85]

Gene Citations: [Kundu97, Arnosti89, Parkinson82, Parkinson78]

Locations: inner membrane

Map Position: [1,967,407 <- 1,969,008] (42.4 centisomes)
Length: 1602 bp / 533 aa

Molecular Weight of Polypeptide: 57.512 kD (from nucleotide sequence), 65.0 kD (experimental) [Slocum83 ]

pI: 5.87

Unification Links: ASAP:ABE-0006288 , CGSC:123 , DIP:DIP-10955N , EchoBASE:EB0980 , EcoGene:EG10987 , EcoliWiki:b1885 , Mint:MINT-1309514 , ModBase:P07018 , OU-Microarray:b1885 , PortEco:tap , PR:PRO_000024025 , Protein Model Portal:P07018 , RefSeq:NP_416399 , RegulonDB:EG10987 , SMR:P07018 , String:511145.b1885 , Swiss-Model:P07018 , UniProt:P07018

Relationship Links: InterPro:IN-FAMILY:IPR003122 , InterPro:IN-FAMILY:IPR003660 , InterPro:IN-FAMILY:IPR004089 , InterPro:IN-FAMILY:IPR004090 , InterPro:IN-FAMILY:IPR004091 , Pfam:IN-FAMILY:PF00015 , Pfam:IN-FAMILY:PF00672 , Pfam:IN-FAMILY:PF02203 , Prints:IN-FAMILY:PR00260 , Prosite:IN-FAMILY:PS00538 , Prosite:IN-FAMILY:PS50111 , Prosite:IN-FAMILY:PS50885 , Smart:IN-FAMILY:SM00283 , Smart:IN-FAMILY:SM00304 , Smart:IN-FAMILY:SM00319

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006935 - chemotaxis Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Manson86]
GO:0007165 - signal transduction Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004871 - signal transducer activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Manson86]
GO:0004888 - transmembrane signaling receptor activity Inferred from experiment Inferred by computational analysis [GOA01a, Manson86]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Zhang07, Daley05]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Krikos83]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: cell processes motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
cell structure membrane
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Essentiality data for tap 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 13-Nov-2013 by Mackie A , Macquarie University


Subunit of: chemotaxis signaling complex - dipeptide sensing

Synonyms: MCP-IV chemotaxis signaling complex

Subunit composition of chemotaxis signaling complex - dipeptide sensing = [(CheA)2][CheW]2[(Tap)2]3
         CheA(L) histidine kinase = (CheA)2
         methyl accepting chemotaxis protein - dipeptide sensing = (Tap)2 (extended summary available)

Summary:
Chemotaxis in Escherichia coli is accomplished with a modified two-component signal transduction complex which transmits controlling signals to the flagellar motor complex. E.coli has four methyl-accepting chemotaxis protein (MCP)-type receptor complexes which recognize the following ligands: Tsr, serine;Tar, aspartate and maltose;Trg, ribose, galactose and glucose and Tap, dipeptides. Serine and aspartate bind directly to the receptor whereas maltose, ribose, galactose, glucose and dipeptides bind first to a periplasmic binding protein which then docks with its individual membrane receptor [Manson98].

The receptor complexes are ternary structures. The receptor-ligand interaction domain is located in the periplasm. Each receptor serves as the organizational framework for a receptor kinase signaling supermolecular complex formed in conjunction with histidine kinase CheA and other components of the signaling pathway [Falke97]. There are two transmembrane (TM) linker domains (CheW) which couple the methylation-dependent receptor to CheA. The receptors form homodimers with or without ligands [Gegner92]. CheA is a histidine kinase capable of autophosphorylation using ATP as a phosphodonor.The receptor complex dimers form trigonal units which in turn form a two-dimensional hexagonal lattice [Shimizu00] located usually at one pole of the cell. The Tsr and Tar receptors are the most abundant and the Tap, Trg receptors are less prevalent [Bren00].

