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Escherichia coli K-12 substr. MG1655 Polypeptide: lipopolysaccharide assembly protein LapB



Gene: lapB Accession Numbers: EG12691 (EcoCyc), b1280, ECK1275

Synonyms: yciM

Regulation Summary Diagram: ?

Regulation summary diagram for lapB

Summary:
Biochemical and genetic analyses suggest that the LapB inner membrane protein functions in the coupling of lipopolysaccharide (LPS) biosynthesis and transport.

lapB (formerly yciM) is essential for growth under standard laboratory conditions. Absence of lapB results in increased LPS production and cell death. Overexpression of lapB results in decreased LPS levels [Mahalakshmi14]. The viability of the lapB mutant from the Keio collection is due to the presence of a suppressor mutation in lpxC [Mahalakshmi14].

Suppressor free ΔlapB mutants can be constructed on minimal medium at 30°C. LPS extracted from these mutants contains increased amounts of precursor forms and various defects in α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A structure: carbon chain length polymorphism, pentaacylation and derivatives with two lauroyl side chains [Klein14]. ΔlapB mutants also have increased levels of LpxC [Klein14].

Mutations in lpxA, lpxC and lpxD which result in decreased lipid IVA synthesis, suppress the essentiality of lapB [Mahalakshmi14]. Extragenic suppressors of lapB essentiality map to genes involved in Lipid A core biosynthesis (waaC, waaQ, waaG) and heptose biosynthesis (lpcA); multicopy suppressors of lapB essentiality include fabZ, fabB (phospholipid and fatty acid biosynthesis), murA (peptidoglycan synthesis), rcsF, hicA, a new small RNA (slrA) and genes of unknown function (yceK, yeaD, nudK, mliC) [Klein14]. A null mutation in lpp which encodes murein lipoprotein, suppresses the essentiality of lapB [Klein14].

LapB is anchored to the cytoplasmic membrane by it's N-terminus with the remainder of the protein located in the cytoplasm. The membrane anchor is essential for LapB function.LapB contains an iron-sulfur center (rubredoxin type) coordinated by 4 cysteine residues located at the C-terminus of the protein. LapB binds zinc in a 1:1 stoichiometry in vitro but is predicted to bind iron in vivo [Nicolaes14]. LapB contains six tetratricopeptide (TPR) repeats and a C-terminal Zinc-finger domain [Mahalakshmi14].

LapB copurifies with LapA, FtsH and WaaC and with the LPS transport system proteins (LptE/D, LptBFGC, LptA). Purified LapB contains LPS [Klein14].

lapAB transcription is subject to heat shock induction via an RpoH-regulated promoter located upstream of lapA [Klein14]. LapB is a post-transcriptional regulator of LpxC - this regulation is dependent on the presence of the FtsH protease [Mahalakshmi14].

lapB: lipopolysaccharide assembly protein B

Citations: [ParadisBleau14]

Gene Citations: [Nonaka06]

Locations: inner membrane, cytosol

Map Position: [1,338,582 -> 1,339,751] (28.85 centisomes, 104°)
Length: 1170 bp / 389 aa

Molecular Weight of Polypeptide: 44.531 kD (from nucleotide sequence), 55.0 kD (experimental) [Nicolaes14 ]

Unification Links: ASAP:ABE-0004300 , DIP:DIP-48161N , EchoBASE:EB2554 , EcoGene:EG12691 , EcoliWiki:b1280 , ModBase:P0AB58 , OU-Microarray:b1280 , PortEco:yciM , Protein Model Portal:P0AB58 , RefSeq:NP_415796 , RegulonDB:EG12691 , SMR:P0AB58 , String:511145.b1280 , UniProt:P0AB58

Relationship Links: InterPro:IN-FAMILY:IPR011990 , InterPro:IN-FAMILY:IPR013026 , InterPro:IN-FAMILY:IPR013105 , InterPro:IN-FAMILY:IPR019734 , Pfam:IN-FAMILY:PF07719 , Pfam:IN-FAMILY:PF13176 , Prosite:IN-FAMILY:PS50005 , Prosite:IN-FAMILY:PS50293 , Smart:IN-FAMILY:SM00028

GO Terms:

Biological Process: GO:0008653 - lipopolysaccharide metabolic process Inferred from experiment Inferred by computational analysis [GOA01, Klein14, Mahalakshmi14]
GO:0046890 - regulation of lipid biosynthetic process Inferred by computational analysis [GOA06]
Molecular Function: GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Nicolaes14]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Zhang07]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Nicolaes14]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]
GO:0031235 - intrinsic component of the cytoplasmic side of the plasma membrane Inferred by computational analysis [GOA06]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents) lipopolysaccharide

Essentiality data for lapB 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 Indeterminate 37 Aerobic 7   No [Mahalakshmi14]
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:
Last-Curated ? 18-May-2014 by Mackie A , Macquarie University


Sequence Features

Protein sequence of lipopolysaccharide assembly protein LapB with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 1 -> 20
[UniProt15]
UniProt: Helical.
Repeat 35 -> 68
[UniProt14a]
UniProt: TPR 1.
Repeat 69 -> 102
[UniProt09]
UniProt: TPR 1;
Repeat 107 -> 140
[UniProt09]
UniProt: TPR 2;
Repeat 142 -> 174
[UniProt14a]
UniProt: TPR 4.
Repeat 180 -> 213
[UniProt09]
UniProt: TPR 4;
Mutagenesis-Variant 184
[Nicolaes14, UniProt14a]
UniProt: Does not affect metal binding; when associated with S-258.
Repeat 214 -> 247
[UniProt09]
UniProt: TPR 5;
Repeat 249 -> 282
[UniProt09]
UniProt: TPR 6;
Mutagenesis-Variant 258
[Nicolaes14, UniProt14a]
UniProt: Does not affect metal binding; when associated with S-184.
Metal-Binding-Site 357
[UniProt15]
UniProt: Iron.
Mutagenesis-Variant 357
[Nicolaes14, UniProt14a]
UniProt: Lack of activity; when associated with S-360; S-371 and S-374.
Metal-Binding-Site 360
[UniProt15]
UniProt: Iron.
Mutagenesis-Variant 360
[Nicolaes14, UniProt14a]
UniProt: Lack of activity; when associated with S-357; S-371 and S-374.
Metal-Binding-Site 371
[UniProt15]
UniProt: Iron.
Mutagenesis-Variant 371
[Nicolaes14, UniProt14a]
UniProt: Lack of activity; when associated with S-357; S-360 and S-374.
Metal-Binding-Site 374
[UniProt15]
UniProt: Iron.
Mutagenesis-Variant 374
[Nicolaes14, UniProt14a]
UniProt: Lack of activity; when associated with S-357; S-360 and S-371.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b1280 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12691; 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

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

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."

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

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

Klein14: Klein G, Kobylak N, Lindner B, Stupak A, Raina S (2014). "Assembly of lipopolysaccharide in Escherichia coli requires the essential LapB heat shock protein." J Biol Chem 289(21);14829-53. PMID: 24722986

Mahalakshmi14: Mahalakshmi S, Sunayana MR, SaiSree L, Reddy M (2014). "yciM is an essential gene required for regulation of lipopolysaccharide synthesis in Escherichia coli." Mol Microbiol 91(1);145-57. PMID: 24266962

Nicolaes14: Nicolaes V, El Hajjaji H, Davis RM, Van der Henst C, Depuydt M, Leverrier P, Aertsen A, Haufroid V, Ollagnier de Choudens S, De Bolle X, Ruiz N, Collet JF (2014). "Insights into the function of YciM, a heat shock membrane protein required to maintain envelope integrity in Escherichia coli." J Bacteriol 196(2);300-9. PMID: 24187084

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

ParadisBleau14: Paradis-Bleau C, Kritikos G, Orlova K, Typas A, Bernhardt TG (2014). "A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism." PLoS Genet 10(1);e1004056. PMID: 24391520

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

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

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

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065


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 19.0 on Fri Aug 28, 2015, biocyc14.