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Applied and Environmental Microbiology, November 2005, p. 7253-7262, Vol. 71, No. 11
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.11.7253-7262.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments

Bas Teusink,1,2,3,{dagger} Frank H. J. van Enckevort,2,3,{dagger} Christof Francke,1,3,{dagger} Anne Wiersma,1,2 Arno Wegkamp,1,2 Eddy J. Smid,1,2 and Roland J. Siezen1,2,3*

Wageningen Centre for Food Sciences, P.O. Box 557, 6700AN Wageningen, The Netherlands,1 NIZO food research, P.O. Box 20, 6710BA Ede, The Netherlands,2 Centre for Molecular and Biomolecular Informatics, Radboud University, P.O. Box 9010, 6500GL Nijmegen, The Netherlands3

Received 12 April 2005/ Accepted 20 June 2005

On the basis of the annotated genome we reconstructed the metabolic pathways of the lactic acid bacterium Lactobacillus plantarum WCFS1. After automatic reconstruction by the Pathologic tool of Pathway Tools (http://bioinformatics.ai.sri.com/ptools/), the resulting pathway-genome database, LacplantCyc, was manually curated extensively. The current database contains refinements to existing routes and new gram-positive bacterium-specific reactions that were not present in the MetaCyc database. These reactions include, for example, reactions related to cell wall biosynthesis, molybdopterin biosynthesis, and transport. At present, LacplantCyc includes 129 pathways and 704 predicted reactions involving some 670 chemical species and 710 enzymes. We tested vitamin and amino acid requirements of L. plantarum experimentally and compared the results with the pathways present in LacplantCyc. In the majority of cases (32 of 37 cases) the experimental results agreed with the final reconstruction. LacplantCyc is the most extensively curated pathway-genome database for gram-positive bacteria and is open to the microbiology community via the World Wide Web (www.lacplantcyc.nl). It can be used as a reference pathway-genome database for gram-positive microbes in general and lactic acid bacteria in particular.

* 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{at}nizo.nl.

{dagger} B.T., F.H.J.V.E., and C.F. contributed equally to this work.

Applied and Environmental Microbiology, November 2005, p. 7253-7262, Vol. 71, No. 11
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.11.7253-7262.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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