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Global profiling of SRP interaction with nascent polypeptides.

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    Signal recognition particle (SRP) targets inner membrane proteins by binding hydrophobic domains during translation. This mechanism efficiently sorts proteins, distinguishing them from those using other cellular pathways.

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    Area of Science:

    • Molecular Biology
    • Cellular Biology
    • Protein Trafficking

    Background:

    • Signal recognition particle (SRP) is a crucial ribonucleoprotein complex for co-translational protein transport to membranes.
    • The existence of parallel protein transport pathways necessitates understanding SRP's substrate pool and selection mechanisms.
    • Current models lack detailed insights into how SRP distinguishes between different protein translocation pathways.

    Purpose of the Study:

    • To determine the precise binding sites of bacterial SRP on nascent proteins at amino acid resolution.
    • To elucidate the molecular basis of substrate selection by SRP within the Escherichia coli proteome.
    • To clarify the role of SRP in pathway decisions for nascent polypeptide chains in bacteria.

    Main Methods:

    • Sequencing of messenger RNA footprints from ribosome-nascent-chain complexes associated with SRP.
    • Analysis of SRP binding sites within the nascent proteome of Escherichia coli.
    • High-resolution mapping of SRP interactions with hydrophobic transmembrane domains (TMDs).

    Main Results:

    • SRP exhibits a strong preference for hydrophobic TMDs, acting as a specific targeting factor for nascent inner membrane proteins (IMPs).
    • SRP selectively recognizes internal TMDs and frequently skips N-terminal TMDs, contrary to existing models.
    • SRP binding is independent of translation speed and the ribosome-associated chaperone trigger factor (TF).

    Conclusions:

    • SRP acts as a dominant gatekeeper, efficiently separating IMPs from proteins targeted by SecA-SecB or TF pathways.
    • SRP's preference for specific hydrophobic features on emerging TMDs dictates pathway selection for nascent proteins.
    • These findings reveal the fundamental principles governing bacterial protein targeting and pathway commitment.