PROBPROT
From genomes to probiotic functions: stripping Lactobacillus rhamnosus using expression proteomics, host interactomics and immunoproteomics
Consortium Leader:
Docent Nisse Kalkkinen, University of Helsinki, Institute of Biotechnology (http://www.biocenter.helsinki.fi/bi)
Other group leaders:
Docent Pekka Varmanen, University of Helsinki, Department of Basic Veterinary Sciences (www.helsinki.fi)
Professor Tapani Alatossava, University of Helsinki, Department of Food Technology (www.helsinki.fi)
Other persons involved in the project:
ABSTRACT
Despite the growing interest towards probiotics and their increasing global economic value, surprisingly little is known about the molecular mechanisms underlying the probiotic properties. Furthermore, the biological mechanisms these bacteria employ to maintain viability during industrial processes and during gastro-intestinal transit, how they interact with the resident microbiota and which proteins play a role during host-microbe interaction are still largely unexplored. Following completion of a genome sequence, a challenge for molecular biology is to find out the functions of the gene products and to understand how they contribute in viability and activity of a given organism. Proteomics has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Compared to measuring of RNA expression levels, proteomic experiments are more challenging. Nevertheless, the potential payoff for proteome analyses is immense, since while RNA can serve as effectors of some biological functions, proteins are the effectors of most biological functions.
The ultimate goal of the project is to get an understanding of the strain specific probiotic properties of L. rhamnosus. The project aims in comprehensive characterization of the entire L. rhamnosus proteome and to address different hypotheses related to probiotic functions, by combination of data from multiple diverse non-gel and gel-based proteomic experiments.
Subprojects:
- Characterization of intracellular subproteomes of an established probiotic strain (L. rhamnosus GG), a potentially probiotic strain with poor adhesion properties (L. rhamnosus LC-705) and a dairy strain isolated from cheese (L. rhamnosus 1/6) under various conditions,
- Characterization of extracellular subproteomes of L. rhamnosus strains,
- Characterization of differences in the proteome of L. rhamnosus during adhesion to cultured human epithelial cells.
- Characterization of immunogenic surface proteins specifically associated with probiotic L. rhamnosus strains.
The project is implemented in co-operation with Valio Ltd and DNA Sequencing Laboratory (University ofHelsinki, Institute of Biotechnology).
Key words: Probiotic, Lactobacillus rhamnosus, functional genomics, proteomics, proteome, secretome, host-microbe interaction, immunoproteomics