LacplantCyc: a Pathway / Genome Database for Lactobacillus plantarum as the model for Lactic Acid Bacteria.

Frank H.J. van Enckevort1,2, Bas Teusink1,3, Roland J. Siezen1,2,3,,
1NIZO food research, Ede, The Netherlands; 2Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands; 3Wageningen Centre for Food Sciences, Wageningen, The Netherlands.

Lactobacillus plantarum is a versatile and flexible lactic acid bacterium that is encountered in various environmental niches, including a number of industrial food and feed fermentation processes. The complete genome sequence of L. plantarum WCFS1, a strain isolated from human saliva, was recently published ( PNAS USA 2003;100:1990-1995) and putative biological functions could be assigned to 2,120 (70%) of the 3,052 predicted protein-encoding genes. This is one of the largest Lactobacillus genomes and it will serve as a model organism for genome annotations and comparisons with other lactic acid bacteria.

LacplantCyc is a newly created pathway/genome database (PGDB). It was automatically generated from the annotated L. plantarum WCFS1 genome (EMBL / GenBank / DDBJ Accession AL935263) and the MetaCyc database using the PathoLogic software from Pathway Tools (Peter Karp and the Bioinformatics Research Group, SRI International, USA). The resulting predicted metabolic network is being manually validated and adjusted with literature and experimentally verified data. This is the first step in creating a model PGDB for other lactic acid bacteria (lactobacilli, lactococci, streptococci). A comparison is being made with the metabolic networks as determined for Bacillus subtilis in BsubCyc.

In addition to the metabolic networks, future steps will focus on the incorporation of protein-protein interactions, signalling and information pathways, transport systems and regulatory networks into a larger set of network databases for lactic acid bacteria. Further annotation and editing of metabolic pathways and interaction networks is in progress.

This project is within a collaboration of: Centre for Molecular and Biomolecular Informatics, University of Nijmegen; NIZO food research, Ede; Wageningen Centre for Food Sciences, Wageningen; The Netherlands