Analysis of a pause transfer sequence from apolipoprotein B.

In contrast to typical secretory proteins, apolipoprotein B pauses at distinct points along the nascent chain during its translocation into the lumen of the endoplasmic reticulum. Specific pause transfer sequences mediate such discrete pauses in the translocation of apolipoprotein B. These sequences have been shown to confer this translocational behavior to heterologous chimeric proteins. To investigate the function of pause transfer sequences, we: (i) examine whether the multiple pause transfer sequences of apolipoprotein B act independently or are dependent upon the action of upstream pause transfer sequences, (ii) identify residues of the prototypical B' pause transfer sequence that are involved in pausing, and (iii) determine whether the stopping step of a translocational pause is a consequence of translational pausing, as has been suggested by other investigators. We conclude that pause transfer sequences act independently of each other and of translation; translocational pausing occurs even in the absence of ongoing protein synthesis. Furthermore, like other topogenic sequences such as signal sequences, pause transfer sequences are degenerate in structure yet have distinctive features necessary for their action. This characterization of the B' pause transfer sequence may aid in the identification of such sequences elsewhere in apolipoprotein B and in other proteins and has implications for the mechanism of translocational pausing.