Escherichia coli K-12 substr. MG1655 Polypeptide: predicted lipoprotein

Gene: yceK Accession Numbers: EG12689 (EcoCyc), b1050, ECK1036

Regulation Summary Diagram: ?

Regulation summary diagram for yceK

Strong aggravating interactions (measured by relative colony size and fitness in rich medium) were observed between lptD and yceK [Babu11]. Deletion of yceK results in impaired outer membrane integrity as evidenced by vancomycin induced morphological defects and lowered outer membrane protein (OMP) abundance [Babu11]. Deletion of yceK and lptD results in cell wall failure/lysis, lowered OMP abundance and increased levels of the DegP stress response protease [Babu11].

Overexpression of yceK suppresses the essentiality of lapB which encodes a protein involved in lipopolysaccharide (LPS) assembly. The defects in LPS composition that occur due to deletion of lapA lapB are exacerbated in a Δ(lapA lapB yceK) [Klein14].

yceK contains a predicted lipoprotein signal [Juncker03, Gonnet04].

Locations: outer membrane

Map Position: [1,112,802 -> 1,113,029] (23.98 centisomes, 86°)
Length: 228 bp / 75 aa

Molecular Weight of Polypeptide: 8.443 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003565 , EchoBASE:EB2552 , EcoGene:EG12689 , EcoliWiki:b1050 , OU-Microarray:b1050 , PortEco:yceK , Protein Model Portal:P0AB31 , RefSeq:NP_415568 , RegulonDB:EG12689 , String:511145.b1050 , UniProt:P0AB31

Relationship Links: InterPro:IN-FAMILY:IPR010780 , Pfam:IN-FAMILY:PF07119

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
Cellular Component: GO:0031246 - intrinsic component of periplasmic side of cell outer membrane Inferred from experiment [Babu11]

Gene Class: ORFs

Essentiality data for yceK 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

Protein sequence of predicted lipoprotein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 21
UniProt: Non-Experimental Qualifier: potential;
Chain 22 -> 75
UniProt: Uncharacterized protein yceK;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b1050 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12689; 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

Babu11: Babu M, Diaz-Mejia JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, Emili A (2011). "Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways." PLoS Genet 7(11);e1002377. PMID: 22125496

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

Gonnet04: Gonnet P, Rudd KE, Lisacek F (2004). "Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins of Escherichia coli K-12." Proteomics 4(6);1597-613. PMID: 15174130

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

Juncker03: Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A (2003). "Prediction of lipoprotein signal peptides in Gram-negative bacteria." Protein Sci 12(8);1652-62. PMID: 12876315

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

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

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

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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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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