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TopicPage for LipoProteome of Escherichia coli K-12

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Membrane Proteome Signal Peptide Proteins         
        

Description:

The LipoProteome of E. coli K-12 is in the process of being fully Verified. The LipoProteome Topic is comprised of the 82 verified (subTopic = LipoProtExp) and the 37 predicted lipoproteins (LipoProtPred) for a total current GeneSet of 119 proven or predicted lipoprotein genes.

Details:

The current estimate of 119 lipoproteins in this Topic is derived from a recently published a bioinformatics analysis and literature review (Gonnet, 2004), who evaluated likely-true and likely-false predictions, and provided a summary table, including a list of 80 verified lipoproteins (and their citations).

The largest set of lipoprotein verifications were performed by Shin-ichi Matsuyama at the University of Tokyo. Although the details of this work has not been published yet, the results have been cited in the Juncker (2003) paper that describes the LipoP lipoprotein prediction algorithm.

Juncker (2003) note that S. Matsuyama experimentally confirmed 90 lipoproteins, but only 76 were named as personal communications, 75 in their Table 4 and CyoA in the text. Juncker et al. also note that 2/90 were plasmid genes and that 7/90 were predicted to be lipoproteins by LipoP when the revised start sites in SwissProt (provided by EcoGene to SwissProt) were used in contrast to the GenBank annotations used in their initial development of LipoP.

Thus 8 additional lipoproteins from the E. coli K-12 genome have been shown to be lipoproteins by S. Matsuyama, but not yet published or identiified. Presumably they are among the 37 additional lipoproteins predicted in EcoGene.

Two additional lipoprotein verifications, out of the 90 unpublished verifications, were cited as unpublished results by Miyadai (2004).
These YafY and YjfS lipoproteins were shown to be localized to the inner membrane, as predicted (Miyadai, 2004). They had been previously predicted to be lipoproteins in 1998 in EcoGene and Swiss-Prot entries, based on choosing alternate start sites that revealed the lipoboxes.
These start site revisions and revised predictions from EcoGene have now been placed in the GenBank U00096.2 annotations.

FtsI is a special case. Although 15% of the molecules been shown to be lipidated, it is listed as a false positive since it is not efficiently lipidated and it is not known if the lipoprotein form has any function.

An additional 7 proteins involved in lipoprotein metabolism that are not lipoproteins include LolACDE (LolB is a lipoprotein), Lgt, Lnt, and LspA.


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