The
presenilin/
gamma-secretase complex, an unusual intramembrane
aspartyl protease, plays an essential role in cellular signaling and
membrane protein turnover. Its ability to liberate numerous
intracellular signaling proteins from the membrane and also mediate the secretion of
amyloid-beta protein (Abeta) has made modulation of
gamma-secretase activity a therapeutic goal for
cancer and
Alzheimer disease. Although the proteolysis of the prototypical substrates Notch and
beta-amyloid precursor
protein (APP) has been intensely studied, the full spectrum of substrates and the determinants that make a transmembrane
protein a substrate remain unclear. Using an unbiased approach to substrate identification, we surveyed the
proteome of a human cell line for targets of
gamma-secretase and found a relatively small population of new substrates, all of which are type I transmembrane
proteins but have diverse
biological roles. By comparing these substrates to type I
proteins not regulated by
gamma-secretase, we determined that besides a short ectodomain,
gamma-secretase requires permissive transmembrane and cytoplasmic domains to bind and cleave its substrates. In addition, we provide evidence for at least two mechanisms that can target a substrate for gamma cleavage: one in which a substrate with a short ectodomain is directly cleaved independent of sheddase association, and a second where a substrate requires ectodomain shedding to instruct subsequent
gamma-secretase processing. These findings expand our understanding of the mechanisms of substrate selection as well as the diverse cellular processes to which
gamma-secretase contributes.