Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015

Escherichia coli K-12 substr. MG1655 Polypeptide: PhoB transcriptional dual regulator

Gene: phoB Accession Numbers: EG10728 (EcoCyc), b0399, ECK0393

Synonyms: phoRc, phoT, PhoB response regulator

Regulation Summary Diagram: ?

Alternative forms of PhoB transcriptional dual regulator: PhoB-Phosphorylated DNA-binding transcriptional dual regulator (extended summary available)

PhoB is a dual transcription regulator that activates expression of the Pho regulon in response to environmental Pi. The Pho regulon includes operons and genes whose products are involved in phosphorus uptake and metabolism [Wanner93, VanBogelen96, Baek06]. Expression of the periplasmic binding proteins for peptide transport, OppA and DppA, is repressed by PhoB [Smith92]. In a proteomic analysis under phosphate-limiting conditions, it was found that up to 400 proteins are differentially expressed [VanBogelen96]. PhoB is also involved in bacterial virulence of pathogenic Escherichia coli [Crepin11].

PhoB is a response regulator and belongs to the two-component system PhoR/PhoB. Under phosphate-limited conditions, the inner membrane sensor kinase PhoR autophosphorylates. Subsequent transfer of the phosphate group to PhoB results in activation of PhoB [Makino89]. When phosphate is in excess, autophosphorylation of PhoR is inhibited and PhoB-P is dephosphorylated. Autoregulation of PhoB/PhoR expression serves as a mechanism for cells to achieve respective optimal densities and fitness under these conditions [Gao13]. This negative regulation requires in addition to PhoR an intact Pst system and PhoU [Wanner96]. In the absence of PhoR, cross-regulation of PhoB by CreC or acetyl phosphate results in phosphorylation of PhoB in response to carbon sources [Wanner92, Amemura90]. A heterodimer formed between a phosphorylated monomer and an unphosphorylated monomer of PhoB plays an important role in PhoB autophosphorylation kinetics [CreagerAllen13].

PhoB consists of two functional domains, the N-terminal receiver domain, which is phosphorylated, and the C-terminal output domain, which binds to DNA and interacts with the σ70 subunit of RNA polymerase to activate transcription [Makino96, Makino93]. The output domain belongs to the winged helix-turn-helix family of transcription factors [MartinezHackert97]. Its activity is silenced by the receiver domain, and phosphorylation relieves inhibition [Ellison00]. The 3D structure of the receiver domain [Sola99] and of two constitutively active mutants of this domain [ArribasBosacoma07] and the 3D structure of the output domain have been solved [MartinezHackert97a]. By using motif binding geometries (MBG), a structural model of the PhoB dimer in the transcription initiation complex PhoB/RNAP/σ factor/DNA has been developed [Tung12].

PhoB binds to the Pho box, which has been described as two direct 11-bp repeats consisting of successive 7-bp direct repeats followed by an A/T-rich region of 4 bp, situated 10 bp upstream of the -10 region [Makino88, Blanco02, Makino86]. The pho promoters contain functional -10 sequences but lack the consensus -35 sequence [Kimura89].

The 3D structure of the PhoB effector domain in complex with its target DNA sequence reveals a novel tandem arrangement in which several monomers bind head to tail to successive 11-bp direct repeat sequences, coating one face of the double helix [Blanco02, Bachhawat05].

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: [Saier94a, Pao95, Parkinson92, Stock90, Parkinson93]

Gene Citations: [Wanner87]

Locations: cytosol

Map Position: [416,366 -> 417,055] (8.97 centisomes)
Length: 690 bp / 229 aa

Molecular Weight of Polypeptide: 26.433 kD (from nucleotide sequence)

pI: 5.51, 5.7

Unification Links: ASAP:ABE-0001389 , CGSC:397 , DIP:DIP-35852N , EchoBASE:EB0721 , EcoGene:EG10728 , EcoliWiki:b0399 , Mint:MINT-1313174 , ModBase:P0AFJ5 , OU-Microarray:b0399 , PortEco:phoB , PR:PRO_000023541 , Protein Model Portal:P0AFJ5 , RegulonDB:EG10728 , SMR:P0AFJ5 , String:511145.b0399 , Swiss-Model:P0AFJ5 , UniProt:P0AFJ5

