NAC controls nascent chain fate through tunnel sensing and chaperone action

Abstract

The nascent polypeptide-associated complex (NAC) is a conserved ribosome-bound factor with essential yet incompletely understood roles in protein biogenesis1. Here we show that NAC is a multi-faceted regulator that coordinates translation elongation, co-translational folding and organelle targeting through distinct interactions with nascent polypeptides both inside and outside the ribosome exit tunnel. Using NAC-selective ribosome profiling in Caenorhabditis elegans, we identify thousands of sequence-specific NAC binding events across the nascent proteome, revealing broad co-translational engagement with hydrophobic and helical motifs in cytosolic, nuclear, endoplasmic reticulum and mitochondrial proteins. Unexpectedly, we discover an intra-tunnel-sensing mode in which NAC engages ribosomes with extremely short nascent polypeptides inside the exit tunnel in a sequence-specific manner. Moreover, initial NAC interactions induce an early elongation slowdown that tunes ribosome flux and prevent ribosome collisions, linking the chaperone activity of NAC to kinetic control of translation. We propose that NAC action protects aggregation-prone intermediates by shielding amphipathic helices, thus promoting cytonuclear folding. NAC also supports mitochondrial membrane protein biogenesis and endoplasmic reticulum targeting by early recognition of signal sequences and transmembrane domains. Our findings establish NAC as an early-acting, multi-faceted orchestrator of co-translational proteostasis, with distinct mechanisms of action on nascent chains depending on their sequence features and subcellular destinations.