Occupying up to 90% of the volume of an individual cell, the vacuole is the most prominent compartment of the plant cell. The plant vacuoles are responsible for the transport and accumulation of nutrients, carbohydrates and storage proteins, and their function directly impacts plant yield and nutritional value. In plants, two types of vacuoles with different properties have been identified, the lytic vacuoles that carry out many of the same processes as yeast and mammalian lysosomes such as the breakdown and recycling of cellular components, and the protein storage vacuoles (PSVs) that carry out an additional number of plant-specific functions such as the accumulation and sequestration of toxic compounds and the storage of defense molecules such as alkaloids, phenolics, and protease inhibitors. Although components of the trafficking machinery to lytic vacuoles are well defined and appear to be conserved in yeast and multicellular eukaryotes, very little is known about the cellular machinery and regulatory mechanisms required for transport of vacuolar soluble proteins to the PSV. To define the genetic element and regulatory mechanisms required for the accumulation and mobilization of reserves into the storage vacuoles we will use a systems biology approach that combines computational tools (algorithm development), analytical tools (Proteomics), and a set of biological tools from the biochemistry, molecular biology and cell biology fields (Classical genetics, microscopy, and molecular biology) in the model plant Arabidopsis thaliana. The basic knowledge derived from this research will allow the design of experimental approaches aimed at improving biomass, production yield, and fitness through the enhancement of various vacuolar reserves in crops of economical interest.