CheA and CheY comprise a two-component signal transduction system where the signal is transmitted via phosphorylation from CheA to CheY (the response regulator). In several ways CheA/CheY differs from the standard two-component paradigm. Most significantly, CheY does not possess a DNA-binding domain and it doesn't act as a transcription factor. In the absence of activator ligand, CheA autophosphorylation is stimulated thus increasing the phosphotransfer from CheA to CheY, the messenger protein. CheY-P has a lower affinity for CheA than CheY, resulting in the dissociation of CheY-P from CheA. CheY-P has a higher affinity than CheY for the flagellar motor protein, FliM, a component of the motor supramolecular complex [Welch93]. Binding of CheY to FliM increases the probability of flagellar rotation in the CW direction [Barak92a]. CCW rotation of the motor induces the flagellar filaments to coalesce into a bundle which propels the cell forward in a fairly straight line (run). CW rotation disrupts the bundle and causes the cell to tumble. The cell typically travels in a three-dimensional walk consisting of runs interspersed with random chaotic tumbling. CheZ is a cytosolic phosphatase which prevents overaccumulation of CheY-P by accelerating the decay of its aspartyl-phosphate residue [Hess87]. CheY-P is thus maintained during steady-state conditions at a level that generates the random walk [Manson98].

When an attractant molecule binds to the receptor, a conformational change is induced [Yeh93] which propagates across the membrane and results in a suppression of CheA autophosphorylation. Levels of CheY-P decrease and the cells tumble less frequently, causing an increase in their run lengths as they enter areas of higher attractant concentrations. The adaptation response is necessary, though, for the cells to respond properly to continually increasing attractant concentration. Adaptive methylation is carried out by two enzymes: the methyltransferase CheR and the methylesterase CheB [Toews79]. CheR is a constitutive enzyme which, through the use of S-adenosylmethionine, methylates glutamate residues in the cytoplasmic domains of the MCPs. CheB is a target for phosphotransfer from CheA, and the activated CheB-P functions as a methyl esterase which removes methyl groups from the MCPs, reducing their kinase activity. Under steady-state conditions, the addition of methyl groups by CheR is balanced by the methyl group removal by CheB-P and an intermediate level of receptor methylation is maintained, resulting in run-tumble behavior of the cell. When an attractant binds to a receptor and inhibits CheA activity, the levels of CheB-P drop. The decrease is slower than that for CheY-P though, since CheB-P is not a phosphate donor to CheZ. The rising level of methyl esters eventually stimulate histidine kinase activity and therefore counteract the effect of attractant binding to the receptor. This resets the receptor signal to its basal level [Falke97].

The components of the chemotaxis sensory system are arranged at one of the cell poles in tight clusters containing thousands of copies of each protein [Sourjik00]. Binding of an attractant results in an increase in the probability that CheA is inactive (unphosphorylated) and methylation of CheA on four specific glutamate residues increases the probability that that it is active (phosphorylated) [Borkovich92]. Lower levels of methylation reduce the activity of CheA but increase the affinity of the receptor for its attractant ligand [Li00a].


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 7 -> 33
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 189 -> 209
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 212 -> 264
[UniProt09]
UniProt: HAMP;
Conserved-Region 269 -> 498
[UniProt09]
UniProt: Methyl-accepting transducer;
Glutamate-methyl-ester-Modification 293
[UniProt11a]
UniProt: Glutamate methyl ester (Gln).
Glutamate-methyl-ester-Modification 300
[UniProt11a]
UniProt: Glutamate methyl ester (Gln).
Glutamate-methyl-ester-Modification 307
[UniProt11a]
UniProt: Glutamate methyl ester (Gln).
Sequence-Conflict 335
[Krikos83, UniProt10]
Alternate sequence: A → G; UniProt: (in Ref. 1; AAA23567);
Glutamate-methyl-ester-Modification 489
[UniProt11a]
UniProt: Glutamate methyl ester (Glu).
Sequence-Conflict 503
[Krikos83, UniProt10]
Alternate sequence: H → R; UniProt: (in Ref. 1; AAA23567);
Sequence-Conflict 527 -> 533
[Krikos83, UniProt10]
Alternate sequence: QIAPVVS → TNCASGILK; UniProt: (in Ref. 1; AAA23567);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1885 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10987; confirmed by SwissProt match.


