A Deubiquitylating Complex Required for Neosynthesis of a Yeast Mitochondrial ATP Synthase Subunit

Sophie Kanga,Ivan Tarassov,Danièle Urban-Grimal,Titia K Sixma,Zoi Erpapazoglou,Francesca Mattiroli,Anne-Marie Mager-Heckel,Rosine Haguenauer-Tsapis,Sébastien Léon,Delphine Bernard

doi:10.1371/journal.pone.0038071

Abstract

The ubiquitin system is known to be involved in maintaining the integrity of mitochondria, but little is known about the role of deubiquitylating (DUB) enzymes in such functions. Budding yeast cells deleted for UBP13 and its close homolog UBP9 displayed a high incidence of petite colonies and slow respiratory growth at 37°C. Both Ubp9 and Ubp13 interacted directly with Duf1 (DUB-associated factor 1), a WD40 motif-containing protein. Duf1 activates the DUB activity of recombinant Ubp9 and Ubp13 in vitro and deletion of DUF1 resulted in the same respiratory phenotype as the deletion of both UBP9 and UBP13. We show that the mitochondrial defects of these mutants resulted from a strong decrease at 37°C in the de novo biosynthesis of Atp9, a membrane-bound component of ATP synthase encoded by mitochondrial DNA. The defect appears at the level of ATP9 mRNA translation, while its maturation remained unchanged in the mutants. This study describes a new role of the ubiquitin system in mitochondrial biogenesis.

Highlights

Ubiquitylation is a posttranslational modification in which ubiquitin, a highly conserved 76-residue polypeptide, is attached to target proteins through a series of enzymatic reactions involving a ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin protein ligases (E3) involved in substrate recognition
We identified a new WD40 protein that interacts with these two deubiquitylating enzymes (DUBs), that we named Duf1 (DUB-associated factor 1), and which is required for mitochondrial function
We checked the incidence of petite colonies (Table 2), a phenotype corresponding to extensive deletions or a complete absence of mitochondrial DNA [23]

Summary

Introduction

Ubiquitylation is a posttranslational modification in which ubiquitin, a highly conserved 76-residue polypeptide, is attached to target proteins through a series of enzymatic reactions involving a ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin protein ligases (E3) involved in substrate recognition. Ubiquitylation is a highly versatile means of regulating protein function, activity, stability, distribution and interactions in the cell. Most of the yeast DUBs belong to the UBP (ubiquitin-specific protease) subfamily. These proteins are cysteine proteases containing two well conserved protein sequences, the Cys and His boxes. These domains contain the catalytic triad residues and other residues of the active site pocket. The regulation of DUB activity and substrate specificity remains poorly understood, most DUBs are found associated with other proteins, suggesting that partner proteins may play a regulatory role [4]

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Conclusion