Relationship Links: InterPro:IN-FAMILY:IPR001789 , InterPro:IN-FAMILY:IPR001867 , InterPro:IN-FAMILY:IPR011006 , InterPro:IN-FAMILY:IPR011879 , InterPro:IN-FAMILY:IPR011991 , PDB:Structure:1B00 , PDB:Structure:1GXP , PDB:Structure:1GXQ , PDB:Structure:1QQI , PDB:Structure:1ZES , PDB:Structure:2IYN , PDB:Structure:2JB9 , PDB:Structure:2JBA , PDB:Structure:2Z33 , PDB:Structure:3T72 , Pfam:IN-FAMILY:PF00072 , Pfam:IN-FAMILY:PF00486 , Prosite:IN-FAMILY:PS50110 , Smart:IN-FAMILY:SM00448 , Smart:IN-FAMILY:SM00862

In Paralogous Gene Group: 121 (40 members)

Reactions known to consume the compound:

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

In Reactions of unknown directionality:

Not in pathways:
CreC sensory histidine kinase - phosphorylated + PhoB = CreC + PhoB-Pasp53

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:2000142 - regulation of DNA-templated transcription, initiation Inferred from experiment [Makino96]
GO:0000160 - phosphorelay signal transduction system Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a]
GO:0006817 - phosphate ion transport Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0001108 - bacterial-type RNA polymerase holo enzyme binding Inferred from experiment [Makino96]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Gao08]
GO:0000156 - phosphorelay response regulator activity Inferred by computational analysis [GOA01a]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism metabolism of other compounds phosphorous metabolism
regulation genetic unit regulated regulon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)
regulation type of regulation transcriptional level repressor

DNA binding site length: 19 base-pairs

Symmetry: Direct Repeat

Transcription Units regulated by related protein PhoB-Phosphorylated DNA-binding transcriptional dual regulator (35 total):

Essentiality data for phoB 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]

Sequence Features

Feature Class Location Citations Comment State
Conserved-Region 1 -> 120
UniProt: Response regulatory;
4-aspartylphosphate-Modification 53
UniProt: 4-aspartylphosphate.

Gene Local Context (not to scale): ?

Transcription Units:


10/20/97 Gene b0399 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10728; confirmed by SwissProt match.


Amemura90: Amemura M, Makino K, Shinagawa H, Nakata A (1990). "Cross talk to the phosphate regulon of Escherichia coli by PhoM protein: PhoM is a histidine protein kinase and catalyzes phosphorylation of PhoB and PhoM-open reading frame 2." J Bacteriol 1990;172(11);6300-7. PMID: 2228961

ArribasBosacoma07: Arribas-Bosacoma R, Kim SK, Ferrer-Orta C, Blanco AG, Pereira PJ, Gomis-Ruth FX, Wanner BL, Coll M, Sola M (2007). "The X-ray crystal structures of two constitutively active mutants of the Escherichia coli PhoB receiver domain give insights into activation." J Mol Biol 366(2);626-41. PMID: 17182055

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

Bachhawat05: Bachhawat P, Swapna GV, Montelione GT, Stock AM (2005). "Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states." Structure 13(9);1353-63. PMID: 16154092

Baek06: Baek JH, Lee SY (2006). "Novel gene members in the Pho regulon of Escherichia coli." FEMS Microbiol Lett 264(1);104-9. PMID: 17020555

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

Blanco02: Blanco AG, Sola M, Gomis-Ruth FX, Coll M (2002). "Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator." Structure 10(5);701-13. PMID: 12015152

CreagerAllen13: Creager-Allen RL, Silversmith RE, Bourret RB (2013). "A link between dimerization and autophosphorylation of the response regulator PhoB." J Biol Chem 288(30);21755-69. PMID: 23760278

Crepin11: Crepin S, Chekabab SM, Le Bihan G, Bertrand N, Dozois CM, Harel J (2011). "The Pho regulon and the pathogenesis of Escherichia coli." Vet Microbiol 153(1-2);82-8. PMID: 21700403

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

Ellison00: Ellison DW, McCleary WR (2000). "The unphosphorylated receiver domain of PhoB silences the activity of its output domain." J Bacteriol 182(23);6592-7. PMID: 11073900

Gao08: Gao R, Tao Y, Stock AM (2008). "System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids." Mol Microbiol 69(6);1358-72. PMID: 18631241

Gao13: Gao R, Stock AM (2013). "Evolutionary tuning of protein expression levels of a positively autoregulated two-component system." PLoS Genet 9(10);e1003927. PMID: 24204322

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."

