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

Gene: yjbF Accession Numbers: EG11924 (EcoCyc), b4027, ECK4019

Regulation Summary Diagram: ?

Regulation summary diagram for yjbF

Sequence similarity suggests that YjbF may be a lipoprotein and/or an outer membrane porin [Zhai02].

Overexpression of yjbEFGH alters colony morphology and leads to increased binding of toluidine blue-O and Congo red, indicating increased production of an EPS that is distinct from colanic acid [Ferrieres07].

Expression of yjbF is positively regulated by RcsC [Ferrieres03]. Disruption of yjbE has a polar effect on expression of yjbFGH, indicating that these genes form an operon; however, a full-length mRNA could not be detected, possibly due to strong secondary structure in the yjbE-yjbF intergenic region [Ferrieres07].

Locations: outer membrane, periplasmic space, inner membrane

Map Position: [4,234,285 -> 4,234,923] (91.26 centisomes, 329°)
Length: 639 bp / 212 aa

Molecular Weight of Polypeptide: 23.755 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013172 , EchoBASE:EB1868 , EcoGene:EG11924 , EcoliWiki:b4027 , OU-Microarray:b4027 , PortEco:yjbF , Protein Model Portal:P32687 , RefSeq:NP_418451 , RegulonDB:EG11924 , SMR:P32687 , String:511145.b4027 , UniProt:P32687

Relationship Links: InterPro:IN-FAMILY:IPR021308 , InterPro:IN-FAMILY:IPR023373 , Pfam:IN-FAMILY:PF11102 , Prosite:IN-FAMILY:PS51257

In Paralogous Gene Group: 565 (2 members)

Genetic Regulation Schematic: ?

Genetic regulation schematic for yjbF

GO Terms:

Biological Process: GO:0045226 - extracellular polysaccharide biosynthetic process Inferred from experiment [Ferrieres07]
Cellular Component: GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09]
GO:0045203 - integral component of cell outer membrane Inferred by computational analysis [Ferrieres07]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents)

Essentiality data for yjbF 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]

Last-Curated ? 30-Mar-2007 by Keseler I , SRI International

Sequence Features

Protein sequence of predicted lipoprotein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 15
UniProt: Non-Experimental Qualifier: potential;
Lipid-Binding-Site 16
UniProt: N-palmitoyl cysteine; Non-Experimental Qualifier: potential;
Chain 16 -> 212
UniProt: Uncharacterized lipoprotein yjbF;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


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 b4027 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11924; 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

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

Ferrieres03: Ferrieres L, Clarke DJ (2003). "The RcsC sensor kinase is required for normal biofilm formation in Escherichia coli K-12 and controls the expression of a regulon in response to growth on a solid surface." Mol Microbiol 50(5);1665-82. PMID: 14651646

Ferrieres07: Ferrieres L, Aslam SN, Cooper RM, Clarke DJ (2007). "The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production." Microbiology 153(Pt 4);1070-80. PMID: 17379715

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

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

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

UniProt10a: 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."

Zhai02: Zhai Y, Saier MH (2002). "The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes." Protein Sci 11(9);2196-207. PMID: 12192075

Other References Related to Gene Regulation

Ihssen04: Ihssen J, Egli T (2004). "Specific growth rate and not cell density controls the general stress response in Escherichia coli." Microbiology 150(Pt 6);1637-48. PMID: 15184550

Ionescu08: Ionescu M, Franchini A, Egli T, Belkin S (2008). "Induction of the yjbEFGH operon is regulated by growth rate and oxygen concentration." Arch Microbiol 189(3):219-26. PMID: 17957352

Ionescu11: Ionescu M, Elgrably-Weiss M, Elad T, Rasouly A, Yagur-Kroll S, Belkin S (2011). "Negative regulation of σ(70)-driven promoters by σ(70)." Res Microbiol. PMID: 21396442

Kamenšek13: Kamenšek S, Žgur-Bertok D (2013). "Global transcriptional responses to the bacteriocin colicin M in Escherichia coli." BMC Microbiol 13;42. PMID: 23421615

Murtin98: Murtin C, Engelhorn M, Geiselmann J, Boccard F (1998). "A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell." J Mol Biol 284(4);949-61. PMID: 9837718

Rozen01: Rozen Y, Dyk TK, LaRossa RA, Belkin S (2001). "Seawater Activation of Escherichia coli Gene Promoter Elements: Dominance of rpoS Control." Microb Ecol 42(4);635-643. PMID: 12024246

Weber05: Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R (2005). "Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity." J Bacteriol 187(5);1591-603. PMID: 15716429

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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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