In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments.
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.
Teusink
Bas
B
Wageningen Centre for Food Sciences, The Netherlands.
van Enckevort
Frank H J
FH
Francke
Christof
C
Wiersma
Anne
A
Wegkamp
Arno
A
Smid
Eddy J
EJ
Siezen
Roland J
RJ
D000596:Amino Acids / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D003470:Culture Media / Q000737:chemistry; D003628:Database Management Systems; D030541:Databases, Genetic; D016680:Genome, Bacterial; D048191:Lactiplantibacillus plantarum / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism*; D009711:Nucleotides / Q000378:metabolism; D011237:Predictive Value of Tests; D014815:Vitamins / Q000378:metabolism
D000596:Amino Acids; D001426:Bacterial Proteins; D003470:Culture Media; D009711:Nucleotides; D014815:Vitamins