$B.T., F.H.J.V.E., and C.F. contributed equally to this work.
*Corresponding author.
Mailing address: Centre for Molecular and Biomolecular Informatics,
Radboud University, P.O. Box 9010, 6500GL Nijmegen, The Netherlands.
Phone: 31 243653379. Fax: 31 24 365 29 77. E-mail: Roland.Siezen@nizo.nl.
Lactobacillus plantarum is a versatile and flexible lactic acid bacterium (LAB) that is important in industrial food fermentation processes. L. plantarum is also one of the LAB species that are important as probiotics in health-promoting food products. We have sequenced and annotated the genome of L. plantarum WCFS1 (PNAS USA 2003; 100:1990-1995), which is one of the largest Lactobacillus genomes. Putative biological functions could be assigned to 2,120 (70%) of the 3,052 predicted protein-encoding genes. L. plantarum will serve as a model organism for genome annotations and comparisons with other LAB (lactobacilli, lactococci, streptococci). This work describes a reference database of the metabolic network, based on the Lactobacillus genome annotation.
LacplantCyc adds an extended dimension to the genome of L. plantarum, providing researchers with a helpful tool for the analysis of the genomic, proteomic, and metabolic information of the organism. Visualization of the data sets in different levels of detail is extremely important to help interpreting these data from a biological viewpoint. Once the connections between genes, proteins and reactions in a metabolic map have been defined, high-throughput transcriptome data can be projected on metabolic maps. Transcriptome data that are superimposed on such a metabolic network provide insight into regulons, regulated pathways and regulatory networks. An additional aim during this process is to formulate which information is useful for improved pathway reconstruction. This should speed up the reconstruction of the metabolic networks of other LAB of which the complete genome has been sequenced. In this way LacplantCyc is envisioned to become the reference Gram-positive PGDB for LAB.
LacplantCyc is available at http://www.lacplantcyc.nl/
The full paper for LacplantCyc is available through this site and directly at the AEM journal site.
The full abstract for LacplantCyc is available at this site.
The pdf poster for LacplantCyc is available at this site.
The short abstract for this poster is available at this site.
Supported by the Netherlands Organisation of Scientific Research (NWO) BioMolecular Informatics Programme, grant 050.50.206.
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