References

Abouhamad91: Abouhamad WN, Manson M, Gibson MM, Higgins CF (1991). "Peptide transport and chemotaxis in Escherichia coli and Salmonella typhimurium: characterization of the dipeptide permease (Dpp) and the dipeptide-binding protein." Mol Microbiol 5(5);1035-47. PMID: 1956284

Alexander07: Alexander RP, Zhulin IB (2007). "Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors." Proc Natl Acad Sci U S A 104(8);2885-90. PMID: 17299051

Arnosti89: Arnosti DN, Chamberlin MJ (1989). "Secondary sigma factor controls transcription of flagellar and chemotaxis genes in Escherichia coli." Proc Natl Acad Sci U S A 86(3);830-4. PMID: 2644646

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

Barak92a: Barak R, Eisenbach M (1992). "Correlation between phosphorylation of the chemotaxis protein CheY and its activity at the flagellar motor." Biochemistry 31(6);1821-6. PMID: 1737035

Borkovich92: Borkovich KA, Alex LA, Simon MI (1992). "Attenuation of sensory receptor signaling by covalent modification." Proc Natl Acad Sci U S A 89(15);6756-60. PMID: 1495964

Bren00: Bren A, Eisenbach M (2000). "How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation." J Bacteriol 182(24);6865-73. PMID: 11092844

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

Falke97: Falke JJ, Bass RB, Butler SL, Chervitz SA, Danielson MA (1997). "The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes." Annu Rev Cell Dev Biol 13;457-512. PMID: 9442881

Gegner92: Gegner JA, Graham DR, Roth AF, Dahlquist FW (1992). "Assembly of an MCP receptor, CheW, and kinase CheA complex in the bacterial chemotaxis signal transduction pathway." Cell 70(6);975-82. PMID: 1326408

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

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

Harayama82: Harayama S, Engstrom P, Wolf-Watz H, Iino T, Hazelbauer GL (1982). "Cloning of trg, a gene for a sensory transducer in Escherichia coli." J Bacteriol 152(1);372-83. PMID: 6749811

Hazelbauer08: Hazelbauer GL, Falke JJ, Parkinson JS (2008). "Bacterial chemoreceptors: high-performance signaling in networked arrays." Trends Biochem Sci 33(1);9-19. PMID: 18165013

Hazelbauer81: Hazelbauer GL, Engstrom P, Harayama S (1981). "Methyl-accepting chemotaxis protein III and transducer gene trg." J Bacteriol 145(1);43-9. PMID: 7007323

Hazelbauer81a: Hazelbauer GL, Engstrom P (1981). "Multiple forms of methyl-accepting chemotaxis proteins distinguished by a factor in addition to multiple methylation." J Bacteriol 145(1);35-42. PMID: 7007319

Hess87: Hess JF, Oosawa K, Matsumura P, Simon MI (1987). "Protein phosphorylation is involved in bacterial chemotaxis." Proc Natl Acad Sci U S A 1987;84(21);7609-13. PMID: 3313398

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

Krikos83: Krikos A, Mutoh N, Boyd A, Simon MI (1983). "Sensory transducers of E. coli are composed of discrete structural and functional domains." Cell 1983;33(2);615-22. PMID: 6305515

Kundu97: Kundu TK, Kusano S, Ishihama A (1997). "Promoter selectivity of Escherichia coli RNA polymerase sigmaF holoenzyme involved in transcription of flagellar and chemotaxis genes." J Bacteriol 179(13);4264-9. PMID: 9209042

Le96: Le Moual H, Koshland DE (1996). "Molecular evolution of the C-terminal cytoplasmic domain of a superfamily of bacterial receptors involved in taxis." J Mol Biol 261(4);568-85. PMID: 8794877

Li00a: Li G, Weis RM (2000). "Covalent modification regulates ligand binding to receptor complexes in the chemosensory system of Escherichia coli." Cell 100(3);357-65. PMID: 10676817

Manson86: Manson MD, Blank V, Brade G, Higgins CF (1986). "Peptide chemotaxis in E. coli involves the Tap signal transducer and the dipeptide permease." Nature 1986;321(6067);253-6. PMID: 3520334

Manson98: Manson MD, Armitage JP, Hoch JA, Macnab RM (1998). "Bacterial locomotion and signal transduction." J Bacteriol 180(5);1009-22. PMID: 9495737

Parkinson10: Parkinson JS (2010). "Signaling mechanisms of HAMP domains in chemoreceptors and sensor kinases." Annu Rev Microbiol 64;101-22. PMID: 20690824

Parkinson78: Parkinson JS (1978). "Complementation analysis and deletion mapping of Escherichia coli mutants defective in chemotaxis." J Bacteriol 135(1);45-53. PMID: 353036

Parkinson82: Parkinson JS, Houts SE (1982). "Isolation and behavior of Escherichia coli deletion mutants lacking chemotaxis functions." J Bacteriol 151(1);106-13. PMID: 7045071

Shimizu00: Shimizu TS, Le Novere N, Levin MD, Beavil AJ, Sutton BJ, Bray D (2000). "Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis." Nat Cell Biol 2(11);792-6. PMID: 11056533

Slocum83: Slocum MK, Parkinson JS (1983). "Genetics of methyl-accepting chemotaxis proteins in Escherichia coli: organization of the tar region." J Bacteriol 155(2);565-77. PMID: 6307970

Slocum85: Slocum MK, Parkinson JS (1985). "Genetics of methyl-accepting chemotaxis proteins in Escherichia coli: null phenotypes of the tar and tap genes." J Bacteriol 163(2);586-94. PMID: 2991198

Sourjik00: Sourjik V, Berg HC (2000). "Localization of components of the chemotaxis machinery of Escherichia coli using fluorescent protein fusions." Mol Microbiol 37(4);740-51. PMID: 10972797

Stock00: Stock J, Levit M (2000). "Signal transduction: hair brains in bacterial chemotaxis." Curr Biol 10(1);R11-4. PMID: 10660286

Toews79: Toews ML, Goy MF, Springer MS, Adler J (1979). "Attractants and repellents control demethylation of methylated chemotaxis proteins in Escherichia coli." Proc Natl Acad Sci U S A 76(11);5544-8. PMID: 392505

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.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 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."

Welch93: Welch M, Oosawa K, Aizawa S, Eisenbach M (1993). "Phosphorylation-dependent binding of a signal molecule to the flagellar switch of bacteria." Proc Natl Acad Sci U S A 90(19);8787-91. PMID: 8415608

Yeh93: Yeh JI, Biemann HP, Pandit J, Koshland DE, Kim SH (1993). "The three-dimensional structure of the ligand-binding domain of a wild-type bacterial chemotaxis receptor. Structural comparison to the cross-linked mutant forms and conformational changes upon ligand binding." J Biol Chem 268(13);9787-92. PMID: 8486661

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Helmann87: Helmann JD, Chamberlin MJ (1987). "DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor." Proc Natl Acad Sci U S A 84(18);6422-4. PMID: 3306678

Ide99: Ide N, Ikebe T, Kutsukake K (1999). "Reevaluation of the promoter structure of the class 3 flagellar operons of Escherichia coli and Salmonella." Genes Genet Syst 74(3);113-6. PMID: 10586520

Ko00a: Ko M, Park C (2000). "Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli." J Mol Biol 303(3);371-82. PMID: 11031114

Liu95a: Liu X, Matsumura P (1995). "An alternative sigma factor controls transcription of flagellar class-III operons in Escherichia coli: gene sequence, overproduction, purification and characterization." Gene 164(1);81-4. PMID: 7590326


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 Fri Dec 19, 2014, BIOCYC14A.