Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

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



Gene: baeR Accession Numbers: EG11618 (EcoCyc), b2079, ECK2075

Synonyms: BaeR response regulator

Regulation Summary Diagram: ?

Alternative forms of BaeR transcriptional regulator: BaeR-Phosphorylated DNA-binding transcriptional activator (extended summary available)

Summary:
An integrated transcriptomic study of the extracytoplasmic stress response, which detects and responds to alterations of the bacterial envelope, was performed by Bury-Moré et al. (2009). They investigated the interconnections and dynamics between Bae, Cpx, Psp, Rcs, and σE pathways and showed that these pathways can be activated simultaneously in response to exogenous or endogenous stimulation, while natural environmental stimuli provoke bacterial modifications that lead to multiple pathway responses [BuryMone09].

Each of these responses might be specialized to ensure a specific aspect of envelope biogenesis and maintenance; on the other hand, CpxR could have a role as a modulator of the response by integrating other endogenous signals. Bury-Moré et al. concluded that all five pathways are needed to mount a full response to extracytoplasmic stress [BuryMone09].

Citations: [Pao95, Parkinson92, Stock90, Parkinson93]

Gene Citations: [Nagakubo02, Nagasawa93]

Locations: cytosol

Map Position: [2,162,300 -> 2,163,022] (46.6 centisomes)
Length: 723 bp / 240 aa

Molecular Weight of Polypeptide: 27.656 kD (from nucleotide sequence)

pI: 5.8

Unification Links: ASAP:ABE-0006884 , CGSC:30764 , EchoBASE:EB1575 , EcoGene:EG11618 , EcoliWiki:b2079 , ModBase:P69228 , OU-Microarray:b2079 , PortEco:baeR , PR:PRO_000022196 , Pride:P69228 , Protein Model Portal:P69228 , RegulonDB:EG11618 , SMR:P69228 , String:511145.b2079 , Swiss-Model:P69228 , UniProt:P69228

Relationship Links: InterPro:IN-FAMILY:IPR001789 , InterPro:IN-FAMILY:IPR001867 , InterPro:IN-FAMILY:IPR011006 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR016032 , PDB:Structure:4B09 , 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:

BaeSR Two-Component Signal Transduction System :
BaeR + BaeS sensory histidine kinase - phosphorylated[inner membrane] → BaeR-Pasp61 + BaeS[inner membrane]

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:2000144 - positive regulation of DNA-templated transcription, initiation Inferred from experiment [Baranova02]
GO:2001023 - regulation of response to drug Inferred from experiment [Baranova02]
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]
Molecular Function: GO:0000986 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding Inferred from experiment [Baranova02]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Gao08]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Transcription Units regulated by related protein BaeR-Phosphorylated DNA-binding transcriptional activator (4 total):

Essentiality data for baeR 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 12 -> 125
[UniProt09]
UniProt: Response regulatory;
 
4-aspartylphosphate-Modification 61
[UniProt11a]
UniProt: 4-aspartylphosphate; Non-Experimental Qualifier: by similarity.
Unmodified
4-aspartylphosphate-Modification 61
[UniProt11a]
UniProt: 4-aspartylphosphate; Non-Experimental Qualifier: by similarity.
 


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2079 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11618; 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

Baranova02: Baranova N, Nikaido H (2002). "The baeSR two-component regulatory system activates transcription of the yegMNOB (mdtABCD) transporter gene cluster in Escherichia coli and increases its resistance to novobiocin and deoxycholate." J Bacteriol 184(15);4168-76. PMID: 12107134

BuryMone09: Bury-Mone S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P (2009). "Global analysis of extracytoplasmic stress signaling in Escherichia coli." PLoS Genet 5(9);e1000651. PMID: 19763168

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

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

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."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Nagakubo02: Nagakubo S, Nishino K, Hirata T, Yamaguchi A (2002). "The putative response regulator BaeR stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, MdtABC." J Bacteriol 184(15);4161-7. PMID: 12107133

Nagasawa93: Nagasawa S, Ishige K, Mizuno T (1993). "Novel members of the two-component signal transduction genes in Escherichia coli." J Biochem (Tokyo) 1993;114(3);350-7. PMID: 8282725

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

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

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

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."

Other References Related to Gene Regulation

GamaCastro08: Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J (2008). "RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation." Nucleic Acids Res 36(Database issue);D120-4. PMID: 18158297

Hirakawa05: Hirakawa H, Inazumi Y, Masaki T, Hirata T, Yamaguchi A (2005). "Indole induces the expression of multidrug exporter genes in Escherichia coli." Mol Microbiol 55(4);1113-26. PMID: 15686558

Nishino05: Nishino K, Honda T, Yamaguchi A (2005). "Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system." J Bacteriol 187(5);1763-72. PMID: 15716448


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 Tue Nov 25, 2014, biocyc13.