First complexomic study of alkane-binding protein complexes in the yeast Yarrowia lipolytica

The yeast Yarrowia lipolytica uses hydrophobic substrates, such as alkanes, fatty acids and oils, for its growth. It has developed a strategy for the use of such substrates, involving the production of hydrophobic binding structures called protrusions on the cell surface. These protrusions are resemble channels connecting the cell wall to the inside of the cell, and are probably involved in transport mechanisms that we do not yet fully understand. The complete genome of the haploid Y. lipolytica strain E150 (CLIB99) was sequenced in 2004 by the Génolevures Consortium. The availability of a complete genome sequence for this species has made it possible to carry out proteomic and other investigations, leading to the characterization of lipid bodies (LB) in terms of (i) their lipid composition, (ii) the major LB proteins, as identified by mass spectrometry, and (iii) differences in protein or lipid composition as a function of the carbon source used. Functional analyses would provide insight into the biological processes associated with these bodies and 2D BN/SDS-PAGE is a highly suitable method for the analysis of protein complexes. This report provides a first description of the analysis and identification of hydrophobic binding protein complexes in Y. lipolytica. For this purpose, we used 2D BN/SDS-PAGE for the separation of protein complexes and HPLC-chip-MS for protein identification. We separated and identified 40 protein complexes (11 heteromultimeric and 29 homomultimeric), providing insight into their function. This study represents a major step forward, as most previous studies identified proteins either on the basis of sequence similarity to proteins from other organisms (44% of the proteins identified in this study) or by prediction (50% of proteins identified in this study) alone.