Escherichia coli K-12 substr. MG1655 Protein: PhoR sensory histidine kinase

Gene: phoR Accession Numbers: EG10733 (EcoCyc), b0400, ECK0394

Synonyms: R1pho, phoR1, nmpB

Regulation Summary Diagram: ?

Regulation summary diagram for phoR

Subunit composition of PhoR sensory histidine kinase = [PhoR]2

Alternative forms of PhoR sensory histidine kinase: PhoR sensory histidine kinase - phosphorylated (summary available)

PhoR is the sensor kinase of the PhoRB two component signal transduction pathway. PhoR indirectly senses and responds to variations in the level of extracellular inorganic phosphate (Pi) by phosphorylating or dephosphorylating its cognate response regulator PhoB.

PhoR is known to be a inner membrane protein comprised of five domains including an N-terminal transmembrane domain, a dimerisation and histidine phosphoacceptor domain and a C-terminal kinase domain [Yamada90a, Hsieh10]. PhoR is an atypical sensor kinase as it does not contain a large periplasmic domain [Scholten93]. The signal sensing and kinase domains of PhoR are located in the cytoplasm [Scholten93].

Under limiting environmental Pi, PhoR is believed to be in an active signalling conformation resulting in the phosphorylation and activation of PhoB and subsequent induction of the Pho regulon. Activation under limiting environmental Pi is considered to be the default state. Excess levels of Pi (>4uM) result in an inhibited form of PhoR which interferes with phosphorylation of PhoB and prevents its activity as a transcription factor [Makino89, Hsieh10]. The Pst transporter PstSCAB and the chaperone like protein PhoU are both necessary for inhibition of the PhoRB system [Cox88, Wanner93]. Accordingly an inhibition complex of PhoR, PhoU and the Pst transporter (PstSCAB) has been proposed but the nature of the interaction between these proteins is not clear [Hsieh10].

Phosphate regulon sensor kinase-phosphotransferase PhoR is probably a dimer or higher oligomer [Hoch95].

Based on DNA microarray analysis, it has been shown that PhoBR and PhoB are responsible for upregulation of phosphonate and glycerol phosphate metabolism and the high-affinity phosphate transport system, respectively, thus showing the complex regulation by the PhoR-PhoB two-component regulatory system [Baek07].

Citations: [Bracha69, Makino85, Baek07a, Carmany03]

Gene Citations: [Wanner87]

Locations: inner membrane

Map Position: [417,113 -> 418,408] (8.99 centisomes, 32°)
Length: 1296 bp / 431 aa

Molecular Weight of Polypeptide: 49.629 kD (from nucleotide sequence), 47.0 kD (experimental) [Tommassen82 ]

pI: 9.75

Unification Links: ASAP:ABE-0001391 , CGSC:394 , DIP:DIP-10502N , EchoBASE:EB0726 , EcoGene:EG10733 , EcoliWiki:b0400 , Mint:MINT-1288861 , ModBase:P08400 , OU-Microarray:b0400 , PortEco:phoR , PR:PRO_000023546 , Protein Model Portal:P08400 , RegulonDB:EG10733 , SMR:P08400 , String:511145.b0400 , UniProt:P08400

Relationship Links: InterPro:IN-FAMILY:IPR000014 , InterPro:IN-FAMILY:IPR003594 , InterPro:IN-FAMILY:IPR003661 , InterPro:IN-FAMILY:IPR004358 , InterPro:IN-FAMILY:IPR005467 , InterPro:IN-FAMILY:IPR009082 , InterPro:IN-FAMILY:IPR013767 , InterPro:IN-FAMILY:IPR014310 , InterPro:IN-FAMILY:IPR021766 , Pfam:IN-FAMILY:PF00512 , Pfam:IN-FAMILY:PF00989 , Pfam:IN-FAMILY:PF02518 , Pfam:IN-FAMILY:PF11808 , Prints:IN-FAMILY:PR00344 , Prosite:IN-FAMILY:PS50109 , Prosite:IN-FAMILY:PS50112 , Smart:IN-FAMILY:SM00091 , Smart:IN-FAMILY:SM00387 , Smart:IN-FAMILY:SM00388

In Paralogous Gene Group: 122 (29 members)

Reactions known to consume the compound:

PhoRB Two-Component Signal Transduction System, phosphate-dependent :
PhoR + ATP → ADP + PhoR sensory histidine kinase - phosphorylated

Reactions known to produce the compound:

PhoRB Two-Component Signal Transduction System, phosphate-dependent :
PhoB + PhoR sensory histidine kinase - phosphorylated → PhoR + PhoB-Pasp53

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for phoR

GO Terms:

Biological Process: GO:0000160 - phosphorelay signal transduction system Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Makino89]
GO:0016036 - cellular response to phosphate starvation Inferred from experiment [Makino85]
GO:0016311 - dephosphorylation Inferred from experiment [Carmany03]
GO:0023014 - signal transduction by protein phosphorylation Inferred from experiment Inferred by computational analysis [GOA01, Makino89]
GO:0046777 - protein autophosphorylation Inferred from experiment [Makino89]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [GOA01]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
GO:0006817 - phosphate ion transport Inferred by computational analysis [UniProtGOA11]
GO:0007165 - signal transduction Inferred by computational analysis [GOA01]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0018106 - peptidyl-histidine phosphorylation Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0000155 - phosphorelay sensor kinase activity Inferred from experiment Inferred by computational analysis [GOA01, Makino89]
GO:0004721 - phosphoprotein phosphatase activity Inferred from experiment [Carmany03]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0004673 - protein histidine kinase activity Inferred by computational analysis [GOA01a, GOA01]
GO:0004871 - signal transducer activity Inferred by computational analysis [GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016772 - transferase activity, transferring phosphorus-containing groups Inferred by computational analysis [GOA01]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis Inferred from experiment [Makino89, UniProtGOA11, GOA01]
GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05, Tommassen82]
GO:0016021 - integral component of membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Scholten93]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell structure membrane
information transfer protein related posttranslational modification
metabolism metabolism of other compounds phosphorous metabolism
regulation type of regulation posttranscriptional covalent modification, demodification, maturation
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

Essentiality data for phoR 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]

Last-Curated ? 22-Jun-2010 by Mackie A , Macquarie University

Sequence Features

Protein sequence of PhoR with features indicated

Feature Class Location Citations Comment State
Transmembrane-Region 10 -> 28
UniProt: Helical;; Non-Experimental Qualifier: probable;
Transmembrane-Region 33 -> 51
UniProt: Helical;; Non-Experimental Qualifier: probable;
Conserved-Region 96 -> 172
UniProt: PAS;
Conserved-Region 210 -> 425
UniProt: Histidine kinase;
Phosphorylation-Modification 213
UniProt: Phosphohistidine; by autocatalysis; Non-Experimental Qualifier: by similarity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b0400 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10733; confirmed by SwissProt match.


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

Baek07: Baek JH, Lee SY (2007). "Transcriptome analysis of phosphate starvation response in Escherichia coli." J Microbiol Biotechnol 17(2);244-52. PMID: 18051755

Baek07a: Baek JH, Kang YJ, Lee SY (2007). "Transcript and protein level analyses of the interactions among PhoB, PhoR, PhoU and CreC in response to phosphate starvation in Escherichia coli." FEMS Microbiol Lett 277(2);254-9. PMID: 18031348

Bracha69: Bracha M, Yagil E (1969). "Genetic mapping of the phoR regulator gene of alkaline phosphatase in Escherichia coli." J Gen Microbiol 59(1);77-81. PMID: 4903904

Carmany03: Carmany DO, Hollingsworth K, McCleary WR (2003). "Genetic and biochemical studies of phosphatase activity of PhoR." J Bacteriol 185(3);1112-5. PMID: 12533489

Cox88: Cox GB, Webb D, Godovac-Zimmermann J, Rosenberg H (1988). "Arg-220 of the PstA protein is required for phosphate transport through the phosphate-specific transport system in Escherichia coli but not for alkaline phosphatase repression." J Bacteriol 170(5);2283-6. PMID: 2896188

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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.

Hoch95: Hoch, JA, Silhavy, TJ "Two-Component Signal Transduction." ASM Press, Washington, D.C. 1995.

Hsieh10: Hsieh YJ, Wanner BL (2010). "Global regulation by the seven-component Pi signaling system." Curr Opin Microbiol 13(2);198-203. PMID: 20171928

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

Makino85: Makino K, Shinagawa H, Nakata A (1985). "Regulation of the phosphate regulon of Escherichia coli K-12: regulation and role of the regulatory gene phoR." J Mol Biol 184(2);231-40. PMID: 2411941

Makino89: Makino K, Shinagawa H, Amemura M, Kawamoto T, Yamada M, Nakata A (1989). "Signal transduction in the phosphate regulon of Escherichia coli involves phosphotransfer between PhoR and PhoB proteins." J Mol Biol 1989;210(3);551-9. PMID: 2693738

Scholten93: Scholten M, Tommassen J (1993). "Topology of the PhoR protein of Escherichia coli and functional analysis of internal deletion mutants." Mol Microbiol 8(2);269-75. PMID: 8391104

Tommassen82: Tommassen J, de Geus P, Lugtenberg B, Hackett J, Reeves P (1982). "Regulation of the pho regulon of Escherichia coli K-12. Cloning of the regulatory genes phoB and phoR and identification of their gene products." J Mol Biol 157(2);265-74. PMID: 7050395

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

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

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

Wanner87: Wanner BL, Chang BD (1987). "The phoBR operon in Escherichia coli K-12." J Bacteriol 1987;169(12);5569-74. PMID: 2824439

Wanner93: Wanner BL (1993). "Gene regulation by phosphate in enteric bacteria." J Cell Biochem 1993;51(1);47-54. PMID: 8432742

Yamada90a: Yamada M, Makino K, Shinagawa H, Nakata A (1990). "Regulation of the phosphate regulon of Escherichia coli: properties of phoR deletion mutants and subcellular localization of PhoR protein." Mol Gen Genet 1990;220(3);366-72. PMID: 2187152

Other References Related to Gene Regulation

Makino86: Makino K, Shinagawa H, Amemura M, Nakata A (1986). "Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12." J Mol Biol 1986;190(1);37-44. PMID: 3537313

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Yang12: Yang C, Huang TW, Wen SY, Chang CY, Tsai SF, Wu WF, Chang CH (2012). "Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli." PLoS One 7(10);e47314. PMID: 23071782

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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