title: The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment.
abstract: The predicted extracellular proteins of the bacterium Lactobacillus plantarum were analysed to gain insight into the mechanisms underlying interactions of this bacterium with its environment. Extracellular proteins play important roles in processes ranging from probiotic effects in the gastrointestinal tract to degradation of complex extracellular carbon sources such as those found in plant materials, and they have a primary role in the adaptation of a bacterium to changing environmental conditions. The functional annotation of extracellular proteins was improved using a wide variety of bioinformatics methods, including domain analysis and phylogenetic profiling. At least 12 proteins are predicted to be directly involved in adherence to host components such as collagen and mucin, and about 30 extracellular enzymes, mainly hydrolases and transglycosylases, might play a role in the degradation of substrates by L. plantarum to sustain its growth in different environmental niches. A comprehensive overview of all predicted extracellular proteins, their domains composition and their predicted function is provided through a database at http://www.cmbi.ru.nl/secretome which could serve as a basis for targeted experimental studies into the function of extracellular proteins.
authors.affiliation: Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, 6500HB Nijmegen, The Netherlands.
authors.forename: Jos
authors.initials: J
authors.lastname: Boekhorst
authors.affiliation: Wageningen Centre for Food Sciences, Wageningen, The Netherlands.|Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, 6500HB Nijmegen, The Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Wels
authors.affiliation: NIZO food research, Ede, The Netherlands.|Wageningen Centre for Food Sciences, Wageningen, The Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
authors.affiliation: NIZO food research, Ede, The Netherlands.|Wageningen Centre for Food Sciences, Wageningen, The Netherlands.|Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, 6500HB Nijmegen, The Netherlands.
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
mesh_terms: D001422:Bacterial Adhesion; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D002876:Chromosomes, Bacterial; D003094:Collagen / Q000378:metabolism; D019295:Computational Biology; D006602:Hexosyltransferases / Q000378:metabolism; D006867:Hydrolases / Q000378:metabolism; D048191:Lactiplantibacillus plantarum / Q000378:metabolism / Q000502:physiology*; D009077:Mucins / Q000378:metabolism; D010802:Phylogeny; D017434:Protein Structure, Tertiary
chemical_list: D001426:Bacterial Proteins; D009077:Mucins; D003094:Collagen; D006602:Hexosyltransferases; D006867:Hydrolases