The Efficiency of Protein Compartmentalization into the Secretory Pathway

Abstract

Numerous proteins targeted for the secretory pathway are increasingly implicated in functional or pathological roles at alternative cellular destinations. The parameters that allow secretory or membrane proteins to reside in intracellular locales outside the secretory pathway remain largely unexplored. In this study, we have used an extremely sensitive and quantitative assay to measure the in vivo efficiency of signal sequence-mediated protein segregation into the secretory pathway. Our findings reveal that segregation efficiency varies tremendously among signals, ranging from >95 to <60%. The nonsegregated fraction is generated by a combination of mechanisms that includes inefficient signal-mediated translocation into the endoplasmic reticulum and leaky ribosomal scanning. The segregation efficiency of some, but not other signal sequences, could be influenced in cis by residues in the mature domain or in trans by yet unidentified cellular factors. These findings imply that protein compartmentalization can be modulated in a substrate-specific manner to generate biologically significant quantities of cytosolically available secretory and membrane proteins. INTRODUCTIONIn mammalian cells, an estimated one-fifth to one-third of all proteins reside in or transit through the secretory pathway. The decisive step in segregating these proteins from the cytosol is their cotranslational targeting to and translocation across the endoplasmic reticulum (ER) membrane (reviewed by Walter and Johnson, 1994;Rapoport et al., 1996;Johnson and van Waes, 1999). Both targeting and initiation of translocation are dependent on a signal sequence, often at the N terminus, encoded in secretory and membrane proteins. Although the primary sequence of signals varies broadly (von Heijne, 1985), they contain shared features (such as hydrophobicity) that allow their common recognition by a ubiquitous machinery for ER translocation. Thus, proteins containing signal sequences are generally considered to have their intended functions at destinations accessed via the secretory pathway.Increasingly, however, many signal-containing proteins have been implicated in functional, pathological, or yet unknown roles at sites outside the secretory pathway. For example, the ER lumenal chaperone calreticulin (CRT) was identified completely independently as a cytosolic integrinbinding protein (Leung-Hagesteijn et al., 1994;Coppolino et al., 1995Coppolino et al., , 1997, a nuclear export factor (Holaska et al., 2001), a regulator of steroid hormone receptor activity (Burns et al., 1994;Dedhar et al., 1994), and an mRNA binding protein that regulates p21 translation (Iakova et al., 2004). In each of these instances, both functional and physical interactions with the respective cytosolic components have been demonstrated. Similarly, a different ER resident protein, the ␤ subunit of glucosidase II (Trombetta et al., 1996), was originally discovered (and given the name 80K-H) as a target of protein kinase C (Sakai et al., 1989;Hirai and Shimizu, 1990). More recentl...

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