Genome-wide view of membrane targeting by Saccharomyces cerevisiae phox homology (PX) and pleckstrin homology (PH) domains

Phosphoinositides constitute a small fraction (∼2%) of the components that make up cellular membranes. However, it is now realized that most of these lipids occupy (and serve as markers for) distinct cellular organelles/membranes where they play critical roles in diverse cellular processes including regulation of cell growth and death, cytoskeletal organization, and vesicular trafficking. With the ongoing characterization of well known and identification of novel phosphoinositide binding modules (PH, FYVE, PX, ENTH domains and others), a role for membrane embedded phosphoinositides as membrane/organelle specific targeting signals has recently become appreciated. Currently, much effort is being placed in identifying ‘effector’ domains (known or novel) that target to any of the seven different phosphoinositides known to occur in cells, determining mechanistically how targeting of these domains is achieved, and understanding the molecular mechanisms of their intact protein at these specific membrane locations. Therefore, in an initial attempt to address these issues and to obtain a genome-wide perspective on the function of two families of highly common phosphoinositide recognition modules, I have focused my work on the phosphoinositide binding and membrane targeting properties of all phox homology (PX) and pleckstrin homology (PH) domains in the yeast S. cerevisiae. Here, I report my finding that all PX domains in yeast selectively recognize PtdIns(3)P (like the well-characterized family of FYVE domains), but with varying affinity, and discuss the functional importance of targeting and assembly of protein complexes by PX domain containing proteins onto PtdIns(3)P enriched membranes. In contrast to these findings, I also report that the great majority of yeast PH domains bind phosphoinositides non-selectively and with low affinity and yet a significant fraction of these domains are still membrane targeted. This finding is in stark contrast to what is currently known about PH domains and suggests a role for alternate ligands (in addition to phosphoinositides) for membrane targeting. These studies as a whole provide an important initial step in understanding the function of these highly prevalent domains in proteins with diverse and critical functions