Bacteriocins are antimicrobial peptides produced by bacteria, which are active against either closely related or more distant species. They provide a defense mechanism for the producing strain as they can kill other bacteria. Therefore, bacteriocins are applied as food preservatives (1
) and are of interest for the development of novel antibiotics (3
). They are exported across the cytoplasmic membrane by dedicated transporters containing an ATP-binding cassette (ABC-transporter), and are often processed by a specific protease, although occasionally these two functions are combined (5
). In many cases the bacteriocin-encoding gene cluster also contains one or more immunity proteins to prevent self-killing. The expression of bacteriocin gene clusters is often under control of a two-component signal transduction system, which is usually part of the cluster. The inducer can be either the bacteriocin itself or a bacteriocin-like peptide. Various classes of over 200 known bacteriocins have been defined, based on features such as the nature of post-translational modifications, specific anti-bacterial activity, formation of oligomers, protein size, presence of sugar moieties, presence of positively charged amino acids and mode of action. Five main classes reported in literature are as follows: (i) lantibiotics, posttranslationally modified peptides (5
); (ii) non-modified heat stable bacteriocins (6
); (iii) large heat-labile bacteriocins; (iv) complex bacteriocins carrying lipid or carbohydrate moieties (9
) and (v) circular bacteriocins (10
) (). A number of classes are divided into subclasses (). These differences in properties reflect the large divergence between bacteriocins (11
Overview of the known classes of bacteriocins and the features that discriminate the different classes
The classical way of identification of a bacteriocin has been by determining its biological activity through extensive testing of the (putative) producer strain for inhibition of the growth of other bacteria. A few reports (5
) describe the identification of putative bacteriocins by screening a genomic DNA sequence for the presence of bacteriocin genes and their genomic context for biosynthetic genes.
Here, we present the web-based software tool BAGEL, which enables the identification of bacteriocins and their biosynthetic clusters through a knowledge-based database. It takes advantage of the fact that accessory genes encoding proteins needed for processing, modification, transport, regulation and/or immunity are commonly located in the vicinity of a putative bacteriocin gene. Furthermore, open reading frame (ORF) detection is provided, which makes BAGEL independent of GenBank annotations and thus prevents the oversight of small non-conserved ORFs (the most probable candidates for bacteriocin genes), which are omitted from many genome annotations. A typical BAGEL search on a genome sequence results in a set of putative bacteriocin gene clusters. These are ranked according to the presence of significant features in the amino acid sequences and their genomic context. The output contains comprehensive information on the predicted putative bacteriocins. BAGEL is the first fully automated and very fast tool for the identification of new bacteriocin gene clusters. We demonstrate the power and versatility of this software by the analysis of a number of annotated and non-annotated bacterial genomes.