BAGEL: a web-based bacteriocin genome mining tool

Abstract

A common problem in the annotation of open reading frames (ORFs) is the identification of genes that are functionally similar but have limited or no sequence homology. This is particularly the case for bacteriocins, a very diverse group of antimicrobial peptides produced by bacteria and usually encoded by small, poorly conserved ORFs. ORFs surrounding bacteriocin genes are often biosynthetic genes. This information can be used to locate putative structural bacteriocin genes. Here, we describe BAGEL, a web server that identifies putative bacteriocin ORFs in a DNA sequence using novel, knowledge-based bacteriocin databases and motif databases. Many bacteriocins are encoded by small genes that are often omitted in the annotation process of bacterial genomes. Thus, we have implemented ORF detection using a number of published ORF prediction tools. In addition, BAGEL takes into account the genomic context, i.e. for each potential bacteriocin-encoding ORF, the sequence of the surrounding region on the genome is analyzed for genes that might encode proteins involved in biosynthesis, transport, regulation and/or immunity. These innovations make BAGEL unique in its ability to detect putative bacteriocin gene clusters in (new) bacterial genomes. BAGEL is freely accessible at: http://bioinformatics.biol.rug.nl/websoftware/bagel.

Figure 1

Schematic overview of BAGEL. (A) A web page where a genome sequence is provided in GenBank file format. Optionally, an annotated reference genome can be selected in case a de novo ORF search was performed on the input genome. (B) A web page with parameters concerning the search and scoring of putative bacteriocins. (C) The actual search for putative bacteriocins takes place through a script which recruits (i) the various search modules; (ii) the peptides with a hit to the various databases (indicated by a plus sign) are further annotated; and (iii) the results concerning putative bacteriocins (indicated by a plus sign) are exported to a results database. (D) This database is used to provide the BAGEL user with the search results in a web page. Annotation (optional): if a genome with new ORF annotations was provided, the (optional) annotated reference genome is used (if possible) to connect the putative bacteriocin ORF to an existing genome annotation.

Figure 2

Distance profiling. Adjacent genes are annotated on the basis of motifs or a hit to one of the databases described in Figure 1C. The presence of ORFs, of which the products are homologous to proteins known to be involved in bacteriocin biosynthesis, contributes to the probability that an ORF encodes a bacteriocin. In this example, the biosynthetic genes (red) are at position −2 (two ORFs upstream) and +4 (four ORFs downstream) of the putative bacteriocin ORF, as indicated by the ruler.