Vetmeduni: MINDY3: A Hub Between Protein Quality Control and DNA Repair
An international team of researchers has uncovered a previously unknown connection between protein quality control and DNA repair. The study identifies the enzyme MINDY3 as a molecular link between these two essential cellular processes, providing new insights into how cells maintain their integrity following DNA damage.
The research was conducted by scientists from the MRC Protein Phosphorylation and Ubiquitylation Unit at the University of Dundee together with collaborators from ETH Zürich, the Małopolska Centre of Biotechnology and the University of Veterinary Medicine Vienna (Vetmeduni). Their findings have been published in EMBO Reports.
The study focuses on MINDY3, a deubiquitinase enzyme involved in regulating protein degradation. Researchers discovered that MINDY3 contains a distinctive EF-hand region that functions as a previously unknown ubiquitin-binding domain. This domain features three binding surfaces that enable MINDY3 to recognize and efficiently cleave long polyubiquitin chains, an essential step in controlling the fate of proteins inside cells.
Importantly, the EF-hand domain not only binds ubiquitin chains but also the ubiquitin-like (UBL) domains of the proteins RAD23A and RAD23B. These proteins transport ubiquitylated proteins to the proteasome for degradation. The newly identified interaction links MINDY3 to the RAD23–proteasome pathway, directing the enzyme to sites of DNA damage and suggesting a coordinated role in protein quality control during DNA repair.
“The key takeaway is that cells have intricate ‘quality-control’ systems to manage damaged proteins and to repair DNA – our work uncovers a new piece of that complex molecular puzzle,” said Sebastian Glatt, Professor of Systems Genetics at Vetmeduni and group leader at the Małopolska Centre of Biotechnology.
Structural Insights into MINDY3 Function
The researchers solved the crystal structure of the MINDY3 EF-hand bound to the RAD23A UBL domain, revealing the molecular basis of this interaction. The structural analysis identified the interface residues that are essential for binding and explained how MINDY3 specifically recognizes RAD23 proteins while remaining distinct from other ubiquitin-binding mechanisms.
MINDY3 Is Recruited to Sites of DNA Damage
Cell-based experiments demonstrated that RAD23A and RAD23B determine where MINDY3 localizes following DNA damage. The findings support a model in which MINDY3 removes ubiquitin chains from RAD23-associated proteins at sites of DNA repair, potentially influencing their stability and function during the repair process.
The study combined structural biology, biochemistry and cell biology techniques, including X-ray crystallography, isothermal titration calorimetry (ITC), pull-down assays and live-cell imaging. Together, these complementary approaches show that the EF-hand of MINDY3 functions as a dedicated ubiquitin-binding module that connects ubiquitin signaling with DNA repair through RAD23A and RAD23B.
The researchers conclude that the newly identified mechanism provides important insights into the molecular coordination of protein quality control and DNA repair and contributes to a better understanding of the cellular response to DNA damage.
Kontakt
Univ.-Prof. Dr. Sebastian Glatt
Zentrum für Biologische Wissenschaften
Veterinärmedizinische Universität Wien (Vetmeduni)
Sebastian.Glatt@vetmeduni.ac.at