LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species

Abstract

Listeria species are ubiquitous in the environment and often contaminate foods because they grow under conditions used for food preservation. Listeria monocytogenes, the human and animal pathogen, causes Listeriosis, an infection with a high mortality rate in risk groups such as immune-compromised individuals. Furthermore, L.monocytogenes is a model organism for the study of intracellular bacterial pathogens. The publication of its genome sequence and that of the non-pathogenic species Listeria innocua initiated numerous comparative studies and efforts to sequence all species comprising the genus. The Proteome database LEGER (http://leger2.gbf.de/cgi-bin/expLeger.pl) was developed to support functional genome analyses by combining information obtained by applying bioinformatics methods and from public databases to improve the original annotations. LEGER offers three unique key features: (i) it is the first comprehensive information system focusing on the functional assignment of genes and proteins; (ii) integrated visualization tools, KEGG pathway and Genome Viewer, alleviate the functional exploration of complex data; and (iii) LEGER presents results of systematic post-genome studies, thus facilitating analyses combining computational and experimental results. Moreover, LEGER provides an unpublished membrane proteome analysis of L.innocua and in total visualizes experimentally validated information about the subcellular localizations of 789 different listerial proteins.

Figure 1

Customized result tables are complemented by MineBlast and visualization tools, such as the Genome Viewer. The MineBlast report (partial) reveals functional descriptions for Lmo1695 found in literature that are currently not available in genome annotations. The Genome Viewer displays the genomic organization around a selected gene (Lmo0433). Each gene symbol provides functional assignments within Pop-up windows (‘Feature’). Graphical tracks point to further computational and experimental information. Green bars above the gene symbols summarize validated knowledge about the subcellular localization of proteins. The Genome Viewer by default comparatively presents both Listeria genomes to highlight differential structures and protein abundances (data not shown).

Figure 2

The integrated KEGG Pathway Viewer facilitates the generation of functional hypotheses. A separate table summarizes affected pathways. Submitted genes or proteins are marked along metabolic or signaling pathway maps. For example, Lmo1986 and Lmo2006, two enzymes out of seventeen that are annotated within the ‘Pantothenate and CoA biosynthesis’ pathway were found to be co-regulated and mediate the first steps of this synthesis (see partial view of the corresponding map).