Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes

Abstract

INTRODUCTIONThe bacterial cell envelope is of major significance as the focal point for interaction between the bacterium and its environment, notably the host in the case of bacterial pathogens. Bacterial cell envelope proteins thus carry out numerous important functions including roles in adhesion, nutrient acquisition and a variety of interactions with host defences. In Gram-positive bacteria the matrix of peptidoglycan and other wall polymers surrounding the cell is not an efficient barrier to the passage of small macromolecules, due both to its inherent structural permeability and to its turnover during normal cell growth. Indeed, peptidoglycan may be sufficiently permeable as to allow the passage of globular proteins of up to "50 kDa in size (Demchick & Koch, 1996 ;Dijkstra & Keck, 1996). Consequently, in the absence of a retentive outer membrane, Grampositive bacteria have evolved distinct mechanisms for retaining proteins within their cell envelopes, including covalent linkage to the peptidoglycan and non-covalent binding to teichoic acids and other cell envelope polymers (Navarre & Schneewind, 1999 ;Cossart & Jonquieres, 2000 ;Janulczyk & Rasmussen, 2001). Also significant among these mechanisms is membraneanchoring of bacterial lipoproteins (Lpps) by covalent N-terminal lipidation (Braun & Wu, 1994 ; Sutcliffe & Russell, 1995). Lpps in Gram-positive bacteria perform important roles as substrate-binding proteins (SBPs) in ABC transporter systems ; in antibiotic resistance ; in cell signalling ; in protein export and folding ; in sporulation and germination ; in conjugation and various other functions (Sutcliffe & Russell, 1995 valent to those carried out by periplasmic proteins of Gram-negative bacteria.The archetypal bacterial Lpp is the murein lipoprotein of Escherichia coli characterized by Braun and coworkers (reviewed in Braun & Wu, 1994). Structural studies revealed that a diacylglycerol moiety is thioether linked to an N-terminal cysteine of this Lpp and that this lipid group serves to orientate the protein by anchoring it to the inner leaflet of the outer membrane. Chemically identical lipid modifications have since been proposed, primarily on the basis of protein sequence analysis (see below), for a great many proteins in both Gram-positive and Gram-negative bacteria, although relatively few have received extensive biochemical characterization.Biosynthesis of bacterial lipoprotein of the ' Braun ' type proceeds via a well conserved pathway that is apparently unique to prokaryotes (Fig. 1). Following signal-peptidedirected export of the prolipoprotein (proLpp), the enzyme prolipoprotein diacylglycerol transferase (Lgt) uses phospholipid substrates and catalyses the addition of a diacylglycerol lipid unit onto the thiol of a crucial conserved cysteine which is located within a ' lipobox ' motif at the cleavage region of the proLpp signal peptide (Sankaran et al., 1995 ; Qi et al., 1995). Subsequently, the signal peptide is removed by a specific lipoprotein signal peptidase II (Lsp) enzyme which ...

Lipoprotein biogenesis in Gram-positive bacteria: knowing when to hold ‘em, knowing when to fold ‘em

“…Moreover, genome analyses have consistently identified putative lipoproteins predicted to have important roles in cell envelope stability and cell wall cross-linking or remodelling such as penicillin binding proteins and peptidoglycan hydrolases [18,54]. For example, ErfK domain (PFAM PF03734) L,D transpeptidases were recently discovered to have roles in the alternative 3-3 cross-linking of peptidoglycan in Enterococcus faecium and M. tuberculosis [72,73], perhaps as a way of recycling or remodelling the peptidoglycan.…”

“…Lipoprotein functions in Gram-positive bacteria Bioinformatic analyses (as described earlier) have indicated that lipoproteins are a relatively abundant family of proteins, typically representing 2% or more of a Grampositive bacterial proteome [18,19,43,54,57]. Functional analyses have revealed several recognisable functional groupings of Gram-positive bacterial lipoproteins [3], with these functions reflecting the localisation of lipoproteins within the cell envelope and more specifically at the interface between the membrane and the cell wall (Box 3).…”

“…F was incorrectly included as a permissible residue in the -2 position when the original pattern was described [54]. b Additional rules apply, i.e.…”

“…type II signal peptides) are highly amenable to bioinformatic analyses, through the identification of the well conserved cysteine-containing lipobox [53][54][55]. Whole genome sequences can be searched for matches to either the Prosite profile PS51257 or the taxon restricted G+LPP sequence pattern (Box 2), which exhibits improved specificity for the identification of lipoproteins from Gram-positive bacteria [54,55].…”

“…Where stretches of amino acids can vary in length, the range is indicated in parentheses. The original G+LPP pattern was described by analysis of the signal peptide features of 33 experimentally verified lipoproteins [54]. An extended dataset of 90 experimentally verified lipoprotein signal peptides was used to revise this pattern (G+LPPv2; [55]).…”