Nashed, S. | Search bioRxiv

bioRxiv2026

Shining a light on the dark Nt-acetylome by integrating omics data

N-terminal acetylation, catalysed by N-terminal acetyltransferases (Nats), is one of the most prevalent protein modifications and is implicated in human diseases. Yet, despite extensive COFRADIC-based proteomics, only [~]5-10% of the proteome has been interrogated, leaving the majority of the Nt-acetylome unexplored. Here, we combined all major COFRADIC datasets with sel-TRAP, a high-sensitivity, orthogonal approach for profiling co-translational Nat targets via selective ribosome purification. This integrated analysis refined the substrate specificities of NatA, NatB, and NatC/E/F and provided the most comprehensive view to date of the canonical human and yeast Nt-acetylomes. Importantly, we also uncovered hundreds of cryptic Nat substrates arising from alternative translation initiation, with unexpected Nt-proteoforms constituting a previously underappreciated source of Nat targets. Collectively, our results revealed the complex landscape of a "dark" Nt-acetylome, the characterization of which, including its functional roles in regulating protein function and in disease, remains a major challenge for future research.

genomics↗

bioRxiv2022

Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import.

N-terminal ends of polypeptides are critical for the selective co-translational recruitment of N-terminal modification enzymes. However, it is unknown whether specific N-terminal signatures differentially regulate protein fate according to their cellular functions. In this work, we developed an in-silico approach to detect functional preferences in cellular N-terminomes, and identified in S. cerevisiae more than 200 Gene Ontology terms with specific N-terminal signatures. In particular, we discovered that Mitochondrial Targeting Sequences (MTS) show a strong and specific over-representation at position 2 of hydrophobic residues known to define potential substrates of the N-terminal acetyltransferase NatC. We validated mitochondrial precursors as co-translational targets of NatC by selective purification of translating ribosomes, and found that their N-terminal signature is conserved in Saccharomycotina yeasts. Finally, systematic mutagenesis of the position 2 in a prototypal yeast mitochondrial protein confirmed its critical role in mitochondrial protein import. Our work highlights the hydrophobicity of MTS N-terminal residues and their modification by NatC as critical features for the definition of the mitochondrial proteome, providing a molecular explanation for mitochondrial defects observed in yeast or human NatC-depleted cells. Functional mapping of N-terminal residues thus has the potential to support the discovery of novel mechanisms of protein regulation or targeting.

genomics↗