Heyde83: Heyde M, Portalier R (1983). "Isolation and characterization of a new type of Escherichia coli K12 phoB mutants." Mol Gen Genet 190(1);122-7. PMID: 6343798

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

Kim00: Kim SK, Kimura S, Shinagawa H, Nakata A, Lee KS, Wanner BL, Makino K (2000). "Dual transcriptional regulation of the Escherichia coli phosphate-starvation-inducible psiE gene of the phosphate regulon by PhoB and the cyclic AMP (cAMP)-cAMP receptor protein complex." J Bacteriol 2000;182(19);5596-9. PMID: 10986267

Kimura89: Kimura S, Makino K, Shinagawa H, Amemura M, Nakata A (1989). "Regulation of the phosphate regulon of Escherichia coli: characterization of the promoter of the pstS gene." Mol Gen Genet 1989;215(3);374-80. PMID: 2651888

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

Makino88: Makino K, Shinagawa H, Amemura M, Kimura S, Nakata A, Ishihama A (1988). "Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro." J Mol Biol 1988;203(1);85-95. PMID: 3054125

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

Makino93: Makino K, Amemura M, Kim SK, Nakata A, Shinagawa H (1993). "Role of the sigma 70 subunit of RNA polymerase in transcriptional activation by activator protein PhoB in Escherichia coli." Genes Dev 7(1);149-60. PMID: 8422984

Makino96: Makino K, Amemura M, Kawamoto T, Kimura S, Shinagawa H, Nakata A, Suzuki M (1996). "DNA binding of PhoB and its interaction with RNA polymerase." J Mol Biol 259(1);15-26. PMID: 8648643

MartinezHackert97: Martinez-Hackert E, Stock AM (1997). "Structural relationships in the OmpR family of winged-helix transcription factors." J Mol Biol 269(3);301-12. PMID: 9199401

MartinezHackert97a: Martinez-Hackert E, Stock AM (1997). "The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor." Structure 5(1);109-24. PMID: 9016718

Pao95: Pao GM, Saier MH (1995). "Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution." J Mol Evol 1995;40(2);136-54. PMID: 7699720

Parkinson92: Parkinson JS, Kofoid EC (1992). "Communication modules in bacterial signaling proteins." Annu Rev Genet 1992;26;71-112. PMID: 1482126

Parkinson93: Parkinson JS (1993). "Signal transduction schemes of bacteria." Cell 1993;73(5);857-71. PMID: 8098993

Pratt77: Pratt C, Torriani A (1977). "Complementation test between alkaline phosphatase regulatory mutations phoB and phoRc in Escherichia coli." Genetics 85(2);203-8. PMID: 324866

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Saier94a: Saier MH (1994). "Bacterial sensor kinase/response regulator systems: an introduction." Res Microbiol 1994;145(5-6);349-55. PMID: 7855419

Shinagawa83: Shinagawa H, Makino K, Nakata A (1983). "Regulation of the pho regulon in Escherichia coli K-12. Genetic and physiological regulation of the positive regulatory gene phoB." J Mol Biol 168(3);477-88. PMID: 6310121

Smith92: Smith MW, Payne JW (1992). "Expression of periplasmic binding proteins for peptide transport is subject to negative regulation by phosphate limitation in Escherichia coli." FEMS Microbiol Lett 79(1-3);183-90. PMID: 1478454

Sola99: Sola M, Gomis-Ruth FX, Serrano L, Gonzalez A, Coll M (1999). "Three-dimensional crystal structure of the transcription factor PhoB receiver domain." J Mol Biol 285(2);675-87. PMID: 9878437

Stock90: Stock JB, Stock AM, Mottonen JM (1990). "Signal transduction in bacteria." Nature 1990;344(6265);395-400. PMID: 2157156

Tung12: Tung CS, McMahon BH (2012). "A structural model of the E. coli PhoB dimer in the transcription initiation complex." BMC Struct Biol 12;3. PMID: 22433509

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

VanBogelen96: VanBogelen RA, Olson ER, Wanner BL, Neidhardt FC (1996). "Global analysis of proteins synthesized during phosphorus restriction in Escherichia coli." J Bacteriol 178(15);4344-66. PMID: 8755861

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

Wanner92: Wanner BL, Wilmes-Riesenberg MR (1992). "Involvement of phosphotransacetylase, acetate kinase, and acetyl phosphate synthesis in control of the phosphate regulon in Escherichia coli." J Bacteriol 174(7);2124-30. PMID: 1551836

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

Wanner96: Wanner BL (1996). "Signal transduction in the control of phosphate-regulated genes of Escherichia coli." Kidney Int 49(4);964-7. PMID: 8691745

Zuckier80: Zuckier G, Ingenito E, Torriani A (1980). "Pleiotropic effects of alkaline phosphatase regulatory mutations phoB and phoT on anaerobic growth of and polyphosphate synthesis in Escherichia coli." J Bacteriol 143(2);934-41. PMID: 7009567

Other References Related to Gene Regulation

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

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 Sun Mar 1, 2015, biocyc13.