Translocational pausing is a common step in the biogenesis of unconventional integral membrane and secretory proteins.

Signal, stop transfer, and signal-anchor sequences direct a nascent polypeptide to a single topology with respect to the membrane of the endoplasmic reticulum. However, other types of sequences direct nascent proteins, either transiently or permanently, to more than one topologic form. Pause transfer sequences direct nascent apolipoprotein B to pause during its translocation, resulting in nonintegrated, transmembrane intermediates that become fully translocated over time. The stop transfer effector sequence (STE) directs the nascent prion protein either to integrate at the hydrophobic domain which immediately follows (TM1) or to become fully translocated, in a manner dependent on cytosolic factors. Although the action of pause transfer sequences has been dissected into stop and restart steps, the mechanism of STE action is unknown. Using chimeric proteins expressed in vitro, we show that STE, independent of TM1, acts as a pause transfer sequence. We also demonstrate that translocational pausing at STE is a common step preceding either complete translocation or integration into the membrane of a chimeric protein containing STE and TM1. These findings have implications for the role of pausing in the biogenesis of both secretory and membrane proteins.