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Escherichia coli K-12 substr. MG1655 Polypeptide: Outer Membrane Protein Assembly Complex - BamE subunit



Gene: bamE Accession Numbers: EG10952 (EcoCyc), b2617, ECK2613

Synonyms: smpA, smqA, small membrane protein A

Regulation Summary Diagram: ?

Component of: Outer Membrane Protein Assembly Complex (extended summary available)

Summary:
Sequence analysis indicates that BamE is a lipoprotein in the outer membrane of Escherichia coli [Brokx04]. Affinity purification experiments have shown BamE copurifies with BamA, BamD, BamB, and BamC. These experiments also show BamE interacts with BamD, BamC, and BamA independently of BamB [Sklar07].

Deletion of bamE results in increased sensitivity to rifampin, cholate, and SDS/EDTA. Deletion of bamE results in reduced levels of the outer membrane proteins (OMPs) LamB and OmpA and an elevated level of DegP suggesting the presence of misfolded OMPs. Large quantities of unfolded LamB monomer accumulate in bamE degP double mutants [Sklar07]. bamE single deletion mutants show only slight defects in OMP assembly and membrane permeability [Rigel12a].

Genetic analysis and biochemical studies suggest that BamE has a function in stabilising the interaction between the BamA and BamD proteins [Sklar07, Rigel12a]. Deletion of BamE results in increased protease sensitivity of BamA [Rigel12a].

Purified BamE exists in both monomeric and dimeric forms which adopt different structures [Kim11]. Whole cell purification of overexpressed BamE yields a mixture of monomeric and dimeric BamE; when expressed in the periplasm, purified BamE is monomeric [Knowles11]. Purified monomeric BamE consists of two N-terminal α-helices and a C-terminal β-sheet containing 3 β-strands [Kim11, Knowles11].

bamE is a member of the σE regulon [Rezuchova03]. bamE expression is upregulated by the presence of autoinducer 2 [DeLisa01].

Comment: [Endo11]

Citations: [Miczak91, Wei01, Sabina03]

Locations: outer membrane

Map Position: [2,751,627 -> 2,751,968] (59.31 centisomes)
Length: 342 bp / 113 aa

Molecular Weight of Polypeptide: 12.302 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008614 , EchoBASE:EB0945 , EcoGene:EG10952 , EcoliWiki:b2617 , Mint:MINT-8141263 , OU-Microarray:b2617 , PortEco:smpA , Pride:P0A937 , Protein Model Portal:P0A937 , RefSeq:NP_417107 , RegulonDB:EG10952 , SMR:P0A937 , String:511145.b2617 , UniProt:P0A937

Relationship Links: InterPro:IN-FAMILY:IPR007450 , InterPro:IN-FAMILY:IPR026592 , PDB:Structure:2KM7 , PDB:Structure:2KXX , PDB:Structure:2YH9 , Pfam:IN-FAMILY:PF04355 , Prosite:IN-FAMILY:PS51257

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0043165 - Gram-negative-bacterium-type cell outer membrane assembly Inferred from experiment Inferred by computational analysis [GOA06, Sklar07, Hagan10]
GO:0046677 - response to antibiotic Inferred from experiment [Sklar07]
GO:0051205 - protein insertion into membrane Inferred from experiment Inferred by computational analysis [GOA06, Sklar07, Hagan10]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Sklar07]
GO:0030674 - protein binding, bridging Inferred from experiment [Sklar07]
GO:0042802 - identical protein binding Inferred from experiment [Knowles11, Albrecht11]
Cellular Component: GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Sklar07]
GO:0045203 - integral component of cell outer membrane Inferred from experiment [Sklar07]
GO:1990063 - Bam protein complex Inferred from experiment [Sklar07]
GO:0009279 - cell outer membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0019867 - outer membrane Inferred by computational analysis [GOA01a]

MultiFun Terms: cell structure membrane

Essentiality data for bamE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Credits:
Curated 17-Oct-2007 by Johnson A , JCVI
Last-Curated ? 14-Apr-2014 by Mackie A , Macquarie University


Subunit of: Outer Membrane Protein Assembly Complex

Subunit composition of Outer Membrane Protein Assembly Complex = [BamE][BamC][BamD][BamA][BamB]
         Outer Membrane Protein Assembly Complex - BamE subunit = BamE (extended summary available)
         Outer Membrane Protein Assembly Complex - BamC subunit = BamC (extended summary available)
         Outer Membrane Protein Assembly Complex - BamD subunit = BamD (extended summary available)
         Outer Membrane Protein Assembly Complex - BamA subunit = BamA (extended summary available)
         Outer Membrane Protein Assembly Complex - BamB subunit = BamB (extended summary available)

Summary:
BamABCDE is an outer membrane, multi-protein complex that is responsible for the assembly and insertion of β-barrel proteins into the outer membrane of E. coli. Following their synthesis in the cytoplasm, unfolded outer membrane proteins (OMPS) are translocated across the inner membrane by the SecYEG translocase and delivered to the Bam complex which folds and inserts β-barrels into the outer membrane. The periplasmic chaperones SurA, Skp and DegP prevent misfolding and aggregation of the OMPS as they cross the periplasm.

BamA is an OMP; BamB, BamC, BamD and BamE are outer membrane lipoproteins. BamA and BamD are essential and depletion of either results in severe outer membrane defects. BamB, BamC and BamE are non-essential and cells lacking these lipoproteins exhibit only minor outer membrane defects [Wu05, Stenberg05, Sklar07]. The relative stoichiometry of the Bam proteins (ABC and D) is believed to be 1:1:1:1 [Hagan10]. Membranes from wild-type cells solubilised in dodecylmaltoside contain the BamABCDE complex plus a BamAB complex or 'module' and a BamCD module [Webb12].

The Bam complex has been reconstituted in vitro from purified components. In the presence of a soluble chaperone (SurA) the reconstituted Bam complex is able to assemble the substrate protein OmpT in proteliposomes without an input of energy [Hagan10].

Reviews: [Schleiff05, Knowles09, Hagan11, Kim12, Rigel12, Ricci12]
Comment: [Stroud10]

Locations: outer membrane

GO Terms:

Biological Process: GO:0043165 - Gram-negative-bacterium-type cell outer membrane assembly Inferred from experiment [Hagan10]
GO:0051205 - protein insertion into membrane Inferred from experiment [Hagan10]
Cellular Component: GO:1990063 - Bam protein complex Inferred from experiment [Stenberg05, Wu05]

Credits:
Last-Curated ? 09-Apr-2014 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 19  
[UniProt10]
UniProt: Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 20 C20G
[Knowles11]
C → G; functionally critical mutation (results in increased sensitivity to vancomycin)
Lipid-Binding-Site 20  
[UniProt10]
UniProt: N-palmitoyl cysteine; Non-Experimental Qualifier: probable;
Chain 20 -> 113  
[UniProt09]
UniProt: Small protein A;
Mutagenesis-Variant 32 I32G
[Knowles11]
I → G; functionally critical mutation (results in increased sensitivity to vancomycin)
Mutagenesis-Variant 34 Q34G/C
[Knowles11]
Q → G or C; functionally critical mutation (results in increased sensitivity to vancomycin)
Mutagenesis-Variant 35 G35C
[Knowles11]
G → C; functionally critical mutation 9results in increased sensitivity to vancomycin)
Mutagenesis-Variant 36 N36G/C
[Knowles11]
N → G or C; functionally critical mutation (results in increased sensitvity to vancomycin)
Mutagenesis-Variant 37 Y37G
[Knowles11]
Y → G; functionally critical mutation (results in increased sensitivity to vancomycin)
Mutagenesis-Variant 38 L38G
[Knowles11]
L → G; functionally critical mutation (results in increased sensitivity to vancomycin)
Alpha-Helix-Region 40 -> 43 α 1
[Kim11]
 
Mutagenesis-Variant 46 I46G
[Knowles11]
I → G; structurally critical mutation (results in diminished levels of BamB)
Alpha-Helix-Region 52 -> 58 α 2
[Kim11]
 
Mutagenesis-Variant 55 V55G
[Knowles11]
V → G; structurally critical mutation (results in diminished levels of BamE)
Mutagenesis-Variant 59 L59G
[Knowles11]
L → G; structurally critical mutation (results in diminished levels of BamE)
Mutagenesis-Variant 64 M64G/C
[Knowles11]
M → G or C; functionally critical mutation (results in increased sensitivity to vancomycin)
Mutagenesis-Variant 66 D66G
[Knowles11]
D → G; functionally critical mutation (results in increased sensitivity to vancomycin)
Mutagenesis-Variant 68 F68G/C
[Knowles11]
F → G or C; functionally critical mutation (results in increased sensitivity to vancomycin)
Beta-Strand-Region 72 -> 75 β 1
[Kim11]
 
Mutagenesis-Variant 73 W73G
[Knowles11]
W → G; functionally critical mutation (results in increased sensitivity to vancomycin)
Mutagenesis-Variant 74 F74G
[Knowles11]
F → G; mutation abolishes phosphatidylglycerol binding and results in increased sensitivity to vancomycin
Mutagenesis-Variant 75 Y75G/C
[Knowles11]
Y → G or C; structurally critical mutation (results in diminished levels of BamE)
Mutagenesis-Variant 76 V76G
[Knowles11]
V → G; functionally critical mutation (results in increased sensitivity to vancomycin)
Mutagenesis-Variant 78 R78G
[Knowles11]
R → G; functionally critical mutation (results in increased sensitivity to vancomycin)
Mutagenesis-Variant 88 Q88C
[Knowles11]
Q → C; functionally critical mutation (results in increased sensitivity to vancomycin)
Beta-Strand-Region 90 -> 95 β 2
[Kim11]
 
Mutagenesis-Variant 91 L91G
[Knowles11]
L → G; structurally critical mutation ( results in diminished levels of BamE)
Mutagenesis-Variant 93 L93G
[Knowles11]
L → G; structurally critical mutation (results in dimished levels of BamE)
Mutagenesis-Variant 95 F95C/G
[Knowles11]
F → C or G; structurally critical mutation (results in dimished levels of BamE)
Mutagenesis-Variant 101 L101G
[Knowles11]
L → G; structurally critical mutation (results in dimished levels of BamE)
Beta-Strand-Region 101 -> 107 β 3
[Kim11]
 


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b2617 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10952; confirmed by SwissProt match.


References

Albrecht11: Albrecht R, Zeth K (2011). "Structural basis of outer membrane protein biogenesis in bacteria." J Biol Chem 286(31);27792-803. PMID: 21586578

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

Brokx04: Brokx SJ, Ellison M, Locke T, Bottorff D, Frost L, Weiner JH (2004). "Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655." J Bacteriol 186(10);3254-8. PMID: 15126489

DeLisa01: DeLisa MP, Wu CF, Wang L, Valdes JJ, Bentley WE (2001). "DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli." J Bacteriol 183(18);5239-47. PMID: 11514505

Endo11: Endo T, Kawano S, Yamano K (2011). "BamE structure: the assembly of β-barrel proteins in the outer membranes of bacteria and mitochondria." EMBO Rep 12(2);94-5. PMID: 21252940

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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hagan10: Hagan CL, Kim S, Kahne D (2010). "Reconstitution of outer membrane protein assembly from purified components." Science 328(5980);890-2. PMID: 20378773

Hagan11: Hagan CL, Silhavy TJ, Kahne D (2011). "β-Barrel membrane protein assembly by the Bam complex." Annu Rev Biochem 80;189-210. PMID: 21370981

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

Kim11: Kim KH, Kang HS, Okon M, Escobar-Cabrera E, McIntosh LP, Paetzel M (2011). "Structural characterization of Escherichia coli BamE, a lipoprotein component of the β-barrel assembly machinery complex." Biochemistry 50(6);1081-90. PMID: 21207987

Kim12: Kim KH, Aulakh S, Paetzel M (2012). "The bacterial outer membrane β-barrel assembly machinery." Protein Sci 21(6);751-68. PMID: 22549918

Knowles09: Knowles TJ, Scott-Tucker A, Overduin M, Henderson IR (2009). "Membrane protein architects: the role of the BAM complex in outer membrane protein assembly." Nat Rev Microbiol 7(3);206-14. PMID: 19182809

Knowles11: Knowles TJ, Browning DF, Jeeves M, Maderbocus R, Rajesh S, Sridhar P, Manoli E, Emery D, Sommer U, Spencer A, Leyton DL, Squire D, Chaudhuri RR, Viant MR, Cunningham AF, Henderson IR, Overduin M (2011). "Structure and function of BamE within the outer membrane and the β-barrel assembly machine." EMBO Rep 12(2);123-8. PMID: 21212804

Miczak91: Miczak A, Chauhan AK, Apirion D (1991). "Two new genes located between 2758 and 2761 kilobase pairs on the Escherichia coli genome." J Bacteriol 173(11);3271-2. PMID: 2045357

Rezuchova03: Rezuchova B, Miticka H, Homerova D, Roberts M, Kormanec J (2003). "New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system." FEMS Microbiol Lett 225(1);1-7. PMID: 12900013

Ricci12: Ricci DP, Silhavy TJ (2012). "The Bam machine: a molecular cooper." Biochim Biophys Acta 1818(4);1067-84. PMID: 21893027

Rigel12: Rigel NW, Silhavy TJ (2012). "Making a beta-barrel: assembly of outer membrane proteins in Gram-negative bacteria." Curr Opin Microbiol 15(2);189-93. PMID: 22221898

Rigel12a: Rigel NW, Schwalm J, Ricci DP, Silhavy TJ (2012). "BamE modulates the Escherichia coli beta-barrel assembly machine component BamA." J Bacteriol 194(5);1002-8. PMID: 22178970

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Sabina03: Sabina J, Dover N, Templeton LJ, Smulski DR, Soll D, LaRossa RA (2003). "Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12." J Bacteriol 185(20);6158-70. PMID: 14526028

Schleiff05: Schleiff E, Soll J (2005). "Membrane protein insertion: mixing eukaryotic and prokaryotic concepts." EMBO Rep 6(11);1023-7. PMID: 16264426

Sklar07: Sklar JG, Wu T, Gronenberg LS, Malinverni JC, Kahne D, Silhavy TJ (2007). "Lipoprotein SmpA is a component of the YaeT complex that assembles outer membrane proteins in Escherichia coli." Proc Natl Acad Sci U S A 104(15);6400-5. PMID: 17404237

Stenberg05: Stenberg F, Chovanec P, Maslen SL, Robinson CV, Ilag LL, von Heijne G, Daley DO (2005). "Protein complexes of the Escherichia coli cell envelope." J Biol Chem 280(41);34409-19. PMID: 16079137

Stroud10: Stroud DA, Meisinger C, Pfanner N, Wiedemann N (2010). "Biochemistry. Assembling the outer membrane." Science 328(5980);831-2. PMID: 20466908

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.

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."

Webb12: Webb CT, Selkrig J, Perry AJ, Noinaj N, Buchanan SK, Lithgow T (2012). "Dynamic association of BAM complex modules includes surface exposure of the lipoprotein BamC." J Mol Biol 422(4);545-55. PMID: 22683355

Wei01: Wei Y, Lee JM, Richmond C, Blattner FR, Rafalski JA, LaRossa RA (2001). "High-density microarray-mediated gene expression profiling of Escherichia coli." J Bacteriol 183(2);545-56. PMID: 11133948

Wu05: Wu T, Malinverni J, Ruiz N, Kim S, Silhavy TJ, Kahne D (2005). "Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli." Cell 121(2);235-45. PMID: 15851030

Other References Related to Gene Regulation

De02: De Wulf P, McGuire AM, Liu X, Lin EC (2002). "Genome-wide profiling of promoter recognition by the two-component response regulator CpxR-P in Escherichia coli." J Biol Chem 277(29);26652-61. PMID: 11953442

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047


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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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