A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins

Abstract

Lipid modification of the N-terminal Cys residue (N-acyl-S-diacylglyceryl-Cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. Such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. Hence, being able to identify such proteins is of great value. To this end, we have created a comprehensive database of bacterial lipoproteins, called DOLOP, which contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. The website also features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include the following: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins. The website, along with additional information on the biosynthetic pathway, statistics on predicted lipoproteins, and related figures, is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop/.

FIG. 1.

(A) The structure of the lipid modification in lipoproteins. The sulfhydryl group of N-terminal cysteine is modified with a diacylglyceryl group attached through a thioether linkage, and the amino group is acylated with a fatty acid. (B) Tripartite structure of the lipoprotein signal sequence. The n-region is made up of five to seven residues and has at least two positively charged residues; the h-region, or the hydrophobic region, is made up of 7 to 22 predominantly hydrophobic and uncharged residues; and the c-region, which has the consensus [LVI][ASTVI][GAS] sequence, along with C, the invariant lipid-modified N-terminal residue in all bacterial lipoproteins, is referred to as the lipobox.

FIG. 2.

(A) Positive charge distribution in the n-region. This graph shows that most lipoproteins have at least two positively charged amino acids in their n-region. (B) Amino acid distribution in the lipobox. Leucine has the highest propensity to occur at the −3 position; alanine and serine at the −2 position; alanine, glycine, or serine at the −1 position; and the invariant cysteine that gets lipid modified. Please refer to the text for details.

FIG. 3.

Plot of the proteome size against the number of predicted lipoproteins for the 234 completely sequenced bacterial genomes used in our analysis. Note that there is a positive correlation between the genome size and the number of lipoproteins encoded. Organisms whose predicted number of lipoproteins falls way above or below the linear trend fitted for the observed data are marked on the graph. The large number of lipoproteins seen in Bacteroides corresponds, in large part, to a lineage-specific expansion of predicted lipoproteins with an N-terminal beta-propeller domain, which may form a specialized adhesion module. In Bdellovibrio, several lipoproteins appear to belong to an expansion of peptidases.

FIG. 4.

(A) Domain architecture for the protein gi 21284057 gb NP_647145.1 from Staphylococcus aureus MW2. This architecture contains two domains: a periplasmic metal-binding protein domain and a lipocalin fold metal-binding domain (in that order). In this case the assignments span the entire protein and provide a complete picture of the protein. (B) Screen shot of the output from PSATool. The program calculates molecular weight, amino acid frequency, composition, and weight composition and displays charge distribution and the nature of the sequence. This tool is available for predicted and verified lipoproteins.