Biology subjects

Devaux, F.

Publications and source records attributed to Devaux, F..

3 recordsLinked to original sources

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↗

bioRxiv2025

Mitochondrial defects result in decreased susceptibility to echinocandins via the transcriptional regulator Pdr1 in Candida glabrata.

In the human fungal pathogen Candida glabrata, the transcription factor Pdr1 controls the expression of genes encoding drug efflux pumps such as Cdr1. Pdr1 also controls its own expression by binding to pleiotropic drug responsive elements (PDREs) located in its promoter. Increased resistance to the antifungal drugs azoles (e.g. fluconazole) is often due to gain-of-function mutations in PDR1 that render the factor hyperactive. Mitochondrial defects also result in increased resistance to azoles via Pdr1. Resistance to another class of antifungals, the echinocandins (e.g. micafungin), is generally due to mutations in the FKS1 and FKS2 genes that encode the catalytic subunit of 1,3-beta-D-glucan synthase, the echinocandin target. We have observed that mitochondrial defects also result in increased resistance to echinocandins and we have shown that this process is mediated by Pdr1. Mitochondrial defects result in increased levels of PDR1 mRNA. Overexpression of PDR1 by replacing its native promoter by the strong ADH1 promoter resulted in increased resistance to micafungin. However, mutations in PDR1 that decrease susceptibility to azoles generally have modest effects on echinocandin resistance. We randomly mutagenized the PDR1 gene and screened for mutants with altered resistance to micafungin. Single amino acid changes downstream of the DNA binding domain result in preferential resistance to micafungin as compared to fluconazole. We also show that auto-regulation of PDR1 expression is necessary for resistance to micafungin. One PDR1 mutant showed over 15-fold increased promoter activity in a PDRE-dependent manner. In summary, we have identified a novel role for the transcriptional regulator Pdr1.

microbiology↗